#!/usr/bin/perl -w
# Copyright (C) 2007,2008,2009,2010,2011,2012 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
# 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);
# GetOptions used in get_options_from_array
use Getopt::Long;
# Used to ensure code quality
use strict;
$::oodebug=0;
$SIG{TERM} ||= sub { exit 0; }; # $SIG{TERM} is not set on Mac OS X
if(not $ENV{SHELL}) {
# $ENV{SHELL} is sometimes not set on Mac OS X
print STDERR ("parallel: Warning: \$SHELL not set. Using /bin/sh\n");
$ENV{SHELL} = "/bin/sh";
}
%Global::original_sig = %SIG;
$SIG{TERM} = sub {}; # Dummy until jobs really start
open $Global::original_stderr, ">&STDERR" or ::die_bug("Can't dup STDERR: $!");
parse_options();
my $number_of_args;
if($Global::max_number_of_args) {
$number_of_args=$Global::max_number_of_args;
} elsif ($::opt_X or $::opt_m) {
$number_of_args = undef;
} else {
$number_of_args = 1;
}
my $command = "";
if(@ARGV) {
if($Global::quoting) {
$command = shell_quote(@ARGV);
} else {
$command = join(" ", @ARGV);
}
}
my @fhlist;
@fhlist = map { open_or_exit($_) } @::opt_a;
if(not @fhlist) {
@fhlist = (*STDIN);
}
if($::opt_skip_first_line) {
# Skip the first line for the first file handle
my $fh = $fhlist[0];
<$fh>;
}
if($::opt_header and not $::opt_pipe) {
my $fh = $fhlist[0];
# split with colsep or \t
# TODO should $header force $colsep = \t if undef?
my $delimiter = $::opt_colsep;
my $id = 1;
for my $fh (@fhlist) {
my $line = <$fh>;
chomp($line);
::debug("Delimiter: '$delimiter'");
for my $s (split /$delimiter/o, $line) {
::debug("Colname: '$s'");
$command =~ s:\{$s(|/|//|\.|/\.)\}:\{$id$1\}:g;
$id++;
}
}
}
if($::opt_nonall or $::opt_onall) {
# Copy all @fhlist into tempfiles
my @argfiles = ();
for my $fh (@fhlist) {
my ($outfh,$name) = ::tempfile(SUFFIX => ".all");
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_P) ? "-P $::opt_P" : ""),
((defined $::opt_u) ? "-u" : ""),
((defined $::opt_group) ? "-g" : ""),
((defined $::opt_D) ? "-D" : ""),
);
my $suboptions =
join(" ",
((defined $::opt_u) ? "-u" : ""),
((defined $::opt_group) ? "-g" : ""),
((defined $::opt_colsep) ? "--colsep ".shell_quote($::opt_colsep) : ""),
((defined @::opt_v) ? "-vv" : ""),
((defined $::opt_D) ? "-D" : ""),
((defined $::opt_timeout) ? "--timeout ".$::opt_timeout : ""),
);
::debug("| parallel");
open(PARALLEL,"| $0 $options") ||
::die_bug("This does not run GNU Parallel: $0 $options");
for my $sshlogin (values %Global::host) {
print PARALLEL "$0 $suboptions -j1 ".
((defined $::opt_tag) ?
"--tagstring ".shell_quote_scalar($sshlogin->string()) : "").
" -S ". shell_quote_scalar($sshlogin->string())." ".
shell_quote_scalar($command)." :::: @argfiles\n";
}
close PARALLEL;
$Global::exitstatus = $? >> 8;
debug("--onall exitvalue ",$?);
if(@::opt_basefile) { cleanup_basefile(); }
unlink(@argfiles);
wait_and_exit(min(undef_as_zero($Global::exitstatus),254));
}
$Global::JobQueue = JobQueue->new(
$command,\@fhlist,$Global::ContextReplace,$number_of_args,\@Global::ret_files);
if($::opt_eta) {
# Count the number of jobs before starting any
$Global::JobQueue->total_jobs();
}
for my $sshlogin (values %Global::host) {
$sshlogin->max_jobs_running();
}
init_run_jobs();
my $sem;
if($Global::semaphore) {
$sem = acquire_semaphore();
}
$SIG{TERM} = \&start_no_new_jobs;
start_more_jobs();
if($::opt_pipe) {
spreadstdin(@fhlist);
}
::debug("Start draining\n");
drain_job_queue();
::debug("Done draining\n");
reaper();
cleanup();
if($Global::semaphore) {
$sem->release();
}
if($::opt_halt_on_error) {
wait_and_exit($Global::halt_on_error_exitstatus);
} else {
wait_and_exit(min(undef_as_zero($Global::exitstatus),254));
}
sub __PIPE_MODE__ {}
sub spreadstdin {
# read a record
# Spawn a job and print the record to it.
my @fhlist = @_; # Filehandles to read from (Defaults to STDIN)
my $record;
my $buf = "";
my $header = "";
if($::opt_header) {
my $non_greedy_regexp = $::opt_header;
# ? , * , + , {} => ?? , *? , +? , {}?
$non_greedy_regexp =~ s/(\?|\*|\+|\})/$1\?/g;
while(read(STDIN,substr($buf,length $buf,0),$::opt_blocksize)) {
if($buf=~s/^(.*?$non_greedy_regexp)//) {
$header = $1; last;
}
}
}
my ($recstart,$recend,$recerror);
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;
$recerror = "parallel: Warning: --recend and --recstart unmatched. Is --blocksize too small?";
} elsif(defined($::opt_recstart)) {
# If --recstart is given it must match start of record
$recstart = $::opt_recstart;
$recend = "";
$recerror = "parallel: Warning: --recstart unmatched. Is --blocksize too small?";
} elsif(defined($::opt_recend)) {
# If --recend is given then it must match end of record
$recstart = "";
$recend = $::opt_recend;
$recerror = "parallel: Warning: --recend unmatched. Is --blocksize too small?";
}
if($::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/\\([rnt'"\\])/"qq|\\$1|"/gee;
$recend =~ s/\\([rnt'"\\])/"qq|\\$1|"/gee;
}
my $recendrecstart = $recend.$recstart;
# Force the while-loop once if everything was read by header reading
my $force_one_time_through = 0;
for my $in (@fhlist) {
while(!$force_one_time_through++ or read($in,substr($buf,length $buf,0),$::opt_blocksize)) {
# substr above = append to $buf
if($::opt_r) {
# Remove empty lines
$buf=~s/^\s*\n//gm;
if(length $buf == 0) {
next;
}
}
if($::opt_regexp) {
if($Global::max_number_of_args) {
# -N => (start..*?end){n}
while($buf =~ s/((?:$recstart.*?$recend){$Global::max_number_of_args})($recstart.*)$/$2/os) {
$record = $header.$1;
::debug("Read record -N: ".length($record)."\n");
write_record_to_pipe(\$record,$recstart,$recend);
}
} else {
# Find the last recend-recstart in $buf
if($buf =~ s/(.*$recend)($recstart.*?)$/$2/os) {
$record = $header.$1;
::debug("Matched record: ".length($record)."/".length($buf)."\n");
write_record_to_pipe(\$record,$recstart,$recend);
}
}
} else {
if($Global::max_number_of_args) {
# -N => (start..*?end){n}
my $i = 0;
while(($i = nindex(\$buf,$recendrecstart,$Global::max_number_of_args)) != -1) {
$i += length $recend; # find the actual splitting location
my $record = $header.substr($buf,0,$i);
substr($buf,0,$i) = "";
::debug("Read record: ".length($record)."\n");
write_record_to_pipe(\$record,$recstart,$recend);
}
} else {
# Find the last recend-recstart in $buf
my $i = rindex($buf,$recendrecstart);
if($i != -1) {
$i += length $recend; # find the actual splitting location
my $record = $header.substr($buf,0,$i);
substr($buf,0,$i) = "";
# ::debug("Read record: ".length($record)."\n");
write_record_to_pipe(\$record,$recstart,$recend);
}
}
}
}
}
# If there is anything left in the buffer write it
substr($buf,0,0) = $header;
write_record_to_pipe(\$buf,$recstart,$recend);
::debug("Done reading input\n");
flush_and_close_pipes();
::debug("Done flushing to children\n");
$Global::start_no_new_jobs = 1;
}
sub nindex {
# See if string is in buffer N times
# Returns:
# the position where the Nth copy is found
my $buf_ref = shift;
my $str = shift;
my $n = shift;
my $i = 0;
for(1..$n) {
$i = index($$buf_ref,$str,$i+1);
if($i == -1) { last }
}
return $i;
}
sub flush_and_close_pipes {
# Flush that that is cached to the open pipes
# and close them.
my $flush_done;
my $sleep = 0.05;
do {
$flush_done = 1;
# Make sure everything is written to the jobs
for my $job (values %Global::running) {
if($job->remaining()) {
if($job->complete_write()) {
# Some data was written - reset sleep timer
$sleep = 0.05;
}
$flush_done = 0;
}
}
$sleep = ::reap_usleep($sleep);
} while (not $flush_done);
for my $job (values %Global::running) {
my $fh = $job->stdin();
close $fh;
}
}
sub write_record_to_pipe {
my $record_ref = shift;
my $recstart = shift;
my $recend = shift;
if(length $$record_ref == 0) { return; }
if($::opt_remove_rec_sep) {
# Remove record separator
$$record_ref =~ s/$recend$recstart//gos;
$$record_ref =~ s/^$recstart//os;
$$record_ref =~ s/$recend$//os;
}
# Keep the pipes hot, but if nothing happens sleep should back off
my $sleep = 0.00001; # 0.00001 ms - better performance on highend
write_record: while(1) {
# Sorting according to sequence is necessary for -k to work
for my $job (sort { $a->seq() <=> $b->seq() } values %Global::running) {
::debug("Looking at ",$job->seq(),"-",$job->remaining(),"-",$job->datawritten(),"\n");
if($job->remaining()) {
# Part of the job's last record has not finished being written
if($job->complete_write()) {
# Something got written - reset sleep timer
$sleep = 0.00001;
}
} else {
if($job->datawritten() > 0) {
# There is no data remaining and we have written data before:
# So this means we have completed writing a block.
# close stdin
# This will cause the job to finish and when it dies we will spawn another job
my $fh = $job->stdin();
close $fh;
} else {
$job->write($record_ref);
# Something got written - reset sleep timer
$sleep = 0.00001;
last write_record;
}
}
}
# Maybe this should be in an if statement: if sleep > 0.001: start more
start_more_jobs(); # These jobs may not be started because of loadavg
$sleep = ::reap_usleep($sleep);
}
return;
}
sub __SEM_MODE__ {}
sub acquire_semaphore {
# Acquires semaphore. If needed: spawns to the background
# 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());
$sem->acquire();
debug("run");
if($Semaphore::fg) {
# skip
} else {
# If run in the background, the PID will change
# therefore release and re-acquire the semaphore
$sem->release();
if(fork()) {
exit(0);
} else {
# child
# Get a semaphore for this pid
::die_bug("Can't start a new session: $!") if setsid() == -1;
$sem = Semaphore->new($Semaphore::name,$Global::host{':'}->max_jobs_running());
$sem->acquire();
}
}
return $sem;
}
sub __PARSE_OPTIONS__ {}
sub options_hash {
# Returns a hash of the GetOptions config
return
("debug|D" => \$::opt_D,
"xargs" => \$::opt_xargs,
"m" => \$::opt_m,
"X" => \$::opt_X,
"v" => \@::opt_v,
"joblog=s" => \$::opt_joblog,
"resume" => \$::opt_resume,
"silent" => \$::opt_silent,
#"silent-error|silenterror" => \$::opt_silent_error,
"keep-order|keeporder|k" => \$::opt_k,
"group" => \$::opt_group,
"g" => \$::opt_retired,
"ungroup|u" => \$::opt_u,
"null|0" => \$::opt_0,
"quote|q" => \$::opt_q,
"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,
"jobs|j=s" => \$::opt_P,
"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-cores" => \$::opt_number_of_cores,
"use-cpus-instead-of-cores" => \$::opt_use_cpus_instead_of_cores,
"shellquote|shell_quote|shell-quote" => \$::opt_shellquote,
"nice=i" => \$::opt_nice,
"timeout=i" => \$::opt_timeout,
"tag" => \$::opt_tag,
"tagstring=s" => \$::opt_tagstring,
"onall" => \$::opt_onall,
"nonall" => \$::opt_nonall,
"sshlogin|S=s" => \@::opt_sshlogin,
"sshloginfile|slf=s" => \@::opt_sshloginfile,
"controlmaster|M" => \$::opt_controlmaster,
"return=s" => \@::opt_return,
"trc=s" => \@::opt_trc,
"transfer" => \$::opt_transfer,
"cleanup" => \$::opt_cleanup,
"basefile|bf=s" => \@::opt_basefile,
"B=s" => \$::opt_retired,
"workdir|wd=s" => \$::opt_workdir,
"W=s" => \$::opt_retired,
"tmpdir=s" => \$::opt_tmpdir,
"tempdir=s" => \$::opt_tmpdir,
"tty" => \$::opt_tty,
"T" => \$::opt_retired,
"halt-on-error|halt=i" => \$::opt_halt_on_error,
"H=i" => \$::opt_retired,
"retries=i" => \$::opt_retries,
"dry-run|dryrun" => \$::opt_dryrun,
"progress" => \$::opt_progress,
"eta" => \$::opt_eta,
"arg-sep|argsep=s" => \$::opt_arg_sep,
"arg-file-sep|argfilesep=s" => \$::opt_arg_file_sep,
"trim=s" => \$::opt_trim,
"profile|J=s" => \@::opt_profile,
"pipe|spreadstdin" => \$::opt_pipe,
"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,
"xapply" => \$::opt_xapply,
"bibtex" => \$::opt_bibtex,
# xargs-compatibility - implemented, man, testsuite
"max-procs|P=s" => \$::opt_P,
"delimiter|d=s" => \$::opt_d,
"max-chars|s=i" => \$::opt_s,
"arg-file|a=s" => \@::opt_a,
"no-run-if-empty|r" => \$::opt_r,
"replace|i:s" => \$::opt_i,
"E=s" => \$::opt_E,
"eof|e:s" => \$::opt_E,
"max-args|n=i" => \$::opt_n,
"max-replace-args|N=i" => \$::opt_N,
"colsep|col-sep|C=s" => \$::opt_colsep,
"help|h" => \$::opt_help,
"L=f" => \$::opt_L,
"max-lines|l:f" => \$::opt_l,
"interactive|p" => \$::opt_p,
"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=i" => \$::opt_semaphoretimeout,
"semaphorename|id=s" => \$::opt_semaphorename,
"fg" => \$::opt_fg,
"bg" => \$::opt_bg,
"wait" => \$::opt_wait,
# Shebang #!/usr/bin/parallel --shebang
"shebang|hashbang" => \$::opt_shebang,
"Y" => \$::opt_retired,
"skip-first-line" => \$::opt_skip_first_line,
"header=s" => \$::opt_header,
);
}
sub get_options_from_array {
# Run GetOptions on @array
# Returns:
# true if parsing worked
# false if parsing failed
# @array is changed
my $array_ref = shift;
# 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};
}
my @retval = GetOptions(options_hash());
if(not $this_is_ARGV) {
@{$array_ref} = @::ARGV;
@::ARGV = @save_argv;
}
return @retval;
}
sub parse_options {
# Returns: N/A
# Defaults:
$Global::version = 20120503;
$Global::progname = 'parallel';
$Global::infinity = 2**31;
$Global::debug = 0;
$Global::verbose = 0;
$Global::grouped = 1;
$Global::keeporder = 0;
$Global::quoting = 0;
$Global::replace{'{}'} = '{}';
$Global::replace{'{.}'} = '{.}';
$Global::replace{'{/}'} = '{/}';
$Global::replace{'{//}'} = '{//}';
$Global::replace{'{/.}'} = '{/.}';
$Global::replace{'{#}'} = '{#}';
$/="\n";
$Global::ignore_empty = 0;
$Global::interactive = 0;
$Global::stderr_verbose = 0;
$Global::default_simultaneous_sshlogins = 9;
$Global::exitstatus = 0;
$Global::halt_on_error_exitstatus = 0;
$Global::arg_sep = ":::";
$Global::arg_file_sep = "::::";
$Global::trim = 'n';
$Global::max_jobs_running = 0;
$Global::job_already_run = '';
@ARGV=read_options();
if(defined $::opt_retired) {
print STDERR "$Global::progname: -g has been retired. Use --group.\n";
print STDERR "$Global::progname: -B has been retired. Use --bf.\n";
print STDERR "$Global::progname: -T has been retired. Use --tty.\n";
print STDERR "$Global::progname: -U has been retired. Use --er.\n";
print STDERR "$Global::progname: -W has been retired. Use --wd.\n";
print STDERR "$Global::progname: -Y has been retired. Use --shebang.\n";
print STDERR "$Global::progname: -H has been retired. Use --halt.\n";
::wait_and_exit(255);
}
if(defined @::opt_v) { $Global::verbose = $#::opt_v+1; } # Convert -v -v to v=2
$Global::debug = (defined $::opt_D);
if(defined $::opt_X) { $Global::ContextReplace = 1; }
if(defined $::opt_silent) { $Global::verbose = 0; }
if(defined $::opt_k) { $Global::keeporder = 1; }
if(defined $::opt_group) { $Global::grouped = 1; }
if(defined $::opt_u) { $Global::grouped = 0; }
if(defined $::opt_0) { $/ = "\0"; }
if(defined $::opt_d) { my $e="sprintf \"$::opt_d\""; $/ = eval $e; }
if(defined $::opt_p) { $Global::interactive = $::opt_p; }
if(defined $::opt_q) { $Global::quoting = 1; }
if(defined $::opt_r) { $Global::ignore_empty = 1; }
if(defined $::opt_verbose) { $Global::stderr_verbose = 1; }
if(defined $::opt_I) { $Global::replace{'{}'} = $::opt_I; }
if(defined $::opt_U) { $Global::replace{'{.}'} = $::opt_U; }
if(defined $::opt_i) {
$Global::replace{'{}'} = $::opt_i eq "" ? "{}" : $::opt_i;
}
if(defined $::opt_basenamereplace) { $Global::replace{'{/}'} = $::opt_basenamereplace; }
if(defined $::opt_dirnamereplace) { $Global::replace{'{//}'} = $::opt_dirnamereplace; }
if(defined $::opt_basenameextensionreplace) {
$Global::replace{'{/.}'} = $::opt_basenameextensionreplace;
}
if(defined $::opt_seqreplace) {
$Global::replace{'{#}'} = $::opt_seqreplace;
}
if(defined $::opt_E) { $Global::end_of_file_string = $::opt_E; }
if(defined $::opt_n) { $Global::max_number_of_args = $::opt_n; }
if(defined $::opt_timeout) { $Global::timeoutq = TimeoutQueue->new($::opt_timeout); }
if(defined $::opt_tmpdir) { $ENV{'TMPDIR'} = $::opt_tmpdir; }
if(defined $::opt_help) { die_usage(); }
if(defined $::opt_colsep) { $Global::trim = 'lr'; }
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_cpus) { print SSHLogin::no_of_cpus(),"\n"; wait_and_exit(0); }
if(defined $::opt_number_of_cores) {
print SSHLogin::no_of_cores(),"\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_bibtex) { bibtex(); wait_and_exit(0); }
if(defined $::opt_show_limits) { show_limits(); }
if(defined @::opt_sshlogin) { @Global::sshlogin = @::opt_sshlogin; }
if(defined @::opt_sshloginfile) { read_sshloginfiles(@::opt_sshloginfile); }
if(defined @::opt_return) { push @Global::ret_files, @::opt_return; }
if(not defined $::opt_recstart and
not defined $::opt_recend) { $::opt_recend = "\n"; }
if(not defined $::opt_blocksize) { $::opt_blocksize = "1M"; }
$::opt_blocksize = multiply_binary_prefix($::opt_blocksize);
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) { $Global::semaphore = 1; }
if(defined $::opt_bg) { $Global::semaphore = 1; }
if(defined $::opt_wait) { $Global::semaphore = 1; }
if(defined $::opt_minversion) {
print $Global::version,"\n";
if($Global::version < $::opt_minversion) {
wait_and_exit(255);
} else {
wait_and_exit(0);
}
}
if(defined $::opt_nonall) {
# Append a dummy empty argument
push @ARGV, ":::", "";
}
if(defined $::opt_tty) {
# Defaults for --tty: -j1 -u
# Can be overridden with -jXXX -g
if(not defined $::opt_P) {
$::opt_P = 1;
}
if(not defined $::opt_group) {
$Global::grouped = 0;
}
}
if(defined @::opt_trc) {
push @Global::ret_files, @::opt_trc;
$::opt_transfer = 1;
$::opt_cleanup = 1;
}
if($::opt_tollef and not $::opt_gnu) {
# Behave like tollef parallel (from moreutils)
if(defined $::opt_l) {
$::opt_load = $::opt_l;
$::opt_l = undef;
}
if(not defined $::opt_arg_sep) {
$Global::arg_sep = "--";
}
}
if(defined $::opt_l) {
if($::opt_l eq "-0") {
# -l -0 (swallowed -0)
$::opt_l = 1;
$::opt_0 = 1;
$/ = "\0";
} elsif ($::opt_l == 0) {
# If not given (or if 0 is given) => 1
$::opt_l = 1;
}
$Global::max_lines = $::opt_l;
$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;
$Global::max_number_of_args ||= $Global::max_lines;
}
if(defined $::opt_N) {
$Global::max_number_of_args = $::opt_N;
$Global::ContextReplace = 1;
}
if((defined $::opt_L or defined $::opt_N)
and
not ($::opt_xargs or $::opt_m)) {
$Global::ContextReplace = 1;
}
for (keys %Global::replace) {
$Global::replace{$_} = ::maybe_quote($Global::replace{$_});
}
%Global::replace_rev = reverse %Global::replace;
if(defined $::opt_tag and not defined $::opt_tagstring) {
$::opt_tagstring = $Global::replace{'{}'};
}
if(grep /^$Global::arg_sep$|^$Global::arg_file_sep$/o, @ARGV) {
# Deal with ::: and ::::
@ARGV=read_args_from_command_line();
}
# 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
$Global::semaphore ||= ($0 =~ m:(^|/)sem$:); # called as 'sem'
if($Global::semaphore) {
# A semaphore does not take input from neither stdin nor file
@::opt_a = ("/dev/null");
push(@Global::unget_argv, [Arg->new("")]);
$Semaphore::timeout = $::opt_semaphoretimeout || 0;
if(defined $::opt_semaphorename) {
$Semaphore::name = $::opt_semaphorename;
} else {
$Semaphore::name = `tty`;
chomp $Semaphore::name;
}
$Semaphore::fg = $::opt_fg;
$Semaphore::wait = $::opt_wait;
$Global::default_simultaneous_sshlogins = 1;
if(not defined $::opt_P) {
$::opt_P = 1;
}
if($Global::interactive and $::opt_bg) {
print STDERR "$Global::progname: Jobs running in the ".
"background cannot be interactive.\n";
::wait_and_exit(255);
}
}
if(defined $::opt_eta) {
$::opt_progress = $::opt_eta;
}
parse_sshlogin();
if(remote_hosts() and ($::opt_X or $::opt_m or $::opt_xargs)) {
# As we do not know the max line length on the remote machine
# long commands generated by xargs may fail
# If opt_N is set, it is probably safe
print STDERR ("$Global::progname: Warning: using -X or -m ",
"with --sshlogin may fail\n");
}
if(not defined $::opt_P) {
$::opt_P = "100%";
}
open_joblog();
}
sub open_joblog {
my $append = 0;
if($::opt_resume and not $::opt_joblog) {
print STDERR ("$Global::progname: --resume requires --joblog\n");
::wait_and_exit(255);
}
if($::opt_joblog) {
if($::opt_resume) {
if(open(JOBLOG, $::opt_joblog)) {
# Read the joblog
$append = ; # If there is a header: Open as append later
while() {
if(/^(\d+)/) {
# This is 30% faster than set_job_already_run($1);
vec($Global::job_already_run,$1,1) = 1;
} else {
print STDERR ("$Global::progname: Format of '$::opt_joblog' is wrong\n");
::wait_and_exit(255);
}
}
close JOBLOG;
}
}
if($append) {
# Append to joblog
if(not open($Global::joblog,">>$::opt_joblog")) {
print STDERR ("$Global::progname: Cannot append to ",
"--joblog $::opt_joblog\n");
::wait_and_exit(255);
}
} else {
# Overwrite the joblog
if(not open($Global::joblog,">$::opt_joblog")) {
print STDERR ("$Global::progname: Cannot write to ",
"--joblog $::opt_joblog\n");
::wait_and_exit(255);
} else {
print $Global::joblog
join("\t", "Seq", "Host", "Starttime", "Runtime",
"Send", "Receive", "Exitval", "Signal", "Command"
). "\n";
}
}
}
}
sub read_options {
# Read options from command line, profile and $PARALLEL
# Returns:
# @ARGV without --options
# This must be done first as this may exec myself
if(defined $ARGV[0] and ($ARGV[0]=~/^--shebang / or
$ARGV[0]=~/^--hashbang /)) {
# Program is called from #! line in script
$ARGV[0]=~s/^--shebang *//; # remove --shebang if it is set
$ARGV[0]=~s/^--hashbang *//; # remove --hashbang if it is set
my $argfile = pop @ARGV;
# exec myself to split $ARGV[0] into separate fields
exec "$0 --skip-first-line -a $argfile @ARGV";
}
Getopt::Long::Configure("bundling","pass_through");
# Check if there is a --profile to set @::opt_profile
GetOptions("profile|J=s" => \@::opt_profile) || die_usage();
# Add options from .parallel/config and other profiles
my @ARGV_profile = ();
my @ARGV_env = ();
my @config_profiles = (
"/etc/parallel/config",
$ENV{'HOME'}."/.parallel/config",
$ENV{'HOME'}."/.parallelrc");
my @profiles = @config_profiles;
if(@::opt_profile) {
# --profile overrides default profiles
@profiles = ();
for my $profile (@::opt_profile) {
push @profiles, $ENV{'HOME'}."/.parallel/".$profile;
}
}
for my $profile (@profiles) {
if(-r $profile) {
open (IN, "<", $profile) || ::die_bug("read-profile: $profile");
while() {
/^\s*\#/ and next;
chomp;
push @ARGV_profile, shell_unquote(split/(? ".arg");
unlink($name);
# Put args into argfile
print $outfh map { $_,$/ } @group;
seek $outfh, 0, 0;
# Append filehandle to -a
push @::opt_a, $outfh;
} elsif($group eq $Global::arg_file_sep) {
# Group of file names on the command line.
# Append args into -a
push @::opt_a, @group;
} else {
::die_bug("Unknown command line group: $group");
}
if(defined($arg)) {
# $arg is ::: or ::::
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
if(@::opt_basefile) { cleanup_basefile(); }
}
sub __QUOTING_ARGUMENTS_FOR_SHELL__ {}
sub shell_quote {
my @strings = (@_);
for my $a (@strings) {
$a =~ s/([\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\*\>\<\~\|\; \"\!\$\&\'])/\\$1/g;
$a =~ s/[\n]/'\n'/g; # filenames with '\n' is quoted using \'
}
return wantarray ? @strings : "@strings";
}
sub shell_quote_scalar {
# Quote the string so shell will not expand any special chars
# Returns:
# string quoted with \ as needed by the shell
my $a = shift;
$a =~ s/([\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\*\>\<\~\|\; \"\!\$\&\'])/\\$1/g;
$a =~ s/[\n]/'\n'/g; # filenames with '\n' is quoted using \'
return $a;
}
sub maybe_quote {
# If $Global::quoting then quote the string so shell will not expand any special chars
# Else do not quote
# Returns:
# if $Global::quoting string quoted with \ as needed by the shell
# else string unaltered
if($Global::quoting) {
return shell_quote_scalar(@_);
} else {
return "@_";
}
}
sub maybe_unquote {
# If $Global::quoting then unquote the string as shell would
# Else do not unquote
# Returns:
# if $Global::quoting string unquoted as done by the shell
# else string unaltered
if($Global::quoting) {
return shell_unquote(@_);
} else {
return "@_";
}
}
sub shell_unquote {
# Unquote strings from shell_quote
# Returns:
# string with shell quoting removed
my @strings = (@_);
my $arg;
for $arg (@strings) {
if(not defined $arg) {
$arg = "";
}
$arg =~ s/'\n'/\n/g; # filenames with '\n' is quoted using \'
$arg =~ s/\\([\002-\011\013-\032])/$1/g;
$arg =~ s/\\([\#\?\`\(\)\{\}\*\>\<\~\|\; \"\!\$\&\'])/$1/g;
$arg =~ s/\\\\/\\/g;
}
return wantarray ? @strings : "@strings";
}
sub __FILEHANDLES__ {}
sub enough_file_handles {
# check that we have enough filehandles available for starting
# another job
# Returns:
# 1 if ungrouped (thus not needing extra filehandles)
# 0 if too few filehandles
# 1 if enough filehandles
if($Global::grouped) {
my %fh;
my $enough_filehandles = 1;
# We need a filehandle for STDOUT and STDERR
# perl uses 7 filehandles for something?
# open3 uses 2 extra filehandles temporarily
for my $i (1..8) {
$enough_filehandles &&= open($fh{$i},"&STDOUT" or
::die_bug("Can't dup STDOUT: $!");
open $Global::original_stderr, ">&STDERR" or
::die_bug("Can't dup STDERR: $!");
open $Global::original_stdin, "<&STDIN" or
::die_bug("Can't dup STDIN: $!");
$Global::total_running = 0;
$Global::total_started = 0;
$Global::tty_taken = 0;
$SIG{USR1} = \&list_running_jobs;
$SIG{USR2} = \&toggle_progress;
if(@::opt_basefile) { setup_basefile(); }
}
sub start_more_jobs {
# Returns:
# number of jobs started
my $jobs_started = 0;
if(not $Global::start_no_new_jobs) {
if($Global::max_procs_file) {
my $mtime = (stat($Global::max_procs_file))[9];
if($mtime > $Global::max_procs_file_last_mod) {
$Global::max_procs_file_last_mod = $mtime;
for my $sshlogin (values %Global::host) {
$sshlogin->set_max_jobs_running(undef);
}
}
}
if($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);
}
}
}
for my $sshlogin (values %Global::host) {
debug("Running jobs before on ".$sshlogin->string().": ".$sshlogin->jobs_running()."\n");
if($::opt_load and $sshlogin->loadavg_too_high()) {
# The load is too high or unknown
next;
}
if($::opt_noswap and $sshlogin->swapping()) {
# The server is swapping
next;
}
while ($sshlogin->jobs_running() < $sshlogin->max_jobs_running()) {
if($Global::JobQueue->empty() and not $::opt_pipe) {
last;
}
debug($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 $sshlogin
debug("No jobs started on ".$sshlogin->string()."\n");
last;
}
debug("Job started on ".$sshlogin->string()."\n");
$sshlogin->inc_jobs_running();
$jobs_started++;
}
debug("Running jobs after on ".$sshlogin->string().": ".$sshlogin->jobs_running()
." of ".$sshlogin->max_jobs_running() ."\n");
}
}
return $jobs_started;
}
sub start_another_job {
# Grab a job from Global::JobQueue, start it at sshlogin
# and remember the pid, the STDOUT and the STDERR handles
# 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("Not starting: JobQueue empty\n");
return 0;
} else {
my $job;
do {
$job = get_job_with_sshlogin($sshlogin);
if(not defined $job) {
# No command available for that sshlogin
debug("Not starting: no jobs available for ".$sshlogin->string()."\n");
return 0;
}
} while ($job->is_already_in_joblog());
debug("Command to run on '".$job->sshlogin()."': '".$job->replaced()."'\n");
if($job->start()) {
$Global::running{$job->pid()} = $job;
debug("Started as seq ",$job->seq()," pid:",$job->pid(),"\n");
return 1;
} else {
# If interactive says: Dont run the job, then skip it and run the next
return start_another_job($sshlogin);
}
}
} else {
# No more file handles
debug("Not starting: no more file handles\n");
return 0;
}
}
sub drain_job_queue {
# Returns: N/A
$Private::first_completed ||= time;
if($::opt_progress) {
print $Global::original_stderr init_progress();
}
my $last_header="";
my $sleep = 0.2;
do {
while($Global::total_running > 0) {
debug("jobs running: ", $Global::total_running, "==", scalar
keys %Global::running," slots: ", $Global::max_jobs_running,
" Memory usage:".my_memory_usage()." ");
if($::opt_pipe) {
# When using --pipe sometimes file handles are not closed properly
for my $job (values %Global::running) {
my $fh = $job->stdin();
close $fh;
}
}
if($::opt_progress) {
my %progress = progress();
if($last_header ne $progress{'header'}) {
print $Global::original_stderr "\n",$progress{'header'},"\n";
$last_header = $progress{'header'};
}
print $Global::original_stderr "\r",$progress{'status'};
}
# Sometimes SIGCHLD is not registered, so force reaper
$sleep = ::reap_usleep($sleep);
}
if(not $Global::JobQueue->empty()) {
start_more_jobs(); # These jobs may not be started because of loadavg
$sleep = ::reap_usleep($sleep);
}
} while ($Global::total_running > 0
or
not $Global::start_no_new_jobs and not $Global::JobQueue->empty());
if($::opt_progress) {
print $Global::original_stderr "\n";
}
}
sub toggle_progress {
# Turn on/off progress view
# Returns: N/A
$::opt_progress = not $::opt_progress;
if($::opt_progress) {
print $Global::original_stderr init_progress();
}
}
sub init_progress {
# Returns:
# list of computers for progress output
$|=1;
my %progress = progress();
return ("\nComputers / CPU cores / Max jobs to run\n",
$progress{'workerlist'});
}
sub progress {
# Returns:
# list of workers
# header that will fit on the screen
# status message that will fit on the screen
my $termcols = terminal_columns();
my ($status, $header) = ("x"x($termcols+1),"");
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";
}
my $eta = "";
if($::opt_eta) {
my $completed = 0;
for(@workers) { $completed += $Global::host{$_}->jobs_completed() }
if($completed) {
my $total = $Global::JobQueue->total_jobs();
my $left = $total - $completed;
my $pctcomplete = $completed / $total;
my $timepassed = (time - $Private::first_completed);
my $avgtime = $timepassed / $completed;
$Private::smoothed_avg_time ||= $avgtime;
# Smooth the eta so it does not jump wildly
$Private::smoothed_avg_time = (1 - $pctcomplete) *
$Private::smoothed_avg_time + $pctcomplete * $avgtime;
my $this_eta;
$Private::last_time ||= $timepassed;
if($timepassed != $Private::last_time
or not defined $Private::last_eta) {
$Private::last_time = $timepassed;
$this_eta = $left * $Private::smoothed_avg_time;
$Private::last_eta = $this_eta;
} else {
$this_eta = $Private::last_eta;
}
$eta = sprintf("ETA: %ds %dleft %.2favg ", $this_eta, $left, $avgtime);
}
}
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
{
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
{ 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
{ 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);
}
sub terminal_columns {
# Get the number of columns of the display
# Returns:
# number of columns of the screen
if(not $Private::columns) {
$Private::columns = $ENV{'COLUMNS'};
if(not $Private::columns) {
my $resize = qx{ resize 2>/dev/null };
$resize =~ /COLUMNS=(\d+);/ and do { $Private::columns = $1; };
}
$Private::columns ||= 80;
}
return $Private::columns;
}
sub get_job_with_sshlogin {
# Returns:
# next command to run with ssh command wrapping if remote
# next command to run with no wrapping (clean_command)
my $sshlogin = shift;
if($::oodebug and $Global::JobQueue->empty()) {
Carp::confess("get_job_with_sshlogin should never be called if empty");
}
my $job = $Global::JobQueue->get();
if(not defined $job) {
# No more jobs
::debug("No more jobs: JobQueue empty\n");
return undef;
}
if($::oodebug and not defined $job->{'commandline'}) {
Carp::confess("get_job_with_sshlogin job->commandline should never be empty");
}
my $clean_command = $job->replaced();
if($clean_command =~ /^\s*$/) {
# Do not run empty lines
if(not $Global::JobQueue->empty()) {
return get_job_with_sshlogin($sshlogin);
} else {
return undef;
}
}
$job->set_sshlogin($sshlogin);
if($::opt_retries and $clean_command and
$job->failed_here()) {
# This command with these args failed for this sshlogin
my ($no_of_failed_sshlogins,$min_failures) = $job->min_failed();
#::my_dump(($no_of_failed_sshlogins,$min_failures));
if($no_of_failed_sshlogins == keys %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 $job;
}
sub __REMOTE_SSH__ {}
sub read_sshloginfiles {
# Returns: N/A
for (@_) {
read_sshloginfile($_);
}
}
sub read_sshloginfile {
# Returns: N/A
my $file = shift;
my $close = 1;
if($file eq "..") {
$file = $ENV{'HOME'}."/.parallel/sshloginfile";
}
if($file eq ".") {
$file = "/etc/parallel/sshloginfile";
}
if($file eq "-") {
*IN = *STDIN;
$close = 0;
} else {
if(not open(IN, $file)) {
print $Global::original_stderr "Cannot open $file\n";
exit(255);
}
}
while() {
chomp;
/^\s*#/ and next;
/^\s*$/ and next;
push @Global::sshlogin, $_;
}
if($close) {
close IN;
}
}
sub parse_sshlogin {
# 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 /,/, $sshlogin) {
if ($s eq ".." or $s eq "-") {
read_sshloginfile($s);
} else {
push (@login, $s);
}
}
}
for my $sshlogin_string (@login) {
my $sshlogin = SSHLogin->new($sshlogin_string);
$sshlogin->set_maxlength(Limits::Command::max_length());
$Global::host{$sshlogin->string()} = $sshlogin;
}
#debug("sshlogin: ", my_dump(%Global::host),"\n");
if($::opt_transfer or @::opt_return or $::opt_cleanup or @::opt_basefile) {
if(not remote_hosts()) {
# There are no remote hosts
if(defined @::opt_trc) {
print $Global::original_stderr
"parallel: Warning: --trc ignored as there are no remote --sshlogin\n";
} elsif (defined $::opt_transfer) {
print $Global::original_stderr
"parallel: Warning: --transfer ignored as there are no remote --sshlogin\n";
} elsif (defined @::opt_return) {
print $Global::original_stderr
"parallel: Warning: --return ignored as there are no remote --sshlogin\n";
} elsif (defined $::opt_cleanup) {
print $Global::original_stderr
"parallel: Warning: --cleanup ignored as there are no remote --sshlogin\n";
} elsif (defined @::opt_basefile) {
print $Global::original_stderr
"parallel: Warning: --basefile ignored as there are no remote --sshlogin\n";
}
}
}
}
sub remote_hosts {
# Return sshlogins that are not ':'
# Returns:
# list of sshlogins with ':' removed
return grep !/^:$/, keys %Global::host;
}
sub setup_basefile {
# Transfer basefiles to each $sshlogin
# This needs to be done before first jobs on $sshlogin is run
# Returns: N/A
my $cmd = "";
for my $sshlogin (values %Global::host) {
if($sshlogin->string() eq ":") { next }
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $rsync_opt = "-rlDzR -e".shell_quote_scalar($sshcmd);
for my $file (@::opt_basefile) {
my $f = $file;
my $relpath = ($f !~ m:^/:); # Is the path relative?
# Use different subdirs depending on abs or rel path
my $rsync_destdir = ($relpath ? "./" : "/");
$f =~ s:/\./:/:g; # Rsync treats /./ special. We dont want that
$f = shell_quote_scalar($f);
$cmd .= "rsync $rsync_opt $f $serverlogin:$rsync_destdir &";
}
}
$cmd .= "wait;";
debug("basesetup: $cmd\n");
print `$cmd`;
}
sub cleanup_basefile {
# Remove the basefiles transferred
# Returns: N/A
my $cmd="";
for my $sshlogin (values %Global::host) {
if($sshlogin->string() eq ":") { next }
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
for my $file (@::opt_basefile) {
$cmd .= "$sshcmd $serverlogin rm -f ".shell_quote_scalar(shell_quote_scalar($file))."&";
}
}
$cmd .= "wait;";
debug("basecleanup: $cmd\n");
print `$cmd`;
}
sub __SIGNAL_HANDLING__ {}
sub list_running_jobs {
# Returns: N/A
for my $v (values %Global::running) {
print $Global::original_stderr "$Global::progname: ",$v->replaced(),"\n";
}
}
sub start_no_new_jobs {
# Returns: N/A
$SIG{TERM} = $Global::original_sig{TERM};
print $Global::original_stderr
("$Global::progname: SIGTERM received. No new jobs will be started.\n",
"$Global::progname: Waiting for these ", scalar(keys %Global::running),
" jobs to finish. Send SIGTERM again to stop now.\n");
list_running_jobs();
$Global::start_no_new_jobs++;
}
sub reaper {
# A job finished.
# Print the output.
# Start another job
# Returns: N/A
my $stiff;
my $children_reaped = 0;
debug("Reaper called ");
while (($stiff = waitpid(-1, &WNOHANG)) > 0) {
$children_reaped++;
if($Global::sshmaster{$stiff}) {
# This is one of the ssh -M: ignore
next;
}
my $job = $Global::running{$stiff};
# '-a <(seq 10)' will give us a pid not in %Global::running
$job or next;
$job->set_exitstatus($? >> 8);
$job->set_exitsignal($? & 127);
debug("died (".$job->exitstatus()."): ".$job->seq());
$job->set_endtime();
if($stiff == $Global::tty_taken) {
# The process that died had the tty => release it
$Global::tty_taken = 0;
}
if(not $job->should_be_retried()) {
# Force printing now if the job failed and we are going to exit
my $print_now = ($job->exitstatus() and
$::opt_halt_on_error and $::opt_halt_on_error == 2);
if($Global::keeporder and not $print_now) {
$Private::print_later{$job->seq()} = $job;
$Private::job_end_sequence ||= 1;
debug("Looking for: $Private::job_end_sequence ".
"Current: ".$job->seq()."\n");
while($Private::print_later{$Private::job_end_sequence}) {
debug("Found job end $Private::job_end_sequence");
$Private::print_later{$Private::job_end_sequence}->print();
delete $Private::print_later{$Private::job_end_sequence};
$Private::job_end_sequence++;
}
} else {
$job->print();
}
if($job->exitstatus()) {
# The jobs had a exit status <> 0, so error
$Global::exitstatus++;
if($::opt_halt_on_error) {
if($::opt_halt_on_error == 1) {
# If halt on error == 1 we should gracefully exit
print $Global::original_stderr
("$Global::progname: Starting no more jobs. ",
"Waiting for ", scalar(keys %Global::running),
" jobs to finish. This job failed:\n",
$job->replaced(),"\n");
$Global::start_no_new_jobs++;
$Global::halt_on_error_exitstatus = $job->exitstatus();
} elsif($::opt_halt_on_error == 2) {
# If halt on error == 2 we should exit immediately
print $Global::original_stderr
("$Global::progname: This job failed:\n",
$job->replaced(),"\n");
exit ($job->exitstatus());
}
}
}
}
my $sshlogin = $job->sshlogin();
$sshlogin->dec_jobs_running();
$sshlogin->inc_jobs_completed();
$Global::total_running--;
delete $Global::running{$stiff};
start_more_jobs();
}
debug("Reaper exit\n");
return $children_reaped;
}
sub timeout {
# SIGALRM was received. Check if there was a timeout
# @Global::timeout is sorted by timeout
while (@Global::timeouts) {
my $t = $Global::timeouts[0];
if($t->timed_out()) {
$t->kill();
shift @Global::timeouts;
} else {
# Because they are sorted by timeout
last;
}
}
}
sub __USAGE__ {}
sub wait_and_exit {
# If we do not wait, we sometimes get segfault
# Returns: N/A
for (keys %Global::unkilled_children) {
kill 9, $_;
waitpid($_,0);
delete $Global::unkilled_children{$_};
}
wait();
exit(shift);
}
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",
"{} {.} {/} {/.} {#} Replacement strings",
"{3} {3.} {3/} {3/.} Positional replacement strings",
"",
"-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",
"",
"When using GNU Parallel for a publication please cite:",
"",
"O. Tange (2011): GNU Parallel - The Command-Line Power Tool,",
";login: The USENIX Magazine, February 2011:42-47.",
"");
}
sub die_bug {
my $bugid = shift;
print STDERR
("$Global::progname: This should not happen. You have found a bug.\n",
"Please contact and include:\n",
"* The version number: $Global::version\n",
"* The bugid: $bugid\n",
"* The command line being run\n",
"* The files being read (put the files on a webserver if they are big)\n",
"\n",
"If you get the error on smaller/fewer files, please include those instead.\n");
::wait_and_exit(255);
}
sub version {
# Returns: N/A
if($::opt_tollef and not $::opt_gnu) {
print "WARNING: YOU ARE USING --tollef. USE --gnu FOR GNU PARALLEL\n\n";
}
print join("\n",
"GNU $Global::progname $Global::version",
"Copyright (C) 2007,2008,2009,2010,2011,2012 Ole Tange and Free Software Foundation, Inc.",
"License GPLv3+: GNU GPL version 3 or later ",
"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 GNU Parallel for a publication please cite:\n",
"O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ",
";login: The USENIX Magazine, February 2011:42-47.\n",
);
}
sub bibtex {
# Returns: N/A
if($::opt_tollef and not $::opt_gnu) {
print "WARNING: YOU ARE USING --tollef. USE --gnu FOR GNU PARALLEL\n\n";
}
print join("\n",
"\@article{Tange2011a,",
" title = {GNU Parallel - The Command-Line Power Tool},",
" author = {O. Tange},",
" address = {Frederiksberg, Denmark},",
" journal = {;login: The USENIX Magazine},",
" month = {Feb},",
" number = {1},",
" volume = {36},",
" url = {http://www.gnu.org/s/parallel},",
" year = {2011},",
" pages = {42-47}",
"}",
"",
);
}
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 __GENERIC_COMMON_FUNCTION__ {}
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 hostname {
if(not $Private::hostname) {
my $hostname = `hostname`;
chomp($hostname);
$Private::hostname = $hostname || "nohostname";
}
return $Private::hostname;
}
sub reap_usleep {
# Reap dead children.
# If no children: Sleep specified amount with exponential backoff
# Returns:
# 0.00001 if children reaped (0.00001 ms works best on highend)
# $ms*1.1 if no children reaped
my $ms = shift;
if(reaper()) {
return 0.00001;
} else {
usleep($ms);
return (($ms < 1000) ? ($ms * 1.1) : ($ms)); # exponential back off
}
}
sub usleep {
# Sleep this many milliseconds.
my $secs = shift;
::debug("Sleeping ",$secs," millisecs\n");
select(undef, undef, undef, $secs/1000);
if($::opt_timeout) {
::debug(my_dump($Global::timeoutq));
$Global::timeoutq->process_timeouts();
}
}
sub multiply_binary_prefix {
# Evalualte numbers with binary prefix
# k=10^3, m=10^6, g=10^9, t=10^12, p=10^15, e=10^18, z=10^21, y=10^24
# K=2^10, M=2^20, G=2^30, T=2^40, P=2^50, E=2^70, Z=2^80, Y=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
# ki=2^10, mi=2^20, gi=2^30, ti=2^40, pi=2^50, ei=2^70, zi=2^80, yi=2^80
# 13G = 13*1024*1024*1024 = 13958643712
my $s = shift;
$s =~ s/k/*1000/g;
$s =~ s/M/*1000*1000/g;
$s =~ s/G/*1000*1000*1000/g;
$s =~ s/T/*1000*1000*1000*1000/g;
$s =~ s/P/*1000*1000*1000*1000*1000/g;
$s =~ s/E/*1000*1000*1000*1000*1000*1000/g;
$s =~ s/Z/*1000*1000*1000*1000*1000*1000*1000/g;
$s =~ s/Y/*1000*1000*1000*1000*1000*1000*1000*1000/g;
$s =~ s/X/*1000*1000*1000*1000*1000*1000*1000*1000*1000/g;
$s =~ s/Ki?/*1024/gi;
$s =~ s/Mi?/*1024*1024/gi;
$s =~ s/Gi?/*1024*1024*1024/gi;
$s =~ s/Ti?/*1024*1024*1024*1024/gi;
$s =~ s/Pi?/*1024*1024*1024*1024*1024/gi;
$s =~ s/Ei?/*1024*1024*1024*1024*1024*1024/gi;
$s =~ s/Zi?/*1024*1024*1024*1024*1024*1024*1024/gi;
$s =~ s/Yi?/*1024*1024*1024*1024*1024*1024*1024*1024/gi;
$s =~ s/Xi?/*1024*1024*1024*1024*1024*1024*1024*1024*1024/gi;
$s = eval $s;
return $s;
}
sub __DEBUGGING__ {}
sub debug {
# Returns: N/A
$Global::debug or return;
@_ = grep { defined $_ ? $_ : "" } @_;
if($Global::original_stdout) {
print $Global::original_stdout @_;
} else {
print @_;
}
}
sub my_memory_usage {
# Returns:
# memory usage if found
# 0 otherwise
use strict;
use FileHandle;
my $pid = $$;
if(-e "/proc/$pid/stat") {
my $fh = FileHandle->new(";
chomp $data;
$fh->close;
my @procinfo = split(/\s+/,$data);
return undef_as_zero($procinfo[22]);
} else {
return 0;
}
}
sub my_size {
# Returns:
# size of object if Devel::Size is installed
# -1 otherwise
my @size_this = (@_);
eval "use Devel::Size qw(size total_size)";
if ($@) {
return -1;
} else {
return total_size(@_);
}
}
sub my_dump {
# Returns:
# ascii expression of object if Data::Dump(er) is installed
# error code otherwise
my @dump_this = (@_);
eval "use Data::Dump qw(dump);";
if ($@) {
# Data::Dump not installed
eval "use Data::Dumper;";
if ($@) {
my $err = "Neither Data::Dump nor Data::Dumper is installed\n".
"Not dumping output\n";
print $Global::original_stderr $err;
return $err;
} else {
return Dumper(@dump_this);
}
} else {
# Create a dummy Data::Dump:dump as Hans Schou sometimes has
# it undefined
eval "sub Data::Dump:dump {}";
eval "use Data::Dump qw(dump);";
return (Data::Dump::dump(@dump_this));
}
}
sub __OBJECT_ORIENTED_PARTS__ {}
package SSHLogin;
sub new {
my $class = shift;
my $sshlogin_string = shift;
my $ncpus;
if($sshlogin_string =~ s:^(\d*)/:: and $1) {
# Override default autodetected ncpus unless zero or missing
$ncpus = $1;
}
my $string = $sshlogin_string;
my @unget = ();
return bless {
'string' => $string,
'jobs_running' => 0,
'jobs_completed' => 0,
'maxlength' => undef,
'max_jobs_running' => undef,
'ncpus' => $ncpus,
'sshcommand' => undef,
'serverlogin' => undef,
'control_path_dir' => undef,
'control_path' => undef,
'loadavg_file' => $ENV{'HOME'} . "/.parallel/tmp/loadavg-" .
$$."-".$string,
'loadavg' => undef,
'last_loadavg_update' => 0,
'swap_activity_file' => $ENV{'HOME'} . "/.parallel/tmp/swap_activity-" .
$$."-".$string,
'swap_activity' => undef,
}, ref($class) || $class;
}
sub DESTROY {
my $self = shift;
# Remove temporary files if they are created.
unlink $self->{'loadavg_file'};
unlink $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_jobs_running {
# my $self = shift;
# $self->{'jobs_running'} = shift;
#}
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 inc_jobs_completed {
my $self = shift;
$self->{'jobs_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'};
}
}
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(SWAP,"<".$self->{'swap_activity_file'}) || ::die_bug("swap_activity_file-r");
my $swap_out = ;
close SWAP;
if($swap_out =~ /^(\d+)$/) {
$self->{'swap_activity'} = $1;
::debug("New swap_activity: ".$self->{'swap_activity'});
}
::debug("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("Older than 10 sec: ".$self->{'swap_activity_file'});
$update_swap_activity_file = 1;
}
} else {
::debug("No swap_activity file: ".$self->{'swap_activity_file'});
$self->{'swap_activity'} = undef;
$update_swap_activity_file = 1;
}
if($update_swap_activity_file) {
::debug("Updating swap_activity file".$self->{'swap_activity_file'});
$self->{'last_swap_activity_update'} = time;
-e $ENV{'HOME'}."/.parallel" or mkdir $ENV{'HOME'}."/.parallel";
-e $ENV{'HOME'}."/.parallel/tmp" or mkdir $ENV{'HOME'}."/.parallel/tmp";
my $swap_activity;
# If the (remote) machine is Mac we should use vm_stat
# swap_in and swap_out on GNU/Linux is $7 and $8
# swap_in and swap_out on Mac is $10 and $11
$swap_activity = q[ { vmstat 1 2> /dev/null || vm_stat 1; } | ].
q[ awk 'NR!=4{next} NF==16{print $7*$8} NF==11{print $10*$11} {exit}' ];
if($self->{'string'} ne ":") {
$swap_activity = $self->sshcommand() . " " . $self->serverlogin() . " " .
::shell_quote_scalar($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 $tmpfile = $self->{'swap_activity_file'}.$$;
qx{ ($swap_activity > $tmpfile; mv $tmpfile $file) & };
}
return $self->{'swap_activity'};
}
sub loadavg_too_high {
my $self = shift;
my $loadavg = $self->loadavg();
return (not defined $loadavg or
$loadavg > $self->max_loadavg());
}
sub loadavg {
# If the currently know loadavg is too old:
# Recompute a new one in the background
# Returns:
# last load average computed
my $self = shift;
# Should we update the loadavg file?
my $update_loadavg_file = 0;
if(-r $self->{'loadavg_file'}) {
open(UPTIME,"<".$self->{'loadavg_file'}) || ::die_bug("loadavg_file-r");
local $/ = undef;
my $uptime_out = ;
close UPTIME;
# load average: 0.76, 1.53, 1.45
if($uptime_out =~ /load average: (\d+.\d+)/) {
$self->{'loadavg'} = $1;
::debug("New loadavg: ".$self->{'loadavg'});
} else {
::die_bug("loadavg_invalid_content: $uptime_out");
}
::debug("Last update: ".$self->{'last_loadavg_update'});
if(time - $self->{'last_loadavg_update'} > 10) {
# last loadavg was started 10 seconds ago
::debug("Older than 10 sec: ".$self->{'loadavg_file'});
$update_loadavg_file = 1;
}
} else {
::debug("No loadavg file: ".$self->{'loadavg_file'});
$self->{'loadavg'} = undef;
$update_loadavg_file = 1;
}
if($update_loadavg_file) {
::debug("Updating loadavg file".$self->{'loadavg_file'}."\n");
$self->{'last_loadavg_update'} = time;
-e $ENV{'HOME'}."/.parallel" or mkdir $ENV{'HOME'}."/.parallel";
-e $ENV{'HOME'}."/.parallel/tmp" or mkdir $ENV{'HOME'}."/.parallel/tmp";
my $uptime;
if($self->{'string'} eq ":") {
$uptime = "LANG=C uptime";
} else {
$uptime = $self->sshcommand() . " " . $self->serverlogin() . " LANG=C uptime";
}
# Run uptime.
# 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->{'loadavg_file'};
my $tmpfile = $self->{'loadavg_file'}.$$;
qx{ ($uptime > $tmpfile && mv $tmpfile $file) & };
}
return $self->{'loadavg'};
}
sub max_loadavg {
my $self = shift;
if(not defined $self->{'max_loadavg'}) {
$self->{'max_loadavg'} =
$self->compute_max_loadavg($::opt_load);
}
::debug("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(IN, $Global::max_load_file)) {
my $opt_load_file = join("",);
close IN;
$load = $self->compute_max_loadavg($opt_load_file);
} else {
print $Global::original_stderr "Cannot open $loadspec\n";
exit(255);
}
} else {
print $Global::original_stderr "Parsing of --load failed\n";
::die_usage();
}
if($load < 0.01) {
$load = 0.01;
}
}
return $load;
}
sub max_jobs_running {
my $self = shift;
if(not defined $self->{'max_jobs_running'}) {
$self->set_max_jobs_running($self->compute_number_of_processes($::opt_P));
}
return $self->{'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("Wanted procs: $wanted_processes\n");
my $system_limit =
$self->processes_available_by_system_limit($wanted_processes);
$system_limit < 1 and ::die_bug('$system_limit < 1');
::debug("Limited to procs: $system_limit\n");
return $system_limit;
}
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 @jobs = ();
my $job;
my @args = ();
my $arg;
my $more_filehandles = 1;
my $max_system_proc_reached = 0;
my $slow_spawining_warning_printed = 0;
my $time = time;
my %fh;
my @children;
# Reserve filehandles
# perl uses 7 filehandles for something?
# parallel uses 1 for memory_usage
for my $i (1..8) {
open($fh{"init-$i"},"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::semaphore) {
# Skip
} 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--;
} 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()) {
last;
} else {
($job) = $Global::JobQueue->get();
push(@jobs, $job);
}
} else {
($arg) = $Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->get();
push(@args, $arg);
}
} else {
# If there are no more command lines, then we have a process
# per command line, so no need to go further
$Global::JobQueue->empty() and last;
($job) = $Global::JobQueue->get();
push(@jobs, $job);
}
}
$wait_time_for_getting_args += time - $before_getting_arg;
$system_limit++;
# Every simultaneous process uses 2 filehandles when grouping
$more_filehandles = open($fh{$system_limit*10}," 10 and
$forktime > 1 and
$forktime > $system_limit * 0.01
and not $slow_spawining_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.
print $Global::original_stderr
("parallel: Warning: Starting $system_limit processes took > $forktime sec.\n",
"Consider adjusting -j. Press CTRL-C to stop.\n");
$slow_spawining_warning_printed = 1;
}
}
if($system_limit < $wanted_processes and not $more_filehandles) {
print $Global::original_stderr
("parallel: Warning: Only enough filehandles to run ",
$system_limit, " jobs in parallel. ",
"Raising ulimit -n may help.\n");
}
if($system_limit < $wanted_processes and $max_system_proc_reached) {
print $Global::original_stderr
("parallel: Warning: Only enough available processes to run ",
$system_limit, " jobs in parallel.\n");
}
if($Global::JobQueue->empty()) {
$system_limit ||= 1;
}
# 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};
}
#wait();
# Cleanup: Unget the command_lines or the @args
$Global::JobQueue->{'commandlinequeue'}->{'arg_queue'}->unget(@args);
$Global::JobQueue->unget(@jobs);
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;
# 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();
print $Global::original_stderr
("parallel: Warning: ssh to $serverlogin only allows ",
"for $ssh_limit simultaneous logins.\n",
"You may raise this by changing ",
"/etc/ssh/sshd_config:MaxStartup on $serverlogin\n",
"Using only ",$ssh_limit-1," connections ",
"to avoid race conditions\n");
}
# 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 simultaneouslogin & ssh host echo simultaneouslogin & ...)|grep simul|wc -l
# Returns:
# Number of succesful logins
my $self = shift;
my $wanted_processes = shift;
my $sshcmd = $self->sshcommand();
my $serverlogin = $self->serverlogin();
my $cmd = "$sshcmd $serverlogin echo simultaneouslogin 2>&1 &"x$wanted_processes;
::debug("Trying $wanted_processes logins at $serverlogin");
open (SIMUL, "($cmd)|grep simultaneouslogin | wc -l|") or
::die_bug("simultaneouslogin");
my $ssh_limit = ;
close SIMUL;
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
# Returns:
# 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+)\%$/) {
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;
$Global::max_procs_file_last_mod = (stat($Global::max_procs_file))[9];
if(open(IN, $Global::max_procs_file)) {
my $opt_P_file = join("",);
close IN;
$processes = $self->user_requested_processes($opt_P_file);
} else {
print $Global::original_stderr "Cannot open $opt_P\n";
exit(255);
}
} else {
print $Global::original_stderr "Parsing of --jobs/-j/--max-procs/-P failed\n";
::die_usage();
}
if($processes < 1) {
$processes = 1;
}
}
return $processes;
}
sub ncpus {
my $self = shift;
if(not defined $self->{'ncpus'}) {
my $sshcmd = $self->sshcommand();
my $serverlogin = $self->serverlogin();
if($serverlogin eq ":") {
if($::opt_use_cpus_instead_of_cores) {
$self->{'ncpus'} = no_of_cpus();
} else {
$self->{'ncpus'} = no_of_cores();
}
} else {
my $ncpu;
if($::opt_use_cpus_instead_of_cores) {
$ncpu = qx(echo|$sshcmd $serverlogin parallel --number-of-cpus);
} else {
$ncpu = qx(echo|$sshcmd $serverlogin parallel --number-of-cores);
}
chomp $ncpu;
if($ncpu =~ /^\s*[0-9]+\s*$/s) {
$self->{'ncpus'} = $ncpu;
} else {
print $Global::original_stderr
("parallel: Warning: Could not figure out ",
"number of cpus on $serverlogin ($ncpu). Using 1\n");
$self->{'ncpus'} = 1;
}
}
}
return $self->{'ncpus'};
}
sub no_of_cpus {
# Returns:
# Number of physical CPUs
local $/="\n"; # If delimiter is set, then $/ will be wrong
my $no_of_cpus;
if ($^O eq 'linux') {
$no_of_cpus = no_of_cpus_gnu_linux();
} elsif ($^O eq 'freebsd') {
$no_of_cpus = no_of_cpus_freebsd();
} elsif ($^O eq 'solaris') {
$no_of_cpus = no_of_cpus_solaris();
} elsif ($^O eq 'aix') {
$no_of_cpus = no_of_cpus_aix();
} elsif ($^O eq 'darwin') {
$no_of_cpus = no_of_cpus_darwin();
} else {
$no_of_cpus = (no_of_cpus_freebsd()
|| no_of_cpus_darwin()
|| no_of_cpus_solaris()
|| no_of_cpus_aix()
|| no_of_cpus_gnu_linux()
);
}
if($no_of_cpus) {
chomp $no_of_cpus;
return $no_of_cpus;
} else {
warn("parallel: Cannot figure out number of cpus. Using 1");
return 1;
}
}
sub no_of_cores {
# Returns:
# Number of CPU cores
local $/="\n"; # If delimiter is set, then $/ will be wrong
my $no_of_cores;
if ($^O eq 'linux') {
$no_of_cores = no_of_cores_gnu_linux();
} elsif ($^O eq 'freebsd') {
$no_of_cores = no_of_cores_freebsd();
} elsif ($^O eq 'solaris') {
$no_of_cores = no_of_cores_solaris();
} elsif ($^O eq 'aix') {
$no_of_cores = no_of_cores_aix();
} elsif ($^O eq 'darwin') {
$no_of_cores = no_of_cores_darwin();
} else {
$no_of_cores = (no_of_cores_freebsd()
|| no_of_cores_darwin()
|| no_of_cores_solaris()
|| no_of_cores_aix()
|| no_of_cores_gnu_linux()
);
}
if($no_of_cores) {
chomp $no_of_cores;
return $no_of_cores;
} else {
warn("parallel: Cannot figure out number of CPU cores. Using 1");
return 1;
}
}
sub no_of_cpus_gnu_linux {
# Returns:
# Number of physical CPUs on GNU/Linux
# undef if not GNU/Linux
my $no_of_cpus;
if(-e "/proc/cpuinfo") {
$no_of_cpus = 0;
my %seen;
open(IN,"cat /proc/cpuinfo|") || return undef;
while() {
if(/^physical id.*[:](.*)/ and not $seen{$1}++) {
$no_of_cpus++;
}
}
close IN;
}
return $no_of_cpus;
}
sub no_of_cores_gnu_linux {
# Returns:
# Number of CPU cores on GNU/Linux
# undef if not GNU/Linux
my $no_of_cores;
if(-e "/proc/cpuinfo") {
$no_of_cores = 0;
open(IN,"cat /proc/cpuinfo|") || return undef;
while() {
/^processor.*[:]/ and $no_of_cores++;
}
close IN;
}
return $no_of_cores;
}
sub no_of_cpus_darwin {
# Returns:
# Number of physical CPUs on Mac Darwin
# undef if not Mac Darwin
my $no_of_cpus =
(`sysctl -n hw.physicalcpu 2>/dev/null`
or
`sysctl -a hw 2>/dev/null | grep -w physicalcpu | awk '{ print \$2 }'`);
return $no_of_cpus;
}
sub no_of_cores_darwin {
# Returns:
# Number of CPU cores on Mac Darwin
# undef if not Mac Darwin
my $no_of_cores =
(`sysctl -n hw.logicalcpu 2>/dev/null`
or
`sysctl -a hw 2>/dev/null | grep -w logicalcpu | awk '{ print \$2 }'`);
return $no_of_cores;
}
sub no_of_cpus_freebsd {
# Returns:
# Number of physical CPUs on FreeBSD
# undef if not FreeBSD
my $no_of_cpus =
(`sysctl -a dev.cpu 2>/dev/null | grep \%parent | awk '{ print \$2 }' | uniq | wc -l | awk '{ print \$1 }'`
or
`sysctl hw.ncpu 2>/dev/null | awk '{ print \$2 }'`);
chomp $no_of_cpus;
return $no_of_cpus;
}
sub no_of_cores_freebsd {
# Returns:
# Number of CPU cores on FreeBSD
# undef if not FreeBSD
my $no_of_cores =
(`sysctl hw.ncpu 2>/dev/null | awk '{ print \$2 }'`
or
`sysctl -a hw 2>/dev/null | grep -w logicalcpu | awk '{ print \$2 }'`);
chomp $no_of_cores;
return $no_of_cores;
}
sub no_of_cpus_solaris {
# Returns:
# Number of physical CPUs on Solaris
# undef if not Solaris
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = `/usr/sbin/psrinfo`;
if($#psrinfo >= 0) {
return $#psrinfo +1;
}
}
if(-x "/usr/sbin/prtconf") {
my @prtconf = `/usr/sbin/prtconf | grep cpu..instance`;
if($#prtconf >= 0) {
return $#prtconf +1;
}
}
return undef;
}
sub no_of_cores_solaris {
# Returns:
# Number of CPU cores on Solaris
# undef if not Solaris
if(-x "/usr/sbin/psrinfo") {
my @psrinfo = `/usr/sbin/psrinfo`;
if($#psrinfo >= 0) {
return $#psrinfo +1;
}
}
if(-x "/usr/sbin/prtconf") {
my @prtconf = `/usr/sbin/prtconf | grep cpu..instance`;
if($#prtconf >= 0) {
return $#prtconf +1;
}
}
return undef;
}
sub no_of_cpus_aix {
# Returns:
# Number of physical CPUs on AIX
# undef if not AIX
my $no_of_cpus = 0;
if(-x "/usr/sbin/lscfg") {
open(IN,"/usr/sbin/lscfg -vs |grep proc | wc -l|tr -d ' ' |")
|| return undef;
$no_of_cpus = ;
chomp ($no_of_cpus);
close IN;
}
return $no_of_cpus;
}
sub no_of_cores_aix {
# Returns:
# Number of CPU cores on AIX
# undef if not AIX
my $no_of_cores;
if(-x "/usr/bin/vmstat") {
open(IN,"/usr/bin/vmstat 1 1|") || return undef;
while() {
/lcpu=([0-9]*) / and $no_of_cores = $1;
}
close IN;
}
return $no_of_cores;
}
sub sshcommand {
my $self = shift;
if (not defined $self->{'sshcommand'}) {
$self->sshcommand_of_sshlogin();
}
return $self->{'sshcommand'};
}
sub serverlogin {
my $self = shift;
if (not defined $self->{'serverlogin'}) {
$self->sshcommand_of_sshlogin();
}
return $self->{'serverlogin'};
}
sub sshcommand_of_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')
# Returns:
# sshcommand - defaults to 'ssh'
# login@host
my $self = shift;
my ($sshcmd, $serverlogin);
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 = "ssh -S ".$control_path;
$serverlogin = $self->{'string'};
my $master = "ssh -MTS $control_path $serverlogin sleep 1";
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}++;
} else {
::debug($master,"\n");
`$master`;
::wait_and_exit(0);
}
}
} else {
$sshcmd = "ssh"; $serverlogin = $self->{'string'};
}
}
$self->{'sshcommand'} = $sshcmd;
$self->{'serverlogin'} = $serverlogin;
}
sub control_path_dir {
# Returns:
# path to directory
my $self = shift;
if(not defined $self->{'control_path_dir'}) {
-e $ENV{'HOME'}."/.parallel" or mkdir $ENV{'HOME'}."/.parallel";
-e $ENV{'HOME'}."/.parallel/tmp" or mkdir $ENV{'HOME'}."/.parallel/tmp";
$self->{'control_path_dir'} =
File::Temp::tempdir($ENV{'HOME'}
. "/.parallel/tmp/control_path_dir-XXXX",
CLEANUP => 1);
}
return $self->{'control_path_dir'};
}
package JobQueue;
sub new {
my $class = shift;
my $command = shift;
my $read_from = shift;
my $context_replace = shift;
my $max_number_of_args = shift;
my $return_files = shift;
my $commandlinequeue = CommandLineQueue->new(
$command,$read_from,$context_replace,$max_number_of_args,$return_files);
my @unget = ();
return bless {
'unget' => \@unget,
'commandlinequeue' => $commandlinequeue,
'total_jobs' => undef,
}, ref($class) || $class;
}
sub get {
my $self = shift;
if(@{$self->{'unget'}}) {
my $job = shift @{$self->{'unget'}};
return ($job);
} else {
my $commandline = $self->{'commandlinequeue'}->get();
if(defined $commandline) {
my $job = Job->new($commandline);
return $job;
} else {
return undef;
}
}
}
sub unget {
my $self = shift;
unshift @{$self->{'unget'}}, @_;
}
sub empty {
my $self = shift;
my $empty = (not @{$self->{'unget'}})
&& $self->{'commandlinequeue'}->empty();
::debug("JobQueue->empty $empty\n");
return $empty;
}
sub total_jobs {
my $self = shift;
if(not defined $self->{'total_jobs'}) {
my $job;
my @queue;
while($job = $self->get()) {
push @queue, $job;
}
$self->unget(@queue);
$self->{'total_jobs'} = $#queue+1;
}
return $self->{'total_jobs'};
}
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 $commandline = shift;
return bless {
'commandline' => $commandline, # The commandline with no args
'workdir' => undef, # --workdir
'stdin' => undef, # filehandle for stdin (used for --pipe)
'stdout' => undef, # filehandle for stdout (used for --group)
# filename for writing stdout to (used for --files)
'stdoutfilename' => undef,
'stderr' => undef, # filehandle for stderr (used for --group)
'remaining' => "", # remaining data not sent to stdin (used for --pipe)
'datawritten' => 0, # 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,
}, ref($class) || $class;
}
sub replaced {
my $self = shift;
$self->{'commandline'} or Carp::croak("cmdline empty");
return $self->{'commandline'}->replaced();
}
sub seq {
my $self = shift;
return $self->{'commandline'}->seq();
}
sub set_stdout {
my $self = shift;
$self->{'stdout'} = shift;
}
sub stdout {
my $self = shift;
return $self->{'stdout'};
}
sub set_stdoutfilename {
my $self = shift;
$self->{'stdoutfilename'} = shift;
}
sub stdoutfilename {
my $self = shift;
return $self->{'stdoutfilename'};
}
sub stderr {
my $self = shift;
return $self->{'stderr'};
}
sub set_stderr {
my $self = shift;
$self->{'stderr'} = shift;
}
sub stdin {
my $self = shift;
return $self->{'stdin'};
}
sub set_stdin {
my $self = shift;
my $stdin = shift;
# set non-blocking
fcntl($stdin, ::F_SETFL, ::O_NONBLOCK) or
::die_bug("Couldn't set flags for HANDLE: $!");
$self->{'stdin'} = $stdin;
}
sub write {
my $self = shift;
my $remaining_ref = shift;
if(length($$remaining_ref)) {
$self->{'remaining'} .= $$remaining_ref;
$self->complete_write();
}
}
sub complete_write {
# Returns:
# number of bytes written (see syswrite)
my $self = shift;
my $in = $self->{'stdin'};
my $len = syswrite($in,$self->{'remaining'});
if (!defined($len) && $! == &::EAGAIN) {
# write would block;
} else {
# Remove the part that was written
substr($self->{'remaining'},0,$len) = "";
$self->{'datawritten'} += $len;
}
return $len;
}
sub remaining {
my $self = shift;
if(defined $self->{'remaining'}) {
return length $self->{'remaining'};
} else {
return undef;
}
}
sub datawritten {
my $self = shift;
return $self->{'datawritten'};
}
sub pid {
my $self = shift;
return $self->{'pid'};
}
sub set_pid {
my $self = shift;
$self->{'pid'} = shift;
}
sub starttime {
my $self = shift;
return $self->{'starttime'};
}
sub set_starttime {
my $self = shift;
my $starttime = shift || time;
$self->{'starttime'} = $starttime;
}
sub runtime {
my $self = shift;
return $self->{'endtime'}-$self->{'starttime'};
}
sub endtime {
my $self = shift;
return $self->{'endtime'};
}
sub set_endtime {
my $self = shift;
my $endtime = shift || time;
$self->{'endtime'} = $endtime;
}
sub set_timeout {
my $self = shift;
my $delta_time = shift;
$self->{'timeout'} = time + $delta_time;
}
sub timeout {
my $self = shift;
return $self->{'timeout'};
}
sub timedout {
my $self = shift;
return time > $self->{'timeout'};
}
sub kill {
# kill the jobs
my $self = shift;
my @family_pids = $self->family_pids();
# Record this jobs as failed
$self->set_exitstatus(1);
# Send two TERMs to give time to clean up
for my $signal ("TERM", "TERM", "KILL") {
my $alive = 0;
for my $pid (@family_pids) {
if(kill 0, $pid) {
# The job still running
kill $signal, $pid;
$alive = 1;
}
}
# Wait 200 ms between TERMs - but only if any pids are alive
if($signal eq "TERM" and $alive) { ::usleep(200); }
}
}
sub family_pids {
# Find the pids with this->pid as (grand)*parent
# TODO test this on different OS as 'ps' is known to be different
my $self = shift;
my $pid = $self->pid();
my $script = q{
family_pids() {
for CHILDPID in `ps --ppid "$@" -o pid --no-headers`; do
family_pids $CHILDPID &
done
echo "$@"
}
} .
"family_pids $pid; wait";
my @pids = qx{$script};
chomp(@pids);
return ($pid,@pids);
}
sub failed {
# return number of times failed for this $sshlogin
my $self = shift;
my $sshlogin = shift;
return $self->{'failed'}{$sshlogin};
}
sub failed_here {
# return number of times failed for the current $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:
# the number of times this command has failed
my $self = shift;
my $total_failures = 0;
for (values %{$self->{'failed'}}) {
$total_failures += $_;
}
return ($total_failures);
}
sub set_sshlogin {
my $self = shift;
my $sshlogin = shift;
$self->{'sshlogin'} = $sshlogin;
delete $self->{'sshlogin_wrap'}; # If sshlogin is changed the wrap is wrong
}
sub sshlogin {
my $self = shift;
return $self->{'sshlogin'};
}
sub sshlogin_wrap {
# Wrap the command with the commands needed to run remotely
my $self = shift;
if(not defined $self->{'sshlogin_wrap'}) {
my $sshlogin = $self->sshlogin();
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $next_command_line = $self->replaced();
my ($pre,$post,$cleanup)=("","","");
if($serverlogin eq ":") {
$self->{'sshlogin_wrap'} = $next_command_line;
} else {
# --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 = '_EXIT_status=$?; ' . $post . ' exit $_EXIT_status;';
}
# If the remote login shell is (t)csh then use 'setenv'
# otherwise use 'export'
my $parallel_env =
q{'eval `echo $SHELL | grep -E "/(t)?csh" > /dev/null}
. q{ && echo setenv PARALLEL_SEQ '$PARALLEL_SEQ'\;}
. q{ setenv PARALLEL_PID '$PARALLEL_PID'}
. q{ || echo PARALLEL_SEQ='$PARALLEL_SEQ'\;export PARALLEL_SEQ\;}
. q{PARALLEL_PID='$PARALLEL_PID'\;export PARALLEL_PID` ;'};
if($::opt_workdir) {
$self->{'sshlogin_wrap'} =
($pre . "$sshcmd $serverlogin $parallel_env "
. ::shell_quote_scalar("cd ".$self->workdir()." && ")
. ::shell_quote_scalar($next_command_line).";".$post);
} else {
$self->{'sshlogin_wrap'} =
($pre . "$sshcmd $serverlogin $parallel_env "
. ::shell_quote_scalar($next_command_line).";".$post);
}
}
}
return $self->{'sshlogin_wrap'};
}
sub transfer {
# Files to transfer
my $self = shift;
my @transfer = ();
$self->{'transfersize'} = 0;
if($::opt_transfer) {
for my $record (@{$self->{'commandline'}{'arg_list'}}) {
# Merge arguments from records into args
for my $arg (@$record) {
CORE::push @transfer, $arg->orig();
# filesize
if(-e $arg->orig()) {
$self->{'transfersize'} += (stat($arg->orig()))[7];
}
}
}
}
return @transfer;
}
sub transfersize {
my $self = shift;
return $self->{'transfersize'};
}
sub sshtransfer {
my $self = shift;
my $sshlogin = $self->sshlogin();
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $rsync_opt = "-rlDzR -e".::shell_quote_scalar($sshcmd);
my $pre = "";
for my $file ($self->transfer()) {
$file =~ s:/\./:/:g; # Rsync treats /./ special. We dont want that
$file =~ s:^\./::g; # Remove ./ if any
my $relpath = ($file !~ m:^/:); # Is the path relative?
# Use different subdirs depending on abs or rel path
# Abs path: rsync -rlDzR /home/tange/dir/subdir/file.gz server:/
# Rel path: rsync -rlDzR ./subdir/file.gz server:.parallel/tmp/tempid/
# Rel path: rsync -rlDzR ./subdir/file.gz server:$workdir/
my $remote_workdir = $self->workdir($file);
my $rsync_destdir = ($relpath ? $remote_workdir : "/");
if($relpath) {
$file = "./".$file;
}
if(-r $file) {
my $mkremote_workdir =
$remote_workdir eq "." ? "true" :
"ssh $serverlogin mkdir -p $rsync_destdir";
$pre .= "$mkremote_workdir; rsync $rsync_opt "
. ::shell_quote_scalar($file)." $serverlogin:$rsync_destdir;";
} else {
print $Global::original_stderr
"parallel: Warning: "
. $file . " is not readable and will not be transferred\n";
}
}
return $pre;
}
sub return {
# Files to return
# Quoted and with {...} substituted
my $self = shift;
my @return = ();
for my $return (@{$self->{'commandline'}{'return_files'}}) {
CORE::push @return,
$self->{'commandline'}->replace_placeholders($return,1);
}
return @return;
}
sub returnsize {
# This is called after the job has finished
my $self = shift;
for my $file ($self->return()) {
if(-e $file) {
$self->{'returnsize'} += (stat($file))[7];
}
}
return $self->{'returnsize'};
}
sub sshreturn {
my $self = shift;
my $sshlogin = $self->sshlogin();
my $sshcmd = $sshlogin->sshcommand();
my $serverlogin = $sshlogin->serverlogin();
my $rsync_opt = "-rlDzR -e".::shell_quote_scalar($sshcmd);
my $pre = "";
for my $file ($self->return()) {
$file =~ s:/\./:/:g; # Rsync treats /./ special. We dont want that
$file =~ s:^\./::g; # Remove ./ if any
my $relpath = ($file !~ m:^/:); # Is the path relative?
# Use different subdirs depending on abs or rel path
# Return or cleanup
my @cmd = ();
my $rsync_destdir = ($relpath ? "./" : "/");
my $ret_file = $file;
my $remove = $::opt_cleanup ? "--remove-source-files" : "";
# If relative path: prepend workdir/./ to avoid problems
# if the dir contains ':' and to get the right relative return path
my $replaced = ($relpath ? $self->workdir()."/./" : "") . $file;
# --return
# Abs path: rsync -rlDzR server:/home/tange/dir/subdir/file.gz /
# Rel path: rsync -rlDzR server:./subsir/file.gz ./
$pre .= "rsync $rsync_opt $remove $serverlogin:".
::shell_quote_scalar($replaced) . " ".$rsync_destdir.";";
}
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 $removeworkdir = "";
my $cleancmd = "";
for my $file ($self->cleanup()) {
my @subworkdirs = parentdirs_of($file);
$file = ::shell_quote_scalar($file);
if(@subworkdirs) {
$removeworkdir = "; rmdir 2>/dev/null ".
join(" ",map { ::shell_quote_scalar($workdir."/".$_) }
@subworkdirs);
}
my $relpath = ($file !~ m:^/:); # Is the path relative?
my $cleandir = ($relpath ? $workdir."/" : "");
$cleancmd .= "$sshcmd $serverlogin rm -f "
. ::shell_quote_scalar($cleandir.$file.$removeworkdir).";";
}
return $cleancmd;
}
sub cleanup {
# Returns:
# Files to remove at cleanup
my $self = shift;
if($::opt_cleanup) {
my @transfer = $self->transfer();
return @transfer;
} else {
return ();
}
}
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();
$::opt_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.
$::opt_workdir = join("/",@dir_parts);
last;
}
}
}
} elsif($::opt_workdir eq "...") {
$workdir = ".parallel/tmp/" . ::hostname() . "-" . $$
. "-" . $self->seq();
} else {
$workdir = $::opt_workdir;
# Rsync treats /./ special. We dont want that
$workdir =~ s:/\./:/:g; # Remove /./
$workdir =~ s:/+$::; # 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
my $job = shift;
my $command = $job->sshlogin_wrap();
if($Global::interactive or $Global::stderr_verbose) {
if($Global::interactive) {
print $Global::original_stderr "$command ?...";
open(TTY,"/dev/tty") || ::die_bug("interactive-tty");
my $answer = ;
close TTY;
my $run_yes = ($answer =~ /^\s*y/i);
if (not $run_yes) {
$command = "true"; # Run the command 'true'
}
} else {
print $Global::original_stderr "$command\n";
}
}
local (*IN,*OUT,*ERR);
my $pid;
if($Global::grouped) {
my ($outfh,$errfh,$name);
# To group we create temporary files for STDOUT and STDERR
# To avoid the cleanup unlink the files immediately (but keep them open)
($outfh,$name) = ::tempfile(SUFFIX => ".par");
$job->set_stdoutfilename($name);
$::opt_files or unlink $name;
($errfh,$name) = ::tempfile(SUFFIX => ".par");
unlink $name;
open OUT, '>&', $outfh or ::die_bug("Can't redirect STDOUT: $!");
open ERR, '>&', $errfh or ::die_bug("Can't dup STDOUT: $!");
$job->set_stdout($outfh);
$job->set_stderr($errfh);
} else {
(*OUT,*ERR)=(*STDOUT,*STDERR);
}
if(($::opt_dryrun or $Global::verbose) and not $Global::grouped) {
if($Global::verbose <= 1) {
print OUT $job->replaced(),"\n";
} else {
# Verbose level > 1: Print the rsync and stuff
print OUT $command,"\n";
}
}
if($::opt_dryrun) {
$command = "true";
}
$Global::total_running++;
$Global::total_started++;
$ENV{'PARALLEL_SEQ'} = $job->seq();
$ENV{'PARALLEL_PID'} = $$;
::debug("$Global::total_running processes. Starting ("
. $job->seq() . "): $command\n");
if($::opt_pipe) {
my ($in);
$pid = ::open3($in, ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
::die_bug("open3-pipe");
$job->set_stdin($in);
} elsif(@::opt_a and not $Global::stdin_in_opt_a and $job->seq() == 1) {
# Give STDIN to the first job if using -a
*IN = *STDIN;
$pid = ::open3("<&IN", ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
::die_bug("open3-a");
# Re-open to avoid complaining
open STDIN, "<&", $Global::original_stdin
or ::die_bug("dup-\$Global::original_stdin: $!");
} elsif ($::opt_tty and not $Global::tty_taken and -c "/dev/tty" and
open(DEVTTY, "/dev/tty")) {
# Give /dev/tty to the command if no one else is using it
*IN = *DEVTTY;
$pid = ::open3("<&IN", ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
::die_bug("open3-/dev/tty");
$Global::tty_taken = $pid;
close DEVTTY;
} else {
$pid = ::open3(::gensym, ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
::die_bug("open3-gensym");
}
$job->set_pid($pid);
$job->set_starttime();
if($::opt_timeout) {
# Timeout must be set before inserting into queue
$job->set_timeout($::opt_timeout);
$Global::timeoutq->insert($job);
}
return $job;
}
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()) {
# 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();
if($self->total_failed() == $::opt_retries) {
# This has been retried enough
return 0;
} else {
# This command should be retried
$Global::JobQueue->unget($self);
::debug("Retry ".$self->seq()."\n");
return 1;
}
}
}
sub print {
# Print the output of the jobs
# Returns: N/A
my $self = shift;
::debug(">>joboutput ".$self->replaced()."\n");
# Only relevant for grouping
$Global::grouped or return;
my $out = $self->stdout();
my $err = $self->stderr();
my $command = $self->sshlogin_wrap();
if($Global::joblog) {
my $cmd;
if($Global::verbose <= 1) {
$cmd = $self->replaced();
} else {
# Verbose level > 1: Print the rsync and stuff
$cmd = $command;
}
printf $Global::joblog
join("\t", $self->seq(), $self->sshlogin()->string(),
$self->starttime(), $self->runtime(),
$self->transfersize(), $self->returnsize(),
$self->exitstatus(), $self->exitsignal(), $cmd
). "\n";
flush $Global::joblog;
$self->set_job_in_joblog();
}
if(($::opt_dryrun or $Global::verbose) and $Global::grouped) {
if($Global::verbose <= 1) {
print STDOUT $self->replaced(),"\n";
} else {
# Verbose level > 1: Print the rsync and stuff
print STDOUT $command,"\n";
}
# If STDOUT and STDERR are merged,
# we want the command to be printed first
# so flush to avoid STDOUT being buffered
flush STDOUT;
}
seek $err, 0, 0;
if($Global::debug) {
print STDERR "ERR:\n";
}
if($::opt_tag or defined $::opt_tagstring) {
my $tag = $self->tag();
while(<$err>) {
print STDERR $tag,$_;
}
} else {
my $buf;
while(sysread($err,$buf,1000_000)) {
print STDERR $buf;
}
}
flush STDERR;
if($::opt_files) {
print STDOUT $self->{'stdoutfilename'},"\n";
} else {
my $buf;
seek $out, 0, 0;
if($Global::debug) {
print STDOUT "OUT:\n";
}
if($::opt_tag or defined $::opt_tagstring) {
my $tag = $self->tag();
while(<$out>) {
print STDOUT $tag,$_;
}
} else {
my $buf;
while(sysread($out,$buf,1000_000)) {
print STDOUT $buf;
}
}
flush STDOUT;
::debug("<{'tag'}) {
$self->{'tag'} = $self->{'commandline'}->
replace_placeholders($::opt_tagstring,0)."\t";
}
return $self->{'tag'};
}
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;
}
}
sub exitsignal {
my $self = shift;
return $self->{'exitsignal'};
}
sub set_exitsignal {
my $self = shift;
my $exitsignal = shift;
$self->{'exitsignal'} = $exitsignal;
}
package CommandLine;
sub new {
my $class = shift;
my $seq = shift;
my $command = ::undef_as_empty(shift);
my $arg_queue = shift;
my $context_replace = shift;
my $max_number_of_args = shift; # for -N and normal (-N1)
my $return_files = shift;
my $len = {
'{}' => 0, # Total length of all {} replaced with all args
'{/}' => 0, # Total length of all {/} replaced with all args
'{//}' => 0, # Total length of all {//} replaced with all args
'{.}' => 0, # Total length of all {.} replaced with all args
'{/.}' => 0, # Total length of all {/.} replaced with all args
'no_args' => undef, # Length of command w/ all replacement args removed
'context' => undef, # Length of context of an additional arg
};
my($sum,%replacecount);
($sum,$len->{'no_args'},$len->{'context'},$len->{'contextgroups'},
%replacecount) = number_of_replacements($command,$context_replace);
if($sum == 0) {
if($command eq "") {
$command = $Global::replace{'{}'};
} else {
# Add {} to the command if there are no {...}'s
$command .=" ".$Global::replace{'{}'};
}
($sum,$len->{'no_args'},$len->{'context'},$len->{'contextgroups'},
%replacecount) = number_of_replacements($command,$context_replace);
}
if(defined $::opt_tagstring) {
my ($dummy1,$dummy2,$dummy3,$dummy4,%repcount) =
number_of_replacements($::opt_tagstring,$context_replace);
# Merge %repcount with %replacecount to get the keys
# for replacing replacement strings in $::opt_tagstring
# The number, however, does not matter.
for (keys %repcount) {
$replacecount{$_} ||= 0;
}
}
my %positional_replace;
my %multi_replace;
for my $used (keys %replacecount) {
if($used =~ /^{(\d+)(\D*)}$/) {
$positional_replace{$1} = '\{'.$2.'\}';
} else {
$multi_replace{$used} = $used;
}
}
return bless {
'command' => $command,
'seq' => $seq,
'len' => $len,
'arg_list' => [],
'arg_queue' => $arg_queue,
'max_number_of_args' => $max_number_of_args,
'replacecount' => \%replacecount,
'context_replace' => $context_replace,
'return_files' => $return_files,
'positional_replace' => \%positional_replace,
'multi_replace' => \%multi_replace,
'replaced' => undef,
}, ref($class) || $class;
}
sub seq {
my $self = shift;
return $self->{'seq'};
}
sub populate {
# Add arguments from arg_queue until the number of arguments or
# max line length is reached
my $self = shift;
if($::opt_pipe) {
# Do no read any args
$self->push([Arg->new("")]);
return;
}
my $next_arg;
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() >= Limits::Command::max_length()) {
# 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);
print STDERR ("$Global::progname: Command line too ",
"long (", $self->len(), " >= ",
Limits::Command::max_length(),
") at number ",
$self->{'arg_queue'}->arg_number(),
": ".
(substr($args,0,50))."...\n");
$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 $CommandLine::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)
$CommandLine::already_spread++;
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());
}
}
}
}
sub push {
# Add one or more records as arguments
my $self = shift;
my $record = shift;
push @{$self->{'arg_list'}}, $record;
#::my_dump($record);
my $arg_no = ($self->number_of_args()-1) * ($#$record+1);
for my $arg (@$record) {
$arg_no++;
if(defined $arg) {
if($self->{'positional_replace'}{$arg_no}) {
# TODO probably bug here if both {1.} and {1} are used
for my $used (keys %{$self->{'replacecount'}}) {
# {} {/} {//} {.} or {/.}
my $replacementfunction =
$self->{'positional_replace'}{$arg_no};
# Find the single replacements
$self->{'len'}{$used} +=
length $arg->replace($replacementfunction);
}
}
for my $used (keys %{$self->{'multi_replace'}}) {
# Add to the multireplacement
$self->{'len'}{$used} += length $arg->replace($used);
}
}
}
}
sub pop {
# Remove last argument
my $self = shift;
my $record = pop @{$self->{'arg_list'}};
for my $arg (@$record) {
if(defined $arg) {
for my $replacement_string (keys %{$self->{'replacecount'}}) {
$self->{'len'}{$replacement_string} -=
length $arg->replace($replacement_string);
}
}
}
return $record;
}
sub pop_all {
# Remove all arguments
my $self = shift;
my @popped = @{$self->{'arg_list'}};
for my $replacement_string (keys %{$self->{'replacecount'}}) {
$self->{'len'}{$replacement_string} = 0;
}
$self->{'arg_list'} = [];
return @popped;
}
sub number_of_args {
my $self = shift;
# This is really number of records
return $#{$self->{'arg_list'}}+1;
}
sub args_as_string {
# Returns:
# all unmodified arguments joined with ' ' (similar to {})
my $self = shift;
return (join " ", map { $_->orig() }
map { @$_ } @{$self->{'arg_list'}});
}
sub len {
# The length of the command line with args substituted
my $self = shift;
my $len = 0;
# Add length of the original command with no args
$len += $self->{'len'}{'no_args'};
if($self->{'context_replace'}) {
$len += $self->number_of_args()*$self->{'len'}{'context'};
for my $replstring (keys %{$self->{'replacecount'}}) {
if(defined $self->{'len'}{$replstring}) {
$len += $self->{'len'}{$replstring} *
$self->{'replacecount'}{$replstring};
}
}
$len += ($self->number_of_args()-1) * $self->{'len'}{'contextgroups'};
} else {
# Each replacement string may occur several times
# Add the length for each time
for my $replstring (keys %{$self->{'replacecount'}}) {
if(defined $self->{'len'}{$replstring}) {
$len += $self->{'len'}{$replstring} *
$self->{'replacecount'}{$replstring};
}
if($Global::replace{$replstring}) {
# This is a multi replacestring ({} {/} {//} {.} {/.})
# Add each space between two arguments
my $number_of_args = ($#{$self->{'arg_list'}[0]}+1) *
$self->number_of_args();
$len += ($number_of_args-1) *
$self->{'replacecount'}{$replstring};
}
}
}
if($::opt_nice) {
# Pessimistic length if --nice is set
# Worse than worst case: every char needs to be quoted with \
$len *= 2;
}
if($::opt_shellquote) {
# Pessimistic length if --shellquote is set
# Worse than worst case: every char needs to be quoted with \ twice
$len *= 4;
}
return $len;
}
sub multi_regexp {
if(not $CommandLine::multi_regexp) {
$CommandLine::multi_regexp =
"(?:".
join("|",map {my $a=$_; $a =~ s/(\W)/\\$1/g; $a}
($Global::replace{"{}"},
$Global::replace{"{.}"},
$Global::replace{"{/}"},
$Global::replace{"{//}"},
$Global::replace{"{/.}"})
).")";
}
return $CommandLine::multi_regexp;
}
sub number_of_replacements {
# Returns:
# sum_of_count, length_of_command_with_no_args,
# length_of_context { 'replacementstring' => count }
my $command = shift;
my $context_replace = shift;
my %count = ();
my $sum = 0;
my $cmd = $command;
my $multi_regexp = multi_regexp();
my $replacement_regexp =
"(?:". ::maybe_quote('\{') .
'\d+(?:|\.|/\.|/|//)?' . # {n} {n.} {n/.} {n/} {n//}
::maybe_quote('\}') .
'|'.
join("|",map {$a=$_;$a=~s/(\W)/\\$1/g; $a} values %Global::replace).
")";
my %c = ();
$cmd =~ s/($replacement_regexp)/$c{$1}++;"\0"/ogex;
for my $k (keys %c) {
if(defined $Global::replace_rev{$k}) {
$count{$Global::replace_rev{$k}} = $c{$k};
} else {
$count{::maybe_unquote($k)} = $c{$k};
}
$sum += $c{$k};
}
my $number_of_context_groups = 0;
my $no_args;
my $context;
if($context_replace) {
$cmd = $command;
while($cmd =~ s/\S*$multi_regexp\S*//o) {
$number_of_context_groups++;
}
$no_args = length $cmd;
$context = length($command) - $no_args;
} else {
$cmd = $command;
$cmd =~ s/$multi_regexp//go;
$cmd =~ s/$replacement_regexp//go;
$no_args = length($cmd);
$context = length($command) - $no_args;
}
for my $k (keys %count) {
if(defined $Global::replace{$k}) {
# {} {/} {//} {.} {/.} {#}
$context -= (length $Global::replace{$k}) * $count{$k};
} else {
# {n}
$context -= (length $k) * $count{$k};
}
}
return ($sum,$no_args,$context,$number_of_context_groups,%count);
}
sub replaced {
my $self = shift;
if(not defined $self->{'replaced'}) {
$self->{'replaced'} = $self->replace_placeholders($self->{'command'},0);
if($self->{'replaced'} =~ /^\s*(-\S+)/) {
# Is this really a command in $PATH starting with '-'?
my $cmd = $1;
if(not grep { -e $_."/".$cmd } split(":",$ENV{'PATH'})) {
print STDERR "parallel: Error:"
. " Command ($cmd) starts with '-'."
. " Is this a wrong option?\n";
::wait_and_exit(255);
}
}
if($::opt_nice) {
# Prepend nice -n19 $SHELL -c
# and quote
$self->{'replaced'} = nice() ." -n" . $::opt_nice . " "
. $ENV{SHELL}." -c "
. ::shell_quote_scalar($self->{'replaced'});
}
if($::opt_shellquote) {
# Prepend echo
# and quote twice
$self->{'replaced'} = "echo " .
::shell_quote_scalar(::shell_quote_scalar($self->{'replaced'}));
}
}
if($::oodebug and length($self->{'replaced'}) != ($self->len())) {
::my_dump($self);
Carp::cluck("replaced len=" . length($self->{'replaced'})
. " computed=" . ($self->len()));
}
return $self->{'replaced'};
}
sub nice {
# Returns:
# path to nice
# Needed because tcsh's built-in nice does not support 'nice -n19'
if(not $Global::path_to_nice) {
$Global::path_to_nice = "nice";
for my $n ((split/:/, $ENV{'PATH'}), "/bin", "/usr/bin") {
if(-x $n."/nice") {
$Global::path_to_nice = $n."/nice";
last;
}
}
}
return $Global::path_to_nice;
}
sub replace_placeholders {
my $self = shift;
my $target = shift;
my $quoteall = shift;
my $context_replace = $self->{'context_replace'};
my $replaced;
if($self->{'context_replace'}) {
$replaced = $self->context_replace_placeholders($target,$quoteall);
} else {
$replaced = $self->simple_replace_placeholders($target,$quoteall);
}
return $replaced;
}
sub context_replace_placeholders {
my $self = shift;
my $target = shift;
my $quoteall = shift;
# -X = context replace
# maybe multiple input sources
# maybe --xapply
# $self->{'arg_list'} = [ [Arg11, Arg12], [Arg21, Arg22], [Arg31, Arg32] ]
my @args=();
my @used_multi;
my %replace;
for my $record (@{$self->{'arg_list'}}) {
# Merge arguments from records into args for easy access
CORE::push @args, @$record;
}
# Replacement functions
my @rep = qw({} {/} {//} {.} {/.});
# Inner part of replacement functions
my @rep_inner = ('', '/', '//', '.', '/.');
# Regexp for replacement functions
my $rep_regexp = "(?:". join('|', map { $_=~s/(\W)/\\$1/g; $_} @rep) . ")";
# Regexp for inner replacement functions
my $rep_inner_regexp = "(?:". join('|', map { $_=~s/(\W)/\\$1/g; $_} @rep_inner) . ")";
# Seq replace string: {#}
my $rep_seq_regexp = '(?:'.::maybe_quote('\{\#\}').")";
# Normal replace strings
my $rep_str_regexp = multi_regexp();
# Positional replace strings
my $rep_str_pos_regexp = ::maybe_quote('\{').'\d+'.$rep_inner_regexp.::maybe_quote('\}');
# Fish out the words that have replacement strings in them
my $tt = $target;
my %word;
while($tt =~ s/(\S*(?:$rep_str_regexp|$rep_str_pos_regexp|$rep_seq_regexp)\S*)/\0/o) {
$word{$1}++;
}
# For each word: Generate the replacement string for that word.
for my $origword (keys %word) {
my @pos_replacements=();
my @replacements=();
my $w;
my $word = $origword; # Make a local modifyable copy
# replace {#} if it exists
$word =~ s/$rep_seq_regexp/$self->seq()/geo;
if($word =~ /$rep_str_pos_regexp/o) {
# There are positional replacement strings
my @argset;
if($#{$self->{'arg_list'}->[0]} == 0) {
# Only one input source: Treat it as a set
@argset = [ @args ];
} else {
@argset = @{$self->{'arg_list'}};
}
# Match 1..n where n = max args in a argset
my $pos_regexp = "(?:".join("|", 1 .. $#{$argset[0]}+1).")";
my $pos_inner_regexp = ::maybe_quote('\{') .
"($pos_regexp)($rep_inner_regexp)" .
::maybe_quote('\}');
for my $argset (@argset) {
# Replace all positional arguments - e.g. {7/.}
# with the replacement function - e.g. {/.}
# of that argument
if(defined $self->{'max_number_of_args'}) {
# Fill up if we have a half completed line, so {n} will be empty
while($#$argset < $self->{'max_number_of_args'}) {
CORE::push @$argset, Arg->new("");
}
}
$w = $word;
$w =~ s/$pos_inner_regexp/$argset->[$1-1]->replace('{'.$2.'}')/geo;
CORE::push @pos_replacements, $w;
}
}
if(not @pos_replacements) {
@pos_replacements = ($word);
}
if($word =~ m:$rep_str_regexp:) {
# There are normal replacement strings
for my $w (@pos_replacements) {
for my $arg (@args) {
my $wmulti = $w;
$wmulti =~ s/($rep_str_regexp)/$arg->replace($Global::replace_rev{$1})/geo;
CORE::push @replacements, $wmulti;
}
}
}
if(@replacements) {
CORE::push @{$replace{$origword}}, @replacements;
} else {
CORE::push @{$replace{$origword}}, @pos_replacements;
}
}
# Substitute the replace strings with the replacement values
# Must be sorted by length if a short word is a substring of a long word
my $regexp = join('|', map { $_=~s/(\W)/\\$1/g; $_}
sort { length $b <=> length $a } keys %word);
$target =~ s/($regexp)/join(" ",@{$replace{$1}})/ge;
return $target;
}
sub simple_replace_placeholders {
# no context (no -X)
# maybe multiple input sources
# maybe --xapply
my $self = shift;
my $target = shift;
my $quoteall = shift;
my @args=();
my @used_multi;
my %replace;
for my $record (@{$self->{'arg_list'}}) {
# Merge arguments from records into args for easy access
CORE::push @args, @$record;
}
# Which replace strings are used?
# {#} {} {/} {//} {.} {/.} {n} {n/} {n//} {n.} {n/.}
for my $used (keys %{$self->{'replacecount'}}) {
# What are the replacement values for the replace strings?
if(grep { $used eq $_ } qw({} {/} {//} {.} {/.})) {
# {} {/} {//} {.} {/.}
$replace{$Global::replace{$used}} =
join(" ", map { $_->replace($used) } @args);
} elsif($used =~ /^\{(\d+)(|\/|\/\/|\.|\/\.)\}$/) {
# {n} {n/} {n//} {n.} {n/.}
my $positional = $1; # number if any
my $replacementfunction = "{".::undef_as_empty($2)."}"; # {} {/} {//} {.} or {/.}
# If -q then the replacementstrings will be quoted, too
# {1.} -> \{1.\}
$Global::replace{$used} ||= ::maybe_quote($used);
if(defined $args[$positional-1]) {
# we have a matching argument for {n}
$replace{$Global::replace{$used}} =
$args[$positional-1]->replace($replacementfunction);
} else {
if($positional <= $self->{'max_number_of_args'}) {
# Fill up if we have a half completed line
$replace{$Global::replace{$used}} = "";
}
}
} elsif($used eq "{#}") {
# {#}
$replace{$Global::replace{$used}} = $self->seq();
} else {
::die_bug('simple_replace_placeholders_20110530');
}
}
# Substitute the replace strings with the replacement values
my $regexp = join('|', map { $_=~s/(\W)/\\$1/g; $_} keys %replace);
if($regexp) {
if($quoteall) {
# This is for --return: The whole expression must be
# quoted - not just the replacements
%replace = map { $_ => ::shell_unquote($replace{$_}) } keys %replace;
$target =~ s/($regexp)/$replace{$1}/g;
$target = ::shell_quote_scalar($target);
} else {
$target =~ s/($regexp)/$replace{$1}/g;
}
}
return $target;
}
package CommandLineQueue;
sub new {
my $class = shift;
my $command = shift;
my $read_from = shift;
my $context_replace = shift;
my $max_number_of_args = shift;
my $return_files = shift;
my @unget = ();
return bless {
'unget' => \@unget,
'command' => $command,
'arg_queue' => RecordQueue->new($read_from,$::opt_colsep),
'context_replace' => $context_replace,
'max_number_of_args' => $max_number_of_args,
'size' => undef,
'return_files' => $return_files,
'seq' => 1,
}, ref($class) || $class;
}
sub get {
my $self = shift;
if(@{$self->{'unget'}}) {
my $cmd_line = shift @{$self->{'unget'}};
return ($cmd_line);
} else {
my $cmd_line;
$cmd_line = CommandLine->new($self->seq(),
$self->{'command'},
$self->{'arg_queue'},
$self->{'context_replace'},
$self->{'max_number_of_args'},
$self->{'return_files'},
);
$cmd_line->populate();
::debug("cmd_line->number_of_args ".$cmd_line->number_of_args()."\n");
if($::opt_pipe) {
if($cmd_line->replaced() eq "") {
# Empty command - pipe requires a command
print STDERR "$Global::progname: --pipe must have a ".
"command to pipe into (e.g. 'cat')\n";
::wait_and_exit(255);
}
} else {
if($cmd_line->number_of_args() == 0) {
# We did not get more args - maybe at EOF string?
return undef;
} elsif($cmd_line->replaced() eq "") {
# Empty command - get the next instead
return $self->get();
}
}
$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("CommandLineQueue->empty $empty\n");
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'};
}
sub size {
my $self = shift;
if(not $self->{'size'}) {
my @all_lines = ();
while(not $self->{'arg_queue'}->empty()) {
push @all_lines, CommandLine->new($self->{'command'},
$self->{'arg_queue'},
$self->{'context_replace'},
$self->{'max_number_of_args'});
}
$self->{'size'} = @all_lines;
$self->unget(@all_lines);
}
return $self->{'size'};
}
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) {
if($::opt_s) {
if(is_acceptable_command_line_length($::opt_s)) {
$Limits::Command::line_max_len = $::opt_s;
} else {
# -s is too long: Find the correct
$Limits::Command::line_max_len = binary_find_max_length(0,$::opt_s);
}
if($::opt_s <= $Limits::Command::line_max_len) {
$Limits::Command::line_max_len = $::opt_s;
} else {
print STDERR "$Global::progname: value for -s option ",
"should be < $Limits::Command::line_max_len\n";
}
} else {
$Limits::Command::line_max_len = real_max_length();
}
}
return $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 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);
}
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("Maxlen: $lower,$upper,$middle\n");
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
# Returns:
# 0 if the command line length is too long
# 1 otherwise
my $len = shift;
$CommandMaxLength::is_acceptable_command_line_length++;
::debug("$CommandMaxLength::is_acceptable_command_line_length $len\n");
local *STDERR;
open (STDERR,">/dev/null");
system "true "."x"x$len;
close STDERR;
::debug("$len $?\n");
return not $?;
}
package RecordQueue;
sub new {
my $class = shift;
my $fhs = shift;
my $colsep = shift;
my @unget = ();
my $arg_sub_queue;
if($colsep) {
# Open one file with colsep
$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'}}) {
return shift @{$self->{'unget'}};
}
$self->{'arg_number'}++;
my $ret = $self->{'arg_sub_queue'}->get();
if(defined $Global::max_number_of_args
and $Global::max_number_of_args == 0) {
::debug("Read 1 but return 0 args\n");
return [Arg->new("")];
} else {
return $ret;
}
}
sub unget {
my $self = shift;
::debug("RecordQueue-unget '@_'\n");
$self->{'arg_number'}--;
unshift @{$self->{'unget'}}, @_;
}
sub empty {
my $self = shift;
my $empty = not @{$self->{'unget'}};
$empty &&= $self->{'arg_sub_queue'}->empty();
::debug("RecordQueue->empty $empty\n");
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("RecordColQueue::arg $arg\n");
my $line = $arg->orig();
::debug("line='$line'\n");
if($line ne "") {
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("RecordColQueue-unget '@_'\n");
unshift @{$self->{'unget'}}, @_;
}
sub empty {
my $self = shift;
my $empty = (not @{$self->{'unget'}} and $self->{'arg_sub_queue'}->empty());
::debug("RecordColQueue->empty $empty");
return $empty;
}
package MultifileQueue;
@Global::unget_argv=();
sub new {
my $class = shift;
my $fhs = shift;
for my $fh (@$fhs) {
if(-t $fh) {
print STDERR "$Global::progname: Input is read from the terminal. ".
"Only experts do this on purpose. ".
"Press CTRL-D to exit.\n";
}
}
return bless {
'unget' => \@Global::unget_argv,
'fhs' => $fhs,
'arg_matrix' => undef,
}, ref($class) || $class;
}
sub get {
my $self = shift;
if($::opt_xapply) {
return $self->xapply_get();
} else {
return $self->nest_get();
}
}
sub unget {
my $self = shift;
::debug("MultifileQueue-unget '@_'\n");
unshift @{$self->{'unget'}}, @_;
}
sub empty {
my $self = shift;
my $empty = (not @Global::unget_argv
and not @{$self->{'unget'}});
for my $fh (@{$self->{'fhs'}}) {
$empty &&= eof($fh);
}
::debug("MultifileQueue->empty $empty\n");
return $empty;
}
sub xapply_get {
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
my @record = ();
my $prepend = undef;
my $empty = 1;
for my $fh (@{$self->{'fhs'}}) {
my $arg = read_arg_from_fh($fh);
if(defined $arg) {
push @record, $arg;
$empty = 0;
} else {
push @record, Arg->new("");
}
}
if($empty) {
return undef;
} else {
return \@record;
}
}
sub nest_get {
my $self = shift;
if(@{$self->{'unget'}}) {
return shift @{$self->{'unget'}};
}
my @record = ();
my $prepend = undef;
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]}];
}
$combarg[$fhno] = [$len,$len]; # Find only combinations with this new entry
# map combinations
# [ 1, 3, 7 ], [ 2, 4, 1 ]
# =>
# [ m[0][1], m[1][3], m[3][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
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 = undef;
my $arg;
do {{
if(eof($fh)) {
if(defined $prepend) {
return Arg->new($prepend);
} else {
return undef;
}
}
$arg = <$fh>;
::debug("read $arg\n");
# Remove delimiter
$arg =~ s:$/$::;
if($Global::end_of_file_string and
$arg eq $Global::end_of_file_string) {
# Ignore the rest of input file
while (<$fh>) {}
::debug("EOF-string $arg\n");
if(defined $prepend) {
return Arg->new($prepend);
} else {
return undef;
}
}
if(defined $prepend) {
$arg = $prepend.$arg; # For line continuation
$prepend = undef; #undef;
}
if($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");
}
}
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 $xmin = $$minmax_ref[0];
my $xmax = $$minmax_ref[1];
my @p;
if(@_) {
# If there are more columns: Compute those recursively
my @rest = expand_combinations(@_);
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 $orig = shift;
if($::oodebug and not defined $orig) {
Carp::cluck($orig);
}
return bless {
'orig' => $orig,
}, ref($class) || $class;
}
sub replace {
my $self = shift;
my $replacement_string = shift; # {} {/} {//} {.} {/.}
if(not defined $self->{$replacement_string}) {
my $s;
if($Global::trim eq "n") {
$s = $self->{'orig'};
} else {
$s = trim_of($self->{'orig'});
}
if($replacement_string eq "{}") {
# skip
} elsif($replacement_string eq "{.}") {
$s =~ s:\.[^/\.]*$::; # Remove .ext from argument
} elsif($replacement_string eq "{/}") {
$s =~ s:^.*/([^/]+)/?$:$1:; # Remove dir from argument. If ending in /, remove final /
} elsif($replacement_string eq "{//}") {
# Only load File::Basename if actually needed
$Global::use{"File::Basename"} ||= eval "use File::Basename;";
$s = dirname($s); # Keep dir from argument.
} elsif($replacement_string eq "{/.}") {
$s =~ s:^.*/([^/]+)/?$:$1:; # Remove dir from argument. If ending in /, remove final /
$s =~ s:\.[^/\.]*$::; # Remove .ext from argument
}
if($Global::JobQueue->quote_args()) {
$s = ::shell_quote_scalar($s);
}
$self->{$replacement_string} = $s;
}
return $self->{$replacement_string};
}
sub orig {
my $self = shift;
return $self->{'orig'};
}
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 $arg (@strings) { $arg =~ s/^\s+//; }
} elsif($Global::trim eq "r") {
for $arg (@strings) { $arg =~ s/\s+$//; }
} elsif($Global::trim eq "rl" or $Global::trim eq "lr") {
for $arg (@strings) { $arg =~ s/^\s+//; $arg =~ s/\s+$//; }
} else {
print STDERR "$Global::progname: --trim must be one of: r l ".
"rl lr\n";
::wait_and_exit(255);
}
return wantarray ? @strings : "@strings";
}
package TimeoutQueue;
sub new {
my $class = shift;
my $delta_time = shift;
return bless {
'queue' => [],
'delta_time' => $delta_time,
}, ref($class) || $class;
}
sub process_timeouts {
# Check if there was a timeout
my $self = shift;
# @Global::timeout is sorted by timeout
while (@{$self->{'queue'}}) {
my $job = $self->{'queue'}[0];
if($job->timedout()) {
# Need to shift off queue before kill
# because kill calls usleep -> process_timeouts
shift @{$self->{'queue'}};
$job->kill();
} else {
# Because they are sorted by timeout
last;
}
}
}
sub insert {
my $self = shift;
my $in = shift;
my $lower = 0;
my $upper = $#{$self->{'queue'}};
my $looking = int(($lower + $upper)/2);
my $in_time = $in->timeout();
# Find the position between $lower and $upper
while($lower < $upper) {
if($self->{'queue'}[$looking]->timeout() < $in_time) {
# Upper half
$lower = $looking+1;
} else {
# Lower half
$upper = $looking;
}
$looking = int(($lower + $upper)/2);
}
# splice at position $looking
splice @{$self->{'queue'}}, $looking, 0, $in;
}
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/semaphores/id- Each
# file in ~/.parallel/semaphores/id-/ 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_dir = $ENV{'HOME'}."/.parallel";
-d $parallel_dir or mkdir $parallel_dir;
my $parallel_locks = $parallel_dir."/semaphores";
-d $parallel_locks or mkdir $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 acquire {
my $self = shift;
my $sleep = 1; # 1 ms
my $start_time = time;
while(1) {
$self->atomic_link_if_count_less_than() and last;
::debug("Remove dead locks");
my $lockdir = $self->{'lockdir'};
for my $d (<$lockdir/*>) {
::debug("Lock $d $lockdir\n");
$d =~ m:$lockdir/([0-9]+)\@([-\._a-z0-9]+)$:o or next;
my ($pid, $host) = ($1,$2);
if($host eq ::hostname()) {
if(not kill 0, $1) {
::debug("Dead: $d");
unlink $d;
} else {
::debug("Alive: $d");
}
}
}
# try again
$self->atomic_link_if_count_less_than() and last;
# 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()*$sleep);
if(defined($::opt_timeout) and
$start_time + $::opt_timeout > time) {
# Acquire the lock anyway
if(not -e $self->{'idfile'}) {
open (A, ">", $self->{'idfile'}) or
::die_bug("write_idfile: $self->{'idfile'}");
close A;
}
link $self->{'idfile'}, $self->{'pidfile'};
last;
}
}
::debug("acquired $self->{'pid'}\n");
}
sub release {
my $self = shift;
unlink $self->{'pidfile'};
if($self->nlinks() == 1) {
# This is the last link, so atomic cleanup
$self->lock();
if($self->nlinks() == 1) {
unlink $self->{'idfile'};
rmdir $self->{'lockdir'};
}
$self->unlock();
}
::debug("released $self->{'pid'}\n");
}
sub atomic_link_if_count_less_than {
# Link $file1 to $file2 if nlinks to $file1 < $count
my $self = shift;
my $retval = 0;
$self->lock();
::debug($self->nlinks()."<".$self->{'count'});
if($self->nlinks() < $self->{'count'}) {
-d $self->{'lockdir'} || mkdir $self->{'lockdir'};
if(not -e $self->{'idfile'}) {
open (A, ">", $self->{'idfile'}) or
::die_bug("write_idfile: $self->{'idfile'}");
close A;
}
$retval = link $self->{'idfile'}, $self->{'pidfile'};
}
$self->unlock();
::debug("atomic $retval");
return $retval;
}
sub nlinks {
my $self = shift;
if(-e $self->{'idfile'}) {
::debug("nlinks".((stat(_))[3])."\n");
return (stat(_))[3];
} else {
return 0;
}
}
sub lock {
my $self = shift;
my $sleep = 100; # 100 ms
open $self->{'lockfh'}, ">", $self->{'lockfile'}
or ::die_bug("Can't open semaphore file $self->{'lockfile'}: $!");
chmod 0666, $self->{'lockfile'}; # assuming you want it a+rw
$Global::use{"Fcntl"} ||= eval "use Fcntl qw(:DEFAULT :flock);";
while(not flock $self->{'lockfh'}, LOCK_EX()|LOCK_NB()) {
if ($! =~ m/Function not implemented/) {
print $Global::original_stderr
("parallel: Warning: flock: $!");
print "parallel: Will wait for a random while\n";
::usleep(rand(5000));
last;
}
::debug("Cannot lock $self->{'lockfile'}");
# TODO if timeout: last
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep);
# Random to avoid every sleeping job waking up at the same time
::usleep(rand()*$sleep);
}
::debug("locked $self->{'lockfile'}");
}
sub unlock {
my $self = shift;
unlink $self->{'lockfile'};
close $self->{'lockfh'};
::debug("unlocked\n");
}
# Keep perl -w happy
$::opt_x = $Semaphore::timeout = $Semaphore::wait = $::opt_shebang =
0;