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Minat/Parallel/parallel
profiteroles 862af085c5 0.1.8
2019-09-27 01:49:14 -07:00

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#!/usr/bin/perl
# Copyright (C) 2007-2019 Ole Tange and Free Software Foundation, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
# or write to the Free Software Foundation, Inc., 51 Franklin St,
# Fifth Floor, Boston, MA 02110-1301 USA
# open3 used in Job::start
use IPC::Open3;
# &WNOHANG used in reaper
use POSIX qw(:sys_wait_h setsid ceil :errno_h);
# gensym used in Job::start
use Symbol qw(gensym);
# tempfile used in Job::start
use File::Temp qw(tempfile tempdir);
# mkpath used in openresultsfile
use File::Path;
# GetOptions used in get_options_from_array
use Getopt::Long;
# Used to ensure code quality
use strict;
use File::Basename;
sub set_input_source_header($$) {
my ($command_ref,$input_source_fh_ref) = @_;
if($opt::header and not $opt::pipe) {
# split with colsep or \t
# $header force $colsep = \t if undef?
my $delimiter = defined $opt::colsep ? $opt::colsep : "\t";
# regexp for {=
my $left = "\Q$Global::parensleft\E";
my $l = $Global::parensleft;
# regexp for =}
my $right = "\Q$Global::parensright\E";
my $r = $Global::parensright;
my $id = 1;
for my $fh (@$input_source_fh_ref) {
my $line = <$fh>;
chomp($line);
::debug("init", "Delimiter: '$delimiter'");
for my $s (split /$delimiter/o, $line) {
::debug("init", "Colname: '$s'");
# Replace {colname} with {2}
for(@$command_ref,@Global::ret_files,@Global::transfer_files,
$opt::tagstring, $opt::workdir, $opt::results,
$opt::retries) {
# Skip if undefined
$_ or next;
s:\{$s(|/|//|\.|/\.)\}:\{$id$1\}:g;
# {=header1 ... =} => {=1 ... =}
s:$left $s (.*?) $right:$l$id$1$r:gx;
}
$Global::input_source_header{$id} = $s;
$id++;
}
}
} else {
my $id = 1;
for my $fh (@$input_source_fh_ref) {
$Global::input_source_header{$id} = $id;
$id++;
}
}
}
sub max_jobs_running() {
# Compute $Global::max_jobs_running as the max number of jobs
# running on each sshlogin.
# Returns:
# $Global::max_jobs_running
if(not $Global::max_jobs_running) {
for my $sshlogin (values %Global::host) {
$sshlogin->max_jobs_running();
}
}
if(not $Global::max_jobs_running) {
::error("Cannot run any jobs.");
wait_and_exit(255);
}
return $Global::max_jobs_running;
}
sub halt() {
# Compute exit value,
# wait for children to complete
# and exit
if($opt::halt and $Global::halt_when ne "never") {
if(not defined $Global::halt_exitstatus) {
if($Global::halt_pct) {
$Global::halt_exitstatus =
::ceil($Global::total_failed /
($Global::total_started || 1) * 100);
} elsif($Global::halt_count) {
$Global::halt_exitstatus =
::min(undef_as_zero($Global::total_failed),101);
}
}
wait_and_exit($Global::halt_exitstatus);
} else {
wait_and_exit(min(undef_as_zero($Global::exitstatus),101));
}
}
sub __PIPE_MODE__() {}
sub pipepart_setup() {
# Compute the blocksize
# Generate the commands to extract the blocks
# Push the commands on queue
# Changes:
# @Global::cat_prepends
# $Global::JobQueue
if($opt::tee) {
# Prepend each command with
# < file
my $cat_string = "< ".Q($opt::a[0]);
for(1..$Global::JobQueue->total_jobs()) {
push @Global::cat_appends, $cat_string;
push @Global::cat_prepends, "";
}
} else {
if(not $opt::blocksize) {
# --blocksize with 10 jobs per jobslot
$opt::blocksize = -10;
}
if($opt::roundrobin) {
# --blocksize with 1 job per jobslot
$opt::blocksize = -1;
}
if($opt::blocksize < 0) {
my $size = 0;
# Compute size of -a
for(@opt::a) {
if(-f $_) {
$size += -s $_;
} elsif(-b $_) {
$size += size_of_block_dev($_);
} else {
::error("$_ is neither a file nor a block device");
wait_and_exit(255);
}
}
# Run in total $job_slots*(- $blocksize) jobs
# Set --blocksize = size / no of proc / (- $blocksize)
$Global::dummy_jobs = 1;
$Global::blocksize = 1 +
int($size / max_jobs_running() / -$opt::blocksize);
}
@Global::cat_prepends = map { pipe_part_files($_) } @opt::a;
# Unget the empty arg as many times as there are parts
$Global::JobQueue->{'commandlinequeue'}{'arg_queue'}->unget(
map { [Arg->new("\0noarg")] } @Global::cat_prepends
);
}
}
sub pipe_tee_setup() {
# Create temporary fifos
# Run 'tee fifo1 fifo2 fifo3 ... fifoN' in the background
# This will spread the input to fifos
# Generate commands that reads from fifo1..N:
# cat fifo | user_command
# Changes:
# @Global::cat_prepends
my @fifos;
for(1..$Global::JobQueue->total_jobs()) {
push @fifos, tmpfifo();
}
# cat foo | tee fifo1 fifo2 fifo3 fifo4 fifo5 > /dev/null
if(not fork()){
# Let tee inherit our stdin
# and redirect stdout to null
open STDOUT, ">","/dev/null";
exec "tee",@fifos;
}
# For each fifo
# (rm fifo1; grep 1) < fifo1
# (rm fifo2; grep 2) < fifo2
# (rm fifo3; grep 3) < fifo3
# Remove the tmpfifo as soon as it is open
@Global::cat_prepends = map { "(rm $_;" } @fifos;
@Global::cat_appends = map { ") < $_" } @fifos;
}
sub parcat_script() {
# TODO if script fails: Use parallel -j0 --plain --lb cat ::: fifos
my $script = q'{
use POSIX qw(:errno_h);
use IO::Select;
use strict;
use threads;
use Thread::Queue;
use Fcntl qw(:DEFAULT :flock);
my $opened :shared;
my $q = Thread::Queue->new();
my $okq = Thread::Queue->new();
my @producers;
if(not @ARGV) {
if(-t *STDIN) {
print "Usage:\n";
print " parcat file(s)\n";
print " cat argfile | parcat\n";
} else {
# Read arguments from stdin
chomp(@ARGV = <STDIN>);
}
}
my $files_to_open = 0;
# Default: fd = stdout
my $fd = 1;
for (@ARGV) {
# --rm = remove file when opened
/^--rm$/ and do { $opt::rm = 1; next; };
# -1 = output to fd 1, -2 = output to fd 2
/^-(\d+)$/ and do { $fd = $1; next; };
push @producers, threads->create("producer", $_, $fd);
$files_to_open++;
}
sub producer {
# Open a file/fifo, set non blocking, enqueue fileno of the file handle
my $file = shift;
my $output_fd = shift;
open(my $fh, "<", $file) || do {
print STDERR "parcat: Cannot open $file\n";
exit(1);
};
# Remove file when it has been opened
if($opt::rm) {
unlink $file;
}
set_fh_non_blocking($fh);
$opened++;
# Pass the fileno to parent
$q->enqueue(fileno($fh),$output_fd);
# Get an OK that the $fh is opened and we can release the $fh
while(1) {
my $ok = $okq->dequeue();
if($ok == fileno($fh)) { last; }
# Not ours - very unlikely to happen
$okq->enqueue($ok);
}
return;
}
my $s = IO::Select->new();
my %buffer;
sub add_file {
my $infd = shift;
my $outfd = shift;
open(my $infh, "<&=", $infd) || die;
open(my $outfh, ">&=", $outfd) || die;
$s->add($infh);
# Tell the producer now opened here and can be released
$okq->enqueue($infd);
# Initialize the buffer
@{$buffer{$infh}{$outfd}} = ();
$Global::fh{$outfd} = $outfh;
}
sub add_files {
# Non-blocking dequeue
my ($infd,$outfd);
do {
($infd,$outfd) = $q->dequeue_nb(2);
if(defined($outfd)) {
add_file($infd,$outfd);
}
} while(defined($outfd));
}
sub add_files_block {
# Blocking dequeue
my ($infd,$outfd) = $q->dequeue(2);
add_file($infd,$outfd);
}
my $fd;
my (@ready,$infh,$rv,$buf);
do {
# Wait until at least one file is opened
add_files_block();
while($q->pending or keys %buffer) {
add_files();
while(keys %buffer) {
@ready = $s->can_read(0.01);
if(not @ready) {
add_files();
}
for $infh (@ready) {
# There is only one key, namely the output file descriptor
for my $outfd (keys %{$buffer{$infh}}) {
$rv = sysread($infh, $buf, 65536);
if (!$rv) {
if($! == EAGAIN) {
# Would block: Nothing read
next;
} else {
# Nothing read, but would not block:
# This file is done
$s->remove($infh);
for(@{$buffer{$infh}{$outfd}}) {
syswrite($Global::fh{$outfd},$_);
}
delete $buffer{$infh};
# Closing the $infh causes it to block
# close $infh;
add_files();
next;
}
}
# Something read.
# Find \n or \r for full line
my $i = (rindex($buf,"\n")+1);
if($i) {
# Print full line
for(@{$buffer{$infh}{$outfd}}, substr($buf,0,$i)) {
syswrite($Global::fh{$outfd},$_);
}
# @buffer = remaining half line
$buffer{$infh}{$outfd} = [substr($buf,$i,$rv-$i)];
} else {
# Something read, but not a full line
push @{$buffer{$infh}{$outfd}}, $buf;
}
redo;
}
}
}
}
} while($opened < $files_to_open);
for (@producers) {
$_->join();
}
sub set_fh_non_blocking {
# Set filehandle as non-blocking
# Inputs:
# $fh = filehandle to be blocking
# Returns:
# N/A
my $fh = shift;
my $flags;
fcntl($fh, &F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
$flags |= &O_NONBLOCK; # Add non-blocking to the flags
fcntl($fh, &F_SETFL, $flags) || die $!; # Set the flags on the filehandle
}
}';
return ::spacefree(3, $script);
}
sub sharder_script() {
my $script = q{
use B;
# Column separator
my $sep = shift;
# Which columns to shard on (count from 1)
my $col = shift;
# Which columns to shard on (count from 0)
my $col0 = $col - 1;
my $bins = @ARGV;
# Open fifos for writing, fh{0..$bins}
my $t = 0;
my %fh;
for(@ARGV) {
open $fh{$t++}, ">", $_;
# open blocks until it is opened by reader
# so unlink only happens when it is ready
unlink $_;
}
while(<STDIN>) {
# Split into $col columns (no need to split into more)
@F = split $sep, $_, $col+1;
$fh = $fh{ hex(B::hash($F[$col0]))%$bins };
print $fh $_;
}
# Close all open fifos
close values %fh;
};
return ::spacefree(1, $script);
}
sub pipe_shard_setup() {
# Create temporary fifos
# Run 'shard.pl sep col fifo1 fifo2 fifo3 ... fifoN' in the background
# This will spread the input to fifos
# Generate commands that reads from fifo1..N:
# cat fifo | user_command
# Changes:
# @Global::cat_prepends
my @shardfifos;
my @parcatfifos;
# TODO $opt::jobs should be evaluated (100%)
# TODO $opt::jobs should be number of total_jobs if there are argugemts
my $njobs = $opt::jobs;
for my $m (0..$njobs-1) {
for my $n (0..$njobs-1) {
# sharding to A B C D
# parcatting all As together
$parcatfifos[$n][$m] = $shardfifos[$m][$n] = tmpfifo();
}
}
my $script = sharder_script();
# cat foo | sharder sep col fifo1 fifo2 fifo3 ... fifoN
if(not fork()) {
# Let the sharder inherit our stdin
# and redirect stdout to null
open STDOUT, ">","/dev/null";
# The PERL_HASH_SEED must be the same for all sharders
# so B::hash will return the same value for any given input
$ENV{'PERL_HASH_SEED'} = $$;
exec qw(parallel --block 100k -q --pipe -j), $njobs,
qw(--roundrobin -u perl -e), $script, ($opt::colsep || ","),
$opt::shard, '{}', (map { (':::+', @{$_}) } @parcatfifos);
}
# For each fifo
# (rm fifo1; grep 1) < fifo1
# (rm fifo2; grep 2) < fifo2
# (rm fifo3; grep 3) < fifo3
my $parcat = Q(parcat_script());
if(not $parcat) {
::error("'parcat' must be in path.");
::wait_and_exit(255);
}
@Global::cat_prepends = map { "perl -e $parcat @$_ | " } @parcatfifos;
}
sub pipe_part_files(@) {
# Given the bigfile
# find header and split positions
# make commands that 'cat's the partial file
# Input:
# $file = the file to read
# Returns:
# @commands that will cat_partial each part
my ($file) = @_;
my $buf = "";
if(not -f $file and not -b $file) {
::error("$file is not a seekable file.");
::wait_and_exit(255);
}
my $header = find_header(\$buf,open_or_exit($file));
# find positions
my @pos = find_split_positions($file,$Global::blocksize,length $header);
# Make @cat_prepends
my @cat_prepends = ();
for(my $i=0; $i<$#pos; $i++) {
push(@cat_prepends,
cat_partial($file, 0, length($header), $pos[$i], $pos[$i+1]));
}
return @cat_prepends;
}
sub find_header($$) {
# Compute the header based on $opt::header
# Input:
# $buf_ref = reference to read-in buffer
# $fh = filehandle to read from
# Uses:
# $opt::header
# $Global::blocksize
# Returns:
# $header string
my ($buf_ref, $fh) = @_;
my $header = "";
if($opt::header) {
if($opt::header eq ":") { $opt::header = "(.*\n)"; }
# Number = number of lines
$opt::header =~ s/^(\d+)$/"(.*\n)"x$1/e;
while(read($fh,substr($$buf_ref,length $$buf_ref,0),
$Global::blocksize)) {
if($$buf_ref=~s/^($opt::header)//) {
$header = $1;
last;
}
}
}
return $header;
}
sub find_split_positions($$$) {
# Find positions in bigfile where recend is followed by recstart
# Input:
# $file = the file to read
# $block = (minimal) --block-size of each chunk
# $headerlen = length of header to be skipped
# Uses:
# $opt::recstart
# $opt::recend
# Returns:
# @positions of block start/end
my($file, $block, $headerlen) = @_;
my $size = -s $file;
if(-b $file) {
# $file is a blockdevice
$size = size_of_block_dev($file);
}
$block = int $block;
# The optimal dd blocksize for mint, redhat, solaris, openbsd = 2^17..2^20
# The optimal dd blocksize for freebsd = 2^15..2^17
my $dd_block_size = 131072; # 2^17
my @pos;
my ($recstart,$recend) = recstartrecend();
my $recendrecstart = $recend.$recstart;
my $fh = ::open_or_exit($file);
push(@pos,$headerlen);
for(my $pos = $block+$headerlen; $pos < $size; $pos += $block) {
my $buf;
if($recendrecstart eq "") {
# records ends anywhere
push(@pos,$pos);
} else {
# Seek the the block start
seek($fh, $pos, 0) || die;
while(read($fh,substr($buf,length $buf,0),$dd_block_size)) {
if($opt::regexp) {
# If match /$recend$recstart/ => Record position
if($buf =~ m:^(.*$recend)$recstart:os) {
# Start looking for next record _after_ this match
$pos += length($1);
push(@pos,$pos);
last;
}
} else {
# If match $recend$recstart => Record position
# TODO optimize to only look at the appended
# $dd_block_size + len $recendrecstart
# TODO increase $dd_block_size to optimize for longer records
my $i = index64(\$buf,$recendrecstart);
if($i != -1) {
# Start looking for next record _after_ this match
$pos += $i + length($recend);
push(@pos,$pos);
last;
}
}
}
}
}
if($pos[$#pos] != $size) {
# Last splitpoint was not at end of the file: add it
push(@pos,$size);
}
close $fh;
return @pos;
}
sub cat_partial($@) {
# Efficient command to copy from byte X to byte Y
# Input:
# $file = the file to read
# ($start, $end, [$start2, $end2, ...]) = start byte, end byte
# Returns:
# Efficient command to copy $start..$end, $start2..$end2, ... to stdout
my($file, @start_end) = @_;
my($start, $i);
# Convert (start,end) to (start,len)
my @start_len = map {
if(++$i % 2) { $start = $_; } else { $_-$start }
} @start_end;
# This can read 7 GB/s using a single core
my $script = spacefree
(0,
q{
while(@ARGV) {
sysseek(STDIN,shift,0) || die;
$left = shift;
while($read =
sysread(STDIN,$buf, $left > 131072 ? 131072 : $left)){
$left -= $read;
syswrite(STDOUT,$buf);
}
}
});
return "<". Q($file) .
" perl -e '$script' @start_len |";
}
sub spreadstdin() {
# read a record
# Spawn a job and print the record to it.
# Uses:
# $Global::blocksize
# STDIN
# $opt::r
# $Global::max_lines
# $Global::max_number_of_args
# $opt::regexp
# $Global::start_no_new_jobs
# $opt::roundrobin
# %Global::running
# Returns: N/A
my $buf = "";
my ($recstart,$recend) = recstartrecend();
my $recendrecstart = $recend.$recstart;
my $chunk_number = 1;
my $one_time_through;
my $two_gb = 2**31-1;
my $blocksize = $Global::blocksize;
my $in = *STDIN;
my $header = find_header(\$buf,$in);
while(1) {
my $anything_written = 0;
my $buflen = length $buf;
my $readsize = ($buflen < $blocksize) ? $blocksize-$buflen : $blocksize;
# If $buf < $blocksize, append so it is $blocksize long after reading.
# Otherwise append a full $blocksize
if(not read($in,substr($buf,$buflen,0),$readsize)) {
# End-of-file
$chunk_number != 1 and last;
# Force the while-loop once if everything was read by header reading
$one_time_through++ and last;
}
if($opt::r) {
# Remove empty lines
$buf =~ s/^\s*\n//gm;
if(length $buf == 0) {
next;
}
}
if($Global::max_lines and not $Global::max_number_of_args) {
# Read n-line records
my $n_lines = $buf =~ tr/\n/\n/;
my $last_newline_pos = rindex64(\$buf,"\n");
# Go backwards until there are full n-line records
while($n_lines % $Global::max_lines) {
$n_lines--;
$last_newline_pos = rindex64(\$buf,"\n",$last_newline_pos-1);
}
# Chop at $last_newline_pos as that is where n-line record ends
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,$last_newline_pos+1);
shorten(\$buf,$last_newline_pos+1);
} elsif($opt::regexp) {
if($Global::max_number_of_args) {
# -N => (start..*?end){n}
# -L -N => (start..*?end){n*l}
my $read_n_lines = -1+
$Global::max_number_of_args * ($Global::max_lines || 1);
# (?!negative lookahead) is needed to avoid backtracking
# See: https://unix.stackexchange.com/questions/439356/
while($buf =~
/(
# Either recstart or at least one char from start
^(?: $recstart | .)
# followed something
(?:(?!$recend$recstart).)*?
# and then recend
$recend
# Then n-1 times recstart.*recend
(?:$recstart(?:(?!$recend$recstart).)*?$recend){$read_n_lines}
)
# Followed by recstart
(?=$recstart)/osx) {
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,length $1);
shorten(\$buf,length $1);
}
} else {
eof($in) and last;
# Find the last recend-recstart in $buf
if($buf =~ /^(.*$recend)$recstart.*?$/os) {
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,length $1);
shorten(\$buf,length $1);
}
}
} elsif($opt::csv) {
# Read a full CSV record
# even number of " + end of line
my $last_newline_pos = length $buf;
do {
# find last EOL
$last_newline_pos = rindex64(\$buf,"\n",$last_newline_pos-1);
# While uneven "
} while((substr($buf,0,$last_newline_pos) =~ y/"/"/)%2
and $last_newline_pos >= 0);
# Chop at $last_newline_pos as that is where CSV record ends
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,$last_newline_pos+1);
shorten(\$buf,$last_newline_pos+1);
} else {
if($Global::max_number_of_args) {
# -N => (start..*?end){n}
my $i = 0;
my $read_n_lines =
$Global::max_number_of_args * ($Global::max_lines || 1);
while(($i = nindex(\$buf,$recendrecstart,$read_n_lines)) != -1
and
length $buf) {
$i += length $recend; # find the actual splitting location
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,$i);
shorten(\$buf,$i);
}
} else {
eof($in) and last;
# Find the last recend+recstart in $buf
my $i = rindex64(\$buf,$recendrecstart);
if($i != -1) {
$i += length $recend; # find the actual splitting location
$anything_written +=
write_record_to_pipe($chunk_number++,\$header,\$buf,
$recstart,$recend,$i);
shorten(\$buf,$i);
}
}
}
if(not $anything_written
and not eof($in)
and not $Global::no_autoexpand_block) {
# Nothing was written - maybe the block size < record size?
# Increase blocksize exponentially up to 2GB-1 (2GB causes problems)
if($blocksize < $two_gb) {
my $old_blocksize = $blocksize;
$blocksize = ::min(ceil($blocksize * 1.3 + 1), $two_gb);
::warning("A record was longer than $old_blocksize. " .
"Increasing to --blocksize $blocksize.");
}
}
}
::debug("init", "Done reading input\n");
# If there is anything left in the buffer write it
write_record_to_pipe($chunk_number++, \$header, \$buf, $recstart,
$recend, length $buf);
if($opt::retries) {
$Global::no_more_input = 1;
# We need to start no more jobs: At most we need to retry some
# of the already running.
my @running = values %Global::running;
# Stop any virgins.
for my $job (@running) {
if(defined $job and $job->virgin()) {
close $job->fh(0,"w");
}
}
# Wait for running jobs to be done
my $sleep =1;
while($Global::total_running > 0) {
$sleep = ::reap_usleep($sleep);
start_more_jobs();
}
}
$Global::start_no_new_jobs ||= 1;
if($opt::roundrobin) {
# Flush blocks to roundrobin procs
my $sleep = 1;
while(%Global::running) {
my $something_written = 0;
for my $job (values %Global::running) {
if($job->block_length()) {
$something_written += $job->non_blocking_write();
} else {
close $job->fh(0,"w");
}
}
if($something_written) {
$sleep = $sleep/2+0.001;
}
$sleep = ::reap_usleep($sleep);
}
}
}
sub recstartrecend() {
# Uses:
# $opt::recstart
# $opt::recend
# Returns:
# $recstart,$recend with default values and regexp conversion
my($recstart,$recend);
if(defined($opt::recstart) and defined($opt::recend)) {
# If both --recstart and --recend is given then both must match
$recstart = $opt::recstart;
$recend = $opt::recend;
} elsif(defined($opt::recstart)) {
# If --recstart is given it must match start of record
$recstart = $opt::recstart;
$recend = "";
} elsif(defined($opt::recend)) {
# If --recend is given then it must match end of record
$recstart = "";
$recend = $opt::recend;
if($opt::regexp and $recend eq '') {
# --regexp --recend ''
$recend = '.';
}
}
if($opt::regexp) {
# If $recstart/$recend contains '|'
# this should only apply to the regexp
$recstart = "(?:".$recstart.")";
$recend = "(?:".$recend.")";
} else {
# $recstart/$recend = printf strings (\n)
$recstart =~ s/\\([0rnt\'\"\\])/"qq|\\$1|"/gee;
$recend =~ s/\\([0rnt\'\"\\])/"qq|\\$1|"/gee;
}
return ($recstart,$recend);
}
sub nindex($$) {
# See if string is in buffer N times
# Returns:
# the position where the Nth copy is found
my ($buf_ref, $str, $n) = @_;
my $i = 0;
for(1..$n) {
$i = index64($buf_ref,$str,$i+1);
if($i == -1) { last }
}
return $i;
}
{
my @robin_queue;
my $sleep = 1;
sub round_robin_write($$$$$) {
# Input:
# $header_ref = ref to $header string
# $block_ref = ref to $block to be written
# $recstart = record start string
# $recend = record end string
# $endpos = end position of $block
# Uses:
# %Global::running
# Returns:
# $something_written = amount of bytes written
my ($header_ref,$buffer_ref,$recstart,$recend,$endpos) = @_;
my $written = 0;
my $block_passed = 0;
while(not $block_passed) {
# Continue flushing existing buffers
# until one is empty and a new block is passed
if(@robin_queue) {
# Rotate queue once so new blocks get a fair chance
# to be given to another block
push @robin_queue, shift @robin_queue;
} else {
# Make a queue to spread the blocks evenly
push @robin_queue, (sort { $a->seq() <=> $b->seq() }
values %Global::running);
}
do {
$written = 0;
for my $job (@robin_queue) {
if($job->block_length() > 0) {
$written += $job->non_blocking_write();
} else {
$job->set_block($header_ref, $buffer_ref,
$endpos, $recstart, $recend);
$block_passed = 1;
$job->set_virgin(0);
$written += $job->non_blocking_write();
last;
}
}
if($written) {
$sleep = $sleep/1.5+0.001;
}
# Don't sleep if something is written
} while($written and not $block_passed);
$sleep = ::reap_usleep($sleep);
}
return $written;
}
}
sub index64($$$) {
# Do index on strings > 2GB.
# index in Perl < v5.22 does not work for > 2GB
# Input:
# as index except STR which must be passed as a reference
# Output:
# as index
my $ref = shift;
my $match = shift;
my $pos = shift || 0;
my $block_size = 2**31-1;
my $strlen = length($$ref);
# No point in doing extra work if we don't need to.
if($strlen < $block_size or $] > 5.022) {
return index($$ref, $match, $pos);
}
my $matchlen = length($match);
my $ret;
my $offset = $pos;
while($offset < $strlen) {
$ret = index(
substr($$ref, $offset, $block_size),
$match, $pos-$offset);
if($ret != -1) {
return $ret + $offset;
}
$offset += ($block_size - $matchlen - 1);
}
return -1;
}
sub rindex64($@) {
# Do rindex on strings > 2GB.
# rindex in Perl < v5.22 does not work for > 2GB
# Input:
# as rindex except STR which must be passed as a reference
# Output:
# as rindex
my $ref = shift;
my $match = shift;
my $pos = shift;
my $block_size = 2**31-1;
my $strlen = length($$ref);
# Default: search from end
$pos = defined $pos ? $pos : $strlen;
# No point in doing extra work if we don't need to.
if($strlen < $block_size) {
return rindex($$ref, $match, $pos);
}
my $matchlen = length($match);
my $ret;
my $offset = $pos - $block_size + $matchlen;
if($offset < 0) {
# The offset is less than a $block_size
# Set the $offset to 0 and
# Adjust block_size accordingly
$block_size = $block_size + $offset;
$offset = 0;
}
while($offset >= 0) {
$ret = rindex(
substr($$ref, $offset, $block_size),
$match);
if($ret != -1) {
return $ret + $offset;
}
$offset -= ($block_size - $matchlen - 1);
}
return -1;
}
sub shorten($$) {
# Do: substr($buf,0,$i) = "";
# Some Perl versions do not support $i > 2GB, so do this in 2GB chunks
# Input:
# $buf_ref = \$buf
# $i = position to shorten to
# Returns: N/A
my ($buf_ref, $i) = @_;
my $two_gb = 2**31-1;
while($i > $two_gb) {
substr($$buf_ref,0,$two_gb) = "";
$i -= $two_gb;
}
substr($$buf_ref,0,$i) = "";
}
sub write_record_to_pipe($$$$$$) {
# Fork then
# Write record from pos 0 .. $endpos to pipe
# Input:
# $chunk_number = sequence number - to see if already run
# $header_ref = reference to header string to prepend
# $buffer_ref = reference to record to write
# $recstart = start string of record
# $recend = end string of record
# $endpos = position in $buffer_ref where record ends
# Uses:
# $Global::job_already_run
# $opt::roundrobin
# @Global::virgin_jobs
# Returns:
# Number of chunks written (0 or 1)
my ($chunk_number, $header_ref, $buffer_ref,
$recstart, $recend, $endpos) = @_;
if($endpos == 0) { return 0; }
if(vec($Global::job_already_run,$chunk_number,1)) { return 1; }
if($opt::roundrobin) {
# Write the block to one of the already running jobs
return round_robin_write($header_ref, $buffer_ref,
$recstart, $recend, $endpos);
}
# If no virgin found, backoff
my $sleep = 0.0001; # 0.01 ms - better performance on highend
while(not @Global::virgin_jobs) {
::debug("pipe", "No virgin jobs");
$sleep = ::reap_usleep($sleep);
# Jobs may not be started because of loadavg
# or too little time between each ssh login
# or retrying failed jobs.
start_more_jobs();
}
my $job = shift @Global::virgin_jobs;
# Job is no longer virgin
$job->set_virgin(0);
if($opt::retries) {
# Copy $buffer[0..$endpos] to $job->{'block'}
# Remove rec_sep
# Run $job->add_transfersize
$job->set_block($header_ref, $buffer_ref, $endpos,
$recstart, $recend);
if(fork()) {
# Skip
} else {
$job->write($job->block_ref());
close $job->fh(0,"w");
exit(0);
}
} else {
# We ignore the removed rec_sep which is technically wrong.
$job->add_transfersize($endpos + length $$header_ref);
if(fork()) {
# Skip
} else {
# Chop of at $endpos as we do not know how many rec_sep will
# be removed.
substr($$buffer_ref,$endpos,length $$buffer_ref) = "";
# Remove rec_sep
if($opt::remove_rec_sep) {
Job::remove_rec_sep($buffer_ref, $recstart, $recend);
}
$job->write($header_ref);
$job->write($buffer_ref);
close $job->fh(0,"w");
exit(0);
}
}
close $job->fh(0,"w");
return 1;
}
sub __SEM_MODE__() {}
sub acquire_semaphore() {
# Acquires semaphore. If needed: spawns to the background
# Uses:
# @Global::host
# Returns:
# The semaphore to be released when jobs is complete
$Global::host{':'} = SSHLogin->new(":");
my $sem = Semaphore->new($Semaphore::name,
$Global::host{':'}->max_jobs_running());
$sem->acquire();
if($Semaphore::fg) {
# skip
} else {
if(fork()) {
exit(0);
} else {
# If run in the background, the PID will change
$sem->pid_change();
}
}
return $sem;
}
sub __PARSE_OPTIONS__() {}
sub options_hash() {
# Returns:
# %hash = the GetOptions config
return
("debug|D=s" => \$opt::D,
"xargs" => \$opt::xargs,
"m" => \$opt::m,
"X" => \$opt::X,
"v" => \@opt::v,
"sql=s" => \$opt::retired,
"sqlmaster=s" => \$opt::sqlmaster,
"sqlworker=s" => \$opt::sqlworker,
"sqlandworker=s" => \$opt::sqlandworker,
"joblog|jl=s" => \$opt::joblog,
"results|result|res=s" => \$opt::results,
"resume" => \$opt::resume,
"resume-failed|resumefailed" => \$opt::resume_failed,
"retry-failed|retryfailed" => \$opt::retry_failed,
"silent" => \$opt::silent,
"keep-order|keeporder|k" => \$opt::keeporder,
"no-keep-order|nokeeporder|nok|no-k" => \$opt::nokeeporder,
"group" => \$opt::group,
"g" => \$opt::retired,
"ungroup|u" => \$opt::ungroup,
"linebuffer|linebuffered|line-buffer|line-buffered|lb"
=> \$opt::linebuffer,
"tmux" => \$opt::tmux,
"tmuxpane" => \$opt::tmuxpane,
"null|0" => \$opt::null,
"quote|q" => \$opt::q,
# Replacement strings
"parens=s" => \$opt::parens,
"rpl=s" => \@opt::rpl,
"plus" => \$opt::plus,
"I=s" => \$opt::I,
"extensionreplace|er=s" => \$opt::U,
"U=s" => \$opt::retired,
"basenamereplace|bnr=s" => \$opt::basenamereplace,
"dirnamereplace|dnr=s" => \$opt::dirnamereplace,
"basenameextensionreplace|bner=s" => \$opt::basenameextensionreplace,
"seqreplace=s" => \$opt::seqreplace,
"slotreplace=s" => \$opt::slotreplace,
"jobs|j=s" => \$opt::jobs,
"delay=s" => \$opt::delay,
"sshdelay=f" => \$opt::sshdelay,
"load=s" => \$opt::load,
"noswap" => \$opt::noswap,
"max-line-length-allowed" => \$opt::max_line_length_allowed,
"number-of-cpus" => \$opt::number_of_cpus,
"number-of-sockets" => \$opt::number_of_sockets,
"number-of-cores" => \$opt::number_of_cores,
"number-of-threads" => \$opt::number_of_threads,
"use-sockets-instead-of-threads"
=> \$opt::use_sockets_instead_of_threads,
"use-cores-instead-of-threads"
=> \$opt::use_cores_instead_of_threads,
"use-cpus-instead-of-cores" => \$opt::use_cpus_instead_of_cores,
"shellquote|shell_quote|shell-quote" => \@opt::shellquote,
"nice=i" => \$opt::nice,
"tag" => \$opt::tag,
"tagstring|tag-string=s" => \$opt::tagstring,
"onall" => \$opt::onall,
"nonall" => \$opt::nonall,
"filter-hosts|filterhosts|filter-host" => \$opt::filter_hosts,
"sshlogin|S=s" => \@opt::sshlogin,
"sshloginfile|slf=s" => \@opt::sshloginfile,
"controlmaster|M" => \$opt::controlmaster,
"ssh=s" => \$opt::ssh,
"transfer-file|transferfile|transfer-files|transferfiles|tf=s"
=> \@opt::transfer_files,
"return=s" => \@opt::return,
"trc=s" => \@opt::trc,
"transfer" => \$opt::transfer,
"cleanup" => \$opt::cleanup,
"basefile|bf=s" => \@opt::basefile,
"B=s" => \$opt::retired,
"ctrlc|ctrl-c" => \$opt::retired,
"noctrlc|no-ctrlc|no-ctrl-c" => \$opt::retired,
"workdir|work-dir|wd=s" => \$opt::workdir,
"W=s" => \$opt::retired,
"rsync-opts|rsyncopts=s" => \$opt::rsync_opts,
"tmpdir|tempdir=s" => \$opt::tmpdir,
"use-compress-program|compress-program=s" => \$opt::compress_program,
"use-decompress-program|decompress-program=s"
=> \$opt::decompress_program,
"compress" => \$opt::compress,
"tty" => \$opt::tty,
"T" => \$opt::retired,
"H=i" => \$opt::retired,
"dry-run|dryrun|dr" => \$opt::dryrun,
"progress" => \$opt::progress,
"eta" => \$opt::eta,
"bar" => \$opt::bar,
"shuf" => \$opt::shuf,
"arg-sep|argsep=s" => \$opt::arg_sep,
"arg-file-sep|argfilesep=s" => \$opt::arg_file_sep,
"trim=s" => \$opt::trim,
"env=s" => \@opt::env,
"recordenv|record-env" => \$opt::record_env,
"session" => \$opt::session,
"plain" => \$opt::plain,
"profile|J=s" => \@opt::profile,
"pipe|spreadstdin" => \$opt::pipe,
"robin|round-robin|roundrobin" => \$opt::roundrobin,
"recstart=s" => \$opt::recstart,
"recend=s" => \$opt::recend,
"regexp|regex" => \$opt::regexp,
"remove-rec-sep|removerecsep|rrs" => \$opt::remove_rec_sep,
"files|output-as-files|outputasfiles" => \$opt::files,
"block|block-size|blocksize=s" => \$opt::blocksize,
"tollef" => \$opt::tollef,
"gnu" => \$opt::gnu,
"link|xapply" => \$opt::link,
"linkinputsource|xapplyinputsource=i" => \@opt::linkinputsource,
# Before changing this line, please read
# https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
"bibtex|citation" => \$opt::citation,
"wc|willcite|will-cite|nn|nonotice|no-notice" => \$opt::willcite,
# Termination and retries
"halt-on-error|halt=s" => \$opt::halt,
"limit=s" => \$opt::limit,
"memfree=s" => \$opt::memfree,
"retries=s" => \$opt::retries,
"timeout=s" => \$opt::timeout,
"termseq|term-seq=s" => \$opt::termseq,
# xargs-compatibility - implemented, man, testsuite
"max-procs|P=s" => \$opt::jobs,
"delimiter|d=s" => \$opt::d,
"max-chars|s=i" => \$opt::max_chars,
"arg-file|a=s" => \@opt::a,
"no-run-if-empty|r" => \$opt::r,
"replace|i:s" => \$opt::i,
"E=s" => \$opt::eof,
"eof|e:s" => \$opt::eof,
"max-args|maxargs|n=i" => \$opt::max_args,
"max-replace-args|N=i" => \$opt::max_replace_args,
"colsep|col-sep|C=s" => \$opt::colsep,
"csv"=> \$opt::csv,
"help|h" => \$opt::help,
"L=f" => \$opt::L,
"max-lines|l:f" => \$opt::max_lines,
"interactive|p" => \$opt::interactive,
"verbose|t" => \$opt::verbose,
"version|V" => \$opt::version,
"minversion|min-version=i" => \$opt::minversion,
"show-limits|showlimits" => \$opt::show_limits,
"exit|x" => \$opt::x,
# Semaphore
"semaphore" => \$opt::semaphore,
"semaphoretimeout|st=i" => \$opt::semaphoretimeout,
"semaphorename|id=s" => \$opt::semaphorename,
"fg" => \$opt::fg,
"bg" => \$opt::bg,
"wait" => \$opt::wait,
# Shebang #!/opt/local/bin/parallel --shebang
"shebang|hashbang" => \$opt::shebang,
"internal-pipe-means-argfiles"
=> \$opt::internal_pipe_means_argfiles,
"Y" => \$opt::retired,
"skip-first-line" => \$opt::skip_first_line,
"bug" => \$opt::bug,
"header=s" => \$opt::header,
"cat" => \$opt::cat,
"fifo" => \$opt::fifo,
"pipepart|pipe-part" => \$opt::pipepart,
"tee" => \$opt::tee,
"shard=s" => \$opt::shard,
"hgrp|hostgrp|hostgroup|hostgroups" => \$opt::hostgroups,
"embed" => \$opt::embed,
);
}
sub get_options_from_array($@) {
# Run GetOptions on @array
# Input:
# $array_ref = ref to @ARGV to parse
# @keep_only = Keep only these options
# Uses:
# @ARGV
# Returns:
# true if parsing worked
# false if parsing failed
# @$array_ref is changed
my ($array_ref, @keep_only) = @_;
if(not @$array_ref) {
# Empty array: No need to look more at that
return 1;
}
# A bit of shuffling of @ARGV needed as GetOptionsFromArray is not
# supported everywhere
my @save_argv;
my $this_is_ARGV = (\@::ARGV == $array_ref);
if(not $this_is_ARGV) {
@save_argv = @::ARGV;
@::ARGV = @{$array_ref};
}
# If @keep_only set: Ignore all values except @keep_only
my %options = options_hash();
if(@keep_only) {
my (%keep,@dummy);
@keep{@keep_only} = @keep_only;
for my $k (grep { not $keep{$_} } keys %options) {
# Store the value of the option in @dummy
$options{$k} = \@dummy;
}
}
my $retval = GetOptions(%options);
if(not $this_is_ARGV) {
@{$array_ref} = @::ARGV;
@::ARGV = @save_argv;
}
return $retval;
}
sub parse_options(@) {
# Returns: N/A
init_globals();
my @argv_before = @ARGV;
@ARGV = read_options();
# Before changing this line, please read
# https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
if(defined $opt::citation) {
citation(\@argv_before,\@ARGV);
wait_and_exit(0);
}
# no-* overrides *
if($opt::nokeeporder) { $opt::keeporder = undef; }
if(@opt::v) { $Global::verbose = $#opt::v+1; } # Convert -v -v to v=2
if($opt::bug) { ::die_bug("test-bug"); }
$Global::debug = $opt::D;
$Global::shell = $ENV{'PARALLEL_SHELL'} || parent_shell($$)
|| $ENV{'SHELL'} || "/bin/sh";
if(not -x $Global::shell and not which($Global::shell)) {
::error("Shell '$Global::shell' not found.");
wait_and_exit(255);
}
::debug("init","Global::shell $Global::shell\n");
$Global::cshell = $Global::shell =~ m:(/[-a-z]*)?csh:;
if(defined $opt::X) { $Global::ContextReplace = 1; }
if(defined $opt::silent) { $Global::verbose = 0; }
if(defined $opt::null) { $/ = "\0"; }
if(defined $opt::d) { $/ = unquote_printf($opt::d) }
if(defined $opt::tagstring) {
$opt::tagstring = unquote_printf($opt::tagstring);
}
if(defined $opt::interactive) { $Global::interactive = $opt::interactive; }
if(defined $opt::q) { $Global::quoting = 1; }
if(defined $opt::r) { $Global::ignore_empty = 1; }
if(defined $opt::verbose) { $Global::stderr_verbose = 1; }
parse_replacement_string_options();
if(defined $opt::eof) { $Global::end_of_file_string = $opt::eof; }
if(defined $opt::max_args) {
$Global::max_number_of_args = $opt::max_args;
}
if(defined $opt::timeout) {
$Global::timeoutq = TimeoutQueue->new($opt::timeout);
}
if(defined $opt::tmpdir) { $ENV{'TMPDIR'} = $opt::tmpdir; }
$ENV{'PARALLEL_RSYNC_OPTS'} = $opt::rsync_opts ||
$ENV{'PARALLEL_RSYNC_OPTS'} || '-rlDzR';
$opt::nice ||= 0;
if(defined $opt::help) { usage(); exit(0); }
if(defined $opt::embed) { embed(); exit(0); }
if(defined $opt::sqlandworker) {
$opt::sqlmaster = $opt::sqlworker = $opt::sqlandworker;
}
if(defined $opt::tmuxpane) { $opt::tmux = $opt::tmuxpane; }
if(defined $opt::colsep) { $Global::trim = 'lr'; }
if(defined $opt::csv) {
$Global::use{"Text::CSV"} ||= eval "use Text::CSV; 1;";
$opt::colsep = defined $opt::colsep ? $opt::colsep : ",";
my $csv_setting = { binary => 1, sep_char => $opt::colsep };
my $sep = $csv_setting->{sep_char};
$Global::csv = Text::CSV->new($csv_setting)
or die "Cannot use CSV: ".Text::CSV->error_diag ();
}
if(defined $opt::header) {
$opt::colsep = defined $opt::colsep ? $opt::colsep : "\t";
}
if(defined $opt::trim) { $Global::trim = $opt::trim; }
if(defined $opt::arg_sep) { $Global::arg_sep = $opt::arg_sep; }
if(defined $opt::arg_file_sep) {
$Global::arg_file_sep = $opt::arg_file_sep;
}
if(defined $opt::number_of_sockets) {
print SSHLogin::no_of_sockets(),"\n"; wait_and_exit(0);
}
if(defined $opt::number_of_cpus) {
print SSHLogin::no_of_cores(),"\n"; wait_and_exit(0);
}
if(defined $opt::number_of_cores) {
print SSHLogin::no_of_cores(),"\n"; wait_and_exit(0);
}
if(defined $opt::number_of_threads) {
print SSHLogin::no_of_threads(),"\n"; wait_and_exit(0);
}
if(defined $opt::max_line_length_allowed) {
print Limits::Command::real_max_length(),"\n"; wait_and_exit(0);
}
if(defined $opt::version) { version(); wait_and_exit(0); }
if(defined $opt::record_env) { record_env(); wait_and_exit(0); }
if(defined $opt::show_limits) { show_limits(); }
if(@opt::sshlogin) { @Global::sshlogin = @opt::sshlogin; }
if(@opt::sshloginfile) { read_sshloginfiles(@opt::sshloginfile); }
if(@opt::return) { push @Global::ret_files, @opt::return; }
if($opt::transfer) {
push @Global::transfer_files, $opt::i || $opt::I || "{}";
}
push @Global::transfer_files, @opt::transfer_files;
if(not defined $opt::recstart and
not defined $opt::recend) { $opt::recend = "\n"; }
$Global::blocksize = multiply_binary_prefix($opt::blocksize || "1M");
if($Global::blocksize > 2**31-1 and not $opt::pipepart) {
warning("--blocksize >= 2G causes problems. Using 2G-1.");
$Global::blocksize = 2**31-1;
}
if($^O eq "cygwin" and
($opt::pipe or $opt::pipepart or $opt::roundrobin)
and $Global::blocksize > 65535) {
warning("--blocksize >= 64K causes problems on Cygwin.");
}
$opt::memfree = multiply_binary_prefix($opt::memfree);
check_invalid_option_combinations();
if((defined $opt::fifo or defined $opt::cat)
and not $opt::pipepart) {
$opt::pipe = 1;
}
if(defined $opt::minversion) {
print $Global::version,"\n";
if($Global::version < $opt::minversion) {
wait_and_exit(255);
} else {
wait_and_exit(0);
}
}
if(not defined $opt::delay) {
# Set --delay to --sshdelay if not set
$opt::delay = $opt::sshdelay;
}
$opt::delay = multiply_time_units($opt::delay);
if($opt::compress_program) {
$opt::compress = 1;
$opt::decompress_program ||= $opt::compress_program." -dc";
}
if(defined $opt::results) {
# Is the output a dir or CSV-file?
if($opt::results =~ /\.csv$/i) {
# CSV with , as separator
$Global::csvsep = ",";
$Global::membuffer ||= 1;
} elsif($opt::results =~ /\.tsv$/i) {
# CSV with TAB as separator
$Global::csvsep = "\t";
$Global::membuffer ||= 1;
}
}
if($opt::compress) {
my ($compress, $decompress) = find_compression_program();
$opt::compress_program ||= $compress;
$opt::decompress_program ||= $decompress;
if(($opt::results and not $Global::csvsep) or $opt::files) {
# No need for decompressing
$opt::decompress_program = "cat >/dev/null";
}
}
if(defined $opt::dryrun) {
# Force grouping due to bug #51039: --dry-run --timeout 3600 -u breaks
$opt::ungroup = 0;
$opt::group = 1;
}
if(defined $opt::nonall) {
# Append a dummy empty argument if there are no arguments
# on the command line to avoid reading from STDIN.
# arg_sep = random 50 char
# \0noarg => nothing (not the empty string)
$Global::arg_sep = join "",
map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..50);
push @ARGV, $Global::arg_sep, "\0noarg";
}
if(defined $opt::tee) {
if(not defined $opt::jobs) {
$opt::jobs = 0;
}
}
if(defined $opt::tty) {
# Defaults for --tty: -j1 -u
# Can be overridden with -jXXX -g
if(not defined $opt::jobs) {
$opt::jobs = 1;
}
if(not defined $opt::group) {
$opt::ungroup = 1;
}
}
if(@opt::trc) {
push @Global::ret_files, @opt::trc;
if(not @Global::transfer_files) {
# Defaults to --transferfile {}
push @Global::transfer_files, $opt::i || $opt::I || "{}";
}
$opt::cleanup = 1;
}
if(defined $opt::max_lines) {
if($opt::max_lines eq "-0") {
# -l -0 (swallowed -0)
$opt::max_lines = 1;
$opt::null = 1;
$/ = "\0";
} elsif ($opt::max_lines == 0) {
# If not given (or if 0 is given) => 1
$opt::max_lines = 1;
}
$Global::max_lines = $opt::max_lines;
if(not $opt::pipe) {
# --pipe -L means length of record - not max_number_of_args
$Global::max_number_of_args ||= $Global::max_lines;
}
}
# Read more than one arg at a time (-L, -N)
if(defined $opt::L) {
$Global::max_lines = $opt::L;
if(not $opt::pipe) {
# --pipe -L means length of record - not max_number_of_args
$Global::max_number_of_args ||= $Global::max_lines;
}
}
if(defined $opt::max_replace_args) {
$Global::max_number_of_args = $opt::max_replace_args;
$Global::ContextReplace = 1;
}
if((defined $opt::L or defined $opt::max_replace_args)
and
not ($opt::xargs or $opt::m)) {
$Global::ContextReplace = 1;
}
if(defined $opt::tag and not defined $opt::tagstring) {
# Default = {}
$opt::tagstring = $Global::parensleft.$Global::parensright;
}
if(grep /^$Global::arg_sep\+?$|^$Global::arg_file_sep\+?$/o, @ARGV) {
# Deal with ::: :::+ :::: and ::::+
@ARGV = read_args_from_command_line();
}
parse_semaphore();
if(defined $opt::eta) { $opt::progress = $opt::eta; }
if(defined $opt::bar) { $opt::progress = $opt::bar; }
# Funding a free software project is hard. GNU Parallel is no
# exception. On top of that it seems the less visible a project
# is, the harder it is to get funding. And the nature of GNU
# Parallel is that it will never be seen by "the guy with the
# checkbook", but only by the people doing the actual work.
#
# This problem has been covered by others - though no solution has
# been found:
# https://www.slideshare.net/NadiaEghbal/consider-the-maintainer
# https://www.numfocus.org/blog/why-is-numpy-only-now-getting-funded/
#
# Before implementing the citation notice it was discussed with
# the users:
# https://lists.gnu.org/archive/html/parallel/2013-11/msg00006.html
#
# Having to spend 10 seconds on running 'parallel --citation' once
# is no doubt not an ideal solution, but no one has so far come up
# with an ideal solution - neither for funding GNU Parallel nor
# other free software.
#
# If you believe you have the perfect solution, you should try it
# out, and if it works, you should post it on the email
# list. Ideas that will cost work and which have not been tested
# are, however, unlikely to be prioritized.
#
# Please note that GPL version 3 gives you the right to fork GNU
# Parallel under a new name, but it does not give you the right to
# distribute modified copies with the citation notice disabled
# under the name GNU Parallel. To do that you need to be the owner
# of the GNU Parallel trademark. The xt:Commerce case shows this.
#
# Description of the xt:Commerce case in OLG Duesseldorf
# http://www.inta.org/INTABulletin/Pages/GERMANYGeneralPublicLicenseDoesNotPermitUseofThird-PartyTrademarksforAdvertisingModifiedVersionsofOpen-SourceSoftware.aspx
# https://web.archive.org/web/20180715073746/http://www.inta.org/INTABulletin/Pages/GERMANYGeneralPublicLicenseDoesNotPermitUseofThird-PartyTrademarksforAdvertisingModifiedVersionsofOpen-SourceSoftware.aspx
#
# The verdict in German
# https://www.admody.com/urteilsdatenbank/cafe6fdaeed3/OLG-Duesseldorf_Urteil_vom_28-September-2010_Az_I-20-U-41-09
# https://web.archive.org/web/20180715073717/https://www.admody.com/urteilsdatenbank/cafe6fdaeed3/OLG-Duesseldorf_Urteil_vom_28-September-2010_Az_I-20-U-41-09
#
# Other free software limiting derivates by the same name
# https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives#Legal_aspects
# https://tm.joomla.org/trademark-faq.html
# https://www.mozilla.org/en-US/foundation/trademarks/faq/
#
# Running 'parallel --citation' one single time takes less than 10
# seconds, and will silence the citation notice for future
# runs. If that is too much trouble for you, why not use one of
# the alternatives instead?
# See a list in: 'man parallel_alternatives'
#
# Please read the above before changing this line.
citation_notice();
parse_halt();
if($ENV{'PARALLEL_ENV'}) {
# Read environment and set $Global::parallel_env
# Must be done before is_acceptable_command_line_length()
my $penv = $ENV{'PARALLEL_ENV'};
# unset $PARALLEL_ENV: It should not be given to children
# because it takes up a lot of env space
delete $ENV{'PARALLEL_ENV'};
if(-e $penv) {
# This is a file/fifo: Replace envvar with content of file
open(my $parallel_env, "<", $penv) ||
::die_bug("Cannot read parallel_env from $penv");
local $/; # Put <> in slurp mode
$penv = <$parallel_env>;
close $parallel_env;
}
# Map \001 to \n to make it easer to quote \n in $PARALLEL_ENV
$penv =~ s/\001/\n/g;
if($penv =~ /\0/) {
::warning('\0 (NUL) in environment is not supported');
}
$Global::parallel_env = $penv;
}
parse_sshlogin();
if(remote_hosts() and ($opt::X or $opt::m or $opt::xargs)) {
# As we do not know the max line length on the remote machine
# long commands generated by xargs may fail
# If $opt::max_replace_args is set, it is probably safe
::warning("Using -X or -m with --sshlogin may fail.");
}
if(not defined $opt::jobs) { $opt::jobs = "100%"; }
open_joblog();
open_csv();
if($opt::sqlmaster or $opt::sqlworker) {
$Global::sql = SQL->new($opt::sqlmaster || $opt::sqlworker);
}
if($opt::sqlworker) { $Global::membuffer ||= 1; }
}
sub check_invalid_option_combinations() {
if(defined $opt::timeout and
$opt::timeout !~ /^\d+(\.\d+)?%?$|^(\d+(\.\d+)?[dhms])+$/i) {
::error("--timeout must be seconds or percentage.");
wait_and_exit(255);
}
if(defined $opt::fifo and defined $opt::cat) {
::error("--fifo cannot be combined with --cat.");
::wait_and_exit(255);
}
if(defined $opt::retries and defined $opt::roundrobin) {
::error("--retries cannot be combined with --roundrobin.");
::wait_and_exit(255);
}
if(defined $opt::pipepart and
(defined $opt::L or defined $opt::max_lines
or defined $opt::max_replace_args)) {
::error("--pipepart is incompatible with --max-replace-args, ".
"--max-lines, and -L.");
wait_and_exit(255);
}
if(defined $opt::group and $opt::ungroup) {
::error("--group cannot be combined with --ungroup.");
::wait_and_exit(255);
}
if(defined $opt::group and $opt::linebuffer) {
::error("--group cannot be combined with --line-buffer.");
::wait_and_exit(255);
}
if(defined $opt::ungroup and $opt::linebuffer) {
::error("--ungroup cannot be combined with --line-buffer.");
::wait_and_exit(255);
}
if(defined $opt::tollef and not $opt::gnu) {
::error("--tollef has been retired.",
"Remove --tollef or use --gnu to override --tollef.");
::wait_and_exit(255);
}
if(defined $opt::retired) {
::error("-g has been retired. Use --group.",
"-B has been retired. Use --bf.",
"-T has been retired. Use --tty.",
"-U has been retired. Use --er.",
"-W has been retired. Use --wd.",
"-Y has been retired. Use --shebang.",
"-H has been retired. Use --halt.",
"--sql has been retired. Use --sqlmaster.",
"--ctrlc has been retired.",
"--noctrlc has been retired.");
::wait_and_exit(255);
}
}
sub init_globals() {
# Defaults:
$Global::version = 20190322;
$Global::progname = 'parallel';
$Global::infinity = 2**31;
$Global::debug = 0;
$Global::verbose = 0;
$Global::quoting = 0;
$Global::total_completed = 0;
# Read only table with default --rpl values
%Global::replace =
(
'{}' => '',
'{#}' => '1 $_=$job->seq()',
'{%}' => '1 $_=$job->slot()',
'{/}' => 's:.*/::',
'{//}' =>
('$Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; '.
'$_ = dirname($_);'),
'{/.}' => 's:.*/::; s:\.[^/.]+$::;',
'{.}' => 's:\.[^/.]+$::',
);
%Global::plus =
(
# {} = {+/}/{/}
# = {.}.{+.} = {+/}/{/.}.{+.}
# = {..}.{+..} = {+/}/{/..}.{+..}
# = {...}.{+...} = {+/}/{/...}.{+...}
'{+/}' => 's:/[^/]*$::',
'{+.}' => 's:.*\.::',
'{+..}' => 's:.*\.([^.]*\.):$1:',
'{+...}' => 's:.*\.([^.]*\.[^.]*\.):$1:',
'{..}' => 's:\.[^/.]+$::; s:\.[^/.]+$::',
'{...}' => 's:\.[^/.]+$::; s:\.[^/.]+$::; s:\.[^/.]+$::',
'{/..}' => 's:.*/::; s:\.[^/.]+$::; s:\.[^/.]+$::',
'{/...}' => 's:.*/::; s:\.[^/.]+$::; s:\.[^/.]+$::; s:\.[^/.]+$::',
'{choose_k}' => 'for $t (2..$#arg){ if($arg[$t-1] ge $arg[$t]) { skip() } }',
# {##} = number of jobs
'{##}' => '$_=total_jobs()',
# Bash ${a:-myval}
'{:-([^}]+?)}' => '$_ ||= $$1',
# Bash ${a:2}
'{:(\d+?)}' => 'substr($_,0,$$1) = ""',
# Bash ${a:2:3}
'{:(\d+?):(\d+?)}' => '$_ = substr($_,$$1,$$2);',
# Bash ${a#bc}
'{#([^#}][^}]*?)}' => 's/^$$1//;',
# Bash ${a%def}
'{%([^}]+?)}' => 's/$$1$//;',
# Bash ${a/def/ghi} ${a/def/}
'{/([^}]+?)/([^}]*?)}' => 's/$$1/$$2/;',
# Bash ${a^a}
'{^([^}]+?)}' => 's/^($$1)/uc($1)/e;',
# Bash ${a^^a}
'{^^([^}]+?)}' => 's/($$1)/uc($1)/eg;',
# Bash ${a,A}
'{,([^}]+?)}' => 's/^($$1)/lc($1)/e;',
# Bash ${a,,A}
'{,,([^}]+?)}' => 's/($$1)/lc($1)/eg;',
);
# Modifiable copy of %Global::replace
%Global::rpl = %Global::replace;
$/ = "\n";
$Global::ignore_empty = 0;
$Global::interactive = 0;
$Global::stderr_verbose = 0;
$Global::default_simultaneous_sshlogins = 9;
$Global::exitstatus = 0;
$Global::arg_sep = ":::";
$Global::arg_file_sep = "::::";
$Global::trim = 'n';
$Global::max_jobs_running = 0;
$Global::job_already_run = '';
$ENV{'TMPDIR'} ||= "/tmp";
$ENV{'OLDPWD'} = $ENV{'PWD'};
if(not $ENV{HOME}) {
# $ENV{HOME} is sometimes not set if called from PHP
::warning("\$HOME not set. Using /tmp.");
$ENV{HOME} = "/tmp";
}
# no warnings to allow for undefined $XDG_*
no warnings 'uninitialized';
# $xdg_config_home is needed to make env_parallel.fish stop complaining
my $xdg_config_home = $ENV{'XDG_CONFIG_HOME'};
# config_dirs = $PARALLEL_HOME, $XDG_CONFIG_HOME/parallel,
# $(each XDG_CONFIG_DIRS)/parallel, $HOME/.parallel
# Keep only dirs that exist
@Global::config_dirs =
(grep { -d $_ }
$ENV{'PARALLEL_HOME'},
(map { "$_/parallel" }
$xdg_config_home,
split /:/, $ENV{'XDG_CONFIG_DIRS'}),
$ENV{'HOME'} . "/.parallel");
# Use first dir as config dir
$Global::config_dir = $Global::config_dirs[0] ||
$ENV{'HOME'} . "/.parallel";
# cache_dirs = $PARALLEL_HOME, $XDG_CACHE_HOME/parallel,
# Keep only dirs that exist
@Global::cache_dirs =
(grep { -d $_ }
$ENV{'PARALLEL_HOME'}, $ENV{'XDG_CACHE_HOME'}."/parallel");
$Global::cache_dir = $Global::cache_dirs[0] ||
$ENV{'HOME'} . "/.parallel";
}
sub parse_halt() {
# $opt::halt flavours
# Uses:
# $opt::halt
# $Global::halt_when
# $Global::halt_fail
# $Global::halt_success
# $Global::halt_pct
# $Global::halt_count
if(defined $opt::halt) {
my %halt_expansion = (
"0" => "never",
"1" => "soon,fail=1",
"2" => "now,fail=1",
"-1" => "soon,success=1",
"-2" => "now,success=1",
);
# Expand -2,-1,0,1,2 into long form
$opt::halt = $halt_expansion{$opt::halt} || $opt::halt;
# --halt 5% == --halt soon,fail=5%
$opt::halt =~ s/^(\d+)%$/soon,fail=$1%/;
# Split: soon,fail=5%
my ($when,$fail_success,$pct_count) = split /[,=]/, $opt::halt;
if(not grep { $when eq $_ } qw(never soon now)) {
::error("--halt must have 'never', 'soon', or 'now'.");
::wait_and_exit(255);
}
$Global::halt_when = $when;
if($when ne "never") {
if($fail_success eq "fail") {
$Global::halt_fail = 1;
} elsif($fail_success eq "success") {
$Global::halt_success = 1;
} elsif($fail_success eq "done") {
$Global::halt_done = 1;
} else {
::error("--halt $when must be followed by ,success or ,fail.");
::wait_and_exit(255);
}
if($pct_count =~ /^(\d+)%$/) {
$Global::halt_pct = $1/100;
} elsif($pct_count =~ /^(\d+)$/) {
$Global::halt_count = $1;
} else {
::error("--halt $when,$fail_success ".
"must be followed by ,number or ,percent%.");
::wait_and_exit(255);
}
}
}
}
sub parse_replacement_string_options() {
# Deal with --rpl
# Uses:
# %Global::rpl
# $Global::parensleft
# $Global::parensright
# $opt::parens
# $Global::parensleft
# $Global::parensright
# $opt::plus
# %Global::plus
# $opt::I
# $opt::U
# $opt::i
# $opt::basenamereplace
# $opt::dirnamereplace
# $opt::seqreplace
# $opt::slotreplace
# $opt::basenameextensionreplace
sub rpl($$) {
# Modify %Global::rpl
# Replace $old with $new
my ($old,$new) = @_;
if($old ne $new) {
$Global::rpl{$new} = $Global::rpl{$old};
delete $Global::rpl{$old};
}
}
my $parens = "{==}";
if(defined $opt::parens) { $parens = $opt::parens; }
my $parenslen = 0.5*length $parens;
$Global::parensleft = substr($parens,0,$parenslen);
$Global::parensright = substr($parens,$parenslen);
if(defined $opt::plus) { %Global::rpl = (%Global::plus,%Global::rpl); }
if(defined $opt::I) { rpl('{}',$opt::I); }
if(defined $opt::i and $opt::i) { rpl('{}',$opt::i); }
if(defined $opt::U) { rpl('{.}',$opt::U); }
if(defined $opt::basenamereplace) { rpl('{/}',$opt::basenamereplace); }
if(defined $opt::dirnamereplace) { rpl('{//}',$opt::dirnamereplace); }
if(defined $opt::seqreplace) { rpl('{#}',$opt::seqreplace); }
if(defined $opt::slotreplace) { rpl('{%}',$opt::slotreplace); }
if(defined $opt::basenameextensionreplace) {
rpl('{/.}',$opt::basenameextensionreplace);
}
for(@opt::rpl) {
# Create $Global::rpl entries for --rpl options
# E.g: "{..} s:\.[^.]+$:;s:\.[^.]+$:;"
my ($shorthand,$long) = split/ /,$_,2;
$Global::rpl{$shorthand} = $long;
}
}
sub parse_semaphore() {
# Semaphore defaults
# Must be done before computing number of processes and max_line_length
# because when running as a semaphore GNU Parallel does not read args
# Uses:
# $opt::semaphore
# $Global::semaphore
# $opt::semaphoretimeout
# $Semaphore::timeout
# $opt::semaphorename
# $Semaphore::name
# $opt::fg
# $Semaphore::fg
# $opt::wait
# $Semaphore::wait
# $opt::bg
# @opt::a
# @Global::unget_argv
# $Global::default_simultaneous_sshlogins
# $opt::jobs
# $Global::interactive
$Global::semaphore ||= ($0 =~ m:(^|/)sem$:); # called as 'sem'
if(defined $opt::semaphore) { $Global::semaphore = 1; }
if(defined $opt::semaphoretimeout) { $Global::semaphore = 1; }
if(defined $opt::semaphorename) { $Global::semaphore = 1; }
if(defined $opt::fg and not $opt::tmux and not $opt::tmuxpane) {
$Global::semaphore = 1;
}
if(defined $opt::bg) { $Global::semaphore = 1; }
if(defined $opt::wait and not $opt::sqlmaster) {
$Global::semaphore = 1; @ARGV = "true";
}
if($Global::semaphore) {
if(@opt::a) {
# A semaphore does not take input from neither stdin nor file
::error("A semaphore does not take input from neither stdin nor a file\n");
::wait_and_exit(255);
}
@opt::a = ("/dev/null");
# Append a dummy empty argument
# \0 => nothing (not the empty string)
push(@Global::unget_argv, [Arg->new("\0noarg")]);
$Semaphore::timeout = $opt::semaphoretimeout || 0;
if(defined $opt::semaphorename) {
$Semaphore::name = $opt::semaphorename;
} else {
local $/ = "\n";
$Semaphore::name = `tty`;
chomp $Semaphore::name;
}
$Semaphore::fg = $opt::fg;
$Semaphore::wait = $opt::wait;
$Global::default_simultaneous_sshlogins = 1;
if(not defined $opt::jobs) {
$opt::jobs = 1;
}
if($Global::interactive and $opt::bg) {
::error("Jobs running in the ".
"background cannot be interactive.");
::wait_and_exit(255);
}
}
}
sub record_env() {
# Record current %ENV-keys in $PARALLEL_HOME/ignored_vars
# Returns: N/A
my $ignore_filename = $Global::config_dir . "/ignored_vars";
if(open(my $vars_fh, ">", $ignore_filename)) {
print $vars_fh map { $_,"\n" } keys %ENV;
} else {
::error("Cannot write to $ignore_filename.");
::wait_and_exit(255);
}
}
sub open_joblog() {
# Open joblog as specified by --joblog
# Uses:
# $opt::resume
# $opt::resume_failed
# $opt::joblog
# $opt::results
# $Global::job_already_run
# %Global::fd
my $append = 0;
if(($opt::resume or $opt::resume_failed)
and
not ($opt::joblog or $opt::results)) {
::error("--resume and --resume-failed require --joblog or --results.");
::wait_and_exit(255);
}
if(defined $opt::joblog and $opt::joblog =~ s/^\+//) {
# --joblog +filename = append to filename
$append = 1;
}
if($opt::joblog
and
($opt::sqlmaster
or
not $opt::sqlworker)) {
# Do not log if --sqlworker
if($opt::resume || $opt::resume_failed || $opt::retry_failed) {
if(open(my $joblog_fh, "<", $opt::joblog)) {
# Read the joblog
# Override $/ with \n because -d might be set
local $/ = "\n";
# If there is a header: Open as append later
$append = <$joblog_fh>;
my $joblog_regexp;
if($opt::retry_failed) {
# Make a regexp that only matches commands with exit+signal=0
# 4 host 1360490623.067 3.445 1023 1222 0 0 command
$joblog_regexp='^(\d+)(?:\t[^\t]+){5}\t0\t0\t';
my @group;
while(<$joblog_fh>) {
if(/$joblog_regexp/o) {
# This is 30% faster than set_job_already_run($1);
vec($Global::job_already_run,($1||0),1) = 1;
$Global::total_completed++;
$group[$1-1] = "true";
} elsif(/(\d+)\s+\S+(\s+[-0-9.]+){6}\s+(.*)$/) {
# Grab out the command
$group[$1-1] = $3;
} else {
chomp;
::error("Format of '$opt::joblog' is wrong: $_");
::wait_and_exit(255);
}
}
if(@group) {
my ($outfh,$name) = ::tmpfile(SUFFIX => ".arg");
unlink($name);
# Put args into argfile
if(grep /\0/, @group) {
# force --null to deal with \n in commandlines
::warning("Command lines contain newline. Forcing --null.");
$opt::null = 1;
$/ = "\0";
}
# Replace \0 with '\n' as used in print_joblog()
print $outfh map { s/\0/\n/g; $_,$/ } map { $_ } @group;
seek $outfh, 0, 0;
exit_if_disk_full();
# Set filehandle to -a
@opt::a = ($outfh);
}
# Remove $command (so -a is run)
@ARGV = ();
}
if($opt::resume || $opt::resume_failed) {
if($opt::resume_failed) {
# Make a regexp that only matches commands with exit+signal=0
# 4 host 1360490623.067 3.445 1023 1222 0 0 command
$joblog_regexp='^(\d+)(?:\t[^\t]+){5}\t0\t0\t';
} else {
# Just match the job number
$joblog_regexp='^(\d+)';
}
while(<$joblog_fh>) {
if(/$joblog_regexp/o) {
# This is 30% faster than set_job_already_run($1);
vec($Global::job_already_run,($1||0),1) = 1;
$Global::total_completed++;
} elsif(not /\d+\s+[^\s]+\s+([-0-9.]+\s+){6}/) {
::error("Format of '$opt::joblog' is wrong: $_");
::wait_and_exit(255);
}
}
}
close $joblog_fh;
}
# $opt::null may be set if the commands contain \n
if($opt::null) { $/ = "\0"; }
}
if($opt::dryrun) {
# Do not write to joblog in a dry-run
if(not open($Global::joblog, ">", "/dev/null")) {
::error("Cannot write to --joblog $opt::joblog.");
::wait_and_exit(255);
}
} elsif($append) {
# Append to joblog
if(not open($Global::joblog, ">>", $opt::joblog)) {
::error("Cannot append to --joblog $opt::joblog.");
::wait_and_exit(255);
}
} else {
if($opt::joblog eq "-") {
# Use STDOUT as joblog
$Global::joblog = $Global::fd{1};
} elsif(not open($Global::joblog, ">", $opt::joblog)) {
# Overwrite the joblog
::error("Cannot write to --joblog $opt::joblog.");
::wait_and_exit(255);
}
print $Global::joblog
join("\t", "Seq", "Host", "Starttime", "JobRuntime",
"Send", "Receive", "Exitval", "Signal", "Command"
). "\n";
}
}
}
sub open_csv() {
if($opt::results) {
# Output as CSV/TSV
if($opt::results eq "-.csv"
or
$opt::results eq "-.tsv") {
# Output as CSV/TSV on stdout
open $Global::csv_fh, ">&", "STDOUT" or
::die_bug("Can't dup STDOUT in csv: $!");
# Do not print any other output to STDOUT
# by forcing all other output to /dev/null
open my $fd, ">", "/dev/null" or
::die_bug("Can't >/dev/null in csv: $!");
$Global::fd{1} = $fd;
$Global::fd{2} = $fd;
} elsif($Global::csvsep) {
if(not open($Global::csv_fh,">",$opt::results)) {
::error("Cannot open results file `$opt::results': ".
"$!.");
wait_and_exit(255);
}
}
}
}
sub find_compression_program() {
# Find a fast compression program
# Returns:
# $compress_program = compress program with options
# $decompress_program = decompress program with options
# Search for these. Sorted by speed on 128 core
# seq 120000000|shuf > 1gb &
# apt-get update
# apt install make g++ htop
# wget -O - pi.dk/3 | bash
# apt install zstd clzip liblz4-tool lzop pigz pxz gzip plzip pbzip2 lzma xz-utils lzip bzip2 lbzip2 lrzip pixz
# git clone https://github.com/facebook/zstd.git
# (cd zstd/contrib/pzstd; make -j; cp pzstd /usr/local/bin)
# echo 'lrzip -L $((-$1))' >/usr/local/bin/lrz
# chmod +x /usr/local/bin/lrz
# wait
# onethread="zstd clzip lz4 lzop gzip lzma xz bzip2"
# multithread="pzstd pigz pxz plzip pbzip2 lzip lbzip2 lrz pixz"
# parallel --shuf -j1 --joblog jl-m --arg-sep , parallel --compress-program \'{3}" "-{2}\' cat ::: 1gb '>'/dev/null , 1 2 3 , {1..3} , $multithread
# parallel --shuf -j50% --delay 1 --joblog jl-s --arg-sep , parallel --compress-program \'{3}" "-{2}\' cat ::: 1gb '>'/dev/null , 1 2 3 , {1..3} , $onethread
# sort -nk4 jl-?
# 1-core:
# 2-cores: pzstd zstd lz4 lzop pigz gzip lbzip2 pbzip2 lrz bzip2 lzma pxz plzip xz lzip clzip
# 4-cores:
# 8-cores: pzstd lz4 zstd pigz lzop lbzip2 pbzip2 gzip lzip lrz plzip pxz bzip2 lzma xz clzip
# 16-cores: pzstd lz4 pigz lzop lbzip2 pbzip2 plzip lzip lrz pxz gzip lzma xz bzip2
# 32-cores: pzstd lbzip2 pbzip2 zstd pigz lz4 lzop plzip lzip lrz gzip pxz lzma bzip2 xz clzip
# 64-cores: pzstd lbzip2 pbzip2 pigz zstd pixz lz4 plzip lzop lzip lrz gzip pxz lzma bzip2 xz clzip
# 128-core: pzstd lbzip2 pbzip2 zstd pixz lz4 pigz lzop plzip lzip gzip lrz pxz bzip2 lzma xz clzip
my @prg = qw(pzstd lbzip2 pbzip2 zstd pixz lz4 pigz lzop plzip lzip gzip
lrz pxz bzip2 lzma xz clzip);
for my $p (@prg) {
if(which($p)) {
return ("$p -c -1","$p -dc");
}
}
# Fall back to cat
return ("cat","cat");
}
sub read_options() {
# Read options from command line, profile and $PARALLEL
# Uses:
# $opt::shebang_wrap
# $opt::shebang
# @ARGV
# $opt::plain
# @opt::profile
# $ENV{'HOME'}
# $ENV{'PARALLEL'}
# Returns:
# @ARGV_no_opt = @ARGV without --options
# This must be done first as this may exec myself
if(defined $ARGV[0] and ($ARGV[0] =~ /^--shebang/ or
$ARGV[0] =~ /^--shebang-?wrap/ or
$ARGV[0] =~ /^--hashbang/)) {
# Program is called from #! line in script
# remove --shebang-wrap if it is set
$opt::shebang_wrap = ($ARGV[0] =~ s/^--shebang-?wrap *//);
# remove --shebang if it is set
$opt::shebang = ($ARGV[0] =~ s/^--shebang *//);
# remove --hashbang if it is set
$opt::shebang .= ($ARGV[0] =~ s/^--hashbang *//);
if($opt::shebang) {
my $argfile = Q(pop @ARGV);
# exec myself to split $ARGV[0] into separate fields
exec "$0 --skip-first-line -a $argfile @ARGV";
}
if($opt::shebang_wrap) {
my @options;
my @parser;
if ($^O eq 'freebsd') {
# FreeBSD's #! puts different values in @ARGV than Linux' does.
my @nooptions = @ARGV;
get_options_from_array(\@nooptions);
while($#ARGV > $#nooptions) {
push @options, shift @ARGV;
}
while(@ARGV and $ARGV[0] ne ":::") {
push @parser, shift @ARGV;
}
if(@ARGV and $ARGV[0] eq ":::") {
shift @ARGV;
}
} else {
@options = shift @ARGV;
}
my $script = Q(shift @ARGV);
# exec myself to split $ARGV[0] into separate fields
exec "$0 --internal-pipe-means-argfiles @options @parser $script ".
"::: @ARGV";
}
}
if($ARGV[0] =~ / --shebang(-?wrap)? /) {
::warning("--shebang and --shebang-wrap must be the first argument.\n");
}
Getopt::Long::Configure("bundling","require_order");
my @ARGV_copy = @ARGV;
my @ARGV_orig = @ARGV;
# Check if there is a --profile to set @opt::profile
get_options_from_array(\@ARGV_copy,"profile|J=s","plain") || die_usage();
my @ARGV_profile = ();
my @ARGV_env = ();
if(not $opt::plain) {
# Add options from $PARALLEL_HOME/config and other profiles
my @config_profiles = (
"/etc/parallel/config",
(map { "$_/config" } @Global::config_dirs),
$ENV{'HOME'}."/.parallelrc");
my @profiles = @config_profiles;
if(@opt::profile) {
# --profile overrides default profiles
@profiles = ();
for my $profile (@opt::profile) {
# Look for the $profile in . and @Global::config_dirs
push @profiles, grep { -r $_ }
map { "$_/$profile" } ".", @Global::config_dirs;
}
}
for my $profile (@profiles) {
if(-r $profile) {
local $/ = "\n";
open (my $in_fh, "<", $profile) ||
::die_bug("read-profile: $profile");
while(<$in_fh>) {
/^\s*\#/ and next;
chomp;
push @ARGV_profile, shell_words($_);
}
close $in_fh;
} else {
if(grep /^$profile$/, @config_profiles) {
# config file is not required to exist
} else {
::error("$profile not readable.");
wait_and_exit(255);
}
}
}
# Add options from shell variable $PARALLEL
if($ENV{'PARALLEL'}) {
push @ARGV_env, shell_words($ENV{'PARALLEL'});
}
# Add options from env_parallel.csh via $PARALLEL_CSH
if($ENV{'PARALLEL_CSH'}) {
push @ARGV_env, shell_words($ENV{'PARALLEL_CSH'});
}
}
Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV_profile) || die_usage();
get_options_from_array(\@ARGV_env) || die_usage();
get_options_from_array(\@ARGV) || die_usage();
# What were the options given on the command line?
# Used to start --sqlworker
my $ai = arrayindex(\@ARGV_orig, \@ARGV);
@Global::options_in_argv = @ARGV_orig[0..$ai-1];
# Prepend non-options to @ARGV (such as commands like 'nice')
unshift @ARGV, @ARGV_profile, @ARGV_env;
return @ARGV;
}
sub arrayindex() {
# Similar to Perl's index function, but for arrays
# Input:
# $arr_ref1 = ref to @array1 to search in
# $arr_ref2 = ref to @array2 to search for
# Returns:
# $pos = position of @array1 in @array2, -1 if not found
my ($arr_ref1,$arr_ref2) = @_;
my $array1_as_string = join "", map { "\0".$_ } @$arr_ref1;
my $array2_as_string = join "", map { "\0".$_ } @$arr_ref2;
my $i = index($array1_as_string,$array2_as_string,0);
if($i == -1) { return -1 }
my @before = split /\0/, substr($array1_as_string,0,$i);
return $#before;
}
sub read_args_from_command_line() {
# Arguments given on the command line after:
# ::: ($Global::arg_sep)
# :::: ($Global::arg_file_sep)
# :::+ ($Global::arg_sep with --link)
# ::::+ ($Global::arg_file_sep with --link)
# Removes the arguments from @ARGV and:
# - puts filenames into -a
# - puts arguments into files and add the files to -a
# - adds --linkinputsource with 0/1 for each -a depending on :::+/::::+
# Input:
# @::ARGV = command option ::: arg arg arg :::: argfiles
# Uses:
# $Global::arg_sep
# $Global::arg_file_sep
# $opt::internal_pipe_means_argfiles
# $opt::pipe
# @opt::a
# Returns:
# @argv_no_argsep = @::ARGV without ::: and :::: and following args
my @new_argv = ();
for(my $arg = shift @ARGV; @ARGV; $arg = shift @ARGV) {
if($arg eq $Global::arg_sep
or
$arg eq $Global::arg_sep."+"
or
$arg eq $Global::arg_file_sep
or
$arg eq $Global::arg_file_sep."+") {
my $group_sep = $arg; # This group of arguments is args or argfiles
my @group;
while(defined ($arg = shift @ARGV)) {
if($arg eq $Global::arg_sep
or
$arg eq $Global::arg_sep."+"
or
$arg eq $Global::arg_file_sep
or
$arg eq $Global::arg_file_sep."+") {
# exit while loop if finding new separator
last;
} else {
# If not hitting ::: :::+ :::: or ::::+
# Append it to the group
push @group, $arg;
}
}
my $is_linked = ($group_sep =~ /\+$/) ? 1 : 0;
my $is_file = ($group_sep eq $Global::arg_file_sep
or
$group_sep eq $Global::arg_file_sep."+");
if($is_file) {
# :::: / ::::+
push @opt::linkinputsource, map { $is_linked } @group;
} else {
# ::: / :::+
push @opt::linkinputsource, $is_linked;
}
if($is_file
or ($opt::internal_pipe_means_argfiles and $opt::pipe)
) {
# Group of file names on the command line.
# Append args into -a
push @opt::a, @group;
} else {
# Group of arguments on the command line.
# Put them into a file.
# Create argfile
my ($outfh,$name) = ::tmpfile(SUFFIX => ".arg");
unlink($name);
# Put args into argfile
print $outfh map { $_,$/ } @group;
seek $outfh, 0, 0;
exit_if_disk_full();
# Append filehandle to -a
push @opt::a, $outfh;
}
if(defined($arg)) {
# $arg is ::: :::+ :::: or ::::+
# so there is another group
redo;
} else {
# $arg is undef -> @ARGV empty
last;
}
}
push @new_argv, $arg;
}
# Output: @ARGV = command to run with options
return @new_argv;
}
sub cleanup() {
# Returns: N/A
unlink keys %Global::unlink;
map { rmdir $_ } keys %Global::unlink;
if(@opt::basefile and $opt::cleanup) { cleanup_basefile(); }
for(keys %Global::sshmaster) {
# If 'ssh -M's are running: kill them
kill "TERM", $_;
}
}
sub __QUOTING_ARGUMENTS_FOR_SHELL__() {}
sub shell_quote(@) {
# Input:
# @strings = strings to be quoted
# Returns:
# @shell_quoted_strings = string quoted as needed by the shell
return wantarray ? (map { Q($_) } @_) : (join" ",map { Q($_) } @_);
}
sub shell_quote_scalar_rc($) {
# Quote for the rc-shell
my $a = $_[0];
if(defined $a) {
if(($a =~ s/'/''/g)
+
($a =~ s/[\n\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]+/'$&'/go)) {
# A string was replaced
# No need to test for "" or \0
} elsif($a eq "") {
$a = "''";
} elsif($a eq "\0") {
$a = "";
}
}
return $a;
}
sub shell_quote_scalar_csh($) {
# Quote for (t)csh
my $a = $_[0];
if(defined $a) {
# $a =~ s/([\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\>\<\~\|\; \"\!\$\&\'\202-\377])/\\$1/g;
# This is 1% faster than the above
if(($a =~ s/[\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]/\\$&/go)
+
# quote newline in csh as \\\n
($a =~ s/[\n]/"\\\n"/go)) {
# A string was replaced
# No need to test for "" or \0
} elsif($a eq "") {
$a = "''";
} elsif($a eq "\0") {
$a = "";
}
}
return $a;
}
sub shell_quote_scalar_default($) {
# Quote for other shells (Bourne compatibles)
# Inputs:
# $string = string to be quoted
# Returns:
# $shell_quoted = string quoted as needed by the shell
my $par = $_[0];
if($par =~ /[^-_.+a-z0-9\/]/i) {
$par =~ s/'/'"'"'/g; # "-quote single quotes
$par = "'$par'"; # '-quote entire string
$par =~ s/^''|''$//g; # Remove unneeded '' at ends
return $par;
} elsif ($par eq "") {
return "''";
} else {
# No quoting needed
return $par;
}
}
sub shell_quote_scalar($) {
# Quote the string so the shell will not expand any special chars
# Inputs:
# $string = string to be quoted
# Returns:
# $shell_quoted = string quoted as needed by the shell
# Speed optimization: Choose the correct shell_quote_scalar_*
# and call that directly from now on
no warnings 'redefine';
if($Global::cshell) {
# (t)csh
*shell_quote_scalar = \&shell_quote_scalar_csh;
} elsif($Global::shell =~ m:(^|/)rc$:) {
# rc-shell
*shell_quote_scalar = \&shell_quote_scalar_rc;
} else {
# other shells
*shell_quote_scalar = \&shell_quote_scalar_default;
}
# The sub is now redefined. Call it
return shell_quote_scalar(@_);
}
sub Q($) {
# Q alias for ::shell_quote_scalar
no warnings 'redefine';
*Q = \&::shell_quote_scalar;
return Q(@_);
}
sub shell_quote_file($) {
# Quote the string so shell will not expand any special chars
# and prepend ./ if needed
# Input:
# $filename = filename to be shell quoted
# Returns:
# $quoted_filename = filename quoted with \ and ./ if needed
my $a = shift;
if(defined $a) {
if($a =~ m:^/: or $a =~ m:^\./:) {
# /abs/path or ./rel/path => skip
} else {
# rel/path => ./rel/path
$a = "./".$a;
}
}
return Q($a);
}
sub shell_words(@) {
# Input:
# $string = shell line
# Returns:
# @shell_words = $string split into words as shell would do
$Global::use{"Text::ParseWords"} ||= eval "use Text::ParseWords; 1;";
return Text::ParseWords::shellwords(@_);
}
sub perl_quote_scalar($) {
# Quote the string so perl's eval will not expand any special chars
# Inputs:
# $string = string to be quoted
# Returns:
# $perl_quoted = string quoted with \ as needed by perl's eval
my $a = $_[0];
if(defined $a) {
$a =~ s/[\\\"\$\@]/\\$&/go;
}
return $a;
}
# -w complains about prototype
sub pQ($) {
# pQ alias for ::perl_quote_scalar
*pQ = \&::perl_quote_scalar;
return pQ(@_);
}
sub unquote_printf() {
# Convert \t \n \r \000 \0
# Inputs:
# $string = string with \t \n \r \num \0
# Returns:
# $replaced = string with TAB NEWLINE CR <ascii-num> NUL
$_ = shift;
s/\\t/\t/g;
s/\\n/\n/g;
s/\\r/\r/g;
s/\\(\d\d\d)/eval 'sprintf "\\'.$1.'"'/ge;
s/\\(\d)/eval 'sprintf "\\'.$1.'"'/ge;
return $_;
}
sub __FILEHANDLES__() {}
sub save_stdin_stdout_stderr() {
# Remember the original STDIN, STDOUT and STDERR
# and file descriptors opened by the shell (e.g. 3>/tmp/foo)
# Uses:
# %Global::fd
# $Global::original_stderr
# $Global::original_stdin
# Returns: N/A
# TODO Disabled until we have an open3 that will take n filehandles
# for my $fdno (1..61) {
# # /dev/fd/62 and above are used by bash for <(cmd)
# # Find file descriptors that are already opened (by the shell)
# Only focus on stdout+stderr for now
for my $fdno (1..2) {
my $fh;
# 2-argument-open is used to be compatible with old perl 5.8.0
# bug #43570: Perl 5.8.0 creates 61 files
if(open($fh,">&=$fdno")) {
$Global::fd{$fdno}=$fh;
}
}
open $Global::original_stderr, ">&", "STDERR" or
::die_bug("Can't dup STDERR: $!");
open $Global::status_fd, ">&", "STDERR" or
::die_bug("Can't dup STDERR: $!");
open $Global::original_stdin, "<&", "STDIN" or
::die_bug("Can't dup STDIN: $!");
}
sub enough_file_handles() {
# Check that we have enough filehandles available for starting
# another job
# Uses:
# $opt::ungroup
# %Global::fd
# Returns:
# 1 if ungrouped (thus not needing extra filehandles)
# 0 if too few filehandles
# 1 if enough filehandles
if(not $opt::ungroup) {
my %fh;
my $enough_filehandles = 1;
# perl uses 7 filehandles for something?
# open3 uses 2 extra filehandles temporarily
# We need a filehandle for each redirected file descriptor
# (normally just STDOUT and STDERR)
for my $i (1..(7+2+keys %Global::fd)) {
$enough_filehandles &&= open($fh{$i}, "<", "/dev/null");
}
for (values %fh) { close $_; }
return $enough_filehandles;
} else {
# Ungrouped does not need extra file handles
return 1;
}
}
sub open_or_exit($) {
# Open a file name or exit if the file cannot be opened
# Inputs:
# $file = filehandle or filename to open
# Uses:
# $Global::original_stdin
# Returns:
# $fh = file handle to read-opened file
my $file = shift;
if($file eq "-") {
return ($Global::original_stdin || *STDIN);
}
if(ref $file eq "GLOB") {
# This is an open filehandle
return $file;
}
my $fh = gensym;
if(not open($fh, "<", $file)) {
::error("Cannot open input file `$file': No such file or directory.");
wait_and_exit(255);
}
return $fh;
}
sub set_fh_blocking($) {
# Set filehandle as blocking
# Inputs:
# $fh = filehandle to be blocking
# Returns:
# N/A
my $fh = shift;
$Global::use{"Fcntl"} ||= eval "use Fcntl qw(:DEFAULT :flock); 1;";
my $flags;
# Get the current flags on the filehandle
fcntl($fh, &F_GETFL, $flags) || die $!;
# Remove non-blocking from the flags
$flags &= ~&O_NONBLOCK;
# Set the flags on the filehandle
fcntl($fh, &F_SETFL, $flags) || die $!;
}
sub set_fh_non_blocking($) {
# Set filehandle as non-blocking
# Inputs:
# $fh = filehandle to be blocking
# Returns:
# N/A
my $fh = shift;
$Global::use{"Fcntl"} ||= eval "use Fcntl qw(:DEFAULT :flock); 1;";
my $flags;
# Get the current flags on the filehandle
fcntl($fh, &F_GETFL, $flags) || die $!;
# Add non-blocking to the flags
$flags |= &O_NONBLOCK;
# Set the flags on the filehandle
fcntl($fh, &F_SETFL, $flags) || die $!;
}
sub __RUNNING_THE_JOBS_AND_PRINTING_PROGRESS__() {}
# Variable structure:
#
# $Global::running{$pid} = Pointer to Job-object
# @Global::virgin_jobs = Pointer to Job-object that have received no input
# $Global::host{$sshlogin} = Pointer to SSHLogin-object
# $Global::total_running = total number of running jobs
# $Global::total_started = total jobs started
# $Global::max_procs_file = filename if --jobs is given a filename
# $Global::JobQueue = JobQueue object for the queue of jobs
# $Global::timeoutq = queue of times where jobs timeout
# $Global::newest_job = Job object of the most recent job started
# $Global::newest_starttime = timestamp of $Global::newest_job
# @Global::sshlogin
# $Global::minimal_command_line_length = minimum length supported by all sshlogins
# $Global::start_no_new_jobs = should more jobs be started?
# $Global::original_stderr = file handle for STDERR when the program started
# $Global::total_started = total number of jobs started
# $Global::joblog = filehandle of joblog
# $Global::debug = Is debugging on?
# $Global::exitstatus = status code of GNU Parallel
# $Global::quoting = quote the command to run
sub init_run_jobs() {
# Set Global variables and progress signal handlers
# Do the copying of basefiles
# Returns: N/A
$Global::total_running = 0;
$Global::total_started = 0;
$SIG{USR1} = \&list_running_jobs;
$SIG{USR2} = \&toggle_progress;
if(@opt::basefile) { setup_basefile(); }
}
{
my $last_time;
my %last_mtime;
my $max_procs_file_last_mod;
sub changed_procs_file {
# If --jobs is a file and it is modfied:
# Force recomputing of max_jobs_running for each $sshlogin
# Uses:
# $Global::max_procs_file
# %Global::host
# Returns: N/A
if($Global::max_procs_file) {
# --jobs filename
my $mtime = (stat($Global::max_procs_file))[9];
$max_procs_file_last_mod ||= 0;
if($mtime > $max_procs_file_last_mod) {
# file changed: Force re-computing max_jobs_running
$max_procs_file_last_mod = $mtime;
for my $sshlogin (values %Global::host) {
$sshlogin->set_max_jobs_running(undef);
}
}
}
}
sub changed_sshloginfile {
# If --slf is changed:
# reload --slf
# filter_hosts
# setup_basefile
# Uses:
# @opt::sshloginfile
# @Global::sshlogin
# %Global::host
# $opt::filter_hosts
# Returns: N/A
if(@opt::sshloginfile) {
# Is --sshloginfile changed?
for my $slf (@opt::sshloginfile) {
my $actual_file = expand_slf_shorthand($slf);
my $mtime = (stat($actual_file))[9];
$last_mtime{$actual_file} ||= $mtime;
if($mtime - $last_mtime{$actual_file} > 1) {
::debug("run","--sshloginfile $actual_file changed. reload\n");
$last_mtime{$actual_file} = $mtime;
# Reload $slf
# Empty sshlogins
@Global::sshlogin = ();
for (values %Global::host) {
# Don't start new jobs on any host
# except the ones added back later
$_->set_max_jobs_running(0);
}
# This will set max_jobs_running on the SSHlogins
read_sshloginfile($actual_file);
parse_sshlogin();
$opt::filter_hosts and filter_hosts();
setup_basefile();
}
}
}
}
sub start_more_jobs {
# Run start_another_job() but only if:
# * not $Global::start_no_new_jobs set
# * not JobQueue is empty
# * not load on server is too high
# * not server swapping
# * not too short time since last remote login
# Uses:
# %Global::host
# $Global::start_no_new_jobs
# $Global::JobQueue
# $opt::pipe
# $opt::load
# $opt::noswap
# $opt::delay
# $Global::newest_starttime
# Returns:
# $jobs_started = number of jobs started
my $jobs_started = 0;
if($Global::start_no_new_jobs) {
return $jobs_started;
}
if(time - ($last_time||0) > 1) {
# At most do this every second
$last_time = time;
changed_procs_file();
changed_sshloginfile();
}
# This will start 1 job on each --sshlogin (if possible)
# thus distribute the jobs on the --sshlogins round robin
for my $sshlogin (values %Global::host) {
if($Global::JobQueue->empty() and not $opt::pipe) {
# No more jobs in the queue
last;
}
debug("run", "Running jobs before on ", $sshlogin->string(), ": ",
$sshlogin->jobs_running(), "\n");
if ($sshlogin->jobs_running() < $sshlogin->max_jobs_running()) {
if($opt::delay
and
$opt::delay > ::now() - $Global::newest_starttime) {
# It has been too short since last start
next;
}
if($opt::load and $sshlogin->loadavg_too_high()) {
# The load is too high or unknown
next;
}
if($opt::noswap and $sshlogin->swapping()) {
# The server is swapping
next;
}
if($opt::limit and $sshlogin->limit()) {
# Over limit
next;
}
if($opt::memfree and $sshlogin->memfree() < $opt::memfree) {
# The server has not enough mem free
::debug("mem", "Not starting job: not enough mem\n");
next;
}
if($sshlogin->too_fast_remote_login()) {
# It has been too short since
next;
}
debug("run", $sshlogin->string(),
" has ", $sshlogin->jobs_running(),
" out of ", $sshlogin->max_jobs_running(),
" jobs running. Start another.\n");
if(start_another_job($sshlogin) == 0) {
# No more jobs to start on this $sshlogin
debug("run","No jobs started on ",
$sshlogin->string(), "\n");
next;
}
$sshlogin->inc_jobs_running();
$sshlogin->set_last_login_at(::now());
$jobs_started++;
}
debug("run","Running jobs after on ", $sshlogin->string(), ": ",
$sshlogin->jobs_running(), " of ",
$sshlogin->max_jobs_running(), "\n");
}
return $jobs_started;
}
}
{
my $no_more_file_handles_warned;
sub start_another_job() {
# If there are enough filehandles
# and JobQueue not empty
# and not $job is in joblog
# Then grab a job from Global::JobQueue,
# start it at sshlogin
# mark it as virgin_job
# Inputs:
# $sshlogin = the SSHLogin to start the job on
# Uses:
# $Global::JobQueue
# $opt::pipe
# $opt::results
# $opt::resume
# @Global::virgin_jobs
# Returns:
# 1 if another jobs was started
# 0 otherwise
my $sshlogin = shift;
# Do we have enough file handles to start another job?
if(enough_file_handles()) {
if($Global::JobQueue->empty() and not $opt::pipe) {
# No more commands to run
debug("start", "Not starting: JobQueue empty\n");
return 0;
} else {
my $job;
# Skip jobs already in job log
# Skip jobs already in results
do {
$job = get_job_with_sshlogin($sshlogin);
if(not defined $job) {
# No command available for that sshlogin
debug("start", "Not starting: no jobs available for ",
$sshlogin->string(), "\n");
return 0;
}
if($job->is_already_in_joblog()) {
$job->free_slot();
}
} while ($job->is_already_in_joblog()
or
($opt::results and $opt::resume and $job->is_already_in_results()));
debug("start", "Command to run on '", $job->sshlogin()->string(), "': '",
$job->replaced(),"'\n");
if($job->start()) {
if($opt::pipe) {
if($job->virgin()) {
push(@Global::virgin_jobs,$job);
} else {
# Block already set: This is a retry
if(fork()) {
::debug("pipe","\n\nWriting ",length ${$job->block_ref()},
" to ", $job->seq(),"\n");
close $job->fh(0,"w");
} else {
$job->write($job->block_ref());
close $job->fh(0,"w");
exit(0);
}
}
}
debug("start", "Started as seq ", $job->seq(),
" pid:", $job->pid(), "\n");
return 1;
} else {
# Not enough processes to run the job.
# Put it back on the queue.
$Global::JobQueue->unget($job);
# Count down the number of jobs to run for this SSHLogin.
my $max = $sshlogin->max_jobs_running();
if($max > 1) { $max--; } else {
my @arg;
for my $record (@{$job->{'commandline'}->{'arg_list'}}) {
push @arg, map { $_->orig() } @$record;
}
::error("No more processes: cannot run a single job. Something is wrong at @arg.");
::wait_and_exit(255);
}
$sshlogin->set_max_jobs_running($max);
# Sleep up to 300 ms to give other processes time to die
::usleep(rand()*300);
::warning("No more processes: ".
"Decreasing number of running jobs to $max.",
"Raising ulimit -u or /etc/security/limits.conf may help.");
return 0;
}
}
} else {
# No more file handles
$no_more_file_handles_warned++ or
::warning("No more file handles. ",
"Raising ulimit -n or /etc/security/limits.conf may help.");
debug("start", "No more file handles. ");
return 0;
}
}
}
sub init_progress() {
# Uses:
# $opt::bar
# Returns:
# list of computers for progress output
$|=1;
if($opt::bar) {
return("","");
}
my %progress = progress();
return ("\nComputers / CPU cores / Max jobs to run\n",
$progress{'workerlist'});
}
sub drain_job_queue(@) {
# Uses:
# $opt::progress
# $Global::total_running
# $Global::max_jobs_running
# %Global::running
# $Global::JobQueue
# %Global::host
# $Global::start_no_new_jobs
# Returns: N/A
my @command = @_;
if($opt::progress) {
::status_no_nl(init_progress());
}
my $last_header = "";
my $sleep = 0.2;
do {
while($Global::total_running > 0) {
debug($Global::total_running, "==", scalar
keys %Global::running," slots: ", $Global::max_jobs_running);
if($opt::pipe) {
# When using --pipe sometimes file handles are not closed properly
for my $job (values %Global::running) {
close $job->fh(0,"w");
}
}
if($opt::progress) {
my %progress = progress();
if($last_header ne $progress{'header'}) {
::status("", $progress{'header'});
$last_header = $progress{'header'};
}
::status_no_nl("\r",$progress{'status'});
}
if($Global::total_running < $Global::max_jobs_running
and not $Global::JobQueue->empty()) {
# These jobs may not be started because of loadavg
# or too little time between each ssh login.
if(start_more_jobs() > 0) {
# Exponential back-on if jobs were started
$sleep = $sleep/2+0.001;
}
}
# Exponential back-off sleeping
$sleep = ::reap_usleep($sleep);
}
if(not $Global::JobQueue->empty()) {
# These jobs may not be started:
# * because there the --filter-hosts has removed all
if(not %Global::host) {
::error("There are no hosts left to run on.");
::wait_and_exit(255);
}
# * because of loadavg
# * because of too little time between each ssh login.
$sleep = ::reap_usleep($sleep);
start_more_jobs();
if($Global::max_jobs_running == 0) {
::warning("There are no job slots available. Increase --jobs.");
}
}
while($opt::sqlmaster and not $Global::sql->finished()) {
# SQL master
$sleep = ::reap_usleep($sleep);
start_more_jobs();
if($Global::start_sqlworker) {
# Start an SQL worker as we are now sure there is work to do
$Global::start_sqlworker = 0;
if(my $pid = fork()) {
$Global::unkilled_sqlworker = $pid;
} else {
# Replace --sql/--sqlandworker with --sqlworker
my @ARGV = map { s/^--sql(andworker)?$/--sqlworker/; $_ } @Global::options_in_argv;
# exec the --sqlworker
exec($0,@ARGV,@command);
}
}
}
} while ($Global::total_running > 0
or
not $Global::start_no_new_jobs and not $Global::JobQueue->empty()
or
$opt::sqlmaster and not $Global::sql->finished());
if($opt::progress) {
my %progress = progress();
::status("\r".$progress{'status'});
}
}
sub toggle_progress() {
# Turn on/off progress view
# Uses:
# $opt::progress
# Returns: N/A
$opt::progress = not $opt::progress;
if($opt::progress) {
::status_no_nl(init_progress());
}
}
sub progress() {
# Uses:
# $opt::bar
# $opt::eta
# %Global::host
# $Global::total_started
# Returns:
# $workerlist = list of workers
# $header = that will fit on the screen
# $status = message that will fit on the screen
if($opt::bar) {
return ("workerlist" => "", "header" => "", "status" => bar());
}
my $eta = "";
my ($status,$header)=("","");
if($opt::eta) {
my($total, $completed, $left, $pctcomplete, $avgtime, $this_eta) =
compute_eta();
$eta = sprintf("ETA: %ds Left: %d AVG: %.2fs ",
$this_eta, $left, $avgtime);
}
my $termcols = terminal_columns();
my @workers = sort keys %Global::host;
my %sshlogin = map { $_ eq ":" ? ($_ => "local") : ($_ => $_) } @workers;
my $workerno = 1;
my %workerno = map { ($_=>$workerno++) } @workers;
my $workerlist = "";
for my $w (@workers) {
$workerlist .=
$workerno{$w}.":".$sshlogin{$w} ." / ".
($Global::host{$w}->ncpus() || "-")." / ".
$Global::host{$w}->max_jobs_running()."\n";
}
$status = "x"x($termcols+1);
# Select an output format that will fit on a single line
if(length $status > $termcols) {
# sshlogin1:XX/XX/XX%/XX.Xs sshlogin2:XX/XX/XX%/XX.Xs sshlogin3:XX/XX/XX%/XX.Xs
$header = "Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete";
$status = $eta .
join(" ",map
{
if($Global::total_started) {
my $completed = ($Global::host{$_}->jobs_completed()||0);
my $running = $Global::host{$_}->jobs_running();
my $time = $completed ? (time-$^T)/($completed) : "0";
sprintf("%s:%d/%d/%d%%/%.1fs ",
$sshlogin{$_}, $running, $completed,
($running+$completed)*100
/ $Global::total_started, $time);
}
} @workers);
}
if(length $status > $termcols) {
# 1:XX/XX/XX%/XX.Xs 2:XX/XX/XX%/XX.Xs 3:XX/XX/XX%/XX.Xs 4:XX/XX/XX%/XX.Xs
$header = "Computer:jobs running/jobs completed/%of started jobs";
$status = $eta .
join(" ",map
{
if($Global::total_started) {
my $completed = ($Global::host{$_}->jobs_completed()||0);
my $running = $Global::host{$_}->jobs_running();
my $time = $completed ? (time-$^T)/($completed) : "0";
sprintf("%s:%d/%d/%d%%/%.1fs ",
$workerno{$_}, $running, $completed,
($running+$completed)*100
/ $Global::total_started, $time);
}
} @workers);
}
if(length $status > $termcols) {
# sshlogin1:XX/XX/XX% sshlogin2:XX/XX/XX% sshlogin3:XX/XX/XX%
$header = "Computer:jobs running/jobs completed/%of started jobs";
$status = $eta .
join(" ",map
{
if($Global::total_started) {
sprintf("%s:%d/%d/%d%%",
$sshlogin{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started)
}
}
@workers);
}
if(length $status > $termcols) {
# 1:XX/XX/XX% 2:XX/XX/XX% 3:XX/XX/XX% 4:XX/XX/XX% 5:XX/XX/XX% 6:XX/XX/XX%
$header = "Computer:jobs running/jobs completed/%of started jobs";
$status = $eta .
join(" ",map
{
if($Global::total_started) {
sprintf("%s:%d/%d/%d%%",
$workerno{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started)
}
}
@workers);
}
if(length $status > $termcols) {
# sshlogin1:XX/XX/XX% sshlogin2:XX/XX/XX% sshlogin3:XX/XX sshlogin4:XX/XX
$header = "Computer:jobs running/jobs completed";
$status = $eta .
join(" ",map
{ sprintf("%s:%d/%d",
$sshlogin{$_}, $Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0)) }
@workers);
}
if(length $status > $termcols) {
# sshlogin1:XX/XX sshlogin2:XX/XX sshlogin3:XX/XX sshlogin4:XX/XX
$header = "Computer:jobs running/jobs completed";
$status = $eta .
join(" ",map
{ sprintf("%s:%d/%d",
$sshlogin{$_}, $Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0)) }
@workers);
}
if(length $status > $termcols) {
# 1:XX/XX 2:XX/XX 3:XX/XX 4:XX/XX 5:XX/XX 6:XX/XX
$header = "Computer:jobs running/jobs completed";
$status = $eta .
join(" ",map
{ sprintf("%s:%d/%d",
$workerno{$_}, $Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0)) }
@workers);
}
if(length $status > $termcols) {
# sshlogin1:XX sshlogin2:XX sshlogin3:XX sshlogin4:XX sshlogin5:XX
$header = "Computer:jobs completed";
$status = $eta .
join(" ",map
{ sprintf("%s:%d",
$sshlogin{$_},
($Global::host{$_}->jobs_completed()||0)) }
@workers);
}
if(length $status > $termcols) {
# 1:XX 2:XX 3:XX 4:XX 5:XX 6:XX
$header = "Computer:jobs completed";
$status = $eta .
join(" ",map
{ sprintf("%s:%d",
$workerno{$_},
($Global::host{$_}->jobs_completed()||0)) }
@workers);
}
return ("workerlist" => $workerlist, "header" => $header, "status" => $status);
}
{
my ($first_completed, $smoothed_avg_time, $last_eta);
sub compute_eta {
# Calculate important numbers for ETA
# Returns:
# $total = number of jobs in total
# $completed = number of jobs completed
# $left = number of jobs left
# $pctcomplete = percent of jobs completed
# $avgtime = averaged time
# $eta = smoothed eta
my $completed = $Global::total_completed;
# In rare cases with -X will $completed > total_jobs()
my $total = ::max($Global::JobQueue->total_jobs(),$completed);
my $left = $total - $completed;
if(not $completed) {
return($total, $completed, $left, 0, 0, 0);
}
my $pctcomplete = ::min($completed / $total,100);
$first_completed ||= time;
my $timepassed = (time - $first_completed);
my $avgtime = $timepassed / $completed;
$smoothed_avg_time ||= $avgtime;
# Smooth the eta so it does not jump wildly
$smoothed_avg_time = (1 - $pctcomplete) * $smoothed_avg_time +
$pctcomplete * $avgtime;
my $eta = int($left * $smoothed_avg_time);
if($eta*0.90 < $last_eta and $last_eta < $eta) {
# Eta jumped less that 10% up: Keep the last eta instead
$eta = $last_eta;
} else {
$last_eta = $eta;
}
return($total, $completed, $left, $pctcomplete, $avgtime, $eta);
}
}
{
my ($rev,$reset);
sub bar() {
# Return:
# $status = bar with eta, completed jobs, arg and pct
$rev ||= "\033[7m";
$reset ||= "\033[0m";
my($total, $completed, $left, $pctcomplete, $avgtime, $eta) =
compute_eta();
my $arg = $Global::newest_job ?
$Global::newest_job->{'commandline'}->
replace_placeholders(["\257<\257>"],0,0) : "";
# These chars mess up display in the terminal
$arg =~ tr/[\011-\016\033\302-\365]//d;
my $eta_dhms = ::seconds_to_time_units($eta);
my $bar_text =
sprintf("%d%% %d:%d=%s %s",
$pctcomplete*100, $completed, $left, $eta_dhms, $arg);
my $terminal_width = terminal_columns();
my $s = sprintf("%-${terminal_width}s",
substr($bar_text." "x$terminal_width,
0,$terminal_width));
my $width = int($terminal_width * $pctcomplete);
substr($s,$width,0) = $reset;
my $zenity = sprintf("%-${terminal_width}s",
substr("# $eta sec $arg",
0,$terminal_width));
$s = "\r" . $zenity . "\r" . $pctcomplete*100 . # Prefix with zenity header
"\r" . $rev . $s . $reset;
return $s;
}
}
{
my ($columns,$last_column_time);
sub terminal_columns() {
# Get the number of columns of the terminal.
# Only update once per second.
# Returns:
# number of columns of the screen
if(not $columns or $last_column_time < time) {
$last_column_time = time;
$columns = $ENV{'COLUMNS'};
if(not $columns) {
my $stty = ::qqx("stty -a </dev/tty");
# FreeBSD/OpenBSD/NetBSD/Dragonfly/MirOS
# MacOSX/IRIX/AIX/Tru64
$stty =~ /(\d+) columns/ and do { $columns = $1; };
# GNU/Linux/Solaris
$stty =~ /columns (\d+)/ and do { $columns = $1; };
# Solaris-x86/HPUX/SCOsysV/UnixWare/OpenIndiana
$stty =~ /columns = (\d+)/ and do { $columns = $1; };
# QNX
$stty =~ /rows=\d+,(\d+)/ and do { $columns = $1; };
}
if(not $columns) {
my $resize = ::qqx("resize");
$resize =~ /COLUMNS=(\d+);/ and do { $columns = $1; };
}
$columns ||= 80;
}
return $columns;
}
}
# Prototype forwarding
sub get_job_with_sshlogin($);
sub get_job_with_sshlogin($) {
# Input:
# $sshlogin = which host should the job be run on?
# Uses:
# $opt::hostgroups
# $Global::JobQueue
# Returns:
# $job = next job object for $sshlogin if any available
my $sshlogin = shift;
my $job;
if ($opt::hostgroups) {
my @other_hostgroup_jobs = ();
while($job = $Global::JobQueue->get()) {
if($sshlogin->in_hostgroups($job->hostgroups())) {
# Found a job to be run on a hostgroup of this
# $sshlogin
last;
} else {
# This job was not in the hostgroups of $sshlogin
push @other_hostgroup_jobs, $job;
}
}
$Global::JobQueue->unget(@other_hostgroup_jobs);
if(not defined $job) {
# No more jobs
return undef;
}
} else {
$job = $Global::JobQueue->get();
if(not defined $job) {
# No more jobs
::debug("start", "No more jobs: JobQueue empty\n");
return undef;
}
}
$job->set_sshlogin($sshlogin);
if($opt::retries and $job->failed_here()) {
# This command with these args failed for this sshlogin
my ($no_of_failed_sshlogins,$min_failures) = $job->min_failed();
# Only look at the Global::host that have > 0 jobslots
if($no_of_failed_sshlogins ==
grep { $_->max_jobs_running() > 0 } values %Global::host
and $job->failed_here() == $min_failures) {
# It failed the same or more times on another host:
# run it on this host
} else {
# If it failed fewer times on another host:
# Find another job to run
my $nextjob;
if(not $Global::JobQueue->empty()) {
# This can potentially recurse for all args
no warnings 'recursion';
$nextjob = get_job_with_sshlogin($sshlogin);
}
# Push the command back on the queue
$Global::JobQueue->unget($job);
return $nextjob;
}
}
return $job;
}
sub __REMOTE_SSH__() {}
sub read_sshloginfiles(@) {
# Read a list of --slf's
# Input:
# @files = files or symbolic file names to read
# Returns: N/A
for my $s (@_) {
read_sshloginfile(expand_slf_shorthand($s));
}
}
sub expand_slf_shorthand($) {
# Expand --slf shorthand into a read file name
# Input:
# $file = file or symbolic file name to read
# Returns:
# $file = actual file name to read
my $file = shift;
if($file eq "-") {
# skip: It is stdin
} elsif($file eq "..") {
$file = $Global::config_dir."/sshloginfile";
} elsif($file eq ".") {
$file = "/etc/parallel/sshloginfile";
} elsif(not -r $file) {
for(@Global::config_dirs) {
if(not -r $_."/".$file) {
# Try prepending $PARALLEL_HOME
::error("Cannot open $file.");
::wait_and_exit(255);
} else {
$file = $_."/".$file;
last;
}
}
}
return $file;
}
sub read_sshloginfile($) {
# Read sshloginfile into @Global::sshlogin
# Input:
# $file = file to read
# Uses:
# @Global::sshlogin
# Returns: N/A
local $/ = "\n";
my $file = shift;
my $close = 1;
my $in_fh;
::debug("init","--slf ",$file);
if($file eq "-") {
$in_fh = *STDIN;
$close = 0;
} else {
if(not open($in_fh, "<", $file)) {
# Try the filename
::error("Cannot open $file.");
::wait_and_exit(255);
}
}
while(<$in_fh>) {
chomp;
/^\s*#/ and next;
/^\s*$/ and next;
push @Global::sshlogin, $_;
}
if($close) {
close $in_fh;
}
}
sub parse_sshlogin() {
# Parse @Global::sshlogin into %Global::host.
# Keep only hosts that are in one of the given ssh hostgroups.
# Uses:
# @Global::sshlogin
# $Global::minimal_command_line_length
# %Global::host
# $opt::transfer
# @opt::return
# $opt::cleanup
# @opt::basefile
# @opt::trc
# Returns: N/A
my @login;
if(not @Global::sshlogin) { @Global::sshlogin = (":"); }
for my $sshlogin (@Global::sshlogin) {
# Split up -S sshlogin,sshlogin
for my $s (split /,|\n/, $sshlogin) {
if ($s eq ".." or $s eq "-") {
# This may add to @Global::sshlogin - possibly bug
read_sshloginfile(expand_slf_shorthand($s));
} else {
$s =~ s/\s*$//;
push (@login, $s);
}
}
}
$Global::minimal_command_line_length = 8_000_000;
my @allowed_hostgroups;
for my $ncpu_sshlogin_string (::uniq(@login)) {
my $sshlogin = SSHLogin->new($ncpu_sshlogin_string);
my $sshlogin_string = $sshlogin->string();
if($sshlogin_string eq "") {
# This is an ssh group: -S @webservers
push @allowed_hostgroups, $sshlogin->hostgroups();
next;
}
if($Global::host{$sshlogin_string}) {
# This sshlogin has already been added:
# It is probably a host that has come back
# Set the max_jobs_running back to the original
debug("run","Already seen $sshlogin_string\n");
if($sshlogin->{'ncpus'}) {
# If ncpus set by '#/' of the sshlogin, overwrite it:
$Global::host{$sshlogin_string}->set_ncpus($sshlogin->ncpus());
}
$Global::host{$sshlogin_string}->set_max_jobs_running(undef);
next;
}
$sshlogin->set_maxlength(Limits::Command::max_length());
$Global::minimal_command_line_length =
::min($Global::minimal_command_line_length, $sshlogin->maxlength());
$Global::host{$sshlogin_string} = $sshlogin;
}
if(@allowed_hostgroups) {
# Remove hosts that are not in these groups
while (my ($string, $sshlogin) = each %Global::host) {
if(not $sshlogin->in_hostgroups(@allowed_hostgroups)) {
delete $Global::host{$string};
}
}
}
# debug("start", "sshlogin: ", my_dump(%Global::host),"\n");
if(@Global::transfer_files or @opt::return or $opt::cleanup or @opt::basefile) {
if(not remote_hosts()) {
# There are no remote hosts
if(@opt::trc) {
::warning("--trc ignored as there are no remote --sshlogin.");
} elsif (defined $opt::transfer) {
::warning("--transfer ignored as there are no remote --sshlogin.");
} elsif (@opt::transfer_files) {
::warning("--transferfile ignored as there are no remote --sshlogin.");
} elsif (@opt::return) {
::warning("--return ignored as there are no remote --sshlogin.");
} elsif (defined $opt::cleanup) {
::warning("--cleanup ignored as there are no remote --sshlogin.");
} elsif (@opt::basefile) {
::warning("--basefile ignored as there are no remote --sshlogin.");
}
}
}
}
sub remote_hosts() {
# Return sshlogins that are not ':'
# Uses:
# %Global::host
# Returns:
# list of sshlogins with ':' removed
return grep !/^:$/, keys %Global::host;
}
sub setup_basefile() {
# Transfer basefiles to each $sshlogin
# This needs to be done before first jobs on $sshlogin is run
# Uses:
# %Global::host
# @opt::basefile
# Returns: N/A
my @cmd;
my $rsync_destdir;
my $workdir;
for my $sshlogin (values %Global::host) {
if($sshlogin->string() eq ":") { next }
for my $file (@opt::basefile) {
if($file !~ m:^/: and $opt::workdir eq "...") {
::error("Work dir '...' will not work with relative basefiles.");
::wait_and_exit(255);
}
if(not $workdir) {
my $dummycmdline = CommandLine->new(1,["true"],{},0,0,[],[],{},{},{});
my $dummyjob = Job->new($dummycmdline);
$workdir = $dummyjob->workdir();
}
push @cmd, $sshlogin->rsync_transfer_cmd($file,$workdir);
}
}
debug("init", "basesetup: @cmd\n");
my ($exitstatus,$stdout_ref,$stderr_ref) =
run_parallel((join "\n",@cmd),"-j0","--retries",5);
if($exitstatus) {
my @stdout = @$stdout_ref;
my @stderr = @$stderr_ref;
::error("Copying of --basefile failed: @stdout@stderr");
::wait_and_exit(255);
}
}
sub cleanup_basefile() {
# Remove the basefiles transferred
# Uses:
# %Global::host
# @opt::basefile
# Returns: N/A
my @cmd;
my $workdir;
if(not $workdir) {
my $dummycmdline = CommandLine->new(1,"true",0,0,0,0,0,{},{},{});
my $dummyjob = Job->new($dummycmdline);
$workdir = $dummyjob->workdir();
}
for my $sshlogin (values %Global::host) {
if($sshlogin->string() eq ":") { next }
for my $file (@opt::basefile) {
push @cmd, $sshlogin->cleanup_cmd($file,$workdir);
}
}
debug("init", "basecleanup: @cmd\n");
my ($exitstatus,$stdout_ref,$stderr_ref) =
run_parallel(join("\n",@cmd),"-j0","--retries",5);
if($exitstatus) {
my @stdout = @$stdout_ref;
my @stderr = @$stderr_ref;
::error("Cleanup of --basefile failed: @stdout@stderr");
::wait_and_exit(255);
}
}
sub run_parallel() {
my ($stdin,@args) = @_;
my $cmd = join "",map { " $_ & " } split /\n/, $stdin;
print $Global::original_stderr ` $cmd wait` ;
return 0
}
sub _run_parallel() {
# Run GNU Parallel
# This should ideally just fork an internal copy
# and not start it through a shell
# Input:
# $stdin = data to provide on stdin for GNU Parallel
# @args = command line arguments
# Returns:
# $exitstatus = exitcode of GNU Parallel run
# \@stdout = standard output
# \@stderr = standard error
my ($stdin,@args) = @_;
my ($exitstatus,@stdout,@stderr);
my ($stdin_fh,$stdout_fh)=(gensym(),gensym());
my ($stderr_fh, $stderrname) = ::tmpfile(SUFFIX => ".par");
unlink $stderrname;
my $pid = ::open3($stdin_fh,$stdout_fh,$stderr_fh,
$0,qw(--plain --shell /bin/sh --will-cite), @args);
if(my $writerpid = fork()) {
close $stdin_fh;
@stdout = <$stdout_fh>;
# Now stdout is closed:
# These pids should be dead or die very soon
while(kill 0, $writerpid) { ::usleep(1); }
die;
# reap $writerpid;
# while(kill 0, $pid) { ::usleep(1); }
# reap $writerpid;
$exitstatus = $?;
seek $stderr_fh, 0, 0;
@stderr = <$stderr_fh>;
close $stdout_fh;
close $stderr_fh;
} else {
close $stdout_fh;
close $stderr_fh;
print $stdin_fh $stdin;
close $stdin_fh;
exit(0);
}
return ($exitstatus,\@stdout,\@stderr);
}
sub filter_hosts() {
# Remove down --sshlogins from active duty.
# Find ncpus, ncores, maxlen, time-to-login for each host.
# Uses:
# %Global::host
# $Global::minimal_command_line_length
# $opt::use_sockets_instead_of_threads
# $opt::use_cores_instead_of_threads
# $opt::use_cpus_instead_of_cores
# Returns: N/A
my ($nsockets_ref,$ncores_ref, $nthreads_ref, $time_to_login_ref,
$maxlen_ref, $echo_ref, $down_hosts_ref) =
parse_host_filtering(parallelized_host_filtering());
delete @Global::host{@$down_hosts_ref};
@$down_hosts_ref and ::warning("Removed @$down_hosts_ref.");
$Global::minimal_command_line_length = 8_000_000;
while (my ($sshlogin, $obj) = each %Global::host) {
if($sshlogin eq ":") { next }
$nsockets_ref->{$sshlogin} or
::die_bug("nsockets missing: ".$obj->serverlogin());
$ncores_ref->{$sshlogin} or
::die_bug("ncores missing: ".$obj->serverlogin());
$nthreads_ref->{$sshlogin} or
::die_bug("nthreads missing: ".$obj->serverlogin());
$time_to_login_ref->{$sshlogin} or
::die_bug("time_to_login missing: ".$obj->serverlogin());
$maxlen_ref->{$sshlogin} or
::die_bug("maxlen missing: ".$obj->serverlogin());
$obj->set_ncpus($nthreads_ref->{$sshlogin});
if($opt::use_cpus_instead_of_cores) {
$obj->set_ncpus($ncores_ref->{$sshlogin});
} elsif($opt::use_sockets_instead_of_threads) {
$obj->set_ncpus($nsockets_ref->{$sshlogin});
} elsif($opt::use_cores_instead_of_threads) {
$obj->set_ncpus($ncores_ref->{$sshlogin});
}
$obj->set_time_to_login($time_to_login_ref->{$sshlogin});
$obj->set_maxlength($maxlen_ref->{$sshlogin});
$Global::minimal_command_line_length =
::min($Global::minimal_command_line_length,
int($maxlen_ref->{$sshlogin}/2));
::debug("init", "Timing from -S:$sshlogin ",
" nsockets:",$nsockets_ref->{$sshlogin},
" ncores:", $ncores_ref->{$sshlogin},
" nthreads:",$nthreads_ref->{$sshlogin},
" time_to_login:", $time_to_login_ref->{$sshlogin},
" maxlen:", $maxlen_ref->{$sshlogin},
" min_max_len:", $Global::minimal_command_line_length,"\n");
}
}
sub parse_host_filtering() {
# Input:
# @lines = output from parallelized_host_filtering()
# Returns:
# \%nsockets = number of sockets of {host}
# \%ncores = number of cores of {host}
# \%nthreads = number of hyperthreaded cores of {host}
# \%time_to_login = time_to_login on {host}
# \%maxlen = max command len on {host}
# \%echo = echo received from {host}
# \@down_hosts = list of hosts with no answer
local $/ = "\n";
my (%nsockets, %ncores, %nthreads, %time_to_login, %maxlen, %echo,
@down_hosts);
for (@_) {
::debug("init","Read: ",$_);
chomp;
my @col = split /\t/, $_;
if($col[0] =~ /^parallel: Warning:/) {
# Timed out job: Ignore it
next;
} elsif(defined $col[6]) {
# This is a line from --joblog
# seq host time spent sent received exit signal command
# 2 : 1372607672.654 0.675 0 0 0 0 eval true\ m\;ssh\ m\ parallel\ --number-of-cores
if($col[0] eq "Seq" and $col[1] eq "Host" and
$col[2] eq "Starttime") {
# Header => skip
next;
}
# Get server from: eval true server\;
$col[8] =~ /eval .?true.?\s([^\;]+);/ or
::die_bug("col8 does not contain host: $col[8]");
my $host = $1;
$host =~ tr/\\//d;
$Global::host{$host} or next;
if($col[6] eq "255" or $col[6] eq "-1" or $col[6] eq "1") {
# exit == 255 or exit == timeout (-1): ssh failed/timedout
# exit == 1: lsh failed
# Remove sshlogin
::debug("init", "--filtered $host\n");
push(@down_hosts, $host);
} elsif($col[6] eq "127") {
# signal == 127: parallel not installed remote
# Set nsockets, ncores, nthreads = 1
::warning("Could not figure out ".
"number of cpus on $host. Using 1.");
$nsockets{$host} = 1;
$ncores{$host} = 1;
$nthreads{$host} = 1;
$maxlen{$host} = Limits::Command::max_length();
} elsif($col[0] =~ /^\d+$/ and $Global::host{$host}) {
# Remember how log it took to log in
# 2 : 1372607672.654 0.675 0 0 0 0 eval true\ m\;ssh\ m\ echo
$time_to_login{$host} = ::min($time_to_login{$host},$col[3]);
} else {
::die_bug("host check unmatched long jobline: $_");
}
} elsif($Global::host{$col[0]}) {
# This output from --number-of-cores, --number-of-cpus,
# --max-line-length-allowed
# ncores: server 8
# ncpus: server 2
# maxlen: server 131071
if(/parallel: Warning: Cannot figure out number of/) {
next;
}
if(not $nsockets{$col[0]}) {
$nsockets{$col[0]} = $col[1];
} elsif(not $ncores{$col[0]}) {
$ncores{$col[0]} = $col[1];
} elsif(not $nthreads{$col[0]}) {
$nthreads{$col[0]} = $col[1];
} elsif(not $maxlen{$col[0]}) {
$maxlen{$col[0]} = $col[1];
} elsif(not $echo{$col[0]}) {
$echo{$col[0]} = $col[1];
} elsif(m/perl: warning:|LANGUAGE =|LC_ALL =|LANG =|are supported and installed/) {
# Skip these:
# perl: warning: Setting locale failed.
# perl: warning: Please check that your locale settings:
# LANGUAGE = (unset),
# LC_ALL = (unset),
# LANG = "en_US.UTF-8"
# are supported and installed on your system.
# perl: warning: Falling back to the standard locale ("C").
} else {
::die_bug("host check too many col0: $_");
}
} else {
::die_bug("host check unmatched short jobline ($col[0]): $_");
}
}
@down_hosts = uniq(@down_hosts);
return(\%nsockets, \%ncores, \%nthreads, \%time_to_login,
\%maxlen, \%echo, \@down_hosts);
}
sub parallelized_host_filtering() {
# Uses:
# %Global::host
# Returns:
# text entries with:
# * joblog line
# * hostname \t number of cores
# * hostname \t number of cpus
# * hostname \t max-line-length-allowed
# * hostname \t empty
sub sshwrapped {
# Wrap with ssh and --env
my $sshlogin = shift;
my $command = shift;
my $commandline = CommandLine->new(1,[$command],{},0,0,[],[],{},{},{});
my $job = Job->new($commandline);
$job->set_sshlogin($sshlogin);
$job->wrapped();
return($job->{'wrapped'});
}
my(@sockets, @cores, @threads, @maxline, @echo);
while (my ($host, $sshlogin) = each %Global::host) {
if($host eq ":") { next }
# The 'true' is used to get the $host out later
push(@sockets, $host."\t"."true $host; ".
sshwrapped($sshlogin,"parallel --number-of-sockets")."\n\0");
push(@cores, $host."\t"."true $host; ".
sshwrapped($sshlogin,"parallel --number-of-cores")."\n\0");
push(@threads, $host."\t"."true $host; ".
sshwrapped($sshlogin,"parallel --number-of-threads")."\n\0");
push(@maxline, $host."\t"."true $host; ".
sshwrapped($sshlogin,"parallel --max-line-length-allowed")."\n\0");
# 'echo' is used to get the fastest possible ssh login time
my $sshcmd = "true $host; exec " .$sshlogin->sshcommand()." ".
$sshlogin->serverlogin();
push(@echo, $host."\t".$sshcmd." -- echo\n\0");
}
# --timeout 10: Setting up an SSH connection and running a simple
# command should never take > 10 sec.
# --delay 0.1: If multiple sshlogins use the same proxy the delay
# will make it less likely to overload the ssh daemon.
# --retries 3: If the ssh daemon is overloaded, try 3 times
my $cmd =
"$0 -j0 --timeout 10 --joblog - --plain --delay 0.1 --retries 3 ".
"--tag --tagstring '{1}' -0 --colsep '\t' -k eval '{2}' && true ";
$cmd = $Global::shell." -c ".Q($cmd);
::debug("init", $cmd, "\n");
my @out;
my $prepend = "";
my ($host_fh,$in,$err);
open3($in, $host_fh, $err, $cmd) || ::die_bug("parallel host check: $cmd");
if(not fork()) {
# Give the commands to run to the $cmd
close $host_fh;
print $in @sockets, @cores, @threads, @maxline, @echo;
close $in;
exit();
}
close $in;
for(<$host_fh>) {
# TODO incompatible with '-quoting. Needs to be fixed differently
#if(/\'$/) {
# # if last char = ' then append next line
# # This may be due to quoting of \n in environment var
# $prepend .= $_;
# next;
#}
$_ = $prepend . $_;
$prepend = "";
push @out, $_;
}
close $host_fh;
return @out;
}
sub onall($@) {
# Runs @command on all hosts.
# Uses parallel to run @command on each host.
# --jobs = number of hosts to run on simultaneously.
# For each host a parallel command with the args will be running.
# Uses:
# $Global::quoting
# @opt::basefile
# $opt::jobs
# $opt::linebuffer
# $opt::ungroup
# $opt::group
# $opt::keeporder
# $opt::D
# $opt::plain
# $opt::max_chars
# $opt::linebuffer
# $opt::files
# $opt::colsep
# $opt::timeout
# $opt::plain
# $opt::retries
# $opt::max_chars
# $opt::arg_sep
# $opt::arg_file_sep
# @opt::v
# @opt::env
# %Global::host
# $Global::exitstatus
# $Global::debug
# $Global::joblog
# $opt::joblog
# $opt::tag
# $opt::tee
# Input:
# @command = command to run on all hosts
# Returns: N/A
sub tmp_joblog {
# Input:
# $joblog = filename of joblog - undef if none
# Returns:
# $tmpfile = temp file for joblog - undef if none
my $joblog = shift;
if(not defined $joblog) {
return undef;
}
my ($fh, $tmpfile) = ::tmpfile(SUFFIX => ".log");
close $fh;
return $tmpfile;
}
my ($input_source_fh_ref,@command) = @_;
if($Global::quoting) {
@command = shell_quote(@command);
}
# Copy all @input_source_fh (-a and :::) into tempfiles
my @argfiles = ();
for my $fh (@$input_source_fh_ref) {
my ($outfh, $name) = ::tmpfile(SUFFIX => ".all", UNLINK => not $opt::D);
print $outfh (<$fh>);
close $outfh;
push @argfiles, $name;
}
if(@opt::basefile) { setup_basefile(); }
# for each sshlogin do:
# parallel -S $sshlogin $command :::: @argfiles
#
# Pass some of the options to the sub-parallels, not all of them as
# -P should only go to the first, and -S should not be copied at all.
my $options =
join(" ",
((defined $opt::memfree) ? "--memfree ".$opt::memfree : ""),
((defined $opt::D) ? "-D $opt::D" : ""),
((defined $opt::group) ? "-g" : ""),
((defined $opt::jobs) ? "-P $opt::jobs" : ""),
((defined $opt::keeporder) ? "--keeporder" : ""),
((defined $opt::linebuffer) ? "--linebuffer" : ""),
((defined $opt::max_chars) ? "--max-chars ".$opt::max_chars : ""),
((defined $opt::plain) ? "--plain" : ""),
((defined $opt::ungroup) ? "-u" : ""),
((defined $opt::tee) ? "--tee" : ""),
);
my $suboptions =
join(" ",
((defined $opt::D) ? "-D $opt::D" : ""),
((defined $opt::arg_file_sep) ? "--arg-file-sep ".$opt::arg_file_sep : ""),
((defined $opt::arg_sep) ? "--arg-sep ".$opt::arg_sep : ""),
((defined $opt::colsep) ? "--colsep ".shell_quote($opt::colsep) : ""),
((defined $opt::files) ? "--files" : ""),
((defined $opt::group) ? "-g" : ""),
((defined $opt::cleanup) ? "--cleanup" : ""),
((defined $opt::keeporder) ? "--keeporder" : ""),
((defined $opt::linebuffer) ? "--linebuffer" : ""),
((defined $opt::max_chars) ? "--max-chars ".$opt::max_chars : ""),
((defined $opt::plain) ? "--plain" : ""),
((defined $opt::retries) ? "--retries ".$opt::retries : ""),
((defined $opt::timeout) ? "--timeout ".$opt::timeout : ""),
((defined $opt::ungroup) ? "-u" : ""),
((defined $opt::tee) ? "--tee" : ""),
((defined $opt::workdir) ? "--wd ".Q($opt::workdir) : ""),
(@Global::transfer_files ? map { "--tf ".Q($_) }
@Global::transfer_files : ""),
(@Global::ret_files ? map { "--return ".Q($_) }
@Global::ret_files : ""),
(@opt::env ? map { "--env ".Q($_) } @opt::env : ""),
(map { "-v" } @opt::v),
);
::debug("init", "| $0 $options\n");
open(my $parallel_fh, "|-", "$0 -0 --will-cite -j0 $options") ||
::die_bug("This does not run GNU Parallel: $0 $options");
my @joblogs;
for my $host (sort keys %Global::host) {
my $sshlogin = $Global::host{$host};
my $joblog = tmp_joblog($opt::joblog);
if($joblog) {
push @joblogs, $joblog;
$joblog = "--joblog $joblog";
}
my $quad = $opt::arg_file_sep || "::::";
# If PARALLEL_ENV is set: Pass it on
my $penv=$Global::parallel_env ?
"PARALLEL_ENV=".Q($Global::parallel_env) :
'';
::debug("init", "$penv $0 $suboptions -j1 $joblog ",
((defined $opt::tag) ?
"--tagstring ".Q($sshlogin->string()) : ""),
" -S ", Q($sshlogin->string())," ",
join(" ",shell_quote(@command))," $quad @argfiles\n");
print $parallel_fh "$penv $0 $suboptions -j1 $joblog ",
((defined $opt::tag) ?
"--tagstring ".Q($sshlogin->string()) : ""),
" -S ", Q($sshlogin->string())," ",
join(" ",shell_quote(@command))," $quad @argfiles\0";
}
close $parallel_fh;
$Global::exitstatus = $? >> 8;
debug("init", "--onall exitvalue ", $?);
if(@opt::basefile and $opt::cleanup) { cleanup_basefile(); }
$Global::debug or unlink(@argfiles);
my %seen;
for my $joblog (@joblogs) {
# Append to $joblog
open(my $fh, "<", $joblog) || ::die_bug("Cannot open tmp joblog $joblog");
# Skip first line (header);
<$fh>;
print $Global::joblog (<$fh>);
close $fh;
unlink($joblog);
}
}
sub __SIGNAL_HANDLING__() {}
sub sigtstp() {
# Send TSTP signal (Ctrl-Z) to all children process groups
# Uses:
# %SIG
# Returns: N/A
signal_children("TSTP");
}
sub sigpipe() {
# Send SIGPIPE signal to all children process groups
# Uses:
# %SIG
# Returns: N/A
signal_children("PIPE");
}
sub signal_children() {
# Send signal to all children process groups
# and GNU Parallel itself
# Uses:
# %SIG
# Returns: N/A
my $signal = shift;
debug("run", "Sending $signal ");
kill $signal, map { -$_ } keys %Global::running;
# Use default signal handler for GNU Parallel itself
$SIG{$signal} = undef;
kill $signal, $$;
}
sub save_original_signal_handler() {
# Remember the original signal handler
# Uses:
# %Global::original_sig
# Returns: N/A
$SIG{INT} = sub {
if($opt::tmux) { ::qqx("tmux kill-session -t p$$"); }
wait_and_exit(255);
};
$SIG{TERM} = sub {
if($opt::tmux) { ::qqx("tmux kill-session -t p$$"); }
wait_and_exit(255);
};
%Global::original_sig = %SIG;
$SIG{TERM} = sub {}; # Dummy until jobs really start
$SIG{ALRM} = 'IGNORE';
# Allow Ctrl-Z to suspend and `fg` to continue
$SIG{TSTP} = \&sigtstp;
$SIG{PIPE} = \&sigpipe;
$SIG{CONT} = sub {
# Set $SIG{TSTP} again (it is undef'ed in sigtstp() )
$SIG{TSTP} = \&sigtstp;
# Send continue signal to all children process groups
kill "CONT", map { -$_ } keys %Global::running;
};
}
sub list_running_jobs() {
# Print running jobs on tty
# Uses:
# %Global::running
# Returns: N/A
for my $job (values %Global::running) {
::status("$Global::progname: ".$job->replaced());
}
}
sub start_no_new_jobs() {
# Start no more jobs
# Uses:
# %Global::original_sig
# %Global::unlink
# $Global::start_no_new_jobs
# Returns: N/A
# $SIG{TERM} = $Global::original_sig{TERM};
unlink keys %Global::unlink;
::status
("$Global::progname: SIGHUP received. No new jobs will be started.",
"$Global::progname: Waiting for these ".(keys %Global::running).
" jobs to finish. Send SIGTERM to stop now.");
list_running_jobs();
$Global::start_no_new_jobs ||= 1;
}
sub reapers() {
# Run reaper until there are no more left
# Returns:
# @pids_reaped = pids of reaped processes
my @pids_reaped;
my $pid;
while($pid = reaper()) {
push @pids_reaped, $pid;
}
return @pids_reaped;
}
sub reaper() {
# A job finished:
# * Set exitstatus, exitsignal, endtime.
# * Free ressources for new job
# * Update median runtime
# * Print output
# * If --halt = now: Kill children
# * Print progress
# Uses:
# %Global::running
# $opt::timeout
# $Global::timeoutq
# $opt::keeporder
# $Global::total_running
# Returns:
# $stiff = PID of child finished
my $stiff;
debug("run", "Reaper ");
if(($stiff = waitpid(-1, &WNOHANG)) <= 0) {
# No jobs waiting to be reaped
return 0;
}
# $stiff = pid of dead process
my $job = $Global::running{$stiff};
# '-a <(seq 10)' will give us a pid not in %Global::running
# The same will one of the ssh -M: ignore
$job or return 0;
delete $Global::running{$stiff};
$Global::total_running--;
if($job->{'commandline'}{'skip'}) {
# $job->skip() was called
$job->set_exitstatus(-2);
$job->set_exitsignal(0);
} else {
$job->set_exitstatus($? >> 8);
$job->set_exitsignal($? & 127);
}
debug("run", "seq ",$job->seq()," died (", $job->exitstatus(), ")");
$job->set_endtime(::now());
my $sshlogin = $job->sshlogin();
$sshlogin->dec_jobs_running();
if($job->should_be_retried()) {
# Free up file handles
$job->free_ressources();
} else {
# The job is done
$sshlogin->inc_jobs_completed();
# Free the jobslot
$job->free_slot();
if($opt::timeout and not $job->exitstatus()) {
# Update average runtime for timeout only for successful jobs
$Global::timeoutq->update_median_runtime($job->runtime());
}
if($opt::keeporder) {
$job->print_earlier_jobs();
} else {
$job->print();
}
if($job->should_we_halt() eq "now") {
# Kill children
::kill_sleep_seq($job->pid());
::killall();
::wait_and_exit($Global::halt_exitstatus);
}
}
$job->cleanup();
if($opt::progress) {
my %progress = progress();
::status_no_nl("\r",$progress{'status'});
}
debug("run", "done ");
return $stiff;
}
sub __USAGE__() {}
sub killall() {
# Kill all jobs by killing their process groups
# Uses:
# $Global::start_no_new_jobs = we are stopping
# $Global::killall = Flag to not run reaper
$Global::start_no_new_jobs ||= 1;
# Do not reap killed children: Ignore them instead
$Global::killall ||= 1;
kill_sleep_seq(keys %Global::running);
}
sub kill_sleep_seq(@) {
# Send jobs TERM,TERM,KILL to processgroups
# Input:
# @pids = list of pids that are also processgroups
# Convert pids to process groups ($processgroup = -$pid)
my @pgrps = map { -$_ } @_;
my @term_seq = split/,/,$opt::termseq;
if(not @term_seq) {
@term_seq = ("TERM",200,"TERM",100,"TERM",50,"KILL",25);
}
while(@term_seq) {
@pgrps = kill_sleep(shift @term_seq, shift @term_seq, @pgrps);
}
}
sub kill_sleep() {
# Kill pids with a signal and wait a while for them to die
# Input:
# $signal = signal to send to @pids
# $sleep_max = number of ms to sleep at most before returning
# @pids = pids to kill (actually process groups)
# Uses:
# $Global::killall = set by killall() to avoid calling reaper
# Returns:
# @pids = pids still alive
my ($signal, $sleep_max, @pids) = @_;
::debug("kill","kill_sleep $signal ",(join " ",sort @pids),"\n");
kill $signal, @pids;
my $sleepsum = 0;
my $sleep = 0.001;
while(@pids and $sleepsum < $sleep_max) {
if($Global::killall) {
# Killall => don't run reaper
while(waitpid(-1, &WNOHANG) > 0) {
$sleep = $sleep/2+0.001;
}
} elsif(reapers()) {
$sleep = $sleep/2+0.001;
}
$sleep *= 1.1;
::usleep($sleep);
$sleepsum += $sleep;
# Keep only living children
@pids = grep { kill(0, $_) } @pids;
}
return @pids;
}
sub wait_and_exit($) {
# If we do not wait, we sometimes get segfault
# Returns: N/A
my $error = shift;
unlink keys %Global::unlink;
if($error) {
# Kill all jobs without printing
killall();
}
for (keys %Global::unkilled_children) {
# Kill any (non-jobs) children (e.g. reserved processes)
kill 9, $_;
waitpid($_,0);
delete $Global::unkilled_children{$_};
}
if($Global::unkilled_sqlworker) {
waitpid($Global::unkilled_sqlworker,0);
}
exit($error);
}
sub die_usage() {
# Returns: N/A
usage();
wait_and_exit(255);
}
sub usage() {
# Returns: N/A
print join
("\n",
"Usage:",
"",
"$Global::progname [options] [command [arguments]] < list_of_arguments",
"$Global::progname [options] [command [arguments]] (::: arguments|:::: argfile(s))...",
"cat ... | $Global::progname --pipe [options] [command [arguments]]",
"",
"-j n Run n jobs in parallel",
"-k Keep same order",
"-X Multiple arguments with context replace",
"--colsep regexp Split input on regexp for positional replacements",
"{} {.} {/} {/.} {#} {%} {= perl code =} Replacement strings",
"{3} {3.} {3/} {3/.} {=3 perl code =} Positional replacement strings",
"With --plus: {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} =",
" {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}",
"",
"-S sshlogin Example: foo\@server.example.com",
"--slf .. Use ~/.parallel/sshloginfile as the list of sshlogins",
"--trc {}.bar Shorthand for --transfer --return {}.bar --cleanup",
"--onall Run the given command with argument on all sshlogins",
"--nonall Run the given command with no arguments on all sshlogins",
"",
"--pipe Split stdin (standard input) to multiple jobs.",
"--recend str Record end separator for --pipe.",
"--recstart str Record start separator for --pipe.",
"",
"See 'man $Global::progname' for details",
"",
"Academic tradition requires you to cite works you base your article on.",
"If you use programs that use GNU Parallel to process data for an article in a",
"scientific publication, please cite:",
"",
" O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,",
" DOI https://doi.org/10.5281/zenodo.1146014",
"",
# Before changing this line, please read
# https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
"This helps funding further development; AND IT WON'T COST YOU A CENT.",
"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
"",
"",);
}
sub citation_notice() {
# if --will-cite or --plain: do nothing
# if stderr redirected: do nothing
# if $PARALLEL_HOME/will-cite: do nothing
# else: print citation notice to stderr
if($opt::willcite
or
$opt::plain
or
not -t $Global::original_stderr
or
grep { -e "$_/will-cite" } @Global::config_dirs) {
# skip
} else {
::status
("Academic tradition requires you to cite works you base your article on.",
"If you use programs that use GNU Parallel to process data for an article in a",
"scientific publication, please cite:",
"",
" O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881,",
" DOI https://doi.org/10.5281/zenodo.1146014",
"",
# Before changing this line, please read
# https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
"This helps funding further development; AND IT WON'T COST YOU A CENT.",
"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
"",
"More about funding GNU Parallel and the citation notice:",
"https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice",
"",
"To silence this citation notice: run 'parallel --citation' once.",
""
);
mkdir $Global::config_dir;
# Number of times the user has run GNU Parallel without showing
# willingness to cite
my $runs = 0;
if(open (my $fh, "<", $Global::config_dir.
"/runs-without-willing-to-cite")) {
$runs = <$fh>;
close $fh;
}
$runs++;
if(open (my $fh, ">", $Global::config_dir.
"/runs-without-willing-to-cite")) {
print $fh $runs;
close $fh;
if($runs >= 10) {
::status("Come on: You have run parallel $runs times. Isn't it about time ",
"you run 'parallel --citation' once to silence the citation notice?",
"");
}
}
}
}
sub status(@) {
my @w = @_;
my $fh = $Global::status_fd || *STDERR;
print $fh map { ($_, "\n") } @w;
flush $fh;
}
sub status_no_nl(@) {
my @w = @_;
my $fh = $Global::status_fd || *STDERR;
print $fh @w;
flush $fh;
}
sub warning(@) {
my @w = @_;
my $prog = $Global::progname || "parallel";
status_no_nl(map { ($prog, ": Warning: ", $_, "\n"); } @w);
}
sub error(@) {
my @w = @_;
my $prog = $Global::progname || "parallel";
status(map { ($prog.": Error: ". $_); } @w);
}
sub die_bug($) {
my $bugid = shift;
print STDERR
("$Global::progname: This should not happen. You have found a bug.\n",
"Please contact <parallel\@gnu.org> and follow\n",
"https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS\n",
"\n",
"Include this in the report:\n",
"* The version number: $Global::version\n",
"* The bugid: $bugid\n",
"* The command line being run\n",
"* The files being read (put the files on a webserver if they are big)\n",
"\n",
"If you get the error on smaller/fewer files, please include those instead.\n");
::wait_and_exit(255);
}
sub version() {
# Returns: N/A
print join
("\n",
"GNU $Global::progname $Global::version",
"Copyright (C) 2007-2019 Ole Tange and Free Software Foundation, Inc.",
"License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>",
"This is free software: you are free to change and redistribute it.",
"GNU $Global::progname comes with no warranty.",
"",
"Web site: http://www.gnu.org/software/${Global::progname}\n",
"When using programs that use GNU Parallel to process data for publication",
"please cite as described in 'parallel --citation'.\n",
);
}
sub citation() {
# Returns: N/A
my ($all_argv_ref,$argv_options_removed_ref) = @_;
my $all_argv = "@$all_argv_ref";
my $no_opts = "@$argv_options_removed_ref";
$all_argv=~s/--citation//;
if($all_argv ne $no_opts) {
::warning("--citation ignores all other options and arguments.");
::status("");
}
::status(
"Academic tradition requires you to cite works you base your article on.",
"If you use programs that use GNU Parallel to process data for an article in a",
"scientific publication, please cite:",
"",
"\@book{tange_ole_2018_1146014,",
" author = {Tange, Ole},",
" title = {GNU Parallel 2018},",
" publisher = {Ole Tange},",
" month = Mar,",
" year = 2018,",
" ISBN = {9781387509881},",
" doi = {10.5281/zenodo.1146014},",
" url = {https://doi.org/10.5281/zenodo.1146014}",
"}",
"",
"(Feel free to use \\nocite{tange_ole_2018_1146014})",
"",
# Before changing this line, please read
# https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
# https://git.savannah.gnu.org/cgit/parallel.git/tree/doc/citation-notice-faq.txt
"This helps funding further development; AND IT WON'T COST YOU A CENT.",
"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
"",
"More about funding GNU Parallel and the citation notice:",
"https://lists.gnu.org/archive/html/parallel/2013-11/msg00006.html",
"https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice",
"https://git.savannah.gnu.org/cgit/parallel.git/tree/doc/citation-notice-faq.txt",
"",
"If you send a copy of your published article to tange\@gnu.org, it will be",
"mentioned in the release notes of next version of GNU Parallel.",
""
);
while(not grep { -e "$_/will-cite" } @Global::config_dirs) {
print "\nType: 'will cite' and press enter.\n> ";
my $input = <STDIN>;
if(not defined $input) {
exit(255);
}
if($input =~ /will cite/i) {
mkdir $Global::config_dir;
if(open (my $fh, ">", $Global::config_dir."/will-cite")) {
close $fh;
::status(
"",
"Thank you for your support: You are the reason why there is funding to",
"continue maintaining GNU Parallel. On behalf of future versions of",
"GNU Parallel, which would not exist without your support:",
"",
" THANK YOU SO MUCH",
"",
"It is really appreciated. The citation notice is now silenced.",
"");
} else {
::status(
"",
"Thank you for your support. It is much appreciated. The citation",
"cannot permanently be silenced. Use '--will-cite' instead.",
"",
"If you use '--will-cite' in scripts to be run by others you are making",
"it harder for others to see the citation notice. The development of",
"GNU parallel is indirectly financed through citations, so if users",
"do not know they should cite then you are making it harder to finance",
"development. However, if you pay 10000 EUR, you should feel free to",
"use '--will-cite' in scripts.",
"");
last;
}
}
}
}
sub show_limits() {
# Returns: N/A
print("Maximal size of command: ",Limits::Command::real_max_length(),"\n",
"Maximal used size of command: ",Limits::Command::max_length(),"\n",
"\n",
"Execution of will continue now, and it will try to read its input\n",
"and run commands; if this is not what you wanted to happen, please\n",
"press CTRL-D or CTRL-C\n");
}
sub embed() {
# Give an embeddable version of GNU Parallel
# Tested with: bash, zsh, ksh, ash, dash, sh
my $randomstring = "cut-here-".join"",
map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..20);
if(not -f $0 or not -r $0) {
::error("--embed only works if parallel is a readable file");
exit(255);
}
if(open(my $fh, "<", $0)) {
# Read the source from $0
my @source = <$fh>;
my $user = $ENV{LOGNAME} || $ENV{USERNAME} || $ENV{USER};
my @env_parallel_source = ();
my $shell = $Global::shell;
$shell =~ s:.*/::;
for(which("env_parallel.$shell")) {
-r $_ or next;
# Read the source of env_parallel.shellname
open(my $env_parallel_source_fh, $_) || die;
@env_parallel_source = <$env_parallel_source_fh>;
close $env_parallel_source_fh;
last;
}
print "#!$Global::shell
# Copyright (C) 2007-2019 $user, Ole Tange and Free Software
# Foundation, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
# or write to the Free Software Foundation, Inc., 51 Franklin St,
# Fifth Floor, Boston, MA 02110-1301 USA
";
print q!
# Embedded GNU Parallel created with --embed
parallel() {
# Start GNU Parallel without leaving temporary files
#
# Not all shells support 'perl <(cat ...)'
# This is a complex way of doing:
# perl <(cat <<'cut-here'
# [...]
# ) "$@"
# and also avoiding:
# [1]+ Done cat
# Make a temporary fifo that perl can read from
_fifo_with_parallel_source=`perl -e 'use POSIX qw(mkfifo);
do {
$f = "/tmp/parallel-".join"",
map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
} while(-e $f);
mkfifo($f,0600);
print $f;'`
# Put source code into temporary file
# so it is easy to copy to the fifo
_file_with_parallel_source=`mktemp`;
!,
"cat <<'$randomstring' > \$_file_with_parallel_source\n",
@source,
$randomstring,"\n",
q!
# Copy the source code from the file to the fifo
# and remove the file and fifo ASAP
# 'sh -c' is needed to avoid
# [1]+ Done cat
sh -c "(rm $_file_with_parallel_source; cat >$_fifo_with_parallel_source; rm $_fifo_with_parallel_source) < $_file_with_parallel_source &"
# Read the source from the fifo
perl $_fifo_with_parallel_source "$@"
}
!,
@env_parallel_source,
q!
# This will call the functions above
parallel -k echo ::: Put your code here
env_parallel --session
env_parallel -k echo ::: Put your code here
parset p,y,c,h -k echo ::: Put your code here
echo $p $y $c $h
!;
} else {
::error("Cannot open $0");
exit(255);
}
::status("Redirect the output to a file and add your changes at the end:",
" $0 --embed > new_script");
}
sub __GENERIC_COMMON_FUNCTION__() {}
sub mkdir_or_die($) {
# If dir is not executable: die
my $dir = shift;
# The eval is needed to catch exception from mkdir
eval { File::Path::mkpath($dir); };
if(not -x $dir) {
::error("Cannot change into non-executable dir $dir: $!");
::wait_and_exit(255);
}
}
sub tmpfile(@) {
# Create tempfile as $TMPDIR/parXXXXX
# Returns:
# $filehandle = opened file handle
# $filename = file name created
my($filehandle,$filename) =
::tempfile(DIR=>$ENV{'TMPDIR'}, TEMPLATE => 'parXXXXX', @_);
if(wantarray) {
return($filehandle,$filename);
} else {
# Separate unlink due to NFS dealing badly with File::Temp
unlink $filename;
return $filehandle;
}
}
sub tmpname($) {
# Select a name that does not exist
# Do not create the file as it may be used for creating a socket (by tmux)
# Remember the name in $Global::unlink to avoid hitting the same name twice
my $name = shift;
my($tmpname);
if(not -w $ENV{'TMPDIR'}) {
if(not -e $ENV{'TMPDIR'}) {
::error("Tmpdir '$ENV{'TMPDIR'}' does not exist.","Try 'mkdir $ENV{'TMPDIR'}'");
} else {
::error("Tmpdir '$ENV{'TMPDIR'}' is not writable.","Try 'chmod +w $ENV{'TMPDIR'}'");
}
::wait_and_exit(255);
}
do {
$tmpname = $ENV{'TMPDIR'}."/".$name.
join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
} while(-e $tmpname or $Global::unlink{$tmpname}++);
return $tmpname;
}
sub tmpfifo() {
# Find an unused name and mkfifo on it
use POSIX qw(mkfifo);
my $tmpfifo = tmpname("fif");
mkfifo($tmpfifo,0600);
return $tmpfifo;
}
sub rm(@) {
# Remove file and remove it from %Global::unlink
# Uses:
# %Global::unlink
delete @Global::unlink{@_};
unlink @_;
}
sub size_of_block_dev() {
# Like -s but for block devices
# Input:
# $blockdev = file name of block device
# Returns:
# $size = in bytes, undef if error
my $blockdev = shift;
if(open(my $fh, "<", $blockdev)) {
seek($fh,0,2) || ::die_bug("cannot seek $blockdev");
my $size = tell($fh);
close $fh;
return $size;
} else {
::error("cannot open $blockdev");
wait_and_exit(255);
}
}
sub qqx(@) {
# Like qx but with clean environment (except for @keep)
# and STDERR ignored
# This is needed if the environment contains functions
# that /bin/sh does not understand
my $PATH = $ENV{'PATH'};
my %env;
# ssh with ssh-agent needs PATH SSH_AUTH_SOCK SSH_AGENT_PID
# ssh with Kerberos needs KRB5CCNAME
# tmux needs LC_CTYPE
my @keep = qw(PATH SSH_AUTH_SOCK SSH_AGENT_PID KRB5CCNAME LC_CTYPE);
@env{@keep} = @ENV{@keep};
local %ENV;
%ENV = %env;
if($Global::debug) {
return qx{ @_ && true };
} else {
return qx{ ( @_ ) 2>/dev/null };
}
}
sub uniq(@) {
# Remove duplicates and return unique values
return keys %{{ map { $_ => 1 } @_ }};
}
sub min(@) {
# Returns:
# Minimum value of array
my $min;
for (@_) {
# Skip undefs
defined $_ or next;
defined $min or do { $min = $_; next; }; # Set $_ to the first non-undef
$min = ($min < $_) ? $min : $_;
}
return $min;
}
sub max(@) {
# Returns:
# Maximum value of array
my $max;
for (@_) {
# Skip undefs
defined $_ or next;
defined $max or do { $max = $_; next; }; # Set $_ to the first non-undef
$max = ($max > $_) ? $max : $_;
}
return $max;
}
sub sum() {
# Returns:
# Sum of values of array
my @args = @_;
my $sum = 0;
for (@args) {
# Skip undefs
$_ and do { $sum += $_; }
}
return $sum;
}
sub undef_as_zero($) {
my $a = shift;
return $a ? $a : 0;
}
sub undef_as_empty($) {
my $a = shift;
return $a ? $a : "";
}
sub undef_if_empty($) {
if(defined($_[0]) and $_[0] eq "") {
return undef;
}
return $_[0];
}
sub multiply_binary_prefix(@) {
# Evalualte numbers with binary prefix
# Ki=2^10, Mi=2^20, Gi=2^30, Ti=2^40, Pi=2^50, Ei=2^70, Zi=2^80, Yi=2^80
# ki=2^10, mi=2^20, gi=2^30, ti=2^40, pi=2^50, ei=2^70, zi=2^80, yi=2^80
# K =2^10, M =2^20, G =2^30, T =2^40, P =2^50, E =2^70, Z =2^80, Y =2^80
# k =10^3, m =10^6, g =10^9, t=10^12, p=10^15, e=10^18, z=10^21, y=10^24
# 13G = 13*1024*1024*1024 = 13958643712
# Input:
# $s = string with prefixes
# Returns:
# $value = int with prefixes multiplied
my @v = @_;
for(@v) {
defined $_ or next;
s/ki/*1024/gi;
s/mi/*1024*1024/gi;
s/gi/*1024*1024*1024/gi;
s/ti/*1024*1024*1024*1024/gi;
s/pi/*1024*1024*1024*1024*1024/gi;
s/ei/*1024*1024*1024*1024*1024*1024/gi;
s/zi/*1024*1024*1024*1024*1024*1024*1024/gi;
s/yi/*1024*1024*1024*1024*1024*1024*1024*1024/gi;
s/xi/*1024*1024*1024*1024*1024*1024*1024*1024*1024/gi;
s/K/*1024/g;
s/M/*1024*1024/g;
s/G/*1024*1024*1024/g;
s/T/*1024*1024*1024*1024/g;
s/P/*1024*1024*1024*1024*1024/g;
s/E/*1024*1024*1024*1024*1024*1024/g;
s/Z/*1024*1024*1024*1024*1024*1024*1024/g;
s/Y/*1024*1024*1024*1024*1024*1024*1024*1024/g;
s/X/*1024*1024*1024*1024*1024*1024*1024*1024*1024/g;
s/k/*1000/g;
s/m/*1000*1000/g;
s/g/*1000*1000*1000/g;
s/t/*1000*1000*1000*1000/g;
s/p/*1000*1000*1000*1000*1000/g;
s/e/*1000*1000*1000*1000*1000*1000/g;
s/z/*1000*1000*1000*1000*1000*1000*1000/g;
s/y/*1000*1000*1000*1000*1000*1000*1000*1000/g;
s/x/*1000*1000*1000*1000*1000*1000*1000*1000*1000/g;
$_ = eval $_;
}
return wantarray ? @v : $v[0];
}
sub multiply_time_units($) {
# Evalualte numbers with time units
# s=1, m=60, h=3600, d=86400
# Input:
# $s = string time units
# Returns:
# $value = int in seconds
my @v = @_;
for(@v) {
defined $_ or next;
if(/[dhms]/i) {
s/s/*1+/gi;
s/m/*60+/gi;
s/h/*3600+/gi;
s/d/*86400+/gi;
$_ = eval $_."0";
}
}
return wantarray ? @v : $v[0];
}
sub seconds_to_time_units() {
# Convert seconds into ??d??h??m??s
# s=1, m=60, h=3600, d=86400
# Input:
# $s = int in seconds
# Returns:
# $str = string time units
my $s = shift;
my $str;
my $d = int($s/86400);
$s -= $d * 86400;
my $h = int($s/3600);
$s -= $h * 3600;
my $m = int($s/60);
$s -= $m * 60;
if($d) {
$str = sprintf("%dd%02dh%02dm%02ds",$d,$h,$m,$s);
} elsif($h) {
$str = sprintf("%dh%02dm%02ds",$h,$m,$s);
} elsif($m) {
$str = sprintf("%dm%02ds",$m,$s);
} else {
$str = sprintf("%ds",$s);
}
return $str;
}
{
my ($disk_full_fh, $b8193, $error_printed);
sub exit_if_disk_full() {
# Checks if $TMPDIR is full by writing 8kb to a tmpfile
# If the disk is full: Exit immediately.
# Returns:
# N/A
if(not $disk_full_fh) {
$disk_full_fh = ::tmpfile(SUFFIX => ".df");
$b8193 = "x"x8193;
}
# Linux does not discover if a disk is full if writing <= 8192
# Tested on:
# bfs btrfs cramfs ext2 ext3 ext4 ext4dev jffs2 jfs minix msdos
# ntfs reiserfs tmpfs ubifs vfat xfs
# TODO this should be tested on different OS similar to this:
#
# doit() {
# sudo mount /dev/ram0 /mnt/loop; sudo chmod 1777 /mnt/loop
# seq 100000 | parallel --tmpdir /mnt/loop/ true &
# seq 6900000 > /mnt/loop/i && echo seq OK
# seq 6980868 > /mnt/loop/i
# seq 10000 > /mnt/loop/ii
# sleep 3
# sudo umount /mnt/loop/ || sudo umount -l /mnt/loop/
# echo >&2
# }
print $disk_full_fh $b8193;
if(not $disk_full_fh
or
tell $disk_full_fh != 8193) {
# On raspbian the disk can be full except for 10 chars.
if(not $error_printed) {
::error("Output is incomplete.",
"Cannot append to buffer file in $ENV{'TMPDIR'}.",
"Is the disk full?",
"Change \$TMPDIR with --tmpdir or use --compress.");
$error_printed = 1;
}
::wait_and_exit(255);
}
truncate $disk_full_fh, 0;
seek($disk_full_fh, 0, 0) || die;
}
}
sub spacefree($$) {
# Remove comments and spaces
# Inputs:
# $spaces = keep 1 space?
# $s = string to remove spaces from
# Returns:
# $s = with spaces removed
my $spaces = shift;
my $s = shift;
$s =~ s/#.*//mg;
if(1 == $spaces) {
$s =~ s/\s+/ /mg;
} elsif(2 == $spaces) {
# Keep newlines
$s =~ s/\n\n+/\n/sg;
$s =~ s/[ \t]+/ /mg;
} elsif(3 == $spaces) {
# Keep perl code required space
$s =~ s{([^a-zA-Z0-9/])\s+}{$1}sg;
$s =~ s{([a-zA-Z0-9/])\s+([^:a-zA-Z0-9/])}{$1$2}sg;
} else {
$s =~ s/\s//mg;
}
return $s;
}
{
my $hostname;
sub hostname() {
local $/ = "\n";
if(not $hostname) {
$hostname = `hostname`;
chomp($hostname);
$hostname ||= "nohostname";
}
return $hostname;
}
}
sub which(@) {
# Input:
# @programs = programs to find the path to
# Returns:
# @full_path = full paths to @programs. Nothing if not found
my @which;
::debug("which", "@_ in $ENV{'PATH'}\n");
for my $prg (@_) {
push(@which, grep { not -d $_ and -x $_ }
map { $_."/".$prg } split(":",$ENV{'PATH'}));
if($prg =~ m:/:) {
# Including path
push(@which, grep { not -d $_ and -x $_ } $prg);
}
}
return wantarray ? @which : $which[0];
}
{
my ($regexp,$shell,%fakename);
sub parent_shell {
# Input:
# $pid = pid to see if (grand)*parent is a shell
# Returns:
# $shellpath = path to shell - undef if no shell found
my $pid = shift;
::debug("init","Parent of $pid\n");
if(not $regexp) {
# All shells known to mankind
#
# ash bash csh dash fdsh fish fizsh ksh ksh93 mksh pdksh
# posh rbash rc rush rzsh sash sh static-sh tcsh yash zsh
my @shells = (qw(ash bash bsd-csh csh dash fdsh fish fizsh
ksh ksh93 lksh mksh pdksh posh rbash rc rush rzsh sash sh
static-sh tcsh yash zsh -sh -csh -bash),
'-sh (sh)' # sh on FreeBSD
);
# Can be formatted as:
# [sh] -sh sh busybox sh -sh (sh)
# /bin/sh /sbin/sh /opt/csw/sh
# But not: foo.sh sshd crash flush pdflush scosh fsflush ssh
$shell = "(?:".join("|",map { "\Q$_\E" } @shells).")";
$regexp = '^((\[)(-?)('. $shell. ')(\])|(|\S+/|busybox )'.
'(-?)('. $shell. '))( *$| [^(])';
%fakename = (
# sh disguises itself as -sh (sh) on FreeBSD
"-sh (sh)" => ["sh"],
# csh and tcsh disguise themselves as -sh/-csh
# E.g.: ssh -tt csh@lo 'ps aux;true' |egrep ^csh
# but sh also disguise itself as -sh
# (TODO When does that happen?)
"-sh" => ["sh"],
"-csh" => ["tcsh", "csh"],
# ash disguises itself as -ash
"-ash" => ["ash", "dash", "sh"],
# dash disguises itself as -dash
"-dash" => ["dash", "ash", "sh"],
# bash disguises itself as -bash
"-bash" => ["bash", "sh"],
# ksh disguises itself as -ksh
"-ksh" => ["ksh", "sh"],
# zsh disguises itself as -zsh
"-zsh" => ["zsh", "sh"],
);
}
# if -sh or -csh try readlink /proc/$$/exe
my ($children_of_ref, $parent_of_ref, $name_of_ref) = pid_table();
my $shellpath;
my $testpid = $pid;
while($testpid) {
if($name_of_ref->{$testpid} =~ /$regexp/o) {
my $shellname = $4 || $8;
my $dash = $3 || $7;
if($shellname eq "sh" and $dash) {
# -sh => csh or sh
if($shellpath = readlink "/proc/$testpid/exe") {
::debug("init","procpath $shellpath\n");
if($shellpath =~ m:/$shell$:o) {
::debug("init", "proc which ".$shellpath." => ");
return $shellpath;
}
}
}
::debug("init", "which ".$shellname." => ");
$shellpath = (which($shellname,@{$fakename{$shellname}}))[0];
::debug("init", "shell path $shellpath\n");
$shellpath and last;
}
if($testpid == $parent_of_ref->{$testpid}) {
# In Solaris zones, the PPID of the zsched process is itself
last;
}
$testpid = $parent_of_ref->{$testpid};
}
return $shellpath;
}
}
{
my %pid_parentpid_cmd;
sub pid_table() {
# Returns:
# %children_of = { pid -> children of pid }
# %parent_of = { pid -> pid of parent }
# %name_of = { pid -> commandname }
if(not %pid_parentpid_cmd) {
# Filter for SysV-style `ps`
my $sysv = q( ps -ef | perl -ane '1..1 and /^(.*)CO?MM?A?N?D/ and $s=length $1;).
q(s/^.{$s}//; print "@F[1,2] $_"' );
# Minix uses cols 2,3 and can have newlines in the command
# so lines not having numbers in cols 2,3 must be ignored
my $minix = q( ps -ef | perl -ane '1..1 and /^(.*)CO?MM?A?N?D/ and $s=length $1;).
q(s/^.{$s}// and $F[2]>0 and $F[3]>0 and print "@F[2,3] $_"' );
# BSD-style `ps`
my $bsd = q(ps -o pid,ppid,command -ax);
%pid_parentpid_cmd =
(
'aix' => $sysv,
'android' => $sysv,
'cygwin' => $sysv,
'darwin' => $bsd,
'dec_osf' => $sysv,
'dragonfly' => $bsd,
'freebsd' => $bsd,
'gnu' => $sysv,
'hpux' => $sysv,
'linux' => $sysv,
'mirbsd' => $bsd,
'minix' => $minix,
'msys' => $sysv,
'MSWin32' => $sysv,
'netbsd' => $bsd,
'nto' => $sysv,
'openbsd' => $bsd,
'solaris' => $sysv,
'svr5' => $sysv,
'syllable' => "echo ps not supported",
);
}
$pid_parentpid_cmd{$^O} or ::die_bug("pid_parentpid_cmd for $^O missing");
my (@pidtable,%parent_of,%children_of,%name_of);
# Table with pid -> children of pid
@pidtable = `$pid_parentpid_cmd{$^O}`;
my $p=$$;
for (@pidtable) {
# must match: 24436 21224 busybox ash
# must match: 24436 21224 <<empty on MacOSX running cubase>>
# must match: 24436 21224 <<empty on system running Viber>>
# or: perl -e 'while($0=" "){}'
if(/^\s*(\S+)\s+(\S+)\s+(\S+.*)/
or
/^\s*(\S+)\s+(\S+)\s+()$/) {
$parent_of{$1} = $2;
push @{$children_of{$2}}, $1;
$name_of{$1} = $3;
} else {
::die_bug("pidtable format: $_");
}
}
return(\%children_of, \%parent_of, \%name_of);
}
}
sub now() {
# Returns time since epoch as in seconds with 3 decimals
# Uses:
# @Global::use
# Returns:
# $time = time now with millisecond accuracy
if(not $Global::use{"Time::HiRes"}) {
if(eval "use Time::HiRes qw ( time );") {
eval "sub TimeHiRestime { return Time::HiRes::time };";
} else {
eval "sub TimeHiRestime { return time() };";
}
$Global::use{"Time::HiRes"} = 1;
}
return (int(TimeHiRestime()*1000))/1000;
}
sub usleep($) {
# Sleep this many milliseconds.
# Input:
# $ms = milliseconds to sleep
my $ms = shift;
::debug("timing",int($ms),"ms ");
select(undef, undef, undef, $ms/1000);
}
sub __KILLER_REAPER__() {}
sub reap_usleep() {
# Reap dead children.
# If no dead children: Sleep specified amount with exponential backoff
# Input:
# $ms = milliseconds to sleep
# Returns:
# $ms/2+0.001 if children reaped
# $ms*1.1 if no children reaped
my $ms = shift;
if(reapers()) {
if(not $Global::total_completed % 100) {
if($opt::timeout) {
# Force cleaning the timeout queue for every 1000 jobs
# Fixes potential memleak
$Global::timeoutq->process_timeouts();
}
}
# Sleep exponentially shorter (1/2^n) if a job finished
return $ms/2+0.001;
} else {
if($opt::timeout) {
$Global::timeoutq->process_timeouts();
}
if($opt::memfree) {
kill_youngster_if_not_enough_mem();
}
if($opt::limit) {
kill_youngest_if_over_limit();
}
if($ms > 0.002) {
# When a child dies, wake up from sleep (or select(,,,))
$SIG{CHLD} = sub { kill "ALRM", $$ };
usleep($ms);
# --compress needs $SIG{CHLD} unset
$SIG{CHLD} = 'DEFAULT';
}
exit_if_disk_full();
if($opt::linebuffer) {
my $something_printed = 0;
if($opt::keeporder) {
for my $job (values %Global::running) {
$something_printed += $job->print_earlier_jobs();
}
} else {
for my $job (values %Global::running) {
$something_printed += $job->print();
}
}
if($something_printed) {
$ms = $ms/2+0.001;
}
}
# Sleep exponentially longer (1.1^n) if a job did not finish,
# though at most 1000 ms.
return (($ms < 1000) ? ($ms * 1.1) : ($ms));
}
}
sub kill_youngest_if_over_limit() {
# Check each $sshlogin we are over limit
# If over limit: kill off the youngest child
# Put the child back in the queue.
# Uses:
# %Global::running
my %jobs_of;
my @sshlogins;
for my $job (values %Global::running) {
if(not $jobs_of{$job->sshlogin()}) {
push @sshlogins, $job->sshlogin();
}
push @{$jobs_of{$job->sshlogin()}}, $job;
}
for my $sshlogin (@sshlogins) {
for my $job (sort { $b->seq() <=> $a->seq() } @{$jobs_of{$sshlogin}}) {
if($sshlogin->limit() == 2) {
$job->kill();
last;
}
}
}
}
sub kill_youngster_if_not_enough_mem() {
# Check each $sshlogin if there is enough mem.
# If less than 50% enough free mem: kill off the youngest child
# Put the child back in the queue.
# Uses:
# %Global::running
my %jobs_of;
my @sshlogins;
for my $job (values %Global::running) {
if(not $jobs_of{$job->sshlogin()}) {
push @sshlogins, $job->sshlogin();
}
push @{$jobs_of{$job->sshlogin()}}, $job;
}
for my $sshlogin (@sshlogins) {
for my $job (sort { $b->seq() <=> $a->seq() } @{$jobs_of{$sshlogin}}) {
if($sshlogin->memfree() < $opt::memfree * 0.5) {
::debug("mem","\n",map { $_->seq()." " }
(sort { $b->seq() <=> $a->seq() }
@{$jobs_of{$sshlogin}}));
::debug("mem","\n", $job->seq(), "killed ",
$sshlogin->memfree()," < ",$opt::memfree * 0.5);
$job->kill();
$sshlogin->memfree_recompute();
} else {
last;
}
}
::debug("mem","Free mem OK ",
$sshlogin->memfree()," > ",$opt::memfree * 0.5);
}
}
sub __DEBUGGING__() {}
sub debug(@) {
# Uses:
# $Global::debug
# %Global::fd
# Returns: N/A
$Global::debug or return;
@_ = grep { defined $_ ? $_ : "" } @_;
if($Global::debug eq "all" or $Global::debug eq $_[0]) {
if($Global::fd{1}) {
# Original stdout was saved
my $stdout = $Global::fd{1};
print $stdout @_[1..$#_];
} else {
print @_[1..$#_];
}
}
}
sub my_memory_usage() {
# Returns:
# memory usage if found
# 0 otherwise
use strict;
use FileHandle;
local $/ = "\n";
my $pid = $$;
if(-e "/proc/$pid/stat") {
my $fh = FileHandle->new("</proc/$pid/stat");
my $data = <$fh>;
chomp $data;
$fh->close;
my @procinfo = split(/\s+/,$data);
return undef_as_zero($procinfo[22]);
} else {
return 0;
}
}
sub my_size() {
# Returns:
# $size = size of object if Devel::Size is installed
# -1 otherwise
my @size_this = (@_);
eval "use Devel::Size qw(size total_size)";
if ($@) {
return -1;
} else {
return total_size(@_);
}
}
sub my_dump(@) {
# Returns:
# ascii expression of object if Data::Dump(er) is installed
# error code otherwise
my @dump_this = (@_);
eval "use Data::Dump qw(dump);";
if ($@) {
# Data::Dump not installed
eval "use Data::Dumper;";
if ($@) {
my $err = "Neither Data::Dump nor Data::Dumper is installed\n".
"Not dumping output\n";
::status($err);
return $err;
} else {
return Dumper(@dump_this);
}
} else {
# Create a dummy Data::Dump:dump as Hans Schou sometimes has
# it undefined
eval "sub Data::Dump:dump {}";
eval "use Data::Dump qw(dump);";
return (Data::Dump::dump(@dump_this));
}
}
sub my_croak(@) {
eval "use Carp; 1";
$Carp::Verbose = 1;
croak(@_);
}
sub my_carp() {
eval "use Carp; 1";
$Carp::Verbose = 1;
carp(@_);
}
sub __OBJECT_ORIENTED_PARTS__() {}
package SSHLogin;
sub new($$) {
my $class = shift;
my $sshlogin_string = shift;
my $ncpus;
my %hostgroups;
# SSHLogins can have these formats:
# @grp+grp/ncpu//usr/bin/ssh user@server
# ncpu//usr/bin/ssh user@server
# /usr/bin/ssh user@server
# user@server
# ncpu/user@server
# @grp+grp/user@server
if($sshlogin_string =~ s:^\@([^/]+)/?::) {
# Look for SSHLogin hostgroups
%hostgroups = map { $_ => 1 } split(/\+/, $1);
}
# An SSHLogin is always in the hostgroup of its "numcpu/host"
$hostgroups{$sshlogin_string} = 1;
if ($sshlogin_string =~ s:^(\d+)/::) {
# Override default autodetected ncpus unless missing
$ncpus = $1;
}
my $string = $sshlogin_string;
# An SSHLogin is always in the hostgroup of its $string-name
$hostgroups{$string} = 1;
@Global::hostgroups{keys %hostgroups} = values %hostgroups;
my @unget = ();
my $no_slash_string = $string;
$no_slash_string =~ s/[^-a-z0-9:]/_/gi;
return bless {
'string' => $string,
'jobs_running' => 0,
'jobs_completed' => 0,
'maxlength' => undef,
'max_jobs_running' => undef,
'orig_max_jobs_running' => undef,
'ncpus' => $ncpus,
'hostgroups' => \%hostgroups,
'sshcommand' => undef,
'serverlogin' => undef,
'control_path_dir' => undef,
'control_path' => undef,
'time_to_login' => undef,
'last_login_at' => undef,
'loadavg_file' => $Global::cache_dir . "/tmp/sshlogin/" .
$no_slash_string . "/loadavg",
'loadavg' => undef,
'last_loadavg_update' => 0,
'swap_activity_file' => $Global::cache_dir . "/tmp/sshlogin/" .
$no_slash_string . "/swap_activity",
'swap_activity' => undef,
}, ref($class) || $class;
}
sub DESTROY($) {
my $self = shift;
# Remove temporary files if they are created.
::rm($self->{'loadavg_file'});
::rm($self->{'swap_activity_file'});
}
sub string($) {
my $self = shift;
return $self->{'string'};
}
sub jobs_running($) {
my $self = shift;
return ($self->{'jobs_running'} || "0");
}
sub inc_jobs_running($) {
my $self = shift;
$self->{'jobs_running'}++;
}
sub dec_jobs_running($) {
my $self = shift;
$self->{'jobs_running'}--;
}
sub set_maxlength($$) {
my $self = shift;
$self->{'maxlength'} = shift;
}
sub maxlength($) {
my $self = shift;
return $self->{'maxlength'};
}
sub jobs_completed() {
my $self = shift;
return $self->{'jobs_completed'};
}
sub in_hostgroups() {
# Input:
# @hostgroups = the hostgroups to look for
# Returns:
# true if intersection of @hostgroups and the hostgroups of this
# SSHLogin is non-empty
my $self = shift;
return grep { defined $self->{'hostgroups'}{$_} } @_;
}
sub hostgroups() {
my $self = shift;
return keys %{$self->{'hostgroups'}};
}
sub inc_jobs_completed($) {
my $self = shift;
$self->{'jobs_completed'}++;
$Global::total_completed++;
}
sub set_max_jobs_running($$) {
my $self = shift;
if(defined $self->{'max_jobs_running'}) {
$Global::max_jobs_running -= $self->{'max_jobs_running'};
}
$self->{'max_jobs_running'} = shift;
if(defined $self->{'max_jobs_running'}) {
# max_jobs_running could be resat if -j is a changed file
$Global::max_jobs_running += $self->{'max_jobs_running'};
}
# Initialize orig to the first non-zero value that comes around
$self->{'orig_max_jobs_running'} ||= $self->{'max_jobs_running'};
}
sub memfree() {
# Returns:
# $memfree in bytes
my $self = shift;
$self->memfree_recompute();
# Return 1 if not defined.
return (not defined $self->{'memfree'} or $self->{'memfree'})
}
sub memfree_recompute() {
my $self = shift;
my $script = memfreescript();
# TODO add sshlogin and backgrounding
# Run the script twice if it gives 0 (typically intermittent error)
$self->{'memfree'} = ::qqx($script) || ::qqx($script);
if(not $self->{'memfree'}) {
::die_bug("Less than 1 byte free");
}
#::debug("mem","New free:",$self->{'memfree'}," ");
}
{
my $script;
sub memfreescript() {
# Returns:
# shellscript for giving available memory in bytes
if(not $script) {
my %script_of = (
# /proc/meminfo
# MemFree: 7012 kB
# Buffers: 19876 kB
# Cached: 431192 kB
# SwapCached: 0 kB
"linux" =>
q[ print 1024 * qx{ ].
q[ awk '/^((Swap)?Cached|MemFree|Buffers):/ ].
q[ { sum += \$2} END { print sum }' ].
q[ /proc/meminfo } ],
# Android uses same code as GNU/Linux
"android" =>
q[ print 1024 * qx{ ].
q[ awk '/^((Swap)?Cached|MemFree|Buffers):/ ].
q[ { sum += \$2} END { print sum }' ].
q[ /proc/meminfo } ],
# $ vmstat 1 1
# procs memory page faults cpu
# r b w avm free re at pi po fr de sr in sy cs us sy id
# 1 0 0 242793 389737 5 1 0 0 0 0 0 107 978 60 1 1 99
"hpux" =>
q[ print (((reverse `vmstat 1 1`)[0] ].
q[ =~ /(?:\d+\D+){4}(\d+)/)[0]*1024) ],
# $ vmstat 1 2
# kthr memory page disk faults cpu
# r b w swap free re mf pi po fr de sr s3 s4 -- -- in sy cs us sy id
# 0 0 0 6496720 5170320 68 260 8 2 1 0 0 -0 3 0 0 309 1371 255 1 2 97
# 0 0 0 6434088 5072656 7 15 8 0 0 0 0 0 261 0 0 1889 1899 3222 0 8 92
#
# The second free value is correct
"solaris" =>
q[ print (((reverse `vmstat 1 2`)[0] ].
q[ =~ /(?:\d+\D+){4}(\d+)/)[0]*1024) ],
"freebsd" => q{
for(qx{/sbin/sysctl -a}) {
if (/^([^:]+):\s+(.+)\s*$/s) {
$sysctl->{$1} = $2;
}
}
print $sysctl->{"hw.pagesize"} *
($sysctl->{"vm.stats.vm.v_cache_count"}
+ $sysctl->{"vm.stats.vm.v_inactive_count"}
+ $sysctl->{"vm.stats.vm.v_free_count"});
},
# Mach Virtual Memory Statistics: (page size of 4096 bytes)
# Pages free: 198061.
# Pages active: 159701.
# Pages inactive: 47378.
# Pages speculative: 29707.
# Pages wired down: 89231.
# "Translation faults": 928901425.
# Pages copy-on-write: 156988239.
# Pages zero filled: 271267894.
# Pages reactivated: 48895.
# Pageins: 1798068.
# Pageouts: 257.
# Object cache: 6603 hits of 1713223 lookups (0% hit rate)
'darwin' =>
q[ $vm = `vm_stat`;
print (($vm =~ /page size of (\d+)/)[0] *
(($vm =~ /Pages free:\s+(\d+)/)[0] +
($vm =~ /Pages inactive:\s+(\d+)/)[0]));
],
);
my $perlscript = "";
# Make a perl script that detects the OS ($^O) and runs
# the appropriate command
for my $os (keys %script_of) {
$perlscript .= 'if($^O eq "'.$os.'") { '.$script_of{$os}.'}';
}
$perlscript =~ s/[\t\n ]+/ /g;
$script = "perl -e " . ::Q($perlscript);
}
return $script;
}
}
sub limit($) {
# Returns:
# 0 = Below limit. Start another job.
# 1 = Over limit. Start no jobs.
# 2 = Kill youngest job
my $self = shift;
if(not defined $self->{'limitscript'}) {
my %limitscripts =
("io" => q!
io() {
limit=$1;
io_file=$2;
# Do the measurement in the background
(tmp=$(tempfile);
LANG=C iostat -x 1 2 > $tmp;
mv $tmp $io_file) &
perl -e '-e $ARGV[0] or exit(1);
for(reverse <>) {
/Device:/ and last;
/(\S+)$/ and $max = $max > $1 ? $max : $1; }
exit ($max < '$limit')' $io_file;
};
export -f io;
io %s %s
!,
"mem" => q!
mem() {
limit=$1;
awk '/^((Swap)?Cached|MemFree|Buffers):/{ sum += $2}
END {
if (sum*1024 < '$limit'/2) { exit 2; }
else { exit (sum*1024 < '$limit') }
}' /proc/meminfo;
};
export -f mem;
mem %s;
!,
"load" => q!
load() {
limit=$1;
ps ax -o state,command |
grep -E '^[DOR].[^[]' |
wc -l |
perl -ne 'exit ('$limit' < $_)';
};
export -f load;
load %s;
!,
);
my ($cmd,@args) = split /\s+/,$opt::limit;
if($limitscripts{$cmd}) {
my $tmpfile = ::tmpname("parlmt");
++$Global::unlink{$tmpfile};
$self->{'limitscript'} =
::spacefree(1, sprintf($limitscripts{$cmd},
::multiply_binary_prefix(@args),$tmpfile));
} else {
$self->{'limitscript'} = $opt::limit;
}
}
my %env = %ENV;
local %ENV = %env;
$ENV{'SSHLOGIN'} = $self->string();
system($Global::shell,"-c",$self->{'limitscript'});
::debug("limit","limit `".$self->{'limitscript'}."` result ".($?>>8)."\n");
return $?>>8;
}
sub swapping($) {
my $self = shift;
my $swapping = $self->swap_activity();
return (not defined $swapping or $swapping)
}
sub swap_activity($) {
# If the currently known swap activity is too old:
# Recompute a new one in the background
# Returns:
# last swap activity computed
my $self = shift;
# Should we update the swap_activity file?
my $update_swap_activity_file = 0;
if(-r $self->{'swap_activity_file'}) {
open(my $swap_fh, "<", $self->{'swap_activity_file'}) ||
::die_bug("swap_activity_file-r");
my $swap_out = <$swap_fh>;
close $swap_fh;
if($swap_out =~ /^(\d+)$/) {
$self->{'swap_activity'} = $1;
::debug("swap", "New swap_activity: ", $self->{'swap_activity'});
}
::debug("swap", "Last update: ", $self->{'last_swap_activity_update'});
if(time - $self->{'last_swap_activity_update'} > 10) {
# last swap activity update was started 10 seconds ago
::debug("swap", "Older than 10 sec: ", $self->{'swap_activity_file'});
$update_swap_activity_file = 1;
}
} else {
::debug("swap", "No swap_activity file: ", $self->{'swap_activity_file'});
$self->{'swap_activity'} = undef;
$update_swap_activity_file = 1;
}
if($update_swap_activity_file) {
::debug("swap", "Updating swap_activity file ", $self->{'swap_activity_file'});
$self->{'last_swap_activity_update'} = time;
my $dir = ::dirname($self->{'swap_activity_file'});
-d $dir or eval { File::Path::mkpath($dir); };
my $swap_activity;
$swap_activity = swapactivityscript();
if($self->{'string'} ne ":") {
$swap_activity = $self->sshcommand() . " " . $self->serverlogin() . " " .
::Q($swap_activity);
}
# Run swap_activity measuring.
# As the command can take long to run if run remote
# save it to a tmp file before moving it to the correct file
my $file = $self->{'swap_activity_file'};
my ($dummy_fh, $tmpfile) = ::tmpfile(SUFFIX => ".swp");
::debug("swap", "\n", $swap_activity, "\n");
::qqx("($swap_activity > $tmpfile && mv $tmpfile $file || rm $tmpfile &)");
}
return $self->{'swap_activity'};
}
{
my $script;
sub swapactivityscript() {
# Returns:
# shellscript for detecting swap activity
#
# arguments for vmstat are OS dependant
# swap_in and swap_out are in different columns depending on OS
#
if(not $script) {
my %vmstat = (
# linux: $7*$8
# $ vmstat 1 2
# procs -----------memory---------- ---swap-- -----io---- -system-- ----cpu----
# r b swpd free buff cache si so bi bo in cs us sy id wa
# 5 0 51208 1701096 198012 18857888 0 0 37 153 28 19 56 11 33 1
# 3 0 51208 1701288 198012 18857972 0 0 0 0 3638 10412 15 3 82 0
'linux' => ['vmstat 1 2 | tail -n1', '$7*$8'],
# solaris: $6*$7
# $ vmstat -S 1 2
# kthr memory page disk faults cpu
# r b w swap free si so pi po fr de sr s3 s4 -- -- in sy cs us sy id
# 0 0 0 4628952 3208408 0 0 3 1 1 0 0 -0 2 0 0 263 613 246 1 2 97
# 0 0 0 4552504 3166360 0 0 0 0 0 0 0 0 0 0 0 246 213 240 1 1 98
'solaris' => ['vmstat -S 1 2 | tail -1', '$6*$7'],
# darwin (macosx): $21*$22
# $ vm_stat -c 2 1
# Mach Virtual Memory Statistics: (page size of 4096 bytes)
# free active specul inactive throttle wired prgable faults copy 0fill reactive purged file-backed anonymous cmprssed cmprssor dcomprs comprs pageins pageout swapins swapouts
# 346306 829050 74871 606027 0 240231 90367 544858K 62343596 270837K 14178 415070 570102 939846 356 370 116 922 4019813 4 0 0
# 345740 830383 74875 606031 0 239234 90369 2696 359 553 0 0 570110 941179 356 370 0 0 0 0 0 0
'darwin' => ['vm_stat -c 2 1 | tail -n1', '$21*$22'],
# ultrix: $12*$13
# $ vmstat -S 1 2
# procs faults cpu memory page disk
# r b w in sy cs us sy id avm fre si so pi po fr de sr s0
# 1 0 0 4 23 2 3 0 97 7743 217k 0 0 0 0 0 0 0 0
# 1 0 0 6 40 8 0 1 99 7743 217k 0 0 3 0 0 0 0 0
'ultrix' => ['vmstat -S 1 2 | tail -1', '$12*$13'],
# aix: $6*$7
# $ vmstat 1 2
# System configuration: lcpu=1 mem=2048MB
#
# kthr memory page faults cpu
# ----- ----------- ------------------------ ------------ -----------
# r b avm fre re pi po fr sr cy in sy cs us sy id wa
# 0 0 333933 241803 0 0 0 0 0 0 10 143 90 0 0 99 0
# 0 0 334125 241569 0 0 0 0 0 0 37 5368 184 0 9 86 5
'aix' => ['vmstat 1 2 | tail -n1', '$6*$7'],
# freebsd: $8*$9
# $ vmstat -H 1 2
# procs memory page disks faults cpu
# r b w avm fre flt re pi po fr sr ad0 ad1 in sy cs us sy id
# 1 0 0 596716 19560 32 0 0 0 33 8 0 0 11 220 277 0 0 99
# 0 0 0 596716 19560 2 0 0 0 0 0 0 0 11 144 263 0 1 99
'freebsd' => ['vmstat -H 1 2 | tail -n1', '$8*$9'],
# mirbsd: $8*$9
# $ vmstat 1 2
# procs memory page disks traps cpu
# r b w avm fre flt re pi po fr sr wd0 cd0 int sys cs us sy id
# 0 0 0 25776 164968 34 0 0 0 0 0 0 0 230 259 38 4 0 96
# 0 0 0 25776 164968 24 0 0 0 0 0 0 0 237 275 37 0 0 100
'mirbsd' => ['vmstat 1 2 | tail -n1', '$8*$9'],
# netbsd: $7*$8
# $ vmstat 1 2
# procs memory page disks faults cpu
# r b avm fre flt re pi po fr sr w0 w1 in sy cs us sy id
# 0 0 138452 6012 54 0 0 0 1 2 3 0 4 100 23 0 0 100
# 0 0 138456 6008 1 0 0 0 0 0 0 0 7 26 19 0 0 100
'netbsd' => ['vmstat 1 2 | tail -n1', '$7*$8'],
# openbsd: $8*$9
# $ vmstat 1 2
# procs memory page disks traps cpu
# r b w avm fre flt re pi po fr sr wd0 wd1 int sys cs us sy id
# 0 0 0 76596 109944 73 0 0 0 0 0 0 1 5 259 22 0 1 99
# 0 0 0 76604 109936 24 0 0 0 0 0 0 0 7 114 20 0 1 99
'openbsd' => ['vmstat 1 2 | tail -n1', '$8*$9'],
# hpux: $8*$9
# $ vmstat 1 2
# procs memory page faults cpu
# r b w avm free re at pi po fr de sr in sy cs us sy id
# 1 0 0 247211 216476 4 1 0 0 0 0 0 102 73005 54 6 11 83
# 1 0 0 247211 216421 43 9 0 0 0 0 0 144 1675 96 25269512791222387000 25269512791222387000 105
'hpux' => ['vmstat 1 2 | tail -n1', '$8*$9'],
# dec_osf (tru64): $11*$12
# $ vmstat 1 2
# Virtual Memory Statistics: (pagesize = 8192)
# procs memory pages intr cpu
# r w u act free wire fault cow zero react pin pout in sy cs us sy id
# 3 181 36 51K 1895 8696 348M 59M 122M 259 79M 0 5 218 302 4 1 94
# 3 181 36 51K 1893 8696 3 15 21 0 28 0 4 81 321 1 1 98
'dec_osf' => ['vmstat 1 2 | tail -n1', '$11*$12'],
# gnu (hurd): $7*$8
# $ vmstat -k 1 2
# (pagesize: 4, size: 512288, swap size: 894972)
# free actv inact wired zeroed react pgins pgouts pfaults cowpfs hrat caobj cache swfree
# 371940 30844 89228 20276 298348 0 48192 19016 756105 99808 98% 876 20628 894972
# 371940 30844 89228 20276 +0 +0 +0 +0 +42 +2 98% 876 20628 894972
'gnu' => ['vmstat -k 1 2 | tail -n1', '$7*$8'],
# -nto (qnx has no swap)
#-irix
#-svr5 (scosysv)
);
my $perlscript = "";
# Make a perl script that detects the OS ($^O) and runs
# the appropriate vmstat command
for my $os (keys %vmstat) {
$vmstat{$os}[1] =~ s/\$/\\\\\\\$/g; # $ => \\\$
$perlscript .= 'if($^O eq "'.$os.'") { print `'.$vmstat{$os}[0].' | awk "{print ' .
$vmstat{$os}[1] . '}"` }';
}
$script = "perl -e " . ::Q($perlscript);
}
return $script;
}
}
sub too_fast_remote_login($) {
my $self = shift;
if($self->{'last_login_at'} and $self->{'time_to_login'}) {
# sshd normally allows 10 simultaneous logins
# A login takes time_to_login
# So time_to_login/5 should be safe
# If now <= last_login + time_to_login/5: Then it is too soon.
my $too_fast = (::now() <= $self->{'last_login_at'}
+ $self->{'time_to_login'}/5);
::debug("run", "Too fast? $too_fast ");
return $too_fast;
} else {
# No logins so far (or time_to_login not computed): it is not too fast
return 0;
}
}
sub last_login_at($) {
my $self = shift;
return $self->{'last_login_at'};
}
sub set_last_login_at($$) {
my $self = shift;
$self->{'last_login_at'} = shift;
}
sub loadavg_too_high($) {
my $self = shift;
my $loadavg = $self->loadavg();
if(defined $loadavg) {
::debug("load", "Load $loadavg > ",$self->max_loadavg());
return $loadavg >= $self->max_loadavg();
} else {
# Unknown load: Assume load is too high
return 1;
}
}
{
my $cmd;
sub loadavg_cmd() {
if(not $cmd) {
# aix => "ps -ae -o state,command" # state wrong
# bsd => "ps ax -o state,command"
# sysv => "ps -ef -o s -o comm"
# cygwin => perl -ne 'close STDERR; /Name/ and print"\n"; \
# /(Name|Pid|Ppid|State):\s+(\S+)/ and print "$2\t";' /proc/*/status |
# awk '{print $2,$1}'
# dec_osf => bsd
# dragonfly => bsd
# freebsd => bsd
# gnu => bsd
# hpux => ps -el|awk '{print $2,$14,$15}'
# irix => ps -ef -o state -o comm
# linux => bsd
# minix => ps el|awk '{print \$1,\$11}'
# mirbsd => bsd
# netbsd => bsd
# openbsd => bsd
# solaris => sysv
# svr5 => sysv
# ultrix => ps -ax | awk '{print $3,$5}'
# unixware => ps -el|awk '{print $2,$14,$15}'
my $ps = ::spacefree(1,q{
$sysv="ps -ef -o s -o comm";
$sysv2="ps -ef -o state -o comm";
$bsd="ps ax -o state,command";
# Treat threads as processes
$bsd2="ps axH -o state,command";
$psel="ps -el|awk '{ print \$2,\$14,\$15 }'";
$cygwin=q{ perl -ne 'close STDERR; /Name/ and print"\n";
/(Name|Pid|Ppid|State):\s+(\S+)/ and print "$2\t";' /proc/*/status |
awk '{print $2,$1}' };
$dummy="echo S COMMAND;echo R dummy";
%ps=(
# TODO Find better code for AIX/Android
'aix' => "uptime",
'android' => "uptime",
'cygwin' => $cygwin,
'darwin' => $bsd,
'dec_osf' => $sysv2,
'dragonfly' => $bsd,
'freebsd' => $bsd2,
'gnu' => $bsd,
'hpux' => $psel,
'irix' => $sysv2,
'linux' => $bsd2,
'minix' => "ps el|awk '{print \$1,\$11}'",
'mirbsd' => $bsd,
'msys' => $cygwin,
'netbsd' => $bsd,
'nto' => $dummy,
'openbsd' => $bsd,
'solaris' => $sysv,
'svr5' => $psel,
'ultrix' => "ps -ax | awk '{print \$3,\$5}'",
'MSWin32' => $sysv,
);
print `$ps{$^O}`;
});
# The command is too long for csh, so base64_wrap the command
$cmd = Job::base64_wrap($ps);
}
return $cmd;
}
}
sub loadavg($) {
# If the currently know loadavg is too old:
# Recompute a new one in the background
# The load average is computed as the number of processes waiting for disk
# or CPU right now. So it is the server load this instant and not averaged over
# several minutes. This is needed so GNU Parallel will at most start one job
# that will push the load over the limit.
#
# Returns:
# $last_loadavg = last load average computed (undef if none)
my $self = shift;
# Should we update the loadavg file?
my $update_loadavg_file = 0;
if(open(my $load_fh, "<", $self->{'loadavg_file'})) {
local $/; # $/ = undef => slurp whole file
my $load_out = <$load_fh>;
close $load_fh;
if($load_out =~ /\S/) {
# Content can be empty if ~/ is on NFS
# due to reading being non-atomic.
#
# Count lines starting with D,O,R but command does not start with [
my $load =()= ($load_out=~/(^\s?[DOR]\S* +(?=[^\[])\S)/gm);
if($load > 0) {
# load is overestimated by 1
$self->{'loadavg'} = $load - 1;
::debug("load", "New loadavg: ", $self->{'loadavg'},"\n");
} elsif ($load_out=~/average: (\d+.\d+)/) {
# AIX does not support instant load average
# 04:11AM up 21 days, 12:55, 1 user, load average: 1.85, 1.57, 1.55
$self->{'loadavg'} = $1;
} else {
::die_bug("loadavg_invalid_content: " .
$self->{'loadavg_file'} . "\n$load_out");
}
}
$update_loadavg_file = 1;
} else {
::debug("load", "No loadavg file: ", $self->{'loadavg_file'});
$self->{'loadavg'} = undef;
$update_loadavg_file = 1;
}
if($update_loadavg_file) {
::debug("load", "Updating loadavg file", $self->{'loadavg_file'}, "\n");
$self->{'last_loadavg_update'} = time;
my $dir = ::dirname($self->{'swap_activity_file'});
-d $dir or eval { File::Path::mkpath($dir); };
-w $dir or ::die_bug("Cannot write to $dir");
my $cmd = "";
if($self->{'string'} ne ":") {
$cmd = $self->sshcommand() . " " . $self->serverlogin() . " " .
::Q(loadavg_cmd());
} else {
$cmd .= loadavg_cmd();
}
# As the command can take long to run if run remote
# save it to a tmp file before moving it to the correct file
::debug("load", "Update load\n");
my $file = $self->{'loadavg_file'};
# tmpfile on same filesystem as $file
my $tmpfile = $file.$$;
::qqx("($cmd > $tmpfile && mv $tmpfile $file || rm $tmpfile & )");
}
return $self->{'loadavg'};
}
sub max_loadavg($) {
my $self = shift;
# If --load is a file it might be changed
if($Global::max_load_file) {
my $mtime = (stat($Global::max_load_file))[9];
if($mtime > $Global::max_load_file_last_mod) {
$Global::max_load_file_last_mod = $mtime;
for my $sshlogin (values %Global::host) {
$sshlogin->set_max_loadavg(undef);
}
}
}
if(not defined $self->{'max_loadavg'}) {
$self->{'max_loadavg'} =
$self->compute_max_loadavg($opt::load);
}
::debug("load", "max_loadavg: ", $self->string(), " ", $self->{'max_loadavg'});
return $self->{'max_loadavg'};
}
sub set_max_loadavg($$) {
my $self = shift;
$self->{'max_loadavg'} = shift;
}
sub compute_max_loadavg($) {
# Parse the max loadaverage that the user asked for using --load
# Returns:
# max loadaverage
my $self = shift;
my $loadspec = shift;
my $load;
if(defined $loadspec) {
if($loadspec =~ /^\+(\d+)$/) {
# E.g. --load +2
my $j = $1;
$load =
$self->ncpus() + $j;
} elsif ($loadspec =~ /^-(\d+)$/) {
# E.g. --load -2
my $j = $1;
$load =
$self->ncpus() - $j;
} elsif ($loadspec =~ /^(\d+)\%$/) {
my $j = $1;
$load =
$self->ncpus() * $j / 100;
} elsif ($loadspec =~ /^(\d+(\.\d+)?)$/) {
$load = $1;
} elsif (-f $loadspec) {
$Global::max_load_file = $loadspec;
$Global::max_load_file_last_mod = (stat($Global::max_load_file))[9];
if(open(my $in_fh, "<", $Global::max_load_file)) {
my $opt_load_file = join("",<$in_fh>);
close $in_fh;
$load = $self->compute_max_loadavg($opt_load_file);
} else {
::error("Cannot open $loadspec.");
::wait_and_exit(255);
}
} else {
::error("Parsing of --load failed.");
::die_usage();
}
if($load < 0.01) {
$load = 0.01;
}
}
return $load;
}
sub time_to_login($) {
my $self = shift;
return $self->{'time_to_login'};
}
sub set_time_to_login($$) {
my $self = shift;
$self->{'time_to_login'} = shift;
}
sub max_jobs_running($) {
my $self = shift;
if(not defined $self->{'max_jobs_running'}) {
my $nproc = $self->compute_number_of_processes($opt::jobs);
$self->set_max_jobs_running($nproc);
}
return $self->{'max_jobs_running'};
}
sub orig_max_jobs_running($) {
my $self = shift;
return $self->{'orig_max_jobs_running'};
}
sub compute_number_of_processes($) {
# Number of processes wanted and limited by system resources
# Returns:
# Number of processes
my $self = shift;
my $opt_P = shift;
my $wanted_processes = $self->user_requested_processes($opt_P);
if(not defined $wanted_processes) {
$wanted_processes = $Global::default_simultaneous_sshlogins;
}
::debug("load", "Wanted procs: $wanted_processes\n");
my $system_limit =
$self->processes_available_by_system_limit($wanted_processes);
::debug("load", "Limited to procs: $system_limit\n");
return $system_limit;
}
{
my @children;
my $max_system_proc_reached;
my $more_filehandles;
my %fh;
my $tmpfhname;
my $count_jobs_already_read;
my @jobs;
my $job;
my @args;
my $arg;
sub reserve_filehandles($) {
# Reserves filehandle
my $n = shift;
for (1..$n) {
$more_filehandles &&= open($fh{$tmpfhname++}, "<", "/dev/null");
}
}
sub reserve_process() {
# Spawn a dummy process
my $child;
if($child = fork()) {
push @children, $child;
$Global::unkilled_children{$child} = 1;
} elsif(defined $child) {
# This is the child
# The child takes one process slot
# It will be killed later
$SIG{'TERM'} = $Global::original_sig{'TERM'};
if($^O eq "cygwin" or $^O eq "msys" or $^O eq "nto") {
# The exec does not work on Cygwin and QNX
sleep 10101010;
} else {
# 'exec sleep' takes less RAM than sleeping in perl
exec 'sleep', 10101;
}
exit(0);
} else {
# Failed to spawn
$max_system_proc_reached = 1;
}
}
sub get_args_or_jobs() {
# Get an arg or a job (depending on mode)
if($Global::semaphore or ($opt::pipe and not $opt::tee)) {
# Skip: No need to get args
return 1;
} elsif(defined $opt::retries and $count_jobs_already_read) {
# For retries we may need to run all jobs on this sshlogin
# so include the already read jobs for this sshlogin
$count_jobs_already_read--;
return 1;
} else {
if($opt::X or $opt::m) {
# The arguments may have to be re-spread over several jobslots
# So pessimistically only read one arg per jobslot
# instead of a full commandline
if($Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->empty()) {
if($Global::JobQueue->empty()) {
return 0;
} else {
$job = $Global::JobQueue->get();
push(@jobs, $job);
return 1;
}
} else {
$arg = $Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->get();
push(@args, $arg);
return 1;
}
} else {
# If there are no more command lines, then we have a process
# per command line, so no need to go further
if($Global::JobQueue->empty()) {
return 0;
} else {
$job = $Global::JobQueue->get();
# Replacement must happen here due to seq()
$job and $job->replaced();
push(@jobs, $job);
return 1;
}
}
}
}
sub cleanup() {
# Cleanup: Close the files
for (values %fh) { close $_ }
# Cleanup: Kill the children
for my $pid (@children) {
kill 9, $pid;
waitpid($pid,0);
delete $Global::unkilled_children{$pid};
}
# Cleanup: Unget the command_lines or the @args
$Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->unget(@args);
@args = ();
$Global::JobQueue->unget(@jobs);
@jobs = ();
}
sub processes_available_by_system_limit($) {
# If the wanted number of processes is bigger than the system limits:
# Limit them to the system limits
# Limits are: File handles, number of input lines, processes,
# and taking > 1 second to spawn 10 extra processes
# Returns:
# Number of processes
my $self = shift;
my $wanted_processes = shift;
my $system_limit = 0;
my $slow_spawning_warning_printed = 0;
my $time = time;
$more_filehandles = 1;
$tmpfhname = "TmpFhNamE";
# perl uses 7 filehandles for something?
# parallel uses 1 for memory_usage
# parallel uses 4 for ?
reserve_filehandles(12);
# Two processes for load avg and ?
reserve_process();
reserve_process();
# For --retries count also jobs already run
$count_jobs_already_read = $Global::JobQueue->next_seq();
my $wait_time_for_getting_args = 0;
my $start_time = time;
while(1) {
$system_limit >= $wanted_processes and last;
not $more_filehandles and last;
$max_system_proc_reached and last;
my $before_getting_arg = time;
if(!$Global::dummy_jobs) {
get_args_or_jobs() or last;
}
$wait_time_for_getting_args += time - $before_getting_arg;
$system_limit++;
# Every simultaneous process uses 2 filehandles to write to
# and 2 filehandles to read from
reserve_filehandles(4);
# System process limit
reserve_process();
my $forktime = time - $time - $wait_time_for_getting_args;
::debug("run", "Time to fork $system_limit procs: $wait_time_for_getting_args ",
$forktime,
" (processes so far: ", $system_limit,")\n");
if($system_limit > 10 and
$forktime > 1 and
$forktime > $system_limit * 0.01
and not $slow_spawning_warning_printed) {
# It took more than 0.01 second to fork a processes on avg.
# Give the user a warning. He can press Ctrl-C if this
# sucks.
::warning("Starting $system_limit processes took > $forktime sec.",
"Consider adjusting -j. Press CTRL-C to stop.");
$slow_spawning_warning_printed = 1;
}
}
cleanup();
if($system_limit < $wanted_processes) {
# The system_limit is less than the wanted_processes
if($system_limit < 1 and not $Global::JobQueue->empty()) {
::warning("Cannot spawn any jobs. ".
"Raising ulimit -u or 'nproc' in /etc/security/limits.conf",
"or /proc/sys/kernel/pid_max may help.");
::wait_and_exit(255);
}
if(not $more_filehandles) {
::warning("Only enough file handles to run ".
$system_limit. " jobs in parallel.",
"Running 'parallel -j0 -N $system_limit --pipe parallel -j0' or",
"raising 'ulimit -n' or 'nofile' in /etc/security/limits.conf",
"or /proc/sys/fs/file-max may help.");
}
if($max_system_proc_reached) {
::warning("Only enough available processes to run ".
$system_limit. " jobs in parallel.",
"Raising ulimit -u or /etc/security/limits.conf ",
"or /proc/sys/kernel/pid_max may help.");
}
}
if($] == 5.008008 and $system_limit > 1000) {
# https://savannah.gnu.org/bugs/?36942
$system_limit = 1000;
}
if($Global::JobQueue->empty()) {
$system_limit ||= 1;
}
if($self->string() ne ":" and
$system_limit > $Global::default_simultaneous_sshlogins) {
$system_limit =
$self->simultaneous_sshlogin_limit($system_limit);
}
return $system_limit;
}
}
sub simultaneous_sshlogin_limit($) {
# Test by logging in wanted number of times simultaneously
# Returns:
# min($wanted_processes,$working_simultaneous_ssh_logins-1)
my $self = shift;
my $wanted_processes = shift;
if($self->{'time_to_login'}) {
return $wanted_processes;
}
# Try twice because it guesses wrong sometimes
# Choose the minimal
my $ssh_limit =
::min($self->simultaneous_sshlogin($wanted_processes),
$self->simultaneous_sshlogin($wanted_processes));
if($ssh_limit < $wanted_processes) {
my $serverlogin = $self->serverlogin();
::warning("ssh to $serverlogin only allows ".
"for $ssh_limit simultaneous logins.",
"You may raise this by changing",
"/etc/ssh/sshd_config:MaxStartups and MaxSessions on $serverlogin.",
"You can also try --sshdelay 0.1",
"Using only ".($ssh_limit-1)." connections ".
"to avoid race conditions.");
# Race condition can cause problem if using all sshs.
if($ssh_limit > 1) { $ssh_limit -= 1; }
}
return $ssh_limit;
}
sub simultaneous_sshlogin($) {
# Using $sshlogin try to see if we can do $wanted_processes
# simultaneous logins
# (ssh host echo simul-login & ssh host echo simul-login & ...) |
# grep simul|wc -l
# Input:
# $wanted_processes = Try for this many logins in parallel
# Returns:
# $ssh_limit = Number of succesful parallel logins
local $/ = "\n";
my $self = shift;
my $wanted_processes = shift;
my $sshcmd = $self->sshcommand();
my $serverlogin = $self->serverlogin();
my $sshdelay = $opt::sshdelay ? "sleep $opt::sshdelay;" : "";
# TODO sh -c wrapper to work for csh
my $cmd = ("$sshdelay$sshcmd $serverlogin -- ".
"echo simultaneouslogin </dev/null 2>&1 &")x$wanted_processes;
::debug("init", "Trying $wanted_processes logins at $serverlogin\n");
open (my $simul_fh, "-|", "($cmd)|grep simultaneouslogin | wc -l") or
::die_bug("simultaneouslogin");
my $ssh_limit = <$simul_fh>;
close $simul_fh;
chomp $ssh_limit;
return $ssh_limit;
}
sub set_ncpus($$) {
my $self = shift;
$self->{'ncpus'} = shift;
}
sub user_requested_processes($) {
# Parse the number of processes that the user asked for using -j
# Input:
# $opt_P = string formatted as for -P
# Returns:
# $processes = the number of processes to run on this sshlogin
my $self = shift;
my $opt_P = shift;
my $processes;
if(defined $opt_P) {
if($opt_P =~ /^\+(\d+)$/) {
# E.g. -P +2
my $j = $1;
$processes =
$self->ncpus() + $j;
} elsif ($opt_P =~ /^-(\d+)$/) {
# E.g. -P -2
my $j = $1;
$processes =
$self->ncpus() - $j;
} elsif ($opt_P =~ /^(\d+(\.\d+)?)\%$/) {
# E.g. -P 10.5%
my $j = $1;
$processes =
$self->ncpus() * $j / 100;
} elsif ($opt_P =~ /^(\d+)$/) {
$processes = $1;
if($processes == 0) {
# -P 0 = infinity (or at least close)
$processes = $Global::infinity;
}
} elsif (-f $opt_P) {
$Global::max_procs_file = $opt_P;
if(open(my $in_fh, "<", $Global::max_procs_file)) {
my $opt_P_file = join("",<$in_fh>);
close $in_fh;
$processes = $self->user_requested_processes($opt_P_file);
} else {
::error("Cannot open $opt_P.");
::wait_and_exit(255);
}
} else {
::error("Parsing of --jobs/-j/--max-procs/-P failed.");
::die_usage();
}
$processes = ::ceil($processes);
}
return $processes;
}
sub ncpus($) {
# Number of CPU threads
# --use_sockets_instead_of_threads = count socket instead
# --use_cores_instead_of_threads = count physical cores instead
# Returns:
# $ncpus = number of cpu (threads) on this sshlogin
local $/ = "\n";
my $self = shift;
if(not defined $self->{'ncpus'}) {
my $sshcmd = $self->sshcommand();
my $serverlogin = $self->serverlogin();
if($serverlogin eq ":") {
if($opt::use_sockets_instead_of_threads) {
$self->{'ncpus'} = socket_core_thread()->{'sockets'};
} elsif($opt::use_cores_instead_of_threads) {
$self->{'ncpus'} = socket_core_thread()->{'cores'};
} else {
$self->{'ncpus'} = socket_core_thread()->{'threads'};
}
} else {
my $ncpu;
if($opt::use_sockets_instead_of_threads
or
$opt::use_cpus_instead_of_cores) {
$ncpu =
::qqx("echo|$sshcmd $serverlogin -- parallel --number-of-sockets");
} elsif($opt::use_cores_instead_of_threads) {
$ncpu =
::qqx("echo|$sshcmd $serverlogin -- parallel --number-of-cores");
} else {
$ncpu =
::qqx("echo|$sshcmd $serverlogin -- parallel --number-of-threads");
}
chomp $ncpu;
if($ncpu =~ /^\s*[0-9]+\s*$/s) {
$self->{'ncpus'} = $ncpu;
} else {
::warning("Could not figure out ".
"number of cpus on $serverlogin ($ncpu). Using 1.");
$self->{'ncpus'} = 1;
}
}
}
return $self->{'ncpus'};
}
sub nproc() {
# Returns:
# Number of threads using `nproc`
my $no_of_threads = ::qqx("nproc");
chomp $no_of_threads;
return $no_of_threads;
}
sub no_of_sockets() {
return socket_core_thread()->{'sockets'};
}
sub no_of_cores() {
return socket_core_thread()->{'cores'};
}
sub no_of_threads() {
return socket_core_thread()->{'threads'};
}
sub socket_core_thread() {
# Returns:
# {
# 'sockets' => #sockets = number of socket with CPU present
# 'cores' => #cores = number of physical cores
# 'threads' => #threads = number of compute cores (hyperthreading)
# 'active' => #taskset_threads = number of taskset limited cores
# }
my $cpu;
if ($^O eq 'linux') {
$cpu = sct_gnu_linux();
} elsif ($^O eq 'android') {
$cpu = sct_android();
} elsif ($^O eq 'freebsd') {
$cpu = sct_freebsd();
} elsif ($^O eq 'netbsd') {
$cpu = sct_netbsd();
} elsif ($^O eq 'openbsd') {
$cpu = sct_openbsd();
} elsif ($^O eq 'gnu') {
$cpu = sct_hurd();
} elsif ($^O eq 'darwin') {
$cpu = sct_darwin();
} elsif ($^O eq 'solaris') {
$cpu = sct_solaris();
} elsif ($^O eq 'aix') {
$cpu = sct_aix();
} elsif ($^O eq 'hpux') {
$cpu = sct_hpux();
} elsif ($^O eq 'nto') {
$cpu = sct_qnx();
} elsif ($^O eq 'svr5') {
$cpu = sct_openserver();
} elsif ($^O eq 'irix') {
$cpu = sct_irix();
} elsif ($^O eq 'dec_osf') {
$cpu = sct_tru64();
} else {
# Try all methods until we find something that works
$cpu = (sct_gnu_linux()
|| sct_android()
|| sct_freebsd()
|| sct_netbsd()
|| sct_openbsd()
|| sct_hurd()
|| sct_darwin()
|| sct_solaris()
|| sct_aix()
|| sct_hpux()
|| sct_qnx()
|| sct_openserver()
|| sct_irix()
|| sct_tru64()
);
}
if(not $cpu) {
my $nproc = nproc();
if($nproc) {
$cpu->{'sockets'} =
$cpu->{'cores'} =
$cpu->{'threads'} =
$cpu->{'active'} =
$nproc;
}
}
if(not $cpu) {
::warning("Cannot figure out number of cpus. Using 1.");
$cpu->{'sockets'} =
$cpu->{'cores'} =
$cpu->{'threads'} =
$cpu->{'active'} =
1
}
# Choose minimum of active and actual
my $mincpu;
$mincpu->{'sockets'} = ::min($cpu->{'sockets'},$cpu->{'active'});
$mincpu->{'cores'} = ::min($cpu->{'cores'},$cpu->{'active'});
$mincpu->{'threads'} = ::min($cpu->{'threads'},$cpu->{'active'});
return $mincpu;
}
sub sct_gnu_linux() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
my $cpu;
local $/ = "\n"; # If delimiter is set, then $/ will be wrong
if($ENV{'PARALLEL_CPUINFO'} or -e "/proc/cpuinfo") {
$cpu->{'sockets'} = 0;
$cpu->{'cores'} = 0;
$cpu->{'threads'} = 0;
my %seen;
my %phy_seen;
my @cpuinfo;
my $physicalid;
if(open(my $in_fh, "<", "/proc/cpuinfo")) {
@cpuinfo = <$in_fh>;
close $in_fh;
}
if($ENV{'PARALLEL_CPUINFO'}) {
# Use CPUINFO from environment - used for testing only
@cpuinfo = split/(?<=\n)/,$ENV{'PARALLEL_CPUINFO'};
}
for(@cpuinfo) {
if(/^physical id.*[:](.*)/) {
$physicalid=$1;
if(not $phy_seen{$1}++) {
$cpu->{'sockets'}++;
}
}
if(/^core id.*[:](.*)/ and not $seen{$physicalid,$1}++) {
$cpu->{'cores'}++;
}
/^processor.*[:]/i and $cpu->{'threads'}++;
}
$cpu->{'sockets'} ||= 1;
$cpu->{'cores'} ||= $cpu->{'threads'};
}
if(-e "/proc/self/status" and not $ENV{'PARALLEL_CPUINFO'}) {
# if 'taskset' is used to limit number of threads
if(open(my $in_fh, "<", "/proc/self/status")) {
while(<$in_fh>) {
if(/^Cpus_allowed:\s*(\S+)/) {
my $a = $1;
$a =~ tr/,//d;
$cpu->{'active'} = unpack ("%32b*", pack ("H*",$a));
}
}
close $in_fh;
}
}
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_android() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
# Use GNU/Linux
return sct_gnu_linux();
}
sub sct_freebsd() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = (::qqx(qq{ sysctl -a dev.cpu | grep \%parent | awk '{ print \$2 }' | uniq | wc -l | awk '{ print \$1 }' })
or
::qqx(qq{ sysctl hw.ncpu | awk '{ print \$2 }' }));
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'threads'} =
(::qqx(qq{ sysctl hw.ncpu | awk '{ print \$2 }' })
or
::qqx(qq{ sysctl -a dev.cpu | grep \%parent | awk '{ print \$2 }' | uniq | wc -l | awk '{ print \$1 }' }));
$cpu->{'threads'} and chomp $cpu->{'threads'};
$cpu->{'sockets'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_netbsd() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = ::qqx("sysctl -n hw.ncpu");
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'threads'} = ::qqx("sysctl -n hw.ncpu");
$cpu->{'threads'} and chomp $cpu->{'threads'};
$cpu->{'sockets'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_openbsd() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = ::qqx('sysctl -n hw.ncpu');
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'threads'} = ::qqx('sysctl -n hw.ncpu');
$cpu->{'threads'} and chomp $cpu->{'threads'};
$cpu->{'sockets'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_hurd() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = ::qqx("nproc");
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'threads'} = ::qqx("nproc");
$cpu->{'threads'} and chomp $cpu->{'threads'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_darwin() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} =
(::qqx('sysctl -n hw.physicalcpu')
or
::qqx(qq{ sysctl -a hw | grep [^a-z]physicalcpu[^a-z] | awk '{ print \$2 }' }));
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'threads'} =
(::qqx('sysctl -n hw.logicalcpu')
or
::qqx(qq{ sysctl -a hw | grep [^a-z]logicalcpu[^a-z] | awk '{ print \$2 }' }));
$cpu->{'threads'} and chomp $cpu->{'threads'};
$cpu->{'sockets'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_solaris() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = ::qqx("/usr/sbin/psrinfo");
if($#psrinfo >= 0) {
$cpu->{'cores'} = $#psrinfo +1;
}
}
if(-x "/usr/sbin/prtconf") {
my @prtconf = ::qqx("/usr/sbin/prtconf | grep cpu..instance");
if($#prtconf >= 0) {
$cpu->{'cores'} = $#prtconf +1;
}
}
if(-x "/usr/sbin/prtconf") {
my @prtconf = ::qqx("/usr/sbin/prtconf | grep cpu..instance");
if($#prtconf >= 0) {
$cpu->{'cores'} = $#prtconf +1;
}
}
$cpu->{'cores'} and chomp $cpu->{'cores'};
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = ::qqx("/usr/sbin/psrinfo");
if($#psrinfo >= 0) {
$cpu->{'threads'} = $#psrinfo +1;
}
}
if(-x "/usr/sbin/prtconf") {
my @prtconf = ::qqx("/usr/sbin/prtconf | grep cpu..instance");
if($#prtconf >= 0) {
$cpu->{'threads'} = $#prtconf +1;
}
}
$cpu->{'threads'} and chomp $cpu->{'threads'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_aix() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
if(-x "/usr/sbin/lscfg") {
if(open(my $in_fh, "-|", "/usr/sbin/lscfg -vs |grep proc | wc -l|tr -d ' '")) {
$cpu->{'cores'} = <$in_fh>;
chomp ($cpu->{'cores'});
close $in_fh;
}
}
if(-x "/usr/bin/vmstat") {
if(open(my $in_fh, "-|", "/usr/bin/vmstat 1 1")) {
while(<$in_fh>) {
/lcpu=([0-9]*) / and $cpu->{'threads'} = $1;
}
close $in_fh;
}
}
if(grep { /\d/ } values %$cpu) {
# BUG It is not not known how to calculate this
$cpu->{'sockets'} = 1;
return $cpu;
} else {
return undef;
}
}
sub sct_hpux() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} =
::qqx(qq{ /usr/bin/mpsched -s 2>&1 | grep 'Locality Domain Count' | awk '{ print \$4 }'});
chomp($cpu->{'cores'});
$cpu->{'threads'} =
::qqx(qq{ /usr/bin/mpsched -s 2>&1 | perl -ne '/Processor Count\\D+(\\d+)/ and print "\$1"'});
if(grep { /\d/ } values %$cpu) {
# BUG It is not not known how to calculate this
$cpu->{'sockets'} = 1;
return $cpu;
} else {
return undef;
}
}
sub sct_qnx() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
# BUG: It is not known how to calculate this.
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_openserver() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = ::qqx("/usr/sbin/psrinfo");
if($#psrinfo >= 0) {
$cpu->{'cores'} = $#psrinfo +1;
}
}
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = ::qqx("/usr/sbin/psrinfo");
if($#psrinfo >= 0) {
$cpu->{'threads'} = $#psrinfo +1;
}
}
$cpu->{'sockets'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_irix() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = ::qqx(qq{ hinv | grep HZ | grep Processor | awk '{print \$1}' });
$cpu->{'cores'} and chomp $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sct_tru64() {
# Returns:
# { 'sockets' => #sockets
# 'cores' => #cores
# 'threads' => #threads
# 'active' => #taskset_threads }
local $/ = "\n";
my $cpu;
$cpu->{'cores'} = ::qqx("sizer -pr");
$cpu->{'cores'} and chomp $cpu->{'cores'};
$cpu->{'cores'} ||= 1;
$cpu->{'sockets'} ||= $cpu->{'cores'};
$cpu->{'threads'} ||= $cpu->{'cores'};
if(grep { /\d/ } values %$cpu) {
return $cpu;
} else {
return undef;
}
}
sub sshcommand($) {
# Returns:
# $sshcommand = the command (incl options) to run when using ssh
my $self = shift;
if (not defined $self->{'sshcommand'}) {
$self->sshcommand_of_sshlogin();
}
return $self->{'sshcommand'};
}
sub serverlogin($) {
# Returns:
# $sshcommand = the command (incl options) to run when using ssh
my $self = shift;
if (not defined $self->{'serverlogin'}) {
$self->sshcommand_of_sshlogin();
}
return $self->{'serverlogin'};
}
sub sshcommand_of_sshlogin($) {
# Compute ssh command and serverlogin from sshlogin
# 'server' -> ('ssh -S /tmp/parallel-ssh-RANDOM/host-','server')
# 'user@server' -> ('ssh','user@server')
# 'myssh user@server' -> ('myssh','user@server')
# 'myssh -l user server' -> ('myssh -l user','server')
# '/usr/bin/myssh -l user server' -> ('/usr/bin/myssh -l user','server')
# Sets:
# $self->{'sshcommand'}
# $self->{'serverlogin'}
my $self = shift;
my ($sshcmd, $serverlogin);
# If $opt::ssh is unset, use $PARALLEL_SSH or 'ssh'
$opt::ssh ||= $ENV{'PARALLEL_SSH'} || "ssh";
if($self->{'string'} =~ /(.+) (\S+)$/) {
# Own ssh command
$sshcmd = $1; $serverlogin = $2;
} else {
# Normal ssh
if($opt::controlmaster) {
# Use control_path to make ssh faster
my $control_path = $self->control_path_dir()."/ssh-%r@%h:%p";
$sshcmd = $opt::ssh." -S ".$control_path;
$serverlogin = $self->{'string'};
if(not $self->{'control_path'}{$control_path}++) {
# Master is not running for this control_path
# Start it
my $pid = fork();
if($pid) {
$Global::sshmaster{$pid} ||= 1;
} else {
$SIG{'TERM'} = undef;
# Ignore the 'foo' being printed
open(STDOUT,">","/dev/null");
# STDERR >/dev/null to ignore
open(STDERR,">","/dev/null");
open(STDIN,"<","/dev/null");
# Run a sleep that outputs data, so it will discover
# if the ssh connection closes.
my $sleep = ::Q('$|=1;while(1){sleep 1;print "foo\n"}');
my @master = ($opt::ssh, "-MTS",
$control_path, $serverlogin, "--", "perl", "-e",
$sleep);
exec(@master);
}
}
} else {
$sshcmd = $opt::ssh; $serverlogin = $self->{'string'};
}
}
if($serverlogin =~ s/(\S+)\@(\S+)/$2/) {
# convert user@server to '-l user server'
# because lsh does not support user@server
$sshcmd = $sshcmd." -l ".$1;
}
$self->{'sshcommand'} = $sshcmd;
$self->{'serverlogin'} = $serverlogin;
}
sub control_path_dir($) {
# Returns:
# $control_path_dir = dir of control path (for -M)
my $self = shift;
if(not defined $self->{'control_path_dir'}) {
$self->{'control_path_dir'} =
# Use $ENV{'TMPDIR'} as that is typically not
# NFS mounted
File::Temp::tempdir($ENV{'TMPDIR'}
. "/control_path_dir-XXXX",
CLEANUP => 1);
}
return $self->{'control_path_dir'};
}
sub rsync_transfer_cmd($) {
# Command to run to transfer a file
# Input:
# $file = filename of file to transfer
# $workdir = destination dir
# Returns:
# $cmd = rsync command to run to transfer $file ("" if unreadable)
my $self = shift;
my $file = shift;
my $workdir = shift;
if(not -r $file) {
::warning($file. " is not readable and will not be transferred.");
return "true";
}
my $rsync_destdir;
my $relpath = ($file !~ m:^/:) || ($file =~ m:/\./:); # Is the path relative or /./?
if($relpath) {
$rsync_destdir = ::shell_quote_file($workdir);
} else {
# rsync /foo/bar /
$rsync_destdir = "/";
}
$file = ::shell_quote_file($file);
my $sshcmd = $self->sshcommand();
my $rsync_opts = $ENV{'PARALLEL_RSYNC_OPTS'}.
" -e".::Q($sshcmd);
my $serverlogin = $self->serverlogin();
# Make dir if it does not exist
return "$sshcmd $serverlogin -- mkdir -p $rsync_destdir && " .
rsync()." $rsync_opts $file $serverlogin:$rsync_destdir";
}
sub cleanup_cmd($$$) {
# Command to run to remove the remote file
# Input:
# $file = filename to remove
# $workdir = destination dir
# Returns:
# $cmd = ssh command to run to remove $file and empty parent dirs
my $self = shift;
my $file = shift;
my $workdir = shift;
my $f = $file;
if($f =~ m:/\./:) {
# foo/bar/./baz/quux => workdir/baz/quux
# /foo/bar/./baz/quux => workdir/baz/quux
$f =~ s:.*/\./:$workdir/:;
} elsif($f =~ m:^[^/]:) {
# foo/bar => workdir/foo/bar
$f = $workdir."/".$f;
}
my @subdirs = split m:/:, ::dirname($f);
my @rmdir;
my $dir = "";
for(@subdirs) {
$dir .= $_."/";
unshift @rmdir, ::shell_quote_file($dir);
}
my $rmdir = @rmdir ? "sh -c ".::Q("rmdir @rmdir 2>/dev/null;") : "";
if(defined $opt::workdir and $opt::workdir eq "...") {
$rmdir .= ::Q("rm -rf " . ::shell_quote_file($workdir).';');
}
$f = ::shell_quote_file($f);
my $sshcmd = $self->sshcommand();
my $serverlogin = $self->serverlogin();
return "$sshcmd $serverlogin -- ".::Q("rm -f $f; $rmdir");
}
{
my $rsync;
sub rsync {
# rsync 3.1.x uses protocol 31 which is unsupported by 2.5.7.
# If the version >= 3.1.0: downgrade to protocol 30
# Returns:
# $rsync = "rsync" or "rsync --protocol 30"
if(not $rsync) {
my @out = `rsync --version`;
for (@out) {
if(/version (\d+.\d+)(.\d+)?/) {
if($1 >= 3.1) {
# Version 3.1.0 or later: Downgrade to protocol 30
$rsync = "rsync --protocol 30";
} else {
$rsync = "rsync";
}
}
}
$rsync or ::die_bug("Cannot figure out version of rsync: @out");
}
return $rsync;
}
}
package JobQueue;
sub new($) {
my $class = shift;
my $commandref = shift;
my $read_from = shift;
my $context_replace = shift;
my $max_number_of_args = shift;
my $transfer_files = shift;
my $return_files = shift;
my $commandlinequeue = CommandLineQueue->new
($commandref, $read_from, $context_replace, $max_number_of_args,
$transfer_files, $return_files);
my @unget = ();
return bless {
'unget' => \@unget,
'commandlinequeue' => $commandlinequeue,
'this_job_no' => 0,
'total_jobs' => undef,
}, ref($class) || $class;
}
sub get($) {
my $self = shift;
$self->{'this_job_no'}++;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
} else {
my $commandline = $self->{'commandlinequeue'}->get();
if(defined $commandline) {
return Job->new($commandline);
} else {
$self->{'this_job_no'}--;
return undef;
}
}
}
sub unget($) {
my $self = shift;
unshift @{$self->{'unget'}}, @_;
$self->{'this_job_no'} -= @_;
}
sub empty($) {
my $self = shift;
my $empty = (not @{$self->{'unget'}}) &&
$self->{'commandlinequeue'}->empty();
::debug("run", "JobQueue->empty $empty ");
return $empty;
}
sub total_jobs($) {
my $self = shift;
if(not defined $self->{'total_jobs'}) {
if($opt::pipe and not $opt::tee) {
::error("--pipe is incompatible with --eta/--bar/--shuf");
::wait_and_exit(255);
}
if($opt::sqlworker) {
$self->{'total_jobs'} = $Global::sql->total_jobs();
} else {
my $record;
my @arg_records;
my $record_queue = $self->{'commandlinequeue'}{'arg_queue'};
my $start = time;
while($record = $record_queue->get()) {
push @arg_records, $record;
if(time - $start > 10) {
::warning("Reading ".scalar(@arg_records).
" arguments took longer than 10 seconds.");
$opt::eta && ::warning("Consider removing --eta.");
$opt::bar && ::warning("Consider removing --bar.");
$opt::shuf && ::warning("Consider removing --shuf.");
last;
}
}
while($record = $record_queue->get()) {
push @arg_records, $record;
}
if($opt::shuf and @arg_records) {
my $i = @arg_records;
while (--$i) {
my $j = int rand($i+1);
@arg_records[$i,$j] = @arg_records[$j,$i];
}
}
$record_queue->unget(@arg_records);
# $#arg_records = number of args - 1
# We have read one @arg_record for this job (so add 1 more)
my $num_args = $#arg_records + 2;
# This jobs is not started so -1
my $started_jobs = $self->{'this_job_no'} - 1;
my $max_args = ::max($Global::max_number_of_args,1);
$self->{'total_jobs'} = ::ceil($num_args / $max_args)
+ $started_jobs;
::debug("init","Total jobs: ".$self->{'total_jobs'}.
" ($num_args/$max_args + $started_jobs)\n");
}
}
return $self->{'total_jobs'};
}
sub flush_total_jobs($) {
# Unset total_jobs to force recomputing
my $self = shift;
::debug("init","flush Total jobs: ");
$self->{'total_jobs'} = undef;
}
sub next_seq($) {
my $self = shift;
return $self->{'commandlinequeue'}->seq();
}
sub quote_args($) {
my $self = shift;
return $self->{'commandlinequeue'}->quote_args();
}
package Job;
sub new($) {
my $class = shift;
my $commandlineref = shift;
return bless {
'commandline' => $commandlineref, # CommandLine object
'workdir' => undef, # --workdir
# filehandle for stdin (used for --pipe)
# filename for writing stdout to (used for --files)
# remaining data not sent to stdin (used for --pipe)
# tmpfiles to cleanup when job is done
'unlink' => [],
# amount of data sent via stdin (used for --pipe)
'transfersize' => 0, # size of files using --transfer
'returnsize' => 0, # size of files using --return
'pid' => undef,
# hash of { SSHLogins => number of times the command failed there }
'failed' => undef,
'sshlogin' => undef,
# The commandline wrapped with rsync and ssh
'sshlogin_wrap' => undef,
'exitstatus' => undef,
'exitsignal' => undef,
# Timestamp for timeout if any
'timeout' => undef,
'virgin' => 1,
# Output used for SQL and CSV-output
'output' => { 1 => [], 2 => [] },
'halfline' => { 1 => [], 2 => [] },
}, ref($class) || $class;
}
sub replaced($) {
my $self = shift;
$self->{'commandline'} or ::die_bug("commandline empty");
return $self->{'commandline'}->replaced();
}
sub seq($) {
my $self = shift;
return $self->{'commandline'}->seq();
}
sub set_seq($$) {
my $self = shift;
return $self->{'commandline'}->set_seq(shift);
}
sub slot($) {
my $self = shift;
return $self->{'commandline'}->slot();
}
sub free_slot($) {
my $self = shift;
push @Global::slots, $self->slot();
}
{
my($cattail);
sub cattail() {
# Returns:
# $cattail = perl program for:
# cattail "decompress program" writerpid [file_to_decompress or stdin] [file_to_unlink]
if(not $cattail) {
$cattail = q{
# cat followed by tail (possibly with rm as soon at the file is opened)
# If $writerpid dead: finish after this round
use Fcntl;
$|=1;
my ($comfile, $cmd, $writerpid, $read_file, $unlink_file) = @ARGV;
if($read_file) {
open(IN,"<",$read_file) || die("cattail: Cannot open $read_file");
} else {
*IN = *STDIN;
}
while(! -s $comfile) {
# Writer has not opened the buffer file, so we cannot remove it yet
$sleep = ($sleep < 30) ? ($sleep * 1.001 + 0.01) : ($sleep);
usleep($sleep);
}
# The writer and we have both opened the file, so it is safe to unlink it
unlink $unlink_file;
unlink $comfile;
my $first_round = 1;
my $flags;
fcntl(IN, F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
$flags |= O_NONBLOCK; # Add non-blocking to the flags
fcntl(IN, F_SETFL, $flags) || die $!; # Set the flags on the filehandle
while(1) {
# clear EOF
seek(IN,0,1);
my $writer_running = kill 0, $writerpid;
$read = sysread(IN,$buf,131072);
if($read) {
if($first_round) {
# Only start the command if there any input to process
$first_round = 0;
open(OUT,"|-",$cmd) || die("cattail: Cannot run $cmd");
}
# Blocking print
while($buf) {
my $bytes_written = syswrite(OUT,$buf);
# syswrite may be interrupted by SIGHUP
substr($buf,0,$bytes_written) = "";
}
# Something printed: Wait less next time
$sleep /= 2;
} else {
if(eof(IN) and not $writer_running) {
# Writer dead: There will never be sent more to the decompressor
close OUT;
exit;
}
# TODO This could probably be done more efficiently using select(2)
# Nothing read: Wait longer before next read
# Up to 100 milliseconds
$sleep = ($sleep < 100) ? ($sleep * 1.001 + 0.01) : ($sleep);
usleep($sleep);
}
}
sub usleep {
# Sleep this many milliseconds.
my $secs = shift;
select(undef, undef, undef, $secs/1000);
}
};
$cattail =~ s/#.*//mg;
$cattail =~ s/\s+/ /g;
}
return $cattail;
}
}
sub openoutputfiles($) {
# Open files for STDOUT and STDERR
# Set file handles in $self->fh
my $self = shift;
my ($outfhw, $errfhw, $outname, $errname);
if($opt::linebuffer and not
($opt::keeporder or $opt::files or $opt::results or
$opt::compress or $opt::compress_program or
$opt::decompress_program)) {
# Do not save to files: Use non-blocking pipe
my ($outfhr, $errfhr);
pipe($outfhr, $outfhw) || die;
pipe($errfhr, $errfhw) || die;
$self->set_fh(1,'w',$outfhw);
$self->set_fh(2,'w',$errfhw);
$self->set_fh(1,'r',$outfhr);
$self->set_fh(2,'r',$errfhr);
# Make it possible to read non-blocking from the pipe
for my $fdno (1,2) {
::set_fh_non_blocking($self->fh($fdno,'r'));
}
# Return immediately because we do not need setting filenames
return;
} elsif($opt::results and not $Global::csvsep) {
my $out = $self->{'commandline'}->results_out();
my $seqname;
if($out eq $opt::results or $out =~ m:/$:) {
# $opt::results = simple string or ending in /
# => $out is a dir/
# prefix/name1/val1/name2/val2/seq
$seqname = $out."seq";
# prefix/name1/val1/name2/val2/stdout
$outname = $out."stdout";
# prefix/name1/val1/name2/val2/stderr
$errname = $out."stderr";
} else {
# $opt::results = replacement string not ending in /
# => $out is a file
$outname = $out;
$errname = "$out.err";
$seqname = "$out.seq";
}
my $seqfhw;
if(not open($seqfhw, "+>", $seqname)) {
::error("Cannot write to `$seqname'.");
::wait_and_exit(255);
}
print $seqfhw $self->seq();
close $seqfhw;
if(not open($outfhw, "+>", $outname)) {
::error("Cannot write to `$outname'.");
::wait_and_exit(255);
}
if(not open($errfhw, "+>", $errname)) {
::error("Cannot write to `$errname'.");
::wait_and_exit(255);
}
$self->set_fh(1,"unlink","");
$self->set_fh(2,"unlink","");
if($opt::sqlworker) {
# Save the filenames in SQL table
$Global::sql->update("SET Stdout = ?, Stderr = ? ".
"WHERE Seq = ". $self->seq(),
$outname, $errname);
}
} elsif(not $opt::ungroup) {
# To group we create temporary files for STDOUT and STDERR
# To avoid the cleanup unlink the files immediately (but keep them open)
if($opt::files) {
($outfhw, $outname) = ::tmpfile(SUFFIX => ".par");
($errfhw, $errname) = ::tmpfile(SUFFIX => ".par");
# --files => only remove stderr
$self->set_fh(1,"unlink","");
$self->set_fh(2,"unlink",$errname);
} else {
($outfhw, $outname) = ::tmpfile(SUFFIX => ".par");
($errfhw, $errname) = ::tmpfile(SUFFIX => ".par");
$self->set_fh(1,"unlink",$outname);
$self->set_fh(2,"unlink",$errname);
}
} else {
# --ungroup
open($outfhw,">&",$Global::fd{1}) || die;
open($errfhw,">&",$Global::fd{2}) || die;
# File name must be empty as it will otherwise be printed
$outname = "";
$errname = "";
$self->set_fh(1,"unlink",$outname);
$self->set_fh(2,"unlink",$errname);
}
# Set writing FD
$self->set_fh(1,'w',$outfhw);
$self->set_fh(2,'w',$errfhw);
$self->set_fh(1,'name',$outname);
$self->set_fh(2,'name',$errname);
if($opt::compress) {
$self->filter_through_compress();
} elsif(not $opt::ungroup) {
$self->grouped();
}
if($opt::linebuffer) {
# Make it possible to read non-blocking from
# the buffer files
# Used for --linebuffer with -k, --files, --res, --compress*
for my $fdno (1,2) {
::set_fh_non_blocking($self->fh($fdno,'r'));
}
}
}
sub print_verbose_dryrun($) {
# If -v set: print command to stdout (possibly buffered)
# This must be done before starting the command
my $self = shift;
if($Global::verbose or $opt::dryrun) {
my $fh = $self->fh(1,"w");
if($Global::verbose <= 1) {
print $fh $self->replaced(),"\n";
} else {
# Verbose level > 1: Print the rsync and stuff
print $fh $self->wrapped(),"\n";
}
}
if($opt::sqlworker) {
$Global::sql->update("SET Command = ? WHERE Seq = ".$self->seq(),
$self->replaced());
}
}
sub add_rm($) {
# Files to remove when job is done
my $self = shift;
push @{$self->{'unlink'}}, @_;
}
sub get_rm($) {
# Files to remove when job is done
my $self = shift;
return @{$self->{'unlink'}};
}
sub cleanup($) {
# Remove files when job is done
my $self = shift;
unlink $self->get_rm();
delete @Global::unlink{$self->get_rm()};
}
sub grouped($) {
my $self = shift;
# Set reading FD if using --group (--ungroup does not need)
for my $fdno (1,2) {
# Re-open the file for reading
# so fdw can be closed seperately
# and fdr can be seeked seperately (for --line-buffer)
open(my $fdr,"<", $self->fh($fdno,'name')) ||
::die_bug("fdr: Cannot open ".$self->fh($fdno,'name'));
$self->set_fh($fdno,'r',$fdr);
# Unlink if not debugging
$Global::debug or ::rm($self->fh($fdno,"unlink"));
}
}
sub empty_input_wrapper($) {
# If no input: exit(0)
# If some input: Pass input as input to command on STDIN
# This avoids starting the command if there is no input.
# Input:
# $command = command to pipe data to
# Returns:
# $wrapped_command = the wrapped command
my $command = shift;
my $script =
::spacefree(0,q{
if(sysread(STDIN, $buf, 1)) {
open($fh, "|-", @ARGV) || die;
syswrite($fh, $buf);
# Align up to 128k block
if($read = sysread(STDIN, $buf, 131071)) {
syswrite($fh, $buf);
}
while($read = sysread(STDIN, $buf, 131072)) {
syswrite($fh, $buf);
}
close $fh;
exit ($?&127 ? 128+($?&127) : 1+$?>>8)
}
});
::debug("run",'Empty wrap: perl -e '.::Q($script)."\n");
if($Global::cshell
and
length $command > 499) {
# csh does not like words longer than 1000 (499 quoted)
# $command = "perl -e '".base64_zip_eval()."' ".
# join" ",string_zip_base64(
# 'exec "'.::perl_quote_scalar($command).'"');
return 'perl -e '.::Q($script)." ".
base64_wrap("exec \"$Global::shell\",'-c',\"".
::perl_quote_scalar($command).'"');
} else {
return 'perl -e '.::Q($script)." ".
$Global::shell." -c ".::Q($command);
}
}
sub filter_through_compress($) {
my $self = shift;
# Send stdout to stdin for $opt::compress_program(1)
# Send stderr to stdin for $opt::compress_program(2)
# cattail get pid: $pid = $self->fh($fdno,'rpid');
my $cattail = cattail();
for my $fdno (1,2) {
# Make a communication file.
my ($fh, $comfile) = ::tmpfile(SUFFIX => ".pac");
close $fh;
# Compressor: (echo > $comfile; compress pipe) > output
# When the echo is written to $comfile,
# it is known that output file is opened,
# thus output file can then be removed by the decompressor.
my $wpid = open(my $fdw,"|-", "(echo > $comfile; ".
empty_input_wrapper($opt::compress_program).") >".
$self->fh($fdno,'name')) || die $?;
$self->set_fh($fdno,'w',$fdw);
$self->set_fh($fdno,'wpid',$wpid);
# Decompressor: open output; -s $comfile > 0: rm $comfile output;
# decompress output > stdout
my $rpid = open(my $fdr, "-|", "perl", "-e", $cattail, $comfile,
$opt::decompress_program, $wpid,
$self->fh($fdno,'name'),$self->fh($fdno,'unlink'))
|| die $?;
$self->set_fh($fdno,'r',$fdr);
$self->set_fh($fdno,'rpid',$rpid);
}
}
sub set_fh($$$$) {
# Set file handle
my ($self, $fd_no, $key, $fh) = @_;
$self->{'fd'}{$fd_no,$key} = $fh;
}
sub fh($) {
# Get file handle
my ($self, $fd_no, $key) = @_;
return $self->{'fd'}{$fd_no,$key};
}
sub write($) {
my $self = shift;
my $remaining_ref = shift;
my $stdin_fh = $self->fh(0,"w");
my $len = length $$remaining_ref;
# syswrite may not write all in one go,
# so make sure everything is written.
my $written;
# If writing is to a closed pipe:
# Do not call signal handler, but let nothing be written
local $SIG{PIPE} = undef;
while($written = syswrite($stdin_fh,$$remaining_ref)){
substr($$remaining_ref,0,$written) = "";
}
}
sub set_block($$$$$$) {
# Copy stdin buffer from $block_ref up to $endpos
# Prepend with $header_ref if virgin (i.e. not --roundrobin)
# Remove $recstart and $recend if needed
# Input:
# $header_ref = ref to $header to prepend
# $buffer_ref = ref to $buffer containing the block
# $endpos = length of $block to pass on
# $recstart = --recstart regexp
# $recend = --recend regexp
# Returns:
# N/A
my $self = shift;
my ($header_ref,$buffer_ref,$endpos,$recstart,$recend) = @_;
$self->{'block'} = ($self->virgin() ? $$header_ref : "").
substr($$buffer_ref,0,$endpos);
if($opt::remove_rec_sep) {
remove_rec_sep(\$self->{'block'},$recstart,$recend);
}
$self->{'block_length'} = length $self->{'block'};
$self->{'block_pos'} = 0;
$self->add_transfersize($self->{'block_length'});
}
sub block_ref($) {
my $self = shift;
return \$self->{'block'};
}
sub block_length($) {
my $self = shift;
return $self->{'block_length'};
}
sub remove_rec_sep($) {
my ($block_ref,$recstart,$recend) = @_;
# Remove record separator
$$block_ref =~ s/$recend$recstart//gos;
$$block_ref =~ s/^$recstart//os;
$$block_ref =~ s/$recend$//os;
}
sub non_blocking_write($) {
my $self = shift;
my $something_written = 0;
use POSIX qw(:errno_h);
my $in = $self->fh(0,"w");
my $rv = syswrite($in,
substr($self->{'block'},$self->{'block_pos'}));
if (!defined($rv) && $! == EAGAIN) {
# would block - but would have written
$something_written = 0;
# avoid triggering auto expanding block
$Global::no_autoexpand_block ||= 1;
} elsif ($self->{'block_pos'}+$rv != $self->{'block_length'}) {
# incomplete write
# Remove the written part
$self->{'block_pos'} += $rv;
$something_written = $rv;
} else {
# successfully wrote everything
# Empty block to free memory
my $a = "";
$self->set_block(\$a,\$a,0,"","");
$something_written = $rv;
}
::debug("pipe", "Non-block: ", $something_written);
return $something_written;
}
sub virgin($) {
my $self = shift;
return $self->{'virgin'};
}
sub set_virgin($$) {
my $self = shift;
$self->{'virgin'} = shift;
}
sub pid($) {
my $self = shift;
return $self->{'pid'};
}
sub set_pid($$) {
my $self = shift;
$self->{'pid'} = shift;
}
sub starttime($) {
# Returns:
# UNIX-timestamp this job started
my $self = shift;
return sprintf("%.3f",$self->{'starttime'});
}
sub set_starttime($@) {
my $self = shift;
my $starttime = shift || ::now();
$self->{'starttime'} = $starttime;
$opt::sqlworker and
$Global::sql->update("SET Starttime = ? WHERE Seq = ".$self->seq(),
$starttime);
}
sub runtime($) {
# Returns:
# Run time in seconds with 3 decimals
my $self = shift;
return sprintf("%.3f",
int(($self->endtime() - $self->starttime())*1000)/1000);
}
sub endtime($) {
# Returns:
# UNIX-timestamp this job ended
# 0 if not ended yet
my $self = shift;
return ($self->{'endtime'} || 0);
}
sub set_endtime($$) {
my $self = shift;
my $endtime = shift;
$self->{'endtime'} = $endtime;
$opt::sqlworker and
$Global::sql->update("SET JobRuntime = ? WHERE Seq = ".$self->seq(),
$self->runtime());
}
sub is_timedout($) {
# Is the job timedout?
# Input:
# $delta_time = time that the job may run
# Returns:
# True or false
my $self = shift;
my $delta_time = shift;
return time > $self->{'starttime'} + $delta_time;
}
sub kill($) {
my $self = shift;
$self->set_exitstatus(-1);
::kill_sleep_seq($self->pid());
}
sub failed($) {
# return number of times failed for this $sshlogin
# Input:
# $sshlogin
# Returns:
# Number of times failed for $sshlogin
my $self = shift;
my $sshlogin = shift;
return $self->{'failed'}{$sshlogin};
}
sub failed_here($) {
# return number of times failed for the current $sshlogin
# Returns:
# Number of times failed for this sshlogin
my $self = shift;
return $self->{'failed'}{$self->sshlogin()};
}
sub add_failed($) {
# increase the number of times failed for this $sshlogin
my $self = shift;
my $sshlogin = shift;
$self->{'failed'}{$sshlogin}++;
}
sub add_failed_here($) {
# increase the number of times failed for the current $sshlogin
my $self = shift;
$self->{'failed'}{$self->sshlogin()}++;
}
sub reset_failed($) {
# increase the number of times failed for this $sshlogin
my $self = shift;
my $sshlogin = shift;
delete $self->{'failed'}{$sshlogin};
}
sub reset_failed_here($) {
# increase the number of times failed for this $sshlogin
my $self = shift;
delete $self->{'failed'}{$self->sshlogin()};
}
sub min_failed($) {
# Returns:
# the number of sshlogins this command has failed on
# the minimal number of times this command has failed
my $self = shift;
my $min_failures =
::min(map { $self->{'failed'}{$_} } keys %{$self->{'failed'}});
my $number_of_sshlogins_failed_on = scalar keys %{$self->{'failed'}};
return ($number_of_sshlogins_failed_on,$min_failures);
}
sub total_failed($) {
# Returns:
# $total_failures = the number of times this command has failed
my $self = shift;
my $total_failures = 0;
for (values %{$self->{'failed'}}) {
$total_failures += $_;
}
return $total_failures;
}
{
my $script;
sub postpone_exit_and_cleanup {
# Command to remove files and dirs (given as args) without
# affecting the exit value in $?/$status.
if(not $script) {
$script = "perl -e '".
::spacefree(0,q{
$bash=shift;
$csh=shift;
for(@ARGV){
unlink;
rmdir;
}
if($bash=~s/h//) {
exit $bash;
}
exit $csh;
}).
"' ".'"$?h" "$status" ';
}
return $script
}
}
{
my $script;
sub fifo_wrap() {
# Script to create a fifo, run a command on the fifo
# while copying STDIN to the fifo, and finally
# remove the fifo and return the exit code of the command.
if(not $script) {
# {} == $PARALLEL_TMP for --fifo
# To make it csh compatible a wrapper needs to:
# * mkfifo
# * spawn $command &
# * cat > fifo
# * waitpid to get the exit code from $command
# * be less than 1000 chars long
$script = "perl -e '".
(::spacefree
(0, q{
($s,$c,$f) = @ARGV;
# mkfifo $PARALLEL_TMP
system "mkfifo", $f;
# spawn $shell -c $command &
$pid = fork || exec $s, "-c", $c;
open($o,">",$f) || die $!;
# cat > $PARALLEL_TMP
while(sysread(STDIN,$buf,131072)){
syswrite $o, $buf;
}
close $o;
# waitpid to get the exit code from $command
waitpid $pid,0;
# Cleanup
unlink $f;
exit $?/256;
}))."'";
}
return $script;
}
}
sub wrapped($) {
# Wrap command with:
# * --shellquote
# * --nice
# * --cat
# * --fifo
# * --sshlogin
# * --pipepart (@Global::cat_prepends)
# * --tee (@Global::cat_prepends)
# * --pipe
# * --tmux
# The ordering of the wrapping is important:
# * --nice/--cat/--fifo should be done on the remote machine
# * --pipepart/--pipe should be done on the local machine inside --tmux
# Uses:
# @opt::shellquote
# $opt::nice
# $Global::shell
# $opt::cat
# $opt::fifo
# @Global::cat_prepends
# $opt::pipe
# $opt::tmux
# Returns:
# $self->{'wrapped'} = the command wrapped with the above
my $self = shift;
if(not defined $self->{'wrapped'}) {
my $command = $self->replaced();
# Bug in Bash and Ksh when running multiline aliases
# This will force them to run correctly, but will fail in
# tcsh so we do not do it.
# $command .= "\n\n";
if(@opt::shellquote) {
# Quote one time for each --shellquote
my $c = $command;
for(@opt::shellquote) {
$c = ::Q($c);
}
# Prepend "echo" (it is written in perl because
# quoting '-e' causes problem in some versions and
# csh's version does something wrong)
$command = q(perl -e '$,=" "; print "@ARGV\n";' -- ) . ::Q($c);
}
if($Global::parallel_env) {
# If $PARALLEL_ENV set, put that in front of the command
# Used for env_parallel.*
if($Global::shell =~ /zsh/) {
# The extra 'eval' will make aliases work, too
$command = $Global::parallel_env."\n".
"eval ".::Q($command);
} else {
$command = $Global::parallel_env."\n".$command;
}
}
if($opt::cat) {
# In '--cat' and '--fifo' {} == $PARALLEL_TMP.
# This is to make it possible to compute $PARALLEL_TMP on
# the fly when running remotely.
# $ENV{PARALLEL_TMP} is set in the remote wrapper before
# the command is run.
#
# Prepend 'cat > $PARALLEL_TMP;'
# Append 'unlink $PARALLEL_TMP without affecting $?'
$command =
'cat > $PARALLEL_TMP;'.
$command.";". postpone_exit_and_cleanup().
'$PARALLEL_TMP';
} elsif($opt::fifo) {
# Prepend fifo-wrapper. In essence:
# mkfifo {}
# ( $command ) &
# # $command must read {}, otherwise this 'cat' will block
# cat > {};
# wait; rm {}
# without affecting $?
$command = fifo_wrap(). " ".
$Global::shell. " ". ::Q($command). ' $PARALLEL_TMP'. ';';
}
# Wrap with ssh + tranferring of files
$command = $self->sshlogin_wrap($command);
if(@Global::cat_prepends) {
# --pipepart: prepend:
# < /tmp/foo perl -e 'while(@ARGV) {
# sysseek(STDIN,shift,0) || die; $left = shift;
# while($read = sysread(STDIN,$buf, ($left > 131072 ? 131072 : $left))){
# $left -= $read; syswrite(STDOUT,$buf);
# }
# }' 0 0 0 11 |
#
# --pipepart --tee: prepend:
# < dash-a-file
#
# --pipe --tee: wrap:
# (rm fifo; ... ) < fifo
#
# --pipe --shard X:
# (rm fifo; ... ) < fifo
$command = (shift @Global::cat_prepends). "($command)".
(shift @Global::cat_appends);
} elsif($opt::pipe and not $opt::roundrobin) {
# Wrap with EOF-detector to avoid starting $command if EOF.
$command = empty_input_wrapper($command);
}
if($opt::tmux) {
# Wrap command with 'tmux'
$command = $self->tmux_wrap($command);
}
if($Global::cshell
and
length $command > 499) {
# csh does not like words longer than 1000 (499 quoted)
# $command = "perl -e '".base64_zip_eval()."' ".
# join" ",string_zip_base64(
# 'exec "'.::perl_quote_scalar($command).'"');
$command = base64_wrap("exec \"$Global::shell\",'-c',\"".
::perl_quote_scalar($command).'"');
}
$self->{'wrapped'} = $command;
}
return $self->{'wrapped'};
}
sub set_sshlogin($$) {
my $self = shift;
my $sshlogin = shift;
$self->{'sshlogin'} = $sshlogin;
delete $self->{'sshlogin_wrap'}; # If sshlogin is changed the wrap is wrong
delete $self->{'wrapped'};
if($opt::sqlworker) {
# Identify worker as --sqlworker often runs on different machines
my $host = $sshlogin->string();
if($host eq ":") {
$host = ::hostname();
}
$Global::sql->update("SET Host = ? WHERE Seq = ".$self->seq(), $host);
}
}
sub sshlogin($) {
my $self = shift;
return $self->{'sshlogin'};
}
sub string_base64($) {
# Base64 encode strings into 1000 byte blocks.
# 1000 bytes is the largest word size csh supports
# Input:
# @strings = to be encoded
# Returns:
# @base64 = 1000 byte block
$Global::use{"MIME::Base64"} ||= eval "use MIME::Base64; 1;";
my @base64 = unpack("(A1000)*",encode_base64((join"",@_),""));
return @base64;
}
sub string_zip_base64($) {
# Pipe string through 'bzip2 -9' and base64 encode it into 1000
# byte blocks.
# 1000 bytes is the largest word size csh supports
# Zipping will make exporting big environments work, too
# Input:
# @strings = to be encoded
# Returns:
# @base64 = 1000 byte block
my($zipin_fh, $zipout_fh,@base64);
::open3($zipin_fh,$zipout_fh,">&STDERR","bzip2 -9");
if(fork) {
close $zipin_fh;
$Global::use{"MIME::Base64"} ||= eval "use MIME::Base64; 1;";
# Split base64 encoded into 1000 byte blocks
@base64 = unpack("(A1000)*",encode_base64((join"",<$zipout_fh>),""));
close $zipout_fh;
} else {
close $zipout_fh;
print $zipin_fh @_;
close $zipin_fh;
exit;
}
::debug("base64","Orig:@_\nAs bzip2 base64:@base64\n");
return @base64;
}
sub base64_zip_eval() {
# Script that:
# * reads base64 strings from @ARGV
# * decodes them
# * pipes through 'bzip2 -dc'
# * evals the result
# Reverse of string_zip_base64 + eval
# Will be wrapped in ' so single quote is forbidden
# Returns:
# $script = 1-liner for perl -e
my $script = ::spacefree(0,q{
@GNU_Parallel = split /_/, "use_IPC::Open3;_use_MIME::Base64";
eval"@GNU_Parallel";
$chld = $SIG{CHLD};
$SIG{CHLD} = "IGNORE";
# Search for bzip2. Not found => use default path
my $zip = (grep { -x $_ } "/usr/local/bin/bzip2")[0] || "bzip2";
# $in = stdin on $zip, $out = stdout from $zip
# Forget my() to save chars for csh
# my($in, $out,$eval);
open3($in,$out,">&STDERR",$zip,"-dc");
if(my $perlpid = fork) {
close $in;
$eval = join "", <$out>;
close $out;
} else {
close $out;
# Pipe decoded base64 into 'bzip2 -dc'
print $in (decode_base64(join"",@ARGV));
close $in;
exit;
}
wait;
$SIG{CHLD} = $chld;
eval $eval;
});
::debug("base64",$script,"\n");
return $script;
}
sub base64_wrap($) {
# base64 encode Perl code
# Split it into chunks of < 1000 bytes
# Prepend it with a decoder that eval's it
# Input:
# $eval_string = Perl code to run
# Returns:
# $shell_command = shell command that runs $eval_string
my $eval_string = shift;
return
"perl -e ".
::Q(base64_zip_eval())." ".
join" ",::shell_quote(string_zip_base64($eval_string));
}
sub base64_eval($) {
# Script that:
# * reads base64 strings from @ARGV
# * decodes them
# * evals the result
# Reverse of string_base64 + eval
# Will be wrapped in ' so single quote is forbidden.
# Spaces are stripped so spaces cannot be significant.
# The funny 'use IPC::Open3'-syntax is to avoid spaces and
# to make it clear that this is a GNU Parallel command
# when looking at the process table.
# Returns:
# $script = 1-liner for perl -e
my $script = ::spacefree(0,q{
@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64");
eval "@GNU_Parallel";
my $eval = decode_base64(join"",@ARGV);
eval $eval;
});
::debug("base64",$script,"\n");
return $script;
}
sub sshlogin_wrap($) {
# Wrap the command with the commands needed to run remotely
# Input:
# $command = command to run
# Returns:
# $self->{'sshlogin_wrap'} = command wrapped with ssh+transfer commands
sub monitor_parent_sshd_script {
# This script is to solve the problem of
# * not mixing STDERR and STDOUT
# * terminating with ctrl-c
# If its parent is ssh: all good
# If its parent is init(1): ssh died, so kill children
my $monitor_parent_sshd_script;
if(not $monitor_parent_sshd_script) {
$monitor_parent_sshd_script =
# This will be packed in ', so only use "
::spacefree(0,'$shell = "'.($ENV{'PARALLEL_SHELL'} || '$ENV{SHELL}').'";'.
'$tmpdir = "'.::perl_quote_scalar($ENV{'TMPDIR'}).'";'.
'$nice = '.$opt::nice.';'.
q{
# Set $PARALLEL_TMP to a non-existent file name in $TMPDIR
do {
$ENV{PARALLEL_TMP} = $tmpdir."/par".
join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
} while(-e $ENV{PARALLEL_TMP});
$SIG{CHLD} = sub { $done = 1; };
$pid = fork;
unless($pid) {
# Make own process group to be able to kill HUP it later
eval { setpgrp };
eval { setpriority(0,0,$nice) };
exec $shell, "-c", ($bashfunc."@ARGV");
die "exec: $!\n";
}
do {
# Parent is not init (ppid=1), so sshd is alive
# Exponential sleep up to 1 sec
$s = $s < 1 ? 0.001 + $s * 1.03 : $s;
select(undef, undef, undef, $s);
} until ($done || getppid == 1);
# Kill HUP the process group if job not done
kill(SIGHUP, -${pid}) unless $done;
wait;
exit ($?&127 ? 128+($?&127) : 1+$?>>8)
});
}
return $monitor_parent_sshd_script;
}
sub vars_to_export {
# Uses:
# @opt::env
my @vars = ("parallel_bash_environment");
for my $varstring (@opt::env) {
# Split up --env VAR1,VAR2
push @vars, split /,/, $varstring;
}
for (@vars) {
if(-r $_ and not -d) {
# Read as environment definition bug #44041
# TODO parse this
my $fh = ::open_or_exit($_);
$Global::envdef = join("",<$fh>);
close $fh;
}
}
if(grep { /^_$/ } @vars) {
local $/ = "\n";
# --env _
# Include all vars that are not in a clean environment
if(open(my $vars_fh, "<", $Global::config_dir . "/ignored_vars")) {
my @ignore = <$vars_fh>;
chomp @ignore;
my %ignore;
@ignore{@ignore} = @ignore;
close $vars_fh;
push @vars, grep { not defined $ignore{$_} } keys %ENV;
@vars = grep { not /^_$/ } @vars;
} else {
::error("Run '$Global::progname --record-env' ".
"in a clean environment first.");
::wait_and_exit(255);
}
}
# Duplicate vars as BASH functions to include post-shellshock functions (v1+v2)
# So --env myfunc should look for BASH_FUNC_myfunc() and BASH_FUNC_myfunc%%
push(@vars, "PARALLEL_PID", "PARALLEL_SEQ",
map { ("BASH_FUNC_$_()", "BASH_FUNC_$_%%") } @vars);
# Keep only defined variables
return grep { defined($ENV{$_}) } @vars;
}
sub env_as_eval {
# Returns:
# $eval = '$ENV{"..."}=...; ...'
my @vars = vars_to_export();
my $csh_friendly = not grep { /\n/ } @ENV{@vars};
my @bash_functions = grep { substr($ENV{$_},0,4) eq "() {" } @vars;
my @non_functions = (grep { !/PARALLEL_ENV/ }
grep { substr($ENV{$_},0,4) ne "() {" } @vars);
# eval of @envset will set %ENV
my $envset = join"", map {
'$ENV{"'.::perl_quote_scalar($_).'"}="'.
::perl_quote_scalar($ENV{$_}).'";'; } @non_functions;
# running @bashfunc on the command line, will set the functions
my @bashfunc = map {
my $v=$_;
s/BASH_FUNC_(.*)(\(\)|%%)/$1/;
"$_$ENV{$v};export -f $_ >/dev/null;" } @bash_functions;
# eval $bashfuncset will set $bashfunc
my $bashfuncset;
if(@bashfunc) {
# Functions are not supported for all shells
if($Global::shell !~ m:(bash|rbash|zsh|rzsh|dash|ksh):) {
::warning("Shell functions may not be supported in $Global::shell.");
}
$bashfuncset =
'@bash_functions=qw('."@bash_functions".");".
::spacefree(1,'$shell="'.($ENV{'PARALLEL_SHELL'} || '$ENV{SHELL}').'";'.q{
if($shell=~/csh/) {
print STDERR "CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset @bash_functions\n";
exec "false";
}
}).
"\n".'$bashfunc = "'.::perl_quote_scalar("@bashfunc").'";';
} else {
$bashfuncset = '$bashfunc = "";'
}
if($ENV{'parallel_bash_environment'}) {
$bashfuncset .= '$bashfunc .= "eval\ \"\$parallel_bash_environment\"\;";';
}
::debug("base64",$envset,$bashfuncset,"\n");
return $csh_friendly,$envset,$bashfuncset;
}
my $self = shift;
my $command = shift;
# TODO test that *sh -c 'parallel --env' use *sh
if(not defined $self->{'sshlogin_wrap'}{$command}) {
my $sshlogin = $self->sshlogin();
my $serverlogin = $sshlogin->serverlogin();
my $quoted_remote_command;
$ENV{'PARALLEL_SEQ'} = $self->seq();
$ENV{'PARALLEL_PID'} = $$;
if($serverlogin eq ":") {
if($opt::workdir) {
# Create workdir if needed. Then cd to it.
my $wd = $self->workdir();
if($opt::workdir eq "." or $opt::workdir eq "...") {
# If $wd does not start with '/': Prepend $HOME
$wd =~ s:^([^/]):$ENV{'HOME'}/$1:;
}
::mkdir_or_die($wd);
my $post = "";
if($opt::workdir eq "...") {
$post = ";".exitstatuswrapper("rm -rf ".::Q($wd).";");
}
$command = "cd ".::Q($wd)." || exit 255; " .
$command . $post;;
}
if(@opt::env) {
# Prepend with environment setter, which sets functions in zsh
my ($csh_friendly,$envset,$bashfuncset) = env_as_eval();
my $perl_code = $envset.$bashfuncset.
'@ARGV="'.::perl_quote_scalar($command).'";'.
"exec\"$Global::shell\",\"-c\",\(\$bashfunc.\"\@ARGV\"\)\;die\"exec:\$\!\\n\"\;";
if(length $perl_code > 999
or
not $csh_friendly
or
$command =~ /\n/) {
# csh does not deal well with > 1000 chars in one word
# csh does not deal well with $ENV with \n
$self->{'sshlogin_wrap'}{$command} = base64_wrap($perl_code);
} else {
$self->{'sshlogin_wrap'}{$command} = "perl -e ".::Q($perl_code);
}
} else {
$self->{'sshlogin_wrap'}{$command} = $command;
}
} else {
my $pwd = "";
if($opt::workdir) {
# Create remote workdir if needed. Then cd to it.
my $wd = ::pQ($self->workdir());
$pwd = qq{system("mkdir","-p","--","$wd"); chdir "$wd" ||}.
qq{print(STDERR "parallel: Cannot chdir to $wd\\n") && exit 255;};
}
my ($csh_friendly,$envset,$bashfuncset) = env_as_eval();
my $remote_command = $pwd.$envset.$bashfuncset.
'@ARGV="'.::perl_quote_scalar($command).'";'.
monitor_parent_sshd_script();
$quoted_remote_command = "perl -e ". ::Q($remote_command);
my $dq_remote_command = ::Q($quoted_remote_command);
if(length $dq_remote_command > 999
or
not $csh_friendly
or
$command =~ /\n/) {
# csh does not deal well with > 1000 chars in one word
# csh does not deal well with $ENV with \n
$quoted_remote_command =
"perl -e ". ::Q(::Q(base64_zip_eval()))." ".
join" ",::shell_quote(::shell_quote(string_zip_base64($remote_command)));
} else {
$quoted_remote_command = $dq_remote_command;
}
my $sshcmd = $sshlogin->sshcommand();
my ($pre,$post,$cleanup)=("","","");
# --transfer
$pre .= $self->sshtransfer();
# --return
$post .= $self->sshreturn();
# --cleanup
$post .= $self->sshcleanup();
if($post) {
# We need to save the exit status of the job
$post = exitstatuswrapper($post);
}
$self->{'sshlogin_wrap'}{$command} =
($pre
. "$sshcmd $serverlogin -- exec "
. $quoted_remote_command
. ";"
. $post);
}
}
return $self->{'sshlogin_wrap'}{$command};
}
sub transfer($) {
# Files to transfer
# Non-quoted and with {...} substituted
# Returns:
# @transfer - File names of files to transfer
my $self = shift;
my $transfersize = 0;
my @transfer = $self->{'commandline'}->
replace_placeholders($self->{'commandline'}{'transfer_files'},0,0);
for(@transfer) {
# filesize
if(-e $_) {
$transfersize += (stat($_))[7];
}
}
$self->add_transfersize($transfersize);
return @transfer;
}
sub transfersize($) {
my $self = shift;
return $self->{'transfersize'};
}
sub add_transfersize($) {
my $self = shift;
my $transfersize = shift;
$self->{'transfersize'} += $transfersize;
$opt::sqlworker and
$Global::sql->update("SET Send = ? WHERE Seq = ".$self->seq(),
$self->{'transfersize'});
}
sub sshtransfer($) {
# Returns for each transfer file:
# rsync $file remote:$workdir
my $self = shift;
my @pre;
my $sshlogin = $self->sshlogin();
my $workdir = $self->workdir();
for my $file ($self->transfer()) {
push @pre, $sshlogin->rsync_transfer_cmd($file,$workdir).";";
}
return join("",@pre);
}
sub return($) {
# Files to return
# Non-quoted and with {...} substituted
# Returns:
# @non_quoted_filenames
my $self = shift;
return $self->{'commandline'}->
replace_placeholders($self->{'commandline'}{'return_files'},0,0);
}
sub returnsize($) {
# This is called after the job has finished
# Returns:
# $number_of_bytes transferred in return
my $self = shift;
for my $file ($self->return()) {
if(-e $file) {
$self->{'returnsize'} += (stat($file))[7];
}
}
return $self->{'returnsize'};
}
sub add_returnsize($) {
my $self = shift;
my $returnsize = shift;
$self->{'returnsize'} += $returnsize;
$opt::sqlworker and
$Global::sql->update("SET Receive = ? WHERE Seq = ".$self->seq(),
$self->{'returnsize'});
}
sub sshreturn($) {
# Returns for each return-file:
# rsync remote:$workdir/$file .
my $self = shift;
my $sshlogin = $self->sshlogin();
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $rsync_opts = $ENV{'PARALLEL_RSYNC_OPTS'}. " -e". ::Q($sshcmd);
my $pre = "";
for my $file ($self->return()) {
$file =~ s:^\./::g; # Remove ./ if any
my $relpath = ($file !~ m:^/:) || ($file =~ m:/\./:); # Is the path relative or /./?
my $cd = "";
my $wd = "";
if($relpath) {
# rsync -avR /foo/./bar/baz.c remote:/tmp/
# == (on old systems)
# rsync -avR --rsync-path="cd /foo; rsync" remote:bar/baz.c /tmp/
$wd = ::shell_quote_file($self->workdir()."/");
}
# Only load File::Basename if actually needed
$Global::use{"File::Basename"} ||= eval "use File::Basename; 1;";
# dir/./file means relative to dir, so remove dir on remote
$file =~ m:(.*)/\./:;
my $basedir = $1 ? ::shell_quote_file($1."/") : "";
my $nobasedir = $file;
$nobasedir =~ s:.*/\./::;
$cd = ::shell_quote_file(::dirname($nobasedir));
my $rsync_cd = '--rsync-path='.::Q("cd $wd$cd; rsync");
my $basename = ::Q(::shell_quote_file(::basename($file)));
# --return
# mkdir -p /home/tange/dir/subdir/;
# rsync (--protocol 30) -rlDzR
# --rsync-path="cd /home/tange/dir/subdir/; rsync"
# server:file.gz /home/tange/dir/subdir/
$pre .= "mkdir -p $basedir$cd && ". $sshlogin->rsync().
" $rsync_cd $rsync_opts $serverlogin:".
$basename . " ".$basedir.$cd.";";
}
return $pre;
}
sub sshcleanup($) {
# Return the sshcommand needed to remove the file
# Returns:
# ssh command needed to remove files from sshlogin
my $self = shift;
my $sshlogin = $self->sshlogin();
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $workdir = $self->workdir();
my $cleancmd = "";
for my $file ($self->remote_cleanup()) {
my @subworkdirs = parentdirs_of($file);
$cleancmd .= $sshlogin->cleanup_cmd($file,$workdir).";";
}
if(defined $opt::workdir and $opt::workdir eq "...") {
$cleancmd .= "$sshcmd $serverlogin -- rm -rf " . ::Q($workdir).';';
}
return $cleancmd;
}
sub remote_cleanup($) {
# Returns:
# Files to remove at cleanup
my $self = shift;
if($opt::cleanup) {
my @transfer = $self->transfer();
my @return = $self->return();
return (@transfer,@return);
} else {
return ();
}
}
sub exitstatuswrapper(@) {
if($Global::cshell) {
return ('set _EXIT_status=$status; ' .
join(" ",@_).
'exit $_EXIT_status;');
} else {
return ('_EXIT_status=$?; ' .
join(" ",@_).
'exit $_EXIT_status;');
}
}
sub workdir($) {
# Returns:
# the workdir on a remote machine
my $self = shift;
if(not defined $self->{'workdir'}) {
my $workdir;
if(defined $opt::workdir) {
if($opt::workdir eq ".") {
# . means current dir
my $home = $ENV{'HOME'};
eval 'use Cwd';
my $cwd = cwd();
$workdir = $cwd;
if($home) {
# If homedir exists: remove the homedir from
# workdir if cwd starts with homedir
# E.g. /home/foo/my/dir => my/dir
# E.g. /tmp/my/dir => /tmp/my/dir
my ($home_dev, $home_ino) = (stat($home))[0,1];
my $parent = "";
my @dir_parts = split(m:/:,$cwd);
my $part;
while(defined ($part = shift @dir_parts)) {
$part eq "" and next;
$parent .= "/".$part;
my ($parent_dev, $parent_ino) = (stat($parent))[0,1];
if($parent_dev == $home_dev and $parent_ino == $home_ino) {
# dev and ino is the same: We found the homedir.
$workdir = join("/",@dir_parts);
last;
}
}
}
if($workdir eq "") {
$workdir = ".";
}
} elsif($opt::workdir eq "...") {
$workdir = ".parallel/tmp/" . ::hostname() . "-" . $$
. "-" . $self->seq();
} else {
$workdir = $self->{'commandline'}->
replace_placeholders([$opt::workdir],0,0);
#$workdir = $opt::workdir;
# Rsync treats /./ special. We dont want that
$workdir =~ s:/\./:/:g; # Remove /./
$workdir =~ s:(.)/+$:$1:; # Remove ending / if any
$workdir =~ s:^\./::g; # Remove starting ./ if any
}
} else {
$workdir = ".";
}
$self->{'workdir'} = $workdir;
}
return $self->{'workdir'};
}
sub parentdirs_of($) {
# Return:
# all parentdirs except . of this dir or file - sorted desc by length
my $d = shift;
my @parents = ();
while($d =~ s:/[^/]+$::) {
if($d ne ".") {
push @parents, $d;
}
}
return @parents;
}
sub start($) {
# Setup STDOUT and STDERR for a job and start it.
# Returns:
# job-object or undef if job not to run
sub open3_setpgrp_internal {
# Run open3+setpgrp followed by the command
# Input:
# $stdin_fh = Filehandle to use as STDIN
# $stdout_fh = Filehandle to use as STDOUT
# $stderr_fh = Filehandle to use as STDERR
# $command = Command to run
# Returns:
# $pid = Process group of job started
my ($stdin_fh,$stdout_fh,$stderr_fh,$command) = @_;
my $pid;
local (*OUT,*ERR);
open OUT, '>&', $stdout_fh or ::die_bug("Can't dup STDOUT: $!");
open ERR, '>&', $stderr_fh or ::die_bug("Can't dup STDERR: $!");
# The eval is needed to catch exception from open3
eval {
if(not $pid = ::open3($stdin_fh, ">&OUT", ">&ERR", "-")) {
# Each child gets its own process group to make it safe to killall
eval{ setpgrp(0,0) };
eval{ setpriority(0,0,$opt::nice) };
exec($Global::shell,"-c",$command)
|| ::die_bug("open3-$stdin_fh $command");
}
};
return $pid;
}
sub open3_setpgrp_external {
# Run open3 on $command wrapped with a perl script doing setpgrp
# Works on systems that do not support open3(,,,"-")
# Input:
# $stdin_fh = Filehandle to use as STDIN
# $stdout_fh = Filehandle to use as STDOUT
# $stderr_fh = Filehandle to use as STDERR
# $command = Command to run
# Returns:
# $pid = Process group of job started
my ($stdin_fh,$stdout_fh,$stderr_fh,$command) = @_;
local (*OUT,*ERR);
open OUT, '>&', $stdout_fh or ::die_bug("Can't dup STDOUT: $!");
open ERR, '>&', $stderr_fh or ::die_bug("Can't dup STDERR: $!");
my $pid;
my @setpgrp_wrap =
('perl','-e',
"eval\{setpgrp\}\;eval\{setpriority\(0,0,$opt::nice\)\}\;".
"exec '$Global::shell', '-c', \@ARGV");
# The eval is needed to catch exception from open3
eval {
$pid = ::open3($stdin_fh, ">&OUT", ">&ERR", @setpgrp_wrap, $command)
|| ::die_bug("open3-$stdin_fh");
1;
};
return $pid;
}
sub open3_setpgrp {
# Select and run open3_setpgrp_internal/open3_setpgrp_external
no warnings 'redefine';
my ($outfh,$name) = ::tmpfile(SUFFIX => ".tst");
# Test to see if open3(x,x,x,"-") is fully supported
# Can an exported bash function be called via open3?
my $script = 'if($pid=::open3($i,$o,$e,"-")) { wait; } '.
'else { exec("bash","-c","testfun && true"); }';
my $bash =
::shell_quote_scalar_default(
"testfun() { rm $name; }; export -f testfun; ".
"perl -MIPC::Open3 -e ".
::shell_quote_scalar_default($script)
);
# Redirect STDERR temporarily,
# so errors on MacOS X are ignored.
open my $saveerr, ">&STDERR";
open STDERR, '>', "/dev/null";
# Run the test
::debug("init",qq{bash -c $bash 2>/dev/null});
qx{ bash -c $bash 2>/dev/null };
open STDERR, ">&", $saveerr;
if(-e $name) {
# Does not support open3(x,x,x,"-")
# or does not have bash:
# Use (slow) external version
unlink($name);
*open3_setpgrp = \&open3_setpgrp_external;
::debug("init","open3_setpgrp_external chosen\n");
} else {
# Supports open3(x,x,x,"-")
# This is 0.5 ms faster to run
*open3_setpgrp = \&open3_setpgrp_internal;
::debug("init","open3_setpgrp_internal chosen\n");
}
# The sub is now redefined. Call it
return open3_setpgrp(@_);
}
my $job = shift;
# Get the shell command to be executed (possibly with ssh infront).
my $command = $job->wrapped();
my $pid;
if($Global::interactive or $Global::stderr_verbose) {
$job->interactive_start();
}
# Must be run after $job->interactive_start():
# $job->interactive_start() may call $job->skip()
if($job->{'commandline'}{'skip'}) {
# $job->skip() was called
$command = "true";
}
$job->openoutputfiles();
$job->print_verbose_dryrun();
# Call slot to store the slot value
$job->slot();
my($stdout_fh,$stderr_fh) = ($job->fh(1,"w"),$job->fh(2,"w"));
if($opt::dryrun or $opt::sqlmaster) { $command = "true"; }
$ENV{'PARALLEL_SEQ'} = $job->seq();
$ENV{'PARALLEL_PID'} = $$;
$ENV{'PARALLEL_TMP'} = ::tmpname("par");
$job->add_rm($ENV{'PARALLEL_TMP'});
::debug("run", $Global::total_running, " processes . Starting (",
$job->seq(), "): $command\n");
if($opt::pipe) {
my ($stdin_fh) = ::gensym();
$pid = open3_setpgrp($stdin_fh,$stdout_fh,$stderr_fh,$command);
if($opt::roundrobin and not $opt::keeporder) {
# --keep-order will make sure the order will be reproducible
::set_fh_non_blocking($stdin_fh);
}
$job->set_fh(0,"w",$stdin_fh);
if($opt::tee or $opt::shard) { $job->set_virgin(0); }
} elsif ($opt::tty and -c "/dev/tty" and
open(my $devtty_fh, "<", "/dev/tty")) {
# Give /dev/tty to the command if no one else is using it
# The eval is needed to catch exception from open3
local (*IN,*OUT,*ERR);
open OUT, '>&', $stdout_fh or ::die_bug("Can't dup STDOUT: $!");
open ERR, '>&', $stderr_fh or ::die_bug("Can't dup STDERR: $!");
*IN = $devtty_fh;
# The eval is needed to catch exception from open3
my @wrap = ('perl','-e',
"eval\{setpriority\(0,0,$opt::nice\)\}\;".
"exec '$Global::shell', '-c', \@ARGV");
eval {
$pid = ::open3("<&IN", ">&OUT", ">&ERR", @wrap, $command)
|| ::die_bug("open3-/dev/tty");
1;
};
close $devtty_fh;
$job->set_virgin(0);
} else {
$pid = open3_setpgrp(::gensym(),$stdout_fh,$stderr_fh,$command);
$job->set_virgin(0);
}
if($pid) {
# A job was started
$Global::total_running++;
$Global::total_started++;
$job->set_pid($pid);
$job->set_starttime();
$Global::running{$job->pid()} = $job;
if($opt::timeout) {
$Global::timeoutq->insert($job);
}
$Global::newest_job = $job;
$Global::newest_starttime = ::now();
return $job;
} else {
# No more processes
::debug("run", "Cannot spawn more jobs.\n");
return undef;
}
}
sub interactive_start($) {
my $self = shift;
my $command = $self->wrapped();
if($Global::interactive) {
my $answer;
::status_no_nl("$command ?...");
do{
open(my $tty_fh, "<", "/dev/tty") || ::die_bug("interactive-tty");
$answer = <$tty_fh>;
close $tty_fh;
# Sometime we get an empty string (not even \n)
# Do not know why, so let us just ignore it and try again
} while(length $answer < 1);
if (not ($answer =~ /^\s*y/i)) {
$self->{'commandline'}->skip();
}
} else {
print $Global::original_stderr "$command\n";
}
}
{
my $tmuxsocket;
sub tmux_wrap($) {
# Wrap command with tmux for session pPID
# Input:
# $actual_command = the actual command being run (incl ssh wrap)
my $self = shift;
my $actual_command = shift;
# Temporary file name. Used for fifo to communicate exit val
my $tmpfifo = ::tmpname("tmx");
$self->add_rm($tmpfifo);
if(length($tmpfifo) >=100) {
::error("tmux does not support sockets with path > 100.");
::wait_and_exit(255);
}
if($opt::tmuxpane) {
# Move the command into a pane in window 0
$actual_command = $ENV{'PARALLEL_TMUX'}.' joinp -t :0 ; '.
$ENV{'PARALLEL_TMUX'}.' select-layout -t :0 tiled ; '.
$actual_command;
}
my $visual_command = $self->replaced();
my $title = $visual_command;
if($visual_command =~ /\0/) {
::error("Command line contains NUL. tmux is confused by NUL.");
::wait_and_exit(255);
}
# ; causes problems
# ascii 194-245 annoys tmux
$title =~ tr/[\011-\016;\302-\365]/ /s;
$title = ::Q($title);
my $l_act = length($actual_command);
my $l_tit = length($title);
my $l_fifo = length($tmpfifo);
# The line to run contains a 118 chars extra code + the title 2x
my $l_tot = 2 * $l_tit + $l_act + $l_fifo;
my $quoted_space75 = ::Q(" ")x75;
while($l_tit < 1000 and
(
(890 < $l_tot and $l_tot < 1350)
or
(9250 < $l_tot and $l_tot < 9800)
)) {
# tmux blocks for certain lengths:
# 900 < title + command < 1200
# 9250 < title + command < 9800
# but only if title < 1000, so expand the title with 75 spaces
# The measured lengths are:
# 996 < (title + whole command) < 1127
# 9331 < (title + whole command) < 9636
$title .= $quoted_space75;
$l_tit = length($title);
$l_tot = 2 * $l_tit + $l_act + $l_fifo;
}
my $tmux;
$ENV{'PARALLEL_TMUX'} ||= "tmux";
if(not $tmuxsocket) {
$tmuxsocket = ::tmpname("tms");
if($opt::fg) {
if(not fork) {
# Run tmux in the foreground
# Wait for the socket to appear
while (not -e $tmuxsocket) { }
`$ENV{'PARALLEL_TMUX'} -S $tmuxsocket attach`;
exit;
}
}
::status("See output with: $ENV{'PARALLEL_TMUX'} -S $tmuxsocket attach");
}
$tmux = "sh -c '".
$ENV{'PARALLEL_TMUX'}." -S $tmuxsocket new-session -s p$$ -d \"sleep .2\" >/dev/null 2>&1';" .
$ENV{'PARALLEL_TMUX'}." -S $tmuxsocket new-window -t p$$ -n $title";
::debug("tmux", "title len:", $l_tit, " act ", $l_act, " max ",
$Limits::Command::line_max_len, " tot ",
$l_tot, "\n");
return "mkfifo $tmpfifo && $tmux ".
# Run in tmux
::Q
(
"(".$actual_command.');'.
# The triple print is needed - otherwise the testsuite fails
q[ perl -e 'while($t++<3){ print $ARGV[0],"\n" }' $?h/$status >> ].$tmpfifo."&".
"echo $title; echo \007Job finished at: `date`;sleep 10"
).
# Run outside tmux
# Read a / separated line: 0h/2 for csh, 2/0 for bash.
# If csh the first will be 0h, so use the second as exit value.
# Otherwise just use the first value as exit value.
q{; exec perl -e '$/="/";$_=<>;$c=<>;unlink $ARGV; /(\d+)h/ and exit($1);exit$c' }.$tmpfifo;
}
}
sub is_already_in_results($) {
# Do we already have results for this job?
# Returns:
# $job_already_run = bool whether there is output for this or not
my $job = $_[0];
my $out = $job->{'commandline'}->results_out();
::debug("run", "Test ${out}stdout", -e "${out}stdout", "\n");
return(-e $out."stdout" or -f $out);
}
sub is_already_in_joblog($) {
my $job = shift;
return vec($Global::job_already_run,$job->seq(),1);
}
sub set_job_in_joblog($) {
my $job = shift;
vec($Global::job_already_run,$job->seq(),1) = 1;
}
sub should_be_retried($) {
# Should this job be retried?
# Returns
# 0 - do not retry
# 1 - job queued for retry
my $self = shift;
if (not $opt::retries) {
return 0;
}
if(not $self->exitstatus() and not $self->exitsignal()) {
# Completed with success. If there is a recorded failure: forget it
$self->reset_failed_here();
return 0;
} else {
# The job failed. Should it be retried?
$self->add_failed_here();
my $retries = $self->{'commandline'}->
replace_placeholders([$opt::retries],0,0);
if($self->total_failed() == $retries) {
# This has been retried enough
return 0;
} else {
# This command should be retried
$self->set_endtime(undef);
$self->reset_exitstatus();
$Global::JobQueue->unget($self);
::debug("run", "Retry ", $self->seq(), "\n");
return 1;
}
}
}
{
my (%print_later,$job_seq_to_print);
sub print_earlier_jobs($) {
# Print jobs whose output is postponed due to --keep-order
# Returns: N/A
my $job = shift;
$print_later{$job->seq()} = $job;
$job_seq_to_print ||= 1;
my $returnsize = 0;
::debug("run", "Looking for: $job_seq_to_print ",
"This: ", $job->seq(), "\n");
for(;vec($Global::job_already_run,$job_seq_to_print,1);
$job_seq_to_print++) {}
while(my $j = $print_later{$job_seq_to_print}) {
$returnsize += $j->print();
if($j->endtime()) {
# Job finished - look at the next
delete $print_later{$job_seq_to_print};
$job_seq_to_print++;
next;
} else {
# Job not finished yet - look at it again next round
last;
}
}
return $returnsize;
}
}
sub print($) {
# Print the output of the jobs
# Returns: N/A
my $self = shift;
::debug("print", ">>joboutput ", $self->replaced(), "\n");
if($opt::dryrun) {
# Nothing was printed to this job:
# cleanup tmp files if --files was set
::rm($self->fh(1,"name"));
}
if($opt::pipe and $self->virgin() and not $opt::tee) {
# Skip --joblog, --dryrun, --verbose
} else {
if($opt::ungroup) {
# NULL returnsize = 0 returnsize
$self->returnsize() or $self->add_returnsize(0);
if($Global::joblog and defined $self->{'exitstatus'}) {
# Add to joblog when finished
$self->print_joblog();
# Printing is only relevant for grouped/--line-buffer output.
$opt::ungroup and return;
}
}
# Check for disk full
::exit_if_disk_full();
}
my $returnsize = $self->returnsize();
for my $fdno (sort { $a <=> $b } keys %Global::fd) {
# Sort by file descriptor numerically: 1,2,3,..,9,10,11
$fdno == 0 and next;
my $out_fd = $Global::fd{$fdno};
my $in_fh = $self->fh($fdno,"r");
if(not $in_fh) {
if(not $Job::file_descriptor_warning_printed{$fdno}++) {
# ::warning("File descriptor $fdno not defined\n");
}
next;
}
::debug("print", "File descriptor $fdno (", $self->fh($fdno,"name"), "):\n");
if($opt::linebuffer) {
# Line buffered print out
$self->print_linebuffer($fdno,$in_fh,$out_fd);
} elsif($opt::files) {
$self->print_files($fdno,$in_fh,$out_fd);
} elsif($opt::tag or defined $opt::tagstring) {
$self->print_tag($fdno,$in_fh,$out_fd);
} else {
$self->print_normal($fdno,$in_fh,$out_fd);
}
flush $out_fd;
}
::debug("print", "<<joboutput\n");
if(defined $self->{'exitstatus'}
and not ($self->virgin() and $opt::pipe)) {
if($Global::joblog and not $opt::sqlworker) {
# Add to joblog when finished
$self->print_joblog();
}
if($opt::sqlworker and not $opt::results) {
$Global::sql->output($self);
}
if($Global::csvsep) {
# Add output to CSV when finished
$self->print_csv();
}
}
return $returnsize - $self->returnsize();
}
{
my $header_printed;
sub print_csv($) {
my $self = shift;
my $cmd;
if($Global::verbose <= 1) {
$cmd = $self->replaced();
} else {
# Verbose level > 1: Print the rsync and stuff
$cmd = join " ", @{$self->{'commandline'}};
}
my $record_ref = $self->{'commandline'}{'arg_list_flat_orig'};
if(not $header_printed) {
# Variable headers
# Normal => V1..Vn
# --header : => first value from column
my @V;
if($opt::header) {
my $i = 1;
@V = (map { $Global::input_source_header{$i++} }
@$record_ref[1..$#$record_ref]);
} else {
my $V = "V1";
@V = (map { $V++ } @$record_ref[1..$#$record_ref]);
}
print $Global::csv_fh
(map { $$_ }
combine_ref("Seq", "Host", "Starttime", "JobRuntime",
"Send", "Receive", "Exitval", "Signal", "Command",
@V,
"Stdout","Stderr"
)),"\n";
$header_printed++;
}
# Memory optimization: Overwrite with the joined output
$self->{'output'}{1} = join("", @{$self->{'output'}{1}});
$self->{'output'}{2} = join("", @{$self->{'output'}{2}});
print $Global::csv_fh
(map { $$_ }
combine_ref
($self->seq(),
$self->sshlogin()->string(),
$self->starttime(), sprintf("%0.3f",$self->runtime()),
$self->transfersize(), $self->returnsize(),
$self->exitstatus(), $self->exitsignal(), \$cmd,
\@$record_ref[1..$#$record_ref],
\$self->{'output'}{1},
\$self->{'output'}{2})),"\n";
}
}
sub combine_ref($) {
# Inspired by Text::CSV_PP::_combine (by Makamaka Hannyaharamitu)
my @part = @_;
my $sep = $Global::csvsep;
my $quot = '"';
my @out = ();
my $must_be_quoted;
for my $column (@part) {
# Memory optimization: Content transferred as reference
if(ref $column ne "SCALAR") {
# Convert all columns to scalar references
my $v = $column;
$column = \$v;
}
if(not defined $$column) {
$$column = '';
next;
}
$must_be_quoted = 0;
if($$column =~ s/$quot/$quot$quot/go){
# Replace " => ""
$must_be_quoted ||=1;
}
if($$column =~ /[\s\Q$sep\E]/o){
# Put quotes around if the column contains ,
$must_be_quoted ||=1;
}
$Global::use{"bytes"} ||= eval "use bytes; 1;";
if ($$column =~ /\0/) {
# Contains \0 => put quotes around
$must_be_quoted ||=1;
}
if($must_be_quoted){
push @out, \$sep, \$quot, $column, \$quot;
} else {
push @out, \$sep, $column;
}
}
# Pop off a $sep
shift @out;
return @out;
}
sub print_files($) {
# Print the name of the file containing stdout on stdout
# Uses:
# $opt::pipe
# $opt::group = Print when job is done
# $opt::linebuffer = Print ASAP
# Returns: N/A
my $self = shift;
my ($fdno,$in_fh,$out_fd) = @_;
# If the job is dead: close printing fh. Needed for --compress
close $self->fh($fdno,"w");
if($? and $opt::compress) {
::error($opt::compress_program." failed.");
$self->set_exitstatus(255);
}
if($opt::compress) {
# Kill the decompressor which will not be needed
CORE::kill "TERM", $self->fh($fdno,"rpid");
}
close $in_fh;
if($opt::pipe and $self->virgin()) {
# Nothing was printed to this job:
# cleanup unused tmp files because --files was set
for my $fdno (1,2) {
::rm($self->fh($fdno,"name"));
::rm($self->fh($fdno,"unlink"));
}
} elsif($fdno == 1 and $self->fh($fdno,"name")) {
print $out_fd $self->tag(),$self->fh($fdno,"name"),"\n";
if($Global::membuffer) {
push @{$self->{'output'}{$fdno}},
$self->tag(), $self->fh($fdno,"name");
}
$self->add_returnsize(-s $self->fh($fdno,"name"));
# Mark as printed - do not print again
$self->set_fh($fdno,"name",undef);
}
}
sub print_linebuffer($) {
my $self = shift;
my ($fdno,$in_fh,$out_fd) = @_;
if(defined $self->{'exitstatus'}) {
# If the job is dead: close printing fh. Needed for --compress
close $self->fh($fdno,"w");
if($? and $opt::compress) {
::error($opt::compress_program." failed.");
$self->set_exitstatus(255);
}
if($opt::compress) {
# Blocked reading in final round
for my $fdno (1,2) {
::set_fh_blocking($self->fh($fdno,'r'));
}
}
}
if(not $self->virgin()) {
if($opt::files or ($opt::results and not $Global::csvsep)) {
# Print filename
if($fdno == 1 and not $self->fh($fdno,"printed")) {
print $out_fd $self->tag(),$self->fh($fdno,"name"),"\n";
if($Global::membuffer) {
push(@{$self->{'output'}{$fdno}}, $self->tag(),
$self->fh($fdno,"name"));
}
$self->set_fh($fdno,"printed",1);
}
# No need for reading $in_fh, as it is from "cat >/dev/null"
} else {
# Read halflines and print full lines
my $outputlength = 0;
my $halfline_ref = $self->{'halfline'}{$fdno};
my ($buf,$i,$rv);
# 1310720 gives 1.2 GB/s
# 131072 gives 0.9 GB/s
while($rv = sysread($in_fh, $buf,1310720)) {
$outputlength += $rv;
# TODO --recend
# Treat both \n and \r as line end
$i = (rindex($buf,"\n")+1) || (rindex($buf,"\r")+1);
if($i) {
# One or more complete lines were found
if($opt::tag or defined $opt::tagstring) {
# Replace ^ with $tag within the full line
my $tag = $self->tag();
# TODO --recend that can be partially in @$halfline_ref
substr($buf,0,$i-1) =~ s/(?<=[\n\r])/$tag/gm;
# The length changed, so find the new ending pos
$i = (rindex($buf,"\n")+1) || (rindex($buf,"\r")+1);
unshift @$halfline_ref, $tag;
}
# Print the partial line (halfline) and the last half
print $out_fd @$halfline_ref, substr($buf,0,$i);
# Buffer in memory for SQL and CSV-output
if($Global::membuffer) {
push(@{$self->{'output'}{$fdno}},
@$halfline_ref, substr($buf,0,$i));
}
# Remove the printed part by keeping the unprinted part
@$halfline_ref = (substr($buf,$i));
} else {
# No newline, so append to the halfline
push @$halfline_ref, $buf;
}
}
$self->add_returnsize($outputlength);
}
if(defined $self->{'exitstatus'}) {
if($opt::files or ($opt::results and not $Global::csvsep)) {
$self->add_returnsize(-s $self->fh($fdno,"name"));
} else {
# If the job is dead: print the remaining partial line
# read remaining
my $halfline_ref = $self->{'halfline'}{$fdno};
if(grep /./, @$halfline_ref) {
my $returnsize = 0;
for(@{$self->{'halfline'}{$fdno}}) {
$returnsize += length $_;
}
$self->add_returnsize($returnsize);
if($opt::tag or defined $opt::tagstring) {
# Prepend $tag the the remaining half line
unshift @$halfline_ref, $self->tag();
}
# Print the partial line (halfline)
print $out_fd @{$self->{'halfline'}{$fdno}};
# Buffer in memory for SQL and CSV-output
if($Global::membuffer) {
push(@{$self->{'output'}{$fdno}}, @$halfline_ref);
}
@$halfline_ref = ();
}
}
if($self->fh($fdno,"rpid") and
CORE::kill 0, $self->fh($fdno,"rpid")) {
# decompress still running
} else {
# decompress done: close fh
close $in_fh;
if($? and $opt::compress) {
::error($opt::decompress_program." failed.");
$self->set_exitstatus(255);
}
}
}
}
}
sub print_tag(@) {
return print_normal(@_);
}
sub free_ressources() {
my $self = shift;
if(not $opt::ungroup) {
for my $fdno (sort { $a <=> $b } keys %Global::fd) {
close $self->fh($fdno,"w");
close $self->fh($fdno,"r");
}
}
}
sub print_normal($) {
my $self = shift;
my ($fdno,$in_fh,$out_fd) = @_;
my $buf;
close $self->fh($fdno,"w");
if($? and $opt::compress) {
::error($opt::compress_program." failed.");
$self->set_exitstatus(255);
}
if(not $self->virgin()) {
seek $in_fh, 0, 0;
# $in_fh is now ready for reading at position 0
my $outputlength = 0;
my @output;
if($opt::tag or $opt::tagstring) {
# Read line by line
local $/ = "\n";
my $tag = $self->tag();
while(<$in_fh>) {
print $out_fd $tag,$_;
$outputlength += length $_;
if($Global::membuffer) {
push @{$self->{'output'}{$fdno}}, $tag, $_;
}
}
} else {
while(sysread($in_fh,$buf,131072)) {
print $out_fd $buf;
$outputlength += length $buf;
if($Global::membuffer) {
push @{$self->{'output'}{$fdno}}, $buf;
}
}
}
if($fdno == 1) {
$self->add_returnsize($outputlength);
}
close $in_fh;
if($? and $opt::compress) {
::error($opt::decompress_program." failed.");
$self->set_exitstatus(255);
}
}
}
sub print_joblog($) {
my $self = shift;
my $cmd;
if($Global::verbose <= 1) {
$cmd = $self->replaced();
} else {
# Verbose level > 1: Print the rsync and stuff
$cmd = join " ", @{$self->{'commandline'}};
}
# Newlines make it hard to parse the joblog
$cmd =~ s/\n/\0/g;
print $Global::joblog
join("\t", $self->seq(), $self->sshlogin()->string(),
$self->starttime(), sprintf("%10.3f",$self->runtime()),
$self->transfersize(), $self->returnsize(),
$self->exitstatus(), $self->exitsignal(), $cmd
). "\n";
flush $Global::joblog;
$self->set_job_in_joblog();
}
sub tag($) {
my $self = shift;
if(not defined $self->{'tag'}) {
if($opt::tag or defined $opt::tagstring) {
$self->{'tag'} = $self->{'commandline'}->
replace_placeholders([$opt::tagstring],0,0)."\t";
} else {
$self->{'tag'} = "";
}
}
return $self->{'tag'};
}
sub hostgroups($) {
my $self = shift;
if(not defined $self->{'hostgroups'}) {
$self->{'hostgroups'} =
$self->{'commandline'}->{'arg_list'}[0][0]->{'hostgroups'};
}
return @{$self->{'hostgroups'}};
}
sub exitstatus($) {
my $self = shift;
return $self->{'exitstatus'};
}
sub set_exitstatus($$) {
my $self = shift;
my $exitstatus = shift;
if($exitstatus) {
# Overwrite status if non-zero
$self->{'exitstatus'} = $exitstatus;
} else {
# Set status but do not overwrite
# Status may have been set by --timeout
$self->{'exitstatus'} ||= $exitstatus;
}
$opt::sqlworker and
$Global::sql->update("SET Exitval = ? WHERE Seq = ".$self->seq(),
$exitstatus);
}
sub reset_exitstatus($) {
my $self = shift;
undef $self->{'exitstatus'};
}
sub exitsignal($) {
my $self = shift;
return $self->{'exitsignal'};
}
sub set_exitsignal($$) {
my $self = shift;
my $exitsignal = shift;
$self->{'exitsignal'} = $exitsignal;
$opt::sqlworker and
$Global::sql->update("SET _Signal = ? WHERE Seq = ".$self->seq(),
$exitsignal);
}
{
my $status_printed;
my $total_jobs;
sub should_we_halt {
# Should we halt? Immediately? Gracefully?
# Returns: N/A
my $job = shift;
my $limit;
if($job->exitstatus() or $job->exitsignal()) {
# Job failed
$Global::exitstatus++;
$Global::total_failed++;
if($Global::halt_fail) {
::status("$Global::progname: This job failed:",
$job->replaced());
$limit = $Global::total_failed;
}
} elsif($Global::halt_success) {
::status("$Global::progname: This job succeeded:",
$job->replaced());
$limit = $Global::total_completed - $Global::total_failed;
}
if($Global::halt_done) {
::status("$Global::progname: This job finished:",
$job->replaced());
$limit = $Global::total_completed;
}
if(not defined $limit) {
return ""
}
# --halt # => 1..100 (number of jobs failed, 101 means > 100)
# --halt % => 1..100 (pct of jobs failed)
if($Global::halt_pct and not $Global::halt_count) {
$total_jobs ||= $Global::JobQueue->total_jobs();
# From the pct compute the number of jobs that must fail/succeed
$Global::halt_count = $total_jobs * $Global::halt_pct;
}
if($limit >= $Global::halt_count) {
# At least N jobs have failed/succeded/completed
# or at least N% have failed/succeded/completed
# So we should prepare for exit
if($Global::halt_fail or $Global::halt_done) {
# Set exit status
if(not defined $Global::halt_exitstatus) {
if($Global::halt_pct) {
# --halt now,fail=X% or soon,fail=X%
# --halt now,done=X% or soon,done=X%
$Global::halt_exitstatus =
::ceil($Global::total_failed / $total_jobs * 100);
} elsif($Global::halt_count) {
# --halt now,fail=X or soon,fail=X
# --halt now,done=X or soon,done=X
$Global::halt_exitstatus =
::min($Global::total_failed,101);
}
if($Global::halt_count and $Global::halt_count == 1) {
# --halt now,fail=1 or soon,fail=1
# --halt now,done=1 or soon,done=1
# Emulate Bash's +128 if there is a signal
$Global::halt_exitstatus =
($job->exitstatus()
or
$job->exitsignal() ? $job->exitsignal() + 128 : 0);
}
}
::debug("halt","Pct: ",$Global::halt_pct,
" count: ",$Global::halt_count,
" status: ",$Global::halt_exitstatus,"\n");
} elsif($Global::halt_success) {
$Global::halt_exitstatus = 0;
}
if($Global::halt_when eq "soon"
and
(scalar(keys %Global::running) > 0
or
$Global::max_jobs_running == 1)) {
::status
("$Global::progname: Starting no more jobs. ".
"Waiting for ". (keys %Global::running).
" jobs to finish.");
$Global::start_no_new_jobs ||= 1;
}
return($Global::halt_when);
}
return "";
}
}
package CommandLine;
sub new($) {
my $class = shift;
my $seq = shift;
my $commandref = shift;
$commandref || die;
my $arg_queue = shift;
my $context_replace = shift;
my $max_number_of_args = shift; # for -N and normal (-n1)
my $transfer_files = shift;
my $return_files = shift;
my $replacecount_ref = shift;
my $len_ref = shift;
my %replacecount = %$replacecount_ref;
my %len = %$len_ref;
for (keys %$replacecount_ref) {
# Total length of this replacement string {} replaced with all args
$len{$_} = 0;
}
return bless {
'command' => $commandref,
'seq' => $seq,
'len' => \%len,
'arg_list' => [],
'arg_list_flat' => [],
'arg_list_flat_orig' => [undef],
'arg_queue' => $arg_queue,
'max_number_of_args' => $max_number_of_args,
'replacecount' => \%replacecount,
'context_replace' => $context_replace,
'transfer_files' => $transfer_files,
'return_files' => $return_files,
'replaced' => undef,
}, ref($class) || $class;
}
sub seq($) {
my $self = shift;
return $self->{'seq'};
}
sub set_seq($$) {
my $self = shift;
$self->{'seq'} = shift;
}
sub slot($) {
# Find the number of a free job slot and return it
# Uses:
# @Global::slots - list with free jobslots
# Returns:
# $jobslot = number of jobslot
my $self = shift;
if(not $self->{'slot'}) {
if(not @Global::slots) {
# $max_slot_number will typically be $Global::max_jobs_running
push @Global::slots, ++$Global::max_slot_number;
}
$self->{'slot'} = shift @Global::slots;
}
return $self->{'slot'};
}
{
my $already_spread;
sub populate($) {
# Add arguments from arg_queue until the number of arguments or
# max line length is reached
# Uses:
# $Global::minimal_command_line_length
# $opt::cat
# $opt::fifo
# $Global::JobQueue
# $opt::m
# $opt::X
# $Global::max_jobs_running
# Returns: N/A
my $self = shift;
my $next_arg;
my $max_len = $Global::minimal_command_line_length
|| Limits::Command::max_length();
if($opt::cat or $opt::fifo) {
# Get the empty arg added by --pipepart (if any)
$Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->get();
# $PARALLEL_TMP will point to a tempfile that will be used as {}
$Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->
unget([Arg->new('$PARALLEL_TMP')]);
}
while (not $self->{'arg_queue'}->empty()) {
$next_arg = $self->{'arg_queue'}->get();
if(not defined $next_arg) {
next;
}
$self->push($next_arg);
if($self->len() >= $max_len) {
# Command length is now > max_length
# If there are arguments: remove the last
# If there are no arguments: Error
# TODO stuff about -x opt_x
if($self->number_of_args() > 1) {
# There is something to work on
$self->{'arg_queue'}->unget($self->pop());
last;
} else {
my $args = join(" ", map { $_->orig() } @$next_arg);
::error("Command line too long (".
$self->len(). " >= ".
$max_len.
") at input ".
$self->{'arg_queue'}->arg_number().
": ".
((length $args > 50) ?
(substr($args,0,50))."..." :
$args));
$self->{'arg_queue'}->unget($self->pop());
::wait_and_exit(255);
}
}
if(defined $self->{'max_number_of_args'}) {
if($self->number_of_args() >= $self->{'max_number_of_args'}) {
last;
}
}
}
if(($opt::m or $opt::X) and not $already_spread
and $self->{'arg_queue'}->empty() and $Global::max_jobs_running) {
# -m or -X and EOF => Spread the arguments over all jobslots
# (unless they are already spread)
$already_spread ||= 1;
if($self->number_of_args() > 1) {
$self->{'max_number_of_args'} =
::ceil($self->number_of_args()/$Global::max_jobs_running);
$Global::JobQueue->{'commandlinequeue'}->{'max_number_of_args'} =
$self->{'max_number_of_args'};
$self->{'arg_queue'}->unget($self->pop_all());
while($self->number_of_args() < $self->{'max_number_of_args'}) {
$self->push($self->{'arg_queue'}->get());
}
}
$Global::JobQueue->flush_total_jobs();
}
if($opt::sqlmaster) {
# Insert the V1..Vn for this $seq in SQL table instead of generating one
$Global::sql->insert_records($self->seq(), $self->{'command'},
$self->{'arg_list_flat_orig'});
}
}
}
sub push($) {
# Add one or more records as arguments
# Returns: N/A
my $self = shift;
my $record = shift;
push @{$self->{'arg_list_flat_orig'}}, map { $_->orig() } @$record;
push @{$self->{'arg_list_flat'}}, @$record;
push @{$self->{'arg_list'}}, $record;
# Make @arg available for {= =}
*Arg::arg = $self->{'arg_list_flat_orig'};
my $quote_arg = $Global::noquote ? 0 : not $Global::quoting;
for my $perlexpr (keys %{$self->{'replacecount'}}) {
if($perlexpr =~ /^(\d+) /) {
# Positional
defined($record->[$1-1]) or next;
$self->{'len'}{$perlexpr} +=
length $record->[$1-1]->replace($perlexpr,$quote_arg,$self);
} else {
for my $arg (@$record) {
if(defined $arg) {
$self->{'len'}{$perlexpr} +=
length $arg->replace($perlexpr,$quote_arg,$self);
}
}
}
}
}
sub pop($) {
# Remove last argument
# Returns:
# the last record
my $self = shift;
my $record = pop @{$self->{'arg_list'}};
# pop off arguments from @$record
splice @{$self->{'arg_list_flat_orig'}}, -($#$record+1), $#$record+1;
splice @{$self->{'arg_list_flat'}}, -($#$record+1), $#$record+1;
my $quote_arg = $Global::noquote ? 0 : not $Global::quoting;
for my $perlexpr (keys %{$self->{'replacecount'}}) {
if($perlexpr =~ /^(\d+) /) {
# Positional
defined($record->[$1-1]) or next;
$self->{'len'}{$perlexpr} -=
length $record->[$1-1]->replace($perlexpr,$quote_arg,$self);
} else {
for my $arg (@$record) {
if(defined $arg) {
$self->{'len'}{$perlexpr} -=
length $arg->replace($perlexpr,$quote_arg,$self);
}
}
}
}
return $record;
}
sub pop_all($) {
# Remove all arguments and zeros the length of replacement perlexpr
# Returns:
# all records
my $self = shift;
my @popped = @{$self->{'arg_list'}};
for my $perlexpr (keys %{$self->{'replacecount'}}) {
$self->{'len'}{$perlexpr} = 0;
}
$self->{'arg_list'} = [];
$self->{'arg_list_flat_orig'} = [undef];
$self->{'arg_list_flat'} = [];
return @popped;
}
sub number_of_args($) {
# The number of records
# Returns:
# number of records
my $self = shift;
# This is really the number of records
return $#{$self->{'arg_list'}}+1;
}
sub number_of_recargs($) {
# The number of args in records
# Returns:
# number of args records
my $self = shift;
my $sum = 0;
my $nrec = scalar @{$self->{'arg_list'}};
if($nrec) {
$sum = $nrec * (scalar @{$self->{'arg_list'}[0]});
}
return $sum;
}
sub args_as_string($) {
# Returns:
# all unmodified arguments joined with ' ' (similar to {})
my $self = shift;
return (join " ", map { $_->orig() }
map { @$_ } @{$self->{'arg_list'}});
}
sub results_out($) {
sub max_file_name_length {
# Figure out the max length of a subdir
# TODO and the max total length
# Ext4 = 255,130816
# Uses:
# $Global::max_file_length is set
# Returns:
# $Global::max_file_length
my $testdir = shift;
my $upper = 8_000_000;
# Dir length of 8 chars is supported everywhere
my $len = 8;
my $dir = "x"x$len;
do {
rmdir($testdir."/".$dir);
$len *= 16;
$dir = "x"x$len;
} while ($len < $upper and mkdir $testdir."/".$dir);
# Then search for the actual max length between $len/16 and $len
my $min = $len/16;
my $max = $len;
while($max-$min > 5) {
# If we are within 5 chars of the exact value:
# it is not worth the extra time to find the exact value
my $test = int(($min+$max)/2);
$dir = "x"x$test;
if(mkdir $testdir."/".$dir) {
rmdir($testdir."/".$dir);
$min = $test;
} else {
$max = $test;
}
}
$Global::max_file_length = $min;
return $min;
}
my $self = shift;
my $out = $self->replace_placeholders([$opt::results],0,0);
if($out eq $opt::results) {
# $opt::results simple string: Append args_as_dirname
my $args_as_dirname = $self->args_as_dirname();
# Output in: prefix/name1/val1/name2/val2/stdout
$out = $opt::results."/".$args_as_dirname;
if(-d $out or eval{ File::Path::mkpath($out); }) {
# OK
} else {
# mkpath failed: Argument probably too long.
# Set $Global::max_file_length, which will keep the individual
# dir names shorter than the max length
max_file_name_length($opt::results);
$args_as_dirname = $self->args_as_dirname();
# prefix/name1/val1/name2/val2/
$out = $opt::results."/".$args_as_dirname;
File::Path::mkpath($out);
}
$out .="/";
} else {
if($out =~ m:/$:) {
# / = dir
if(-d $out or eval{ File::Path::mkpath($out); }) {
# OK
} else {
::error("Cannot make dir '$out'.");
::wait_and_exit(255);
}
} else {
$out =~ m:(.*)/:;
File::Path::mkpath($1);
}
}
return $out;
}
sub args_as_dirname($) {
# Returns:
# all unmodified arguments joined with '/' (similar to {})
# \t \0 \\ and / are quoted as: \t \0 \\ \_
# If $Global::max_file_length: Keep subdirs < $Global::max_file_length
my $self = shift;
my @res = ();
for my $rec_ref (@{$self->{'arg_list'}}) {
# If headers are used, sort by them.
# Otherwise keep the order from the command line.
my @header_indexes_sorted = header_indexes_sorted($#$rec_ref+1);
for my $n (@header_indexes_sorted) {
CORE::push(@res,
$Global::input_source_header{$n},
map { my $s = $_;
# \t \0 \\ and / are quoted as: \t \0 \\ \_
$s =~ s/\\/\\\\/g;
$s =~ s/\t/\\t/g;
$s =~ s/\0/\\0/g;
$s =~ s:/:\\_:g;
if($Global::max_file_length) {
# Keep each subdir shorter than the longest
# allowed file name
$s = substr($s,0,$Global::max_file_length);
}
$s; }
$rec_ref->[$n-1]->orig());
}
}
return join "/", @res;
}
sub header_indexes_sorted($) {
# Sort headers first by number then by name.
# E.g.: 1a 1b 11a 11b
# Returns:
# Indexes of %Global::input_source_header sorted
my $max_col = shift;
no warnings 'numeric';
for my $col (1 .. $max_col) {
# Make sure the header is defined. If it is not: use column number
if(not defined $Global::input_source_header{$col}) {
$Global::input_source_header{$col} = $col;
}
}
my @header_indexes_sorted = sort {
# Sort headers numerically then asciibetically
$Global::input_source_header{$a} <=> $Global::input_source_header{$b}
or
$Global::input_source_header{$a} cmp $Global::input_source_header{$b}
} 1 .. $max_col;
return @header_indexes_sorted;
}
sub len($) {
# Uses:
# @opt::shellquote
# The length of the command line with args substituted
my $self = shift;
my $len = 0;
# Add length of the original command with no args
# Length of command w/ all replacement args removed
$len += $self->{'len'}{'noncontext'} + @{$self->{'command'}} -1;
::debug("length", "noncontext + command: $len\n");
my $recargs = $self->number_of_recargs();
if($self->{'context_replace'}) {
# Context is duplicated for each arg
$len += $recargs * $self->{'len'}{'context'};
for my $replstring (keys %{$self->{'replacecount'}}) {
# If the replacements string is more than once: mulitply its length
$len += $self->{'len'}{$replstring} *
$self->{'replacecount'}{$replstring};
::debug("length", $replstring, " ", $self->{'len'}{$replstring}, "*",
$self->{'replacecount'}{$replstring}, "\n");
}
# echo 11 22 33 44 55 66 77 88 99 1010
# echo 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
# 5 + ctxgrp*arg
::debug("length", "Ctxgrp: ", $self->{'len'}{'contextgroups'},
" Groups: ", $self->{'len'}{'noncontextgroups'}, "\n");
# Add space between context groups
$len += ($recargs-1) * ($self->{'len'}{'contextgroups'});
} else {
# Each replacement string may occur several times
# Add the length for each time
$len += 1*$self->{'len'}{'context'};
::debug("length", "context+noncontext + command: $len\n");
for my $replstring (keys %{$self->{'replacecount'}}) {
# (space between regargs + length of replacement)
# * number this replacement is used
$len += ($recargs -1 + $self->{'len'}{$replstring}) *
$self->{'replacecount'}{$replstring};
}
}
if(defined $Global::parallel_env) {
# If we are using --env, add the prefix for that, too.
$len += length $Global::parallel_env;
}
if($Global::quoting) {
# Pessimistic length if -q is set
# Worse than worst case: ' => "'" + " => '"'
# TODO can we count the number of expanding chars?
# and count them in arguments, too?
$len *= 3;
}
if(@opt::shellquote) {
# Pessimistic length if --shellquote is set
# Worse than worst case: ' => "'"
for(@opt::shellquote) {
$len *= 3;
}
$len *= 5;
}
if(@opt::sshlogin) {
# Pessimistic length if remote
# Worst case is BASE64 encoding 3 bytes -> 4 bytes
$len = int($len*4/3);
}
return $len;
}
sub replaced($) {
# Uses:
# $Global::noquote
# $Global::quoting
# Returns:
# $replaced = command with place holders replaced and prepended
my $self = shift;
if(not defined $self->{'replaced'}) {
# Don't quote arguments if the input is the full command line
my $quote_arg = $Global::noquote ? 0 : not $Global::quoting;
# or if ($opt::cat or $opt::pipe) as they use $PARALLEL_TMP
$quote_arg = ($opt::cat || $opt::fifo) ? 0 : $quote_arg;
$self->{'replaced'} = $self->
replace_placeholders($self->{'command'},$Global::quoting,
$quote_arg);
my $len = length $self->{'replaced'};
if ($len != $self->len()) {
::debug("length", $len, " != ", $self->len(),
" ", $self->{'replaced'}, "\n");
} else {
::debug("length", $len, " == ", $self->len(),
" ", $self->{'replaced'}, "\n");
}
}
return $self->{'replaced'};
}
sub replace_placeholders($$$$) {
# Replace foo{}bar with fooargbar
# Input:
# $targetref = command as shell words
# $quote = should everything be quoted?
# $quote_arg = should replaced arguments be quoted?
# Uses:
# @Arg::arg = arguments as strings to be use in {= =}
# Returns:
# @target with placeholders replaced
my $self = shift;
my $targetref = shift;
my $quote = shift;
my $quote_arg = shift;
my %replace;
# Token description:
# \0spc = unquoted space
# \0end = last token element
# \0ign = dummy token to be ignored
# \257<...\257> = replacement expression
# " " = quoted space, that splits -X group
# text = normal text - possibly part of -X group
my $spacer = 0;
my @tokens = grep { length $_ > 0 } map {
if(/^\257<|^ $/) {
# \257<...\257> or space
$_
} else {
# Split each space/tab into a token
split /(?=\s)|(?<=\s)/
}
}
# Split \257< ... \257> into own token
map { split /(?=\257<)|(?<=\257>)/ }
# Insert "\0spc" between every element
# This space should never be quoted
map { $spacer++ ? ("\0spc",$_) : $_ }
map { $_ eq "" ? "\0empty" : $_ }
@$targetref;
if(not @tokens) {
# @tokens is empty: Return empty array
return @tokens;
}
::debug("replace", "Tokens ".join":",@tokens,"\n");
# Make it possible to use $arg[2] in {= =}
*Arg::arg = $self->{'arg_list_flat_orig'};
# Flat list:
# $self->{'arg_list'} = [ [Arg11, Arg12], [Arg21, Arg22], [Arg31, Arg32] ]
# $self->{'arg_list_flat'} = [ Arg11, Arg12, Arg21, Arg22, Arg31, Arg32 ]
if(not @{$self->{'arg_list_flat'}}) {
@{$self->{'arg_list_flat'}} = Arg->new("");
}
my $argref = $self->{'arg_list_flat'};
# Number of arguments - used for positional arguments
my $n = $#$argref+1;
# $self is actually a CommandLine-object,
# but it looks nice to be able to say {= $job->slot() =}
my $job = $self;
# @replaced = tokens with \257< \257> replaced
my @replaced;
if($self->{'context_replace'}) {
my @ctxgroup;
for my $t (@tokens,"\0end") {
# \0end = last token was end of tokens.
if($t eq "\t" or $t eq " " or $t eq "\0end" or $t eq "\0spc") {
# Context group complete: Replace in it
if(grep { /^\257</ } @ctxgroup) {
# Context group contains a replacement string:
# Copy once per arg
my $space = "\0ign";
for my $arg (@$argref) {
my $normal_replace;
# Push output
# Put unquoted space before each context group
# except the first
CORE::push @replaced, $space, map {
$a = $_;
$a =~
s{\257<(-?\d+)?(.*)\257>}
{
if($1) {
# Positional replace
# Find the relevant arg and replace it
($argref->[$1 > 0 ? $1-1 : $n+$1] ? # If defined: replace
$argref->[$1 > 0 ? $1-1 : $n+$1]->
replace($2,$quote_arg,$self)
: "");
} else {
# Normal replace
$normal_replace ||= 1;
($arg ? $arg->replace($2,$quote_arg,$self) : "");
}
}sgxe;
$a
} @ctxgroup;
$normal_replace or last;
$space = "\0spc";
}
} else {
# Context group has no a replacement string: Copy it once
CORE::push @replaced, @ctxgroup;
}
# New context group
@ctxgroup=();
}
if($t eq "\0spc" or $t eq " ") {
CORE::push @replaced,$t;
} else {
CORE::push @ctxgroup,$t;
}
}
} else {
# @group = @token
# Replace in group
# Push output
# repquote = no if {} first on line, no if $quote, yes otherwise
for my $t (@tokens) {
if($t =~ /^\257</) {
my $space = "\0ign";
for my $arg (@$argref) {
my $normal_replace;
$a = $t;
$a =~
s{\257<(-?\d+)?(.*)\257>}
{
if($1) {
# Positional replace
# Find the relevant arg and replace it
($argref->[$1 > 0 ? $1-1 : $n+$1] ? # If defined: replace
$argref->[$1 > 0 ? $1-1 : $n+$1]->
replace($2,$quote_arg,$self)
: "");
} else {
# Normal replace
$normal_replace ||= 1;
($arg ? $arg->replace($2,$quote_arg,$self) : "");
}
}sgxe;
CORE::push @replaced, $space, $a;
$normal_replace or last;
$space = "\0spc";
}
} else {
# No replacement
CORE::push @replaced, $t;
}
}
}
*Arg::arg = [];
::debug("replace","Replaced: ".join":",@replaced,"\n");
if($Global::escape_string_present) {
# Command line contains \257: Unescape it \257\256 => \257
# If a replacement resulted in \257\256
# it will have been escaped into \\\257\\\\256
# and will not be matched below
for(@replaced) {
s/\257\256/\257/g;
}
}
# Put tokens into groups that may be quoted.
my @quotegroup;
my @quoted;
for (map { $_ eq "\0empty" ? "" : $_ }
grep { $_ ne "\0ign" and $_ ne "\0noarg" and $_ ne "'\0noarg'" }
@replaced, "\0end") {
if($_ eq "\0spc" or $_ eq "\0end") {
# \0spc splits quotable groups
if($quote) {
if(@quotegroup) {
CORE::push @quoted, ::Q(join"",@quotegroup);;
}
} else {
CORE::push @quoted, join"",@quotegroup;
}
@quotegroup = ();
} else {
CORE::push @quotegroup, $_;
}
}
::debug("replace","Quoted: ".join":",@quoted,"\n");
return wantarray ? @quoted : "@quoted";
}
sub skip($) {
# Skip this job
my $self = shift;
$self->{'skip'} = 1;
}
package CommandLineQueue;
sub new($) {
my $class = shift;
my $commandref = shift;
my $read_from = shift;
my $context_replace = shift || 0;
my $max_number_of_args = shift;
my $transfer_files = shift;
my $return_files = shift;
my @unget = ();
my $posrpl;
my ($replacecount_ref, $len_ref);
my @command = @$commandref;
my $seq = 1;
# Replace replacement strings with {= perl expr =}
# '{=' 'perlexpr' '=}' => '{= perlexpr =}'
@command = merge_rpl_parts(@command);
# Protect matching inside {= perl expr =}
# by replacing {= and =} with \257< and \257>
# in options that can contain replacement strings:
# @command, --transferfile, --return,
# --tagstring, --workdir, --results
for(@command, @$transfer_files, @$return_files,
$opt::tagstring, $opt::workdir, $opt::results, $opt::retries) {
# Skip if undefined
$_ or next;
# Escape \257 => \257\256
$Global::escape_string_present += s/\257/\257\256/g;
# Needs to match rightmost left parens (Perl defaults to leftmost)
# to deal with: {={==} and {={==}=}
# Replace {= -> \257< and =} -> \257>
#
# Complex way to do:
# s/{=(.*)=}/\257<$1\257>/g
# which would not work
s[\Q$Global::parensleft\E # Match {=
# Match . unless the next string is {= or =}
# needed to force matching the shortest {= =}
((?:(?! \Q$Global::parensleft\E|\Q$Global::parensright\E ).)*?)
\Q$Global::parensright\E ] # Match =}
{\257<$1\257>}gxs;
for my $rpl (sort { length $b <=> length $a } keys %Global::rpl) {
# Replace long --rpl's before short ones, as a short may be a
# substring of a long:
# --rpl '% s/a/b/' --rpl '%% s/b/a/'
#
# Replace the shorthand string (--rpl)
# with the {= perl expr =}
#
# Avoid searching for shorthand strings inside existing {= perl expr =}
#
# Replace $$1 in {= perl expr =} with groupings in shorthand string
#
# --rpl '{/(\.\S+)/(\.\S+)} s/$$1/$$2/g;'
# echo {/.tar/.gz} ::: UU.tar.gz
my ($prefix,$grp_regexp,$postfix) =
$rpl =~ /^( [^(]* ) # Prefix - e.g. {%%
( \(.*\) )? # Group capture regexp - e.g (.*)
( [^)]* )$ # Postfix - e.g }
/xs;
$grp_regexp ||= '';
my $rplval = $Global::rpl{$rpl};
while(s{( (?: ^|\257> ) (?: [^\257]*|[\257][^<>] )*? )
# Don't replace after \257 unless \257>
\Q$prefix\E $grp_regexp \Q$postfix\E}
{
# The start remains the same
my $unchanged = $1;
# Dummy entry to start at 1.
my @grp = (1);
# $2 = first ()-group in $grp_regexp
# Put $2 in $grp[1], Put $3 in $grp[2]
# so first ()-group in $grp_regexp is $grp[1];
for(my $i = 2; defined $grp[$#grp]; $i++) {
push @grp, eval '$'.$i;
}
my $rv = $rplval;
# replace $$1 with $_pAr_gRp1, $$2 with $_pAr_gRp2
# in the code to be executed
$rv =~ s/\$\$ (\d+)/\$_pAr_gRp$1/gx;
# prepend with $_pAr_gRp1 = perlquote($1),
my $set_args = "";
for(my $i = 1;defined $grp[$i]; $i++) {
$set_args .= "\$_pAr_gRp$i = \"" .
::perl_quote_scalar($grp[$i]) . "\";";
}
$unchanged . "\257<" . $set_args . $rv . "\257>"
}gxes) {
}
# Do the same for the positional replacement strings
$posrpl = $rpl;
if($posrpl =~ s/^\{//) {
# Only do this if the shorthand start with {
$prefix=~s/^\{//;
# Don't replace after \257 unless \257>
while(s{( (?: ^|\257> ) (?: [^\257]*|[\257][^<>] )*? )
\{(-?\d+) \s* \Q$prefix\E $grp_regexp \Q$postfix\E}
{
# The start remains the same
my $unchanged = $1;
my $position = $2;
# Dummy entry to start at 1.
my @grp = (1);
# $3 = first ()-group in $grp_regexp
# Put $3 in $grp[1], Put $4 in $grp[2]
# so first ()-group in $grp_regexp is $grp[1];
for(my $i = 3; defined $grp[$#grp]; $i++) {
push @grp, eval '$'.$i;
}
my $rv = $rplval;
# replace $$1 with $_pAr_gRp1, $$2 with $_pAr_gRp2
# in the code to be executed
$rv =~ s/\$\$ (\d+)/\$_pAr_gRp$1/gx;
# prepend with $_pAr_gRp1 = perlquote($1),
my $set_args = "";
for(my $i = 1;defined $grp[$i]; $i++) {
$set_args .= "\$_pAr_gRp$i = \"" .
::perl_quote_scalar($grp[$i]) . "\";";
}
$unchanged . "\257<" . $position . $set_args . $rv . "\257>"
}gxes) {
}
}
}
}
# Add {} if no replacement strings in @command
($replacecount_ref, $len_ref, @command) =
replacement_counts_and_lengths($transfer_files,$return_files,@command);
if("@command" =~ /^[^ \t\n=]*\257</) {
# Replacement string is (part of) the command (and not just
# argument or variable definition V1={})
# E.g. parallel {}, parallel my_{= s/_//=}, parallel {2}
# Do no quote (Otherwise it will fail if the input contains spaces)
$Global::noquote = 1;
}
if($opt::sqlmaster and $Global::sql->append()) {
$seq = $Global::sql->max_seq() + 1;
}
return bless {
'unget' => \@unget,
'command' => \@command,
'replacecount' => $replacecount_ref,
'arg_queue' => RecordQueue->new($read_from,$opt::colsep),
'context_replace' => $context_replace,
'len' => $len_ref,
'max_number_of_args' => $max_number_of_args,
'size' => undef,
'transfer_files' => $transfer_files,
'return_files' => $return_files,
'seq' => $seq,
}, ref($class) || $class;
}
sub merge_rpl_parts($) {
# '{=' 'perlexpr' '=}' => '{= perlexpr =}'
# Input:
# @in = the @command as given by the user
# Uses:
# $Global::parensleft
# $Global::parensright
# Returns:
# @command with parts merged to keep {= and =} as one
my @in = @_;
my @out;
my $l = quotemeta($Global::parensleft);
my $r = quotemeta($Global::parensright);
while(@in) {
my $s = shift @in;
$_ = $s;
# Remove matching (right most) parens
while(s/(.*)$l.*?$r/$1/os) {}
if(/$l/o) {
# Missing right parens
while(@in) {
$s .= " ".shift @in;
$_ = $s;
while(s/(.*)$l.*?$r/$1/os) {}
if(not /$l/o) {
last;
}
}
}
push @out, $s;
}
return @out;
}
sub replacement_counts_and_lengths($$@) {
# Count the number of different replacement strings.
# Find the lengths of context for context groups and non-context
# groups.
# If no {} found in @command: add it to @command
#
# Input:
# \@transfer_files = array of filenames to transfer
# \@return_files = array of filenames to return
# @command = command template
# Output:
# \%replacecount, \%len, @command
my $transfer_files = shift;
my $return_files = shift;
my @command = @_;
my (%replacecount,%len);
my $sum = 0;
while($sum == 0) {
# Count how many times each replacement string is used
my @cmd = @command;
my $contextlen = 0;
my $noncontextlen = 0;
my $contextgroups = 0;
for my $c (@cmd) {
while($c =~ s/ \257<( (?: [^\257]*|[\257][^<>] )*?)\257> /\000/xs) {
# %replacecount = { "perlexpr" => number of times seen }
# e.g { "s/a/b/" => 2 }
$replacecount{$1}++;
$sum++;
}
# Measure the length of the context around the {= perl expr =}
# Use that {=...=} has been replaced with \000 above
# So there is no need to deal with \257<
while($c =~ s/ (\S*\000\S*) //xs) {
my $w = $1;
$w =~ tr/\000//d; # Remove all \000's
$contextlen += length($w);
$contextgroups++;
}
# All {= perl expr =} have been removed: The rest is non-context
$noncontextlen += length $c;
}
for(@$transfer_files, @$return_files,
$opt::tagstring, $opt::workdir, $opt::results, $opt::retries) {
# Options that can contain replacement strings
$_ or next;
my $t = $_;
while($t =~ s/ \257<( (?: [^\257]*|[\257][^<>] )* )\257> //xs) {
# %replacecount = { "perlexpr" => number of times seen }
# e.g { "$_++" => 2 }
# But for tagstring we just need to mark it as seen
$replacecount{$1} ||= 1;
}
}
if($opt::bar) {
# If the command does not contain {} force it to be computed
# as it is being used by --bar
$replacecount{""} ||= 1;
}
$len{'context'} = 0+$contextlen;
$len{'noncontext'} = $noncontextlen;
$len{'contextgroups'} = $contextgroups;
$len{'noncontextgroups'} = @cmd-$contextgroups;
::debug("length", "@command Context: ", $len{'context'},
" Non: ", $len{'noncontext'}, " Ctxgrp: ", $len{'contextgroups'},
" NonCtxGrp: ", $len{'noncontextgroups'}, "\n");
if($sum == 0) {
if(not @command) {
# Default command = {}
@command = ("\257<\257>");
} elsif(($opt::pipe or $opt::pipepart)
and not $opt::fifo and not $opt::cat) {
# With --pipe / --pipe-part you can have no replacement
last;
} else {
# Append {} to the command if there are no {...}'s and no {=...=}
push @command, ("\257<\257>");
}
}
}
return(\%replacecount,\%len,@command);
}
sub get($) {
my $self = shift;
if(@{$self->{'unget'}}) {
my $cmd_line = shift @{$self->{'unget'}};
return ($cmd_line);
} else {
if($opt::sqlworker) {
# Get the sequence number from the SQL table
$self->set_seq($SQL::next_seq);
# Get the command from the SQL table
$self->{'command'} = $SQL::command_ref;
my @command;
# Recompute replace counts based on the read command
($self->{'replacecount'},
$self->{'len'}, @command) =
replacement_counts_and_lengths($self->{'transfer_files'},
$self->{'return_files'},
@$SQL::command_ref);
if("@command" =~ /^[^ \t\n=]*\257</) {
# Replacement string is (part of) the command (and not just
# argument or variable definition V1={})
# E.g. parallel {}, parallel my_{= s/_//=}, parallel {2}
# Do no quote (Otherwise it will fail if the input contains spaces)
$Global::noquote = 1;
}
}
my $cmd_line = CommandLine->new($self->seq(),
$self->{'command'},
$self->{'arg_queue'},
$self->{'context_replace'},
$self->{'max_number_of_args'},
$self->{'transfer_files'},
$self->{'return_files'},
$self->{'replacecount'},
$self->{'len'},
);
$cmd_line->populate();
::debug("init","cmd_line->number_of_args ",
$cmd_line->number_of_args(), "\n");
if(not $Global::no_more_input and ($opt::pipe or $opt::pipepart)) {
if($cmd_line->replaced() eq "") {
# Empty command - pipe requires a command
::error("--pipe/--pipepart must have a command to pipe into ".
"(e.g. 'cat').");
::wait_and_exit(255);
}
} elsif($cmd_line->number_of_args() == 0) {
# We did not get more args - maybe at EOF string?
return undef;
}
$self->set_seq($self->seq()+1);
return $cmd_line;
}
}
sub unget($) {
my $self = shift;
unshift @{$self->{'unget'}}, @_;
}
sub empty($) {
my $self = shift;
my $empty = (not @{$self->{'unget'}}) &&
$self->{'arg_queue'}->empty();
::debug("run", "CommandLineQueue->empty $empty");
return $empty;
}
sub seq($) {
my $self = shift;
return $self->{'seq'};
}
sub set_seq($$) {
my $self = shift;
$self->{'seq'} = shift;
}
sub quote_args($) {
my $self = shift;
# If there is not command emulate |bash
return $self->{'command'};
}
package Limits::Command;
# Maximal command line length (for -m and -X)
sub max_length($) {
# Find the max_length of a command line and cache it
# Returns:
# number of chars on the longest command line allowed
if(not $Limits::Command::line_max_len) {
# Disk cache of max command line length
my $len_cache = $Global::cache_dir . "/tmp/sshlogin/" . ::hostname() .
"/linelen";
my $cached_limit;
if(-e $len_cache) {
open(my $fh, "<", $len_cache) || ::die_bug("Cannot read $len_cache");
$cached_limit = <$fh>;
close $fh;
} else {
$cached_limit = real_max_length();
# If $HOME is write protected: Do not fail
my $dir = ::dirname($len_cache);
-d $dir or eval { File::Path::mkpath($dir); };
open(my $fh, ">", $len_cache);
print $fh $cached_limit;
close $fh;
}
$Limits::Command::line_max_len = tmux_length($cached_limit);
if($opt::max_chars) {
if($opt::max_chars <= $cached_limit) {
$Limits::Command::line_max_len = $opt::max_chars;
} else {
::warning("Value for -s option should be < $cached_limit.");
}
}
}
return int($Limits::Command::line_max_len);
}
sub real_max_length($) {
# Find the max_length of a command line
# Returns:
# The maximal command line length
# Use an upper bound of 8 MB if the shell allows for infinite long lengths
my $upper = 8_000_000;
my $len = 8;
do {
if($len > $upper) { return $len };
$len *= 16;
} while (is_acceptable_command_line_length($len));
# Then search for the actual max length between 0 and upper bound
return binary_find_max_length(int($len/16),$len);
}
# Prototype forwarding
sub binary_find_max_length($$);
sub binary_find_max_length($$) {
# Given a lower and upper bound find the max_length of a command line
# Returns:
# number of chars on the longest command line allowed
my ($lower, $upper) = (@_);
if($lower == $upper or $lower == $upper-1) { return $lower; }
my $middle = int (($upper-$lower)/2 + $lower);
::debug("init", "Maxlen: $lower,$upper,$middle : ");
if (is_acceptable_command_line_length($middle)) {
return binary_find_max_length($middle,$upper);
} else {
return binary_find_max_length($lower,$middle);
}
}
sub is_acceptable_command_line_length($) {
# Test if a command line of this length can run
# in the current environment
# Returns:
# 0 if the command line length is too long
# 1 otherwise
my $len = shift;
if($Global::parallel_env) {
$len += length $Global::parallel_env;
}
::qqx("true "."x"x$len);
::debug("init", "$len=$? ");
return not $?;
}
sub tmux_length($) {
# If $opt::tmux set, find the limit for tmux
# tmux 1.8 has a 2kB limit
# tmux 1.9 has a 16kB limit
# tmux 2.0 has a 16kB limit
# tmux 2.1 has a 16kB limit
# tmux 2.2 has a 16kB limit
# Input:
# $len = maximal command line length
# Returns:
# $tmux_len = maximal length runable in tmux
local $/ = "\n";
my $len = shift;
if($opt::tmux) {
$ENV{'PARALLEL_TMUX'} ||= "tmux";
if(not ::which($ENV{'PARALLEL_TMUX'})) {
::error($ENV{'PARALLEL_TMUX'}." not found in \$PATH.");
::wait_and_exit(255);
}
my @out;
for my $l (1, 2020, 16320, 100000, $len) {
my $tmpfile = ::tmpname("tms");
my $tmuxcmd = $ENV{'PARALLEL_TMUX'}.
" -S $tmpfile new-session -d -n echo $l".
("x"x$l). " && echo $l; rm -f $tmpfile";
push @out, ::qqx($tmuxcmd);
::rm($tmpfile);
}
::debug("tmux","tmux-out ",@out);
chomp @out;
# The arguments is given 3 times on the command line
# and the wrapping is around 30 chars
# (29 for tmux1.9, 33 for tmux1.8)
my $tmux_len = ::max(@out);
$len = ::min($len,int($tmux_len/4-33));
::debug("tmux","tmux-length ",$len);
}
return $len;
}
package RecordQueue;
sub new($) {
my $class = shift;
my $fhs = shift;
my $colsep = shift;
my @unget = ();
my $arg_sub_queue;
if($opt::sqlworker) {
# Open SQL table
$arg_sub_queue = SQLRecordQueue->new();
} elsif(defined $colsep) {
# Open one file with colsep or CSV
$arg_sub_queue = RecordColQueue->new($fhs);
} else {
# Open one or more files if multiple -a
$arg_sub_queue = MultifileQueue->new($fhs);
}
return bless {
'unget' => \@unget,
'arg_number' => 0,
'arg_sub_queue' => $arg_sub_queue,
}, ref($class) || $class;
}
sub get($) {
# Returns:
# reference to array of Arg-objects
my $self = shift;
if(@{$self->{'unget'}}) {
$self->{'arg_number'}++;
# Flush cached computed replacements in Arg-objects
# To fix: parallel --bar echo {%} ::: a b c ::: d e f
my $ret = shift @{$self->{'unget'}};
if($ret) {
map { $_->flush_cache() } @$ret;
}
return $ret;
}
my $ret = $self->{'arg_sub_queue'}->get();
if($ret) {
if(grep { index($_->orig(),"\0") > 0 } @$ret) {
# Allow for \0 in position 0 because GNU Parallel uses "\0noarg"
# to mean no-string
::warning("A NUL character in the input was replaced with \\0.",
"NUL cannot be passed through in the argument list.",
"Did you mean to use the --null option?");
for(grep { index($_->orig(),"\0") > 0 } @$ret) {
# Replace \0 with \\0
my $a = $_->orig();
$a =~ s/\0/\\0/g;
$_->set_orig($a);
}
}
if(defined $Global::max_number_of_args
and $Global::max_number_of_args == 0) {
::debug("run", "Read 1 but return 0 args\n");
# \0noarg => nothing (not the empty string)
map { $_->set_orig("\0noarg"); } @$ret;
}
# Flush cached computed replacements in Arg-objects
# To fix: parallel --bar echo {%} ::: a b c ::: d e f
map { $_->flush_cache() } @$ret;
}
return $ret;
}
sub unget($) {
my $self = shift;
::debug("run", "RecordQueue-unget\n");
$self->{'arg_number'} -= @_;
unshift @{$self->{'unget'}}, @_;
}
sub empty($) {
my $self = shift;
my $empty = (not @{$self->{'unget'}}) &&
$self->{'arg_sub_queue'}->empty();
::debug("run", "RecordQueue->empty $empty");
return $empty;
}
sub arg_number($) {
my $self = shift;
return $self->{'arg_number'};
}
package RecordColQueue;
sub new($) {
my $class = shift;
my $fhs = shift;
my @unget = ();
my $arg_sub_queue = MultifileQueue->new($fhs);
return bless {
'unget' => \@unget,
'arg_sub_queue' => $arg_sub_queue,
}, ref($class) || $class;
}
sub get($) {
# Returns:
# reference to array of Arg-objects
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
my $unget_ref = $self->{'unget'};
if($self->{'arg_sub_queue'}->empty()) {
return undef;
}
my $in_record = $self->{'arg_sub_queue'}->get();
if(defined $in_record) {
my @out_record = ();
for my $arg (@$in_record) {
::debug("run", "RecordColQueue::arg $arg\n");
my $line = $arg->orig();
::debug("run", "line='$line'\n");
if($line ne "") {
if($opt::csv) {
# Parse CSV
chomp $line;
if(not $Global::csv->parse($line)) {
die "CSV has unexpected format: ^$line^";
}
for($Global::csv->fields()) {
push @out_record, Arg->new($_);
}
} else {
for my $s (split /$opt::colsep/o, $line, -1) {
push @out_record, Arg->new($s);
}
}
} else {
push @out_record, Arg->new("");
}
}
return \@out_record;
} else {
return undef;
}
}
sub unget($) {
my $self = shift;
::debug("run", "RecordColQueue-unget '@_'\n");
unshift @{$self->{'unget'}}, @_;
}
sub empty($) {
my $self = shift;
my $empty = (not @{$self->{'unget'}}) &&
$self->{'arg_sub_queue'}->empty();
::debug("run", "RecordColQueue->empty $empty");
return $empty;
}
package SQLRecordQueue;
sub new($) {
my $class = shift;
my @unget = ();
return bless {
'unget' => \@unget,
}, ref($class) || $class;
}
sub get($) {
# Returns:
# reference to array of Arg-objects
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
return $Global::sql->get_record();
}
sub unget($) {
my $self = shift;
::debug("run", "SQLRecordQueue-unget '@_'\n");
unshift @{$self->{'unget'}}, @_;
}
sub empty($) {
my $self = shift;
if(@{$self->{'unget'}}) { return 0; }
my $get = $self->get();
if(defined $get) {
$self->unget($get);
}
my $empty = not $get;
::debug("run", "SQLRecordQueue->empty $empty");
return $empty;
}
package MultifileQueue;
@Global::unget_argv=();
sub new($$) {
my $class = shift;
my $fhs = shift;
for my $fh (@$fhs) {
if(-t $fh and -t ($Global::status_fd || *STDERR)) {
::warning("Input is read from the terminal. You are either an expert",
"(in which case: YOU ARE AWESOME!) or maybe you forgot",
"::: or :::: or -a or to pipe data into parallel. If so",
"consider going through the tutorial: man parallel_tutorial",
"Press CTRL-D to exit.");
}
}
return bless {
'unget' => \@Global::unget_argv,
'fhs' => $fhs,
'arg_matrix' => undef,
}, ref($class) || $class;
}
sub get($) {
my $self = shift;
if($opt::link) {
return $self->link_get();
} else {
return $self->nest_get();
}
}
sub unget($) {
my $self = shift;
::debug("run", "MultifileQueue-unget '@_'\n");
unshift @{$self->{'unget'}}, @_;
}
sub empty($) {
my $self = shift;
my $empty = (not @Global::unget_argv) &&
not @{$self->{'unget'}};
for my $fh (@{$self->{'fhs'}}) {
$empty &&= eof($fh);
}
::debug("run", "MultifileQueue->empty $empty ");
return $empty;
}
sub link_get($) {
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
my @record = ();
my $prepend;
my $empty = 1;
for my $fh (@{$self->{'fhs'}}) {
my $arg = read_arg_from_fh($fh);
if(defined $arg) {
# Record $arg for recycling at end of file
push @{$self->{'arg_matrix'}{$fh}}, $arg;
push @record, $arg;
$empty = 0;
} else {
::debug("run", "EOA ");
# End of file: Recycle arguments
push @{$self->{'arg_matrix'}{$fh}}, shift @{$self->{'arg_matrix'}{$fh}};
# return last @{$args->{'args'}{$fh}};
push @record, @{$self->{'arg_matrix'}{$fh}}[-1];
}
}
if($empty) {
return undef;
} else {
return \@record;
}
}
sub nest_get($) {
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
my @record = ();
my $prepend;
my $empty = 1;
my $no_of_inputsources = $#{$self->{'fhs'}} + 1;
if(not $self->{'arg_matrix'}) {
# Initialize @arg_matrix with one arg from each file
# read one line from each file
my @first_arg_set;
my $all_empty = 1;
for (my $fhno = 0; $fhno < $no_of_inputsources ; $fhno++) {
my $arg = read_arg_from_fh($self->{'fhs'}[$fhno]);
if(defined $arg) {
$all_empty = 0;
}
$self->{'arg_matrix'}[$fhno][0] = $arg || Arg->new("");
push @first_arg_set, $self->{'arg_matrix'}[$fhno][0];
}
if($all_empty) {
# All filehandles were at eof or eof-string
return undef;
}
return [@first_arg_set];
}
# Treat the case with one input source special. For multiple
# input sources we need to remember all previously read values to
# generate all combinations. But for one input source we can
# forget the value after first use.
if($no_of_inputsources == 1) {
my $arg = read_arg_from_fh($self->{'fhs'}[0]);
if(defined($arg)) {
return [$arg];
}
return undef;
}
for (my $fhno = $no_of_inputsources - 1; $fhno >= 0; $fhno--) {
if(eof($self->{'fhs'}[$fhno])) {
next;
} else {
# read one
my $arg = read_arg_from_fh($self->{'fhs'}[$fhno]);
defined($arg) || next; # If we just read an EOF string: Treat this as EOF
my $len = $#{$self->{'arg_matrix'}[$fhno]} + 1;
$self->{'arg_matrix'}[$fhno][$len] = $arg;
# make all new combinations
my @combarg = ();
for (my $fhn = 0; $fhn < $no_of_inputsources; $fhn++) {
push(@combarg, [0, $#{$self->{'arg_matrix'}[$fhn]}],
# Is input source --link'ed to the next?
$opt::linkinputsource[$fhn+1]);
}
# Find only combinations with this new entry
$combarg[2*$fhno] = [$len,$len];
# map combinations
# [ 1, 3, 7 ], [ 2, 4, 1 ]
# =>
# [ m[0][1], m[1][3], m[2][7] ], [ m[0][2], m[1][4], m[2][1] ]
my @mapped;
for my $c (expand_combinations(@combarg)) {
my @a;
for my $n (0 .. $no_of_inputsources - 1 ) {
push @a, $self->{'arg_matrix'}[$n][$$c[$n]];
}
push @mapped, \@a;
}
# append the mapped to the ungotten arguments
push @{$self->{'unget'}}, @mapped;
# get the first
if(@mapped) {
return shift @{$self->{'unget'}};
}
}
}
# all are eof or at EOF string; return from the unget queue
return shift @{$self->{'unget'}};
}
sub read_arg_from_fh($) {
# Read one Arg from filehandle
# Returns:
# Arg-object with one read line
# undef if end of file
my $fh = shift;
my $prepend;
my $arg;
my $half_record = 0;
do {{
# This makes 10% faster
if(not defined ($arg = <$fh>)) {
if(defined $prepend) {
return Arg->new($prepend);
} else {
return undef;
}
}
if($opt::csv) {
# We need to read a full CSV line.
if(($arg =~ y/"/"/) % 2 ) {
# The number of " on the line is uneven:
# If we were in a half_record => we have a full record now
# If we were ouside a half_record => we are in a half record now
$half_record = not $half_record;
}
if($half_record) {
# CSV half-record with quoting:
# col1,"col2 2""x3"" board newline <-this one
# cont",col3
$prepend .= $arg;
redo;
} else {
# Now we have a full CSV record
}
}
# Remove delimiter
chomp $arg;
if($Global::end_of_file_string and
$arg eq $Global::end_of_file_string) {
# Ignore the rest of input file
close $fh;
::debug("run", "EOF-string ($arg) met\n");
if(defined $prepend) {
return Arg->new($prepend);
} else {
return undef;
}
}
if(defined $prepend) {
$arg = $prepend.$arg; # For line continuation
undef $prepend;
}
if($Global::ignore_empty) {
if($arg =~ /^\s*$/) {
redo; # Try the next line
}
}
if($Global::max_lines) {
if($arg =~ /\s$/) {
# Trailing space => continued on next line
$prepend = $arg;
redo;
}
}
}} while (1 == 0); # Dummy loop {{}} for redo
if(defined $arg) {
return Arg->new($arg);
} else {
::die_bug("multiread arg undefined");
}
}
# Prototype forwarding
sub expand_combinations(@);
sub expand_combinations(@) {
# Input:
# ([xmin,xmax], [ymin,ymax], ...)
# Returns: ([x,y,...],[x,y,...])
# where xmin <= x <= xmax and ymin <= y <= ymax
my $minmax_ref = shift;
my $link = shift; # This is linked to the next input source
my $xmin = $$minmax_ref[0];
my $xmax = $$minmax_ref[1];
my @p;
if(@_) {
my @rest = expand_combinations(@_);
if($link) {
# Linked to next col with --link/:::+/::::+
# TODO BUG does not wrap values if not same number of vals
push(@p, map { [$$_[0], @$_] }
grep { $xmin <= $$_[0] and $$_[0] <= $xmax } @rest);
} else {
# If there are more columns: Compute those recursively
for(my $x = $xmin; $x <= $xmax; $x++) {
push @p, map { [$x, @$_] } @rest;
}
}
} else {
for(my $x = $xmin; $x <= $xmax; $x++) {
push @p, [$x];
}
}
return @p;
}
package Arg;
sub new($) {
my $class = shift;
my $orig = shift;
my @hostgroups;
if($opt::hostgroups) {
if($orig =~ s:@(.+)::) {
# We found hostgroups on the arg
@hostgroups = split(/\+/, $1);
if(not grep { defined $Global::hostgroups{$_} } @hostgroups) {
# This hostgroup is not defined using -S
# Add it
::warning("Adding hostgroups: @hostgroups");
# Add sshlogin
for(grep { not defined $Global::hostgroups{$_} } @hostgroups) {
my $sshlogin = SSHLogin->new($_);
my $sshlogin_string = $sshlogin->string();
$Global::host{$sshlogin_string} = $sshlogin;
$Global::hostgroups{$sshlogin_string} = 1;
}
}
} else {
# No hostgroup on the arg => any hostgroup
@hostgroups = (keys %Global::hostgroups);
}
}
return bless {
'orig' => $orig,
'hostgroups' => \@hostgroups,
}, ref($class) || $class;
}
sub Q($) {
# Q alias for ::shell_quote_scalar
no warnings 'redefine';
*Q = \&::shell_quote_scalar;
return Q(@_);
}
sub pQ($) {
# pQ alias for ::perl_quote_scalar
*pQ = \&::perl_quote_scalar;
return pQ(@_);
}
sub total_jobs() {
return $Global::JobQueue->total_jobs();
}
{
my %perleval;
my $job;
sub skip() {
# shorthand for $job->skip();
$job->skip();
}
sub slot() {
# shorthand for $job->slot();
$job->slot();
}
sub seq() {
# shorthand for $job->seq();
$job->seq();
}
sub replace($$$$) {
# Calculates the corresponding value for a given perl expression
# Returns:
# The calculated string (quoted if asked for)
my $self = shift;
my $perlexpr = shift; # E.g. $_=$_ or s/.gz//
my $quote = (shift) ? 1 : 0; # should the string be quoted?
# This is actually a CommandLine-object,
# but it looks nice to be able to say {= $job->slot() =}
$job = shift;
$perlexpr =~ s/^(-?\d+)? *//; # Positional replace treated as normal replace
if(not $self->{'cache'}{$perlexpr}) {
# Only compute the value once
# Use $_ as the variable to change
local $_;
if($Global::trim eq "n") {
$_ = $self->{'orig'};
} else {
# Trim the input
$_ = trim_of($self->{'orig'});
}
::debug("replace", "eval ", $perlexpr, " ", $_, "\n");
if(not $perleval{$perlexpr}) {
# Make an anonymous function of the $perlexpr
# And more importantly: Compile it only once
if($perleval{$perlexpr} =
eval('sub { no strict; no warnings; my $job = shift; '.
$perlexpr.' }')) {
# All is good
} else {
# The eval failed. Maybe $perlexpr is invalid perl?
::error("Cannot use $perlexpr: $@");
::wait_and_exit(255);
}
}
# Execute the function
$perleval{$perlexpr}->($job);
$self->{'cache'}{$perlexpr} = $_;
}
# Return the value quoted if needed
return($quote ? Q($self->{'cache'}{$perlexpr})
: $self->{'cache'}{$perlexpr});
}
}
sub flush_cache($) {
# Flush cache of computed values
my $self = shift;
$self->{'cache'} = undef;
}
sub orig($) {
my $self = shift;
return $self->{'orig'};
}
sub set_orig($$) {
my $self = shift;
$self->{'orig'} = shift;
}
sub trim_of($) {
# Removes white space as specifed by --trim:
# n = nothing
# l = start
# r = end
# lr|rl = both
# Returns:
# string with white space removed as needed
my @strings = map { defined $_ ? $_ : "" } (@_);
my $arg;
if($Global::trim eq "n") {
# skip
} elsif($Global::trim eq "l") {
for my $arg (@strings) { $arg =~ s/^\s+//; }
} elsif($Global::trim eq "r") {
for my $arg (@strings) { $arg =~ s/\s+$//; }
} elsif($Global::trim eq "rl" or $Global::trim eq "lr") {
for my $arg (@strings) { $arg =~ s/^\s+//; $arg =~ s/\s+$//; }
} else {
::error("--trim must be one of: r l rl lr.");
::wait_and_exit(255);
}
return wantarray ? @strings : "@strings";
}
package TimeoutQueue;
sub new($) {
my $class = shift;
my $delta_time = shift;
my ($pct);
if($delta_time =~ /(\d+(\.\d+)?)%/) {
# Timeout in percent
$pct = $1/100;
$delta_time = 1_000_000;
}
$delta_time = ::multiply_time_units($delta_time);
return bless {
'queue' => [],
'delta_time' => $delta_time,
'pct' => $pct,
'remedian_idx' => 0,
'remedian_arr' => [],
'remedian' => undef,
}, ref($class) || $class;
}
sub delta_time($) {
my $self = shift;
return $self->{'delta_time'};
}
sub set_delta_time($$) {
my $self = shift;
$self->{'delta_time'} = shift;
}
sub remedian($) {
my $self = shift;
return $self->{'remedian'};
}
sub set_remedian($$) {
# Set median of the last 999^3 (=997002999) values using Remedian
#
# Rousseeuw, Peter J., and Gilbert W. Bassett Jr. "The remedian: A
# robust averaging method for large data sets." Journal of the
# American Statistical Association 85.409 (1990): 97-104.
my $self = shift;
my $val = shift;
my $i = $self->{'remedian_idx'}++;
my $rref = $self->{'remedian_arr'};
$rref->[0][$i%999] = $val;
$rref->[1][$i/999%999] = (sort @{$rref->[0]})[$#{$rref->[0]}/2];
$rref->[2][$i/999/999%999] = (sort @{$rref->[1]})[$#{$rref->[1]}/2];
$self->{'remedian'} = (sort @{$rref->[2]})[$#{$rref->[2]}/2];
}
sub update_median_runtime($) {
# Update delta_time based on runtime of finished job if timeout is
# a percentage
my $self = shift;
my $runtime = shift;
if($self->{'pct'}) {
$self->set_remedian($runtime);
$self->{'delta_time'} = $self->{'pct'} * $self->remedian();
::debug("run", "Timeout: $self->{'delta_time'}s ");
}
}
sub process_timeouts($) {
# Check if there was a timeout
my $self = shift;
# $self->{'queue'} is sorted by start time
while (@{$self->{'queue'}}) {
my $job = $self->{'queue'}[0];
if($job->endtime()) {
# Job already finished. No need to timeout the job
# This could be because of --keep-order
shift @{$self->{'queue'}};
} elsif($job->is_timedout($self->{'delta_time'})) {
# Need to shift off queue before kill
# because kill calls usleep that calls process_timeouts
shift @{$self->{'queue'}};
::warning("This job was killed because it timed out:",
$job->replaced());
$job->kill();
} else {
# Because they are sorted by start time the rest are later
last;
}
}
}
sub insert($) {
my $self = shift;
my $in = shift;
push @{$self->{'queue'}}, $in;
}
package SQL;
sub new($) {
my $class = shift;
my $dburl = shift;
$Global::use{"DBI"} ||= eval "use DBI; 1;";
# +DBURL = append to this DBURL
my $append = $dburl=~s/^\+//;
my %options = parse_dburl(get_alias($dburl));
my %driveralias = ("sqlite" => "SQLite",
"sqlite3" => "SQLite",
"pg" => "Pg",
"postgres" => "Pg",
"postgresql" => "Pg",
"csv" => "CSV",
"oracle" => "Oracle",
"ora" => "Oracle");
my $driver = $driveralias{$options{'databasedriver'}} ||
$options{'databasedriver'};
my $database = $options{'database'};
my $host = $options{'host'} ? ";host=".$options{'host'} : "";
my $port = $options{'port'} ? ";port=".$options{'port'} : "";
my $dsn = "DBI:$driver:dbname=$database$host$port";
my $userid = $options{'user'};
my $password = $options{'password'};;
my $dbh = DBI->connect($dsn, $userid, $password,
{ RaiseError => 1, AutoInactiveDestroy => 1 })
or die $DBI::errstr;
$dbh->{'PrintWarn'} = $Global::debug || 0;
$dbh->{'PrintError'} = $Global::debug || 0;
$dbh->{'RaiseError'} = 1;
$dbh->{'ShowErrorStatement'} = 1;
$dbh->{'HandleError'} = sub {};
if(not defined $options{'table'}) {
::error("The DBURL ($dburl) must contain a table.");
::wait_and_exit(255);
}
return bless {
'dbh' => $dbh,
'driver' => $driver,
'max_number_of_args' => undef,
'table' => $options{'table'},
'append' => $append,
}, ref($class) || $class;
}
# Prototype forwarding
sub get_alias($);
sub get_alias($) {
my $alias = shift;
$alias =~ s/^(sql:)*//; # Accept aliases prepended with sql:
if ($alias !~ /^:/) {
return $alias;
}
# Find the alias
my $path;
if (-l $0) {
($path) = readlink($0) =~ m|^(.*)/|;
} else {
($path) = $0 =~ m|^(.*)/|;
}
my @deprecated = ("$ENV{HOME}/.dburl.aliases",
"$path/dburl.aliases", "$path/dburl.aliases.dist");
for (@deprecated) {
if(-r $_) {
::warning("$_ is deprecated. ".
"Use .sql/aliases instead (read man sql).");
}
}
my @urlalias=();
check_permissions("$ENV{HOME}/.sql/aliases");
check_permissions("$ENV{HOME}/.dburl.aliases");
my @search = ("$ENV{HOME}/.sql/aliases",
"$ENV{HOME}/.dburl.aliases", "/etc/sql/aliases",
"$path/dburl.aliases", "$path/dburl.aliases.dist");
for my $alias_file (@search) {
# local $/ needed if -0 set
local $/ = "\n";
if(-r $alias_file) {
open(my $in, "<", $alias_file) || die;
push @urlalias, <$in>;
close $in;
}
}
my ($alias_part,$rest) = $alias=~/(:\w*)(.*)/;
# If we saw this before: we have an alias loop
if(grep {$_ eq $alias_part } @Private::seen_aliases) {
::error("$alias_part is a cyclic alias.");
exit -1;
} else {
push @Private::seen_aliases, $alias_part;
}
my $dburl;
for (@urlalias) {
/^$alias_part\s+(\S+.*)/ and do { $dburl = $1; last; }
}
if($dburl) {
return get_alias($dburl.$rest);
} else {
::error("$alias is not defined in @search");
exit(-1);
}
}
sub check_permissions($) {
my $file = shift;
if(-e $file) {
if(not -o $file) {
my $username = (getpwuid($<))[0];
::warning("$file should be owned by $username: ".
"chown $username $file");
}
my ($dev,$ino,$mode,$nlink,$uid,$gid,$rdev,$size,
$atime,$mtime,$ctime,$blksize,$blocks) = stat($file);
if($mode & 077) {
my $username = (getpwuid($<))[0];
::warning("$file should be only be readable by $username: ".
"chmod 600 $file");
}
}
}
sub parse_dburl($) {
my $url = shift;
my %options = ();
# sql:mysql://[[user][:password]@][host][:port]/[database[/table][?query]]
if($url=~m!^(?:sql:)? # You can prefix with 'sql:'
((?:oracle|ora|mysql|pg|postgres|postgresql)(?:s|ssl|)|
(?:sqlite|sqlite2|sqlite3|csv)):// # Databasedriver ($1)
(?:
([^:@/][^:@]*|) # Username ($2)
(?:
:([^@]*) # Password ($3)
)?
@)?
([^:/]*)? # Hostname ($4)
(?:
:
([^/]*)? # Port ($5)
)?
(?:
/
([^/?]*)? # Database ($6)
)?
(?:
/
([^?]*)? # Table ($7)
)?
(?:
\?
(.*)? # Query ($8)
)?
$!ix) {
$options{databasedriver} = ::undef_if_empty(lc(uri_unescape($1)));
$options{user} = ::undef_if_empty(uri_unescape($2));
$options{password} = ::undef_if_empty(uri_unescape($3));
$options{host} = ::undef_if_empty(uri_unescape($4));
$options{port} = ::undef_if_empty(uri_unescape($5));
$options{database} = ::undef_if_empty(uri_unescape($6));
$options{table} = ::undef_if_empty(uri_unescape($7));
$options{query} = ::undef_if_empty(uri_unescape($8));
::debug("sql", "dburl $url\n");
::debug("sql", "databasedriver ", $options{databasedriver},
" user ", $options{user},
" password ", $options{password}, " host ", $options{host},
" port ", $options{port}, " database ", $options{database},
" table ", $options{table}, " query ", $options{query}, "\n");
} else {
::error("$url is not a valid DBURL");
exit 255;
}
return %options;
}
sub uri_unescape($) {
# Copied from http://cpansearch.perl.org/src/GAAS/URI-1.55/URI/Escape.pm
# to avoid depending on URI::Escape
# This section is (C) Gisle Aas.
# Note from RFC1630: "Sequences which start with a percent sign
# but are not followed by two hexadecimal characters are reserved
# for future extension"
my $str = shift;
if (@_ && wantarray) {
# not executed for the common case of a single argument
my @str = ($str, @_); # need to copy
foreach (@str) {
s/%([0-9A-Fa-f]{2})/chr(hex($1))/eg;
}
return @str;
}
$str =~ s/%([0-9A-Fa-f]{2})/chr(hex($1))/eg if defined $str;
$str;
}
sub run($) {
my $self = shift;
my $stmt = shift;
if($self->{'driver'} eq "CSV") {
$stmt=~ s/;$//;
if($stmt eq "BEGIN" or
$stmt eq "COMMIT") {
return undef;
}
}
my @retval;
my $dbh = $self->{'dbh'};
::debug("sql","$opt::sqlmaster$opt::sqlworker run $stmt\n");
# Execute with the rest of the args - if any
my $rv;
my $sth;
my $lockretry = 0;
while($lockretry < 10) {
$sth = $dbh->prepare($stmt);
if($sth
and
eval { $rv = $sth->execute(@_) }) {
last;
} else {
if($@ =~ /no such table|Table .* doesn.t exist|relation ".*" does not exist/
or
$DBI::errstr =~ /no such table|Table .* doesn.t exist|relation ".*" does not exist/) {
# This is fine:
# It is just a worker that reported back too late -
# another worker had finished the job first
# and the table was then dropped
$rv = $sth = 0;
last;
}
if($DBI::errstr =~ /locked/) {
::debug("sql", "Lock retry: $lockretry");
$lockretry++;
::usleep(rand()*300);
} elsif(not $sth) {
# Try again
$lockretry++;
} else {
::error($DBI::errstr);
::wait_and_exit(255);
}
}
}
if($lockretry >= 10) {
::die_bug("retry > 10: $DBI::errstr");
}
if($rv < 0 and $DBI::errstr){
::error($DBI::errstr);
::wait_and_exit(255);
}
return $sth;
}
sub get($) {
my $self = shift;
my $sth = $self->run(@_);
my @retval;
# If $sth = 0 it means the table was dropped by another process
while($sth) {
my @row = $sth->fetchrow_array();
@row or last;
push @retval, \@row;
}
return \@retval;
}
sub table($) {
my $self = shift;
return $self->{'table'};
}
sub append($) {
my $self = shift;
return $self->{'append'};
}
sub update($) {
my $self = shift;
my $stmt = shift;
my $table = $self->table();
$self->run("UPDATE $table $stmt",@_);
}
sub output($) {
my $self = shift;
my $commandline = shift;
$self->update("SET Stdout = ?, Stderr = ? WHERE Seq = ".
$commandline->seq(),
join("",@{$commandline->{'output'}{1}}),
join("",@{$commandline->{'output'}{2}}));
}
sub max_number_of_args($) {
# Maximal number of args for this table
my $self = shift;
if(not $self->{'max_number_of_args'}) {
# Read the number of args from the SQL table
my $table = $self->table();
my $v = $self->get("SELECT * FROM $table LIMIT 1;");
my @reserved_columns = qw(Seq Host Starttime JobRuntime Send
Receive Exitval _Signal Command Stdout Stderr);
if(not $v) {
::error("$table contains no records");
}
# Count the number of Vx columns
$self->{'max_number_of_args'} = $#{$v->[0]} - $#reserved_columns;
}
return $self->{'max_number_of_args'};
}
sub set_max_number_of_args($$) {
my $self = shift;
$self->{'max_number_of_args'} = shift;
}
sub create_table($) {
my $self = shift;
if($self->append()) { return; }
my $max_number_of_args = shift;
$self->set_max_number_of_args($max_number_of_args);
my $table = $self->table();
$self->run(qq(DROP TABLE IF EXISTS $table;));
# BIGINT and TEXT are not supported in these databases or are too small
my %vartype = (
"Oracle" => { "BIGINT" => "NUMBER(19,0)",
"TEXT" => "CLOB", },
"mysql" => { "TEXT" => "LONGTEXT", },
"CSV" => { "BIGINT" => "INT",
"FLOAT" => "REAL", },
);
my $BIGINT = $vartype{$self->{'driver'}}{"BIGINT"} || "BIGINT";
my $TEXT = $vartype{$self->{'driver'}}{"TEXT"} || "TEXT";
my $FLOAT = $vartype{$self->{'driver'}}{"FLOAT"} || "FLOAT(44)";
my $v_def = join "", map { "V$_ $TEXT," } (1..$self->max_number_of_args());
$self->run(qq{CREATE TABLE $table
(Seq $BIGINT,
Host $TEXT,
Starttime $FLOAT,
JobRuntime $FLOAT,
Send $BIGINT,
Receive $BIGINT,
Exitval $BIGINT,
_Signal $BIGINT,
Command $TEXT,}.
$v_def.
qq{Stdout $TEXT,
Stderr $TEXT);});
}
sub insert_records($) {
my $self = shift;
my $seq = shift;
my $command_ref = shift;
my $record_ref = shift;
my $table = $self->table();
# For SQL encode the command with \257 space as split points
my $command = join("\257 ",@$command_ref);
my @v_cols = map { ", V$_" } (1..$self->max_number_of_args());
# Two extra value due to $seq, Exitval, Send
my $v_vals = join ",", map { "?" } (1..$self->max_number_of_args()+4);
$self->run("INSERT INTO $table (Seq,Command,Exitval,Send @v_cols) ".
"VALUES ($v_vals);", $seq, $command, -1000,
0, @$record_ref[1..$#$record_ref]);
}
sub get_record($) {
my $self = shift;
my @retval;
my $table = $self->table();
my @v_cols = map { ", V$_" } (1..$self->max_number_of_args());
my $v = $self->get("SELECT Seq, Command @v_cols FROM $table ".
"WHERE Exitval = -1000 ORDER BY Seq LIMIT 1;");
if($v->[0]) {
my $val_ref = $v->[0];
# Mark record as taken
my $seq = shift @$val_ref;
# Save the sequence number to use when running the job
$SQL::next_seq = $seq;
$self->update("SET Exitval = ? WHERE Seq = ".$seq, -1220);
my @command = split /\257 /, shift @$val_ref;
$SQL::command_ref = \@command;
for (@$val_ref) {
push @retval, Arg->new($_);
}
}
if(@retval) {
return \@retval;
} else {
return undef;
}
}
sub total_jobs($) {
my $self = shift;
my $table = $self->table();
my $v = $self->get("SELECT count(*) FROM $table;");
if($v->[0]) {
return $v->[0]->[0];
} else {
::die_bug("SQL::total_jobs");
}
}
sub max_seq($) {
my $self = shift;
my $table = $self->table();
my $v = $self->get("SELECT max(Seq) FROM $table;");
if($v->[0]) {
return $v->[0]->[0];
} else {
::die_bug("SQL::max_seq");
}
}
sub finished($) {
# Check if there are any jobs left in the SQL table that do not
# have a "real" exitval
my $self = shift;
if($opt::wait or $Global::start_sqlworker) {
my $table = $self->table();
my $rv = $self->get("select Seq,Exitval from $table ".
"where Exitval <= -1000 limit 1");
return not $rv->[0];
} else {
return 1;
}
}
package Semaphore;
# This package provides a counting semaphore
#
# If a process dies without releasing the semaphore the next process
# that needs that entry will clean up dead semaphores
#
# The semaphores are stored in $PARALLEL_HOME/semaphores/id-<name> Each
# file in $PARALLEL_HOME/semaphores/id-<name>/ is the process ID of the
# process holding the entry. If the process dies, the entry can be
# taken by another process.
sub new($) {
my $class = shift;
my $id = shift;
my $count = shift;
$id =~ s/([^-_a-z0-9])/unpack("H*",$1)/ige; # Convert non-word chars to hex
$id = "id-".$id; # To distinguish it from a process id
my $parallel_locks = $Global::cache_dir . "/semaphores";
-d $parallel_locks or ::mkdir_or_die($parallel_locks);
my $lockdir = "$parallel_locks/$id";
my $lockfile = $lockdir.".lock";
if($count < 1) { ::die_bug("semaphore-count: $count"); }
return bless {
'lockfile' => $lockfile,
'lockfh' => Symbol::gensym(),
'lockdir' => $lockdir,
'id' => $id,
'idfile' => $lockdir."/".$id,
'pid' => $$,
'pidfile' => $lockdir."/".$$.'@'.::hostname(),
'count' => $count + 1 # nlinks returns a link for the 'id-' as well
}, ref($class) || $class;
}
sub remove_dead_locks($) {
my $self = shift;
my $lockdir = $self->{'lockdir'};
for my $d (glob "$lockdir/*") {
$d =~ m:$lockdir/([0-9]+)\@([-\._a-z0-9]+)$:o or next;
my ($pid, $host) = ($1, $2);
if($host eq ::hostname()) {
if(kill 0, $pid) {
::debug("sem", "Alive: $pid $d\n");
} else {
::debug("sem", "Dead: $d\n");
::rm($d);
}
}
}
}
sub acquire($) {
my $self = shift;
my $sleep = 1; # 1 ms
my $start_time = time;
while(1) {
# Can we get a lock?
$self->atomic_link_if_count_less_than() and last;
$self->remove_dead_locks();
# Retry slower and slower up to 1 second
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep);
# Random to avoid every sleeping job waking up at the same time
::usleep(rand()*$sleep);
if($opt::semaphoretimeout) {
if($opt::semaphoretimeout > 0
and
time - $start_time > $opt::semaphoretimeout) {
# Timeout: Take the semaphore anyway
::warning("Semaphore timed out. Stealing the semaphore.");
if(not -e $self->{'idfile'}) {
open (my $fh, ">", $self->{'idfile'}) or
::die_bug("timeout_write_idfile: $self->{'idfile'}");
close $fh;
}
link $self->{'idfile'}, $self->{'pidfile'};
last;
}
if($opt::semaphoretimeout < 0
and
time - $start_time > -$opt::semaphoretimeout) {
# Timeout: Exit
::warning("Semaphore timed out. Exiting.");
exit(1);
last;
}
}
}
::debug("sem", "acquired $self->{'pid'}\n");
}
sub release($) {
my $self = shift;
::rm($self->{'pidfile'});
if($self->nlinks() == 1) {
# This is the last link, so atomic cleanup
$self->lock();
if($self->nlinks() == 1) {
::rm($self->{'idfile'});
rmdir $self->{'lockdir'};
}
$self->unlock();
}
::debug("run", "released $self->{'pid'}\n");
}
sub pid_change($) {
# This should do what release()+acquire() would do without having
# to re-acquire the semaphore
my $self = shift;
my $old_pidfile = $self->{'pidfile'};
$self->{'pid'} = $$;
$self->{'pidfile'} = $self->{'lockdir'}."/".$$.'@'.::hostname();
my $retval = link $self->{'idfile'}, $self->{'pidfile'};
::debug("sem","link($self->{'idfile'},$self->{'pidfile'})=$retval\n");
::rm($old_pidfile);
}
sub atomic_link_if_count_less_than($) {
# Link $file1 to $file2 if nlinks to $file1 < $count
my $self = shift;
my $retval = 0;
$self->lock();
my $nlinks = $self->nlinks();
::debug("sem","$nlinks<$self->{'count'} ");
if($nlinks < $self->{'count'}) {
-d $self->{'lockdir'} or ::mkdir_or_die($self->{'lockdir'});
if(not -e $self->{'idfile'}) {
open (my $fh, ">", $self->{'idfile'}) or
::die_bug("write_idfile: $self->{'idfile'}");
close $fh;
}
$retval = link $self->{'idfile'}, $self->{'pidfile'};
::debug("sem","link($self->{'idfile'},$self->{'pidfile'})=$retval\n");
}
$self->unlock();
::debug("sem", "atomic $retval");
return $retval;
}
sub nlinks($) {
my $self = shift;
if(-e $self->{'idfile'}) {
return (stat(_))[3];
} else {
return 0;
}
}
sub lock($) {
my $self = shift;
my $sleep = 100; # 100 ms
my $total_sleep = 0;
$Global::use{"Fcntl"} ||= eval "use Fcntl qw(:DEFAULT :flock); 1;";
my $locked = 0;
while(not $locked) {
if(tell($self->{'lockfh'}) == -1) {
# File not open
open($self->{'lockfh'}, ">", $self->{'lockfile'})
or ::debug("run", "Cannot open $self->{'lockfile'}");
}
if($self->{'lockfh'}) {
# File is open
chmod 0666, $self->{'lockfile'}; # assuming you want it a+rw
if(flock($self->{'lockfh'}, LOCK_EX()|LOCK_NB())) {
# The file is locked: No need to retry
$locked = 1;
last;
} else {
if ($! =~ m/Function not implemented/) {
::warning("flock: $!",
"Will wait for a random while.");
::usleep(rand(5000));
# File cannot be locked: No need to retry
$locked = 2;
last;
}
}
}
# Locking failed in first round
# Sleep and try again
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep);
# Random to avoid every sleeping job waking up at the same time
::usleep(rand()*$sleep);
$total_sleep += $sleep;
if($opt::semaphoretimeout) {
if($opt::semaphoretimeout > 0
and
$total_sleep/1000 > $opt::semaphoretimeout) {
# Timeout: Take the semaphore anyway
::warning("Semaphore timed out. Taking the semaphore.");
$locked = 3;
last;
}
if($opt::semaphoretimeout < 0
and
$total_sleep/1000 > -$opt::semaphoretimeout) {
# Timeout: Exit
::warning("Semaphore timed out. Exiting.");
$locked = 4;
last;
}
} else {
if($total_sleep/1000 > 30) {
::warning("Semaphore stuck for 30 seconds. ".
"Consider using --semaphoretimeout.");
}
}
}
::debug("run", "locked $self->{'lockfile'}");
}
sub unlock($) {
my $self = shift;
::rm($self->{'lockfile'});
close $self->{'lockfh'};
::debug("run", "unlocked\n");
}
# Keep perl -w happy
$opt::x = $Semaphore::timeout = $Semaphore::wait =
$Job::file_descriptor_warning_printed = $Global::envdef = @Arg::arg =
$Global::max_slot_number = $opt::session;
package main;
sub main() {
save_stdin_stdout_stderr();
save_original_signal_handler();
parse_options();
::debug("init", "Open file descriptors: ", join(" ",keys %Global::fd), "\n");
my $number_of_args;
if($Global::max_number_of_args) {
$number_of_args = $Global::max_number_of_args;
} elsif ($opt::X or $opt::m or $opt::xargs) {
$number_of_args = undef;
} else {
$number_of_args = 1;
}
my @command = @ARGV;
my @input_source_fh;
if($opt::pipepart) {
if($opt::tee) {
@input_source_fh = map { open_or_exit($_) } @opt::a;
# Remove the first: It will be the file piped.
shift @input_source_fh;
if(not @input_source_fh and not $opt::pipe) {
@input_source_fh = (*STDIN);
}
} else {
# -a is used for data - not for command line args
@input_source_fh = map { open_or_exit($_) } "/dev/null";
}
} else {
@input_source_fh = map { open_or_exit($_) } @opt::a;
if(not @input_source_fh and not $opt::pipe) {
@input_source_fh = (*STDIN);
}
}
if($opt::sqlmaster) {
# Create SQL table to hold joblog + output
$Global::sql->create_table($#input_source_fh+1);
if($opt::sqlworker) {
# Start a real --sqlworker in the background later
$Global::start_sqlworker = 1;
$opt::sqlworker = undef;
}
}
if($opt::skip_first_line) {
# Skip the first line for the first file handle
my $fh = $input_source_fh[0];
<$fh>;
}
set_input_source_header(\@command,\@input_source_fh);
if($opt::filter_hosts and (@opt::sshlogin or @opt::sshloginfile)) {
# Parallel check all hosts are up. Remove hosts that are down
filter_hosts();
}
if($opt::nonall or $opt::onall) {
onall(\@input_source_fh,@command);
wait_and_exit(min(undef_as_zero($Global::exitstatus),254));
}
$Global::JobQueue = JobQueue->new(
\@command,\@input_source_fh,$Global::ContextReplace,
$number_of_args,\@Global::transfer_files,\@Global::ret_files);
if($opt::pipepart) {
pipepart_setup();
} elsif($opt::pipe and $opt::tee) {
pipe_tee_setup();
} elsif($opt::pipe and $opt::shard) {
pipe_shard_setup();
}
if($opt::eta or $opt::bar or $opt::shuf or $Global::halt_pct) {
# Count the number of jobs or shuffle all jobs
# before starting any.
# Must be done after ungetting any --pipepart jobs.
$Global::JobQueue->total_jobs();
}
# Compute $Global::max_jobs_running
# Must be done after ungetting any --pipepart jobs.
max_jobs_running();
init_run_jobs();
my $sem;
if($Global::semaphore) {
$sem = acquire_semaphore();
}
$SIG{TERM} = $Global::original_sig{TERM};
$SIG{HUP} = \&start_no_new_jobs;
if($opt::tee or $opt::shard) {
# All jobs must be running in parallel for --tee/--shard
while(start_more_jobs()) {}
$Global::start_no_new_jobs = 1;
if(not $Global::JobQueue->empty()) {
::error("--tee requres --jobs to be higher. Try --jobs 0.");
::wait_and_exit(255);
}
} elsif($opt::pipe and not $opt::pipepart) {
# Fill all jobslots
while(start_more_jobs()) {}
spreadstdin();
} else {
# Reap one - start one
while(reaper() + start_more_jobs()) {}
}
::debug("init", "Start draining\n");
drain_job_queue(@command);
::debug("init", "Done draining\n");
reapers();
::debug("init", "Done reaping\n");
if($Global::semaphore) {
$sem->release();
}
cleanup();
::debug("init", "Halt\n");
halt();
}
main();
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