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Diffstat (limited to 'kaldi_decode/utils/queue.pl')
| -rwxr-xr-x | kaldi_decode/utils/queue.pl | 580 |
1 files changed, 0 insertions, 580 deletions
diff --git a/kaldi_decode/utils/queue.pl b/kaldi_decode/utils/queue.pl deleted file mode 100755 index 1e36de6..0000000 --- a/kaldi_decode/utils/queue.pl +++ /dev/null @@ -1,580 +0,0 @@ -#!/usr/bin/env perl -use strict; -use warnings; - -# Copyright 2012 Johns Hopkins University (Author: Daniel Povey). -# 2014 Vimal Manohar (Johns Hopkins University) -# Apache 2.0. - -use File::Basename; -use Cwd; -use Getopt::Long; - -# queue.pl has the same functionality as run.pl, except that -# it runs the job in question on the queue (Sun GridEngine). -# This version of queue.pl uses the task array functionality -# of the grid engine. Note: it's different from the queue.pl -# in the s4 and earlier scripts. - -# The script now supports configuring the queue system using a config file -# (default in conf/queue.conf; but can be passed specified with --config option) -# and a set of command line options. -# The current script handles: -# 1) Normal configuration arguments -# For e.g. a command line option of "--gpu 1" could be converted into the option -# "-q g.q -l gpu=1" to qsub. How the CLI option is handled is determined by a -# line in the config file like -# gpu=* -q g.q -l gpu=$0 -# $0 here in the line is replaced with the argument read from the CLI and the -# resulting string is passed to qsub. -# 2) Special arguments to options such as -# gpu=0 -# If --gpu 0 is given in the command line, then no special "-q" is given. -# 3) Default argument -# default gpu=0 -# If --gpu option is not passed in the command line, then the script behaves as -# if --gpu 0 was passed since 0 is specified as the default argument for that -# option -# 4) Arbitrary options and arguments. -# Any command line option starting with '--' and its argument would be handled -# as long as its defined in the config file. -# 5) Default behavior -# If the config file that is passed using is not readable, then the script -# behaves as if the queue has the following config file: -# $ cat conf/queue.conf -# # Default configuration -# command qsub -v PATH -cwd -S /bin/bash -j y -l arch=*64* -# option mem=* -l mem_free=$0,ram_free=$0 -# option mem=0 # Do not add anything to qsub_opts -# option num_threads=* -pe smp $0 -# option num_threads=1 # Do not add anything to qsub_opts -# option max_jobs_run=* -tc $0 -# default gpu=0 -# option gpu=0 -q all.q -# option gpu=* -l gpu=$0 -q g.q - -my $qsub_opts = ""; -my $sync = 0; -my $num_threads = 1; -my $gpu = 0; - -my $config = "conf/queue.conf"; - -my %cli_options = (); - -my $jobname; -my $jobstart; -my $jobend; - -my $array_job = 0; - -sub print_usage() { - print STDERR - "Usage: queue.pl [options] [JOB=1:n] log-file command-line arguments...\n" . - "e.g.: queue.pl foo.log echo baz\n" . - " (which will echo \"baz\", with stdout and stderr directed to foo.log)\n" . - "or: queue.pl -q all.q\@xyz foo.log echo bar \| sed s/bar/baz/ \n" . - " (which is an example of using a pipe; you can provide other escaped bash constructs)\n" . - "or: queue.pl -q all.q\@qyz JOB=1:10 foo.JOB.log echo JOB \n" . - " (which illustrates the mechanism to submit parallel jobs; note, you can use \n" . - " another string other than JOB)\n" . - "Note: if you pass the \"-sync y\" option to qsub, this script will take note\n" . - "and change its behavior. Otherwise it uses qstat to work out when the job finished\n" . - "Options:\n" . - " --config <config-file> (default: $config)\n" . - " --mem <mem-requirement> (e.g. --mem 2G, --mem 500M, \n" . - " also support K and numbers mean bytes)\n" . - " --num-threads <num-threads> (default: $num_threads)\n" . - " --max-jobs-run <num-jobs>\n" . - " --gpu <0|1> (default: $gpu)\n"; - exit 1; -} - -if (@ARGV < 2) { - print_usage(); -} - -for (my $x = 1; $x <= 3; $x++) { # This for-loop is to - # allow the JOB=1:n option to be interleaved with the - # options to qsub. - while (@ARGV >= 2 && $ARGV[0] =~ m:^-:) { - my $switch = shift @ARGV; - - if ($switch eq "-V") { - $qsub_opts .= "-V "; - } else { - my $argument = shift @ARGV; - if ($argument =~ m/^--/) { - print STDERR "WARNING: suspicious argument '$argument' to $switch; starts with '-'\n"; - } - if ($switch eq "-sync" && $argument =~ m/^[yY]/) { - $sync = 1; - $qsub_opts .= "$switch $argument "; - } elsif ($switch eq "-pe") { # e.g. -pe smp 5 - my $argument2 = shift @ARGV; - $qsub_opts .= "$switch $argument $argument2 "; - $num_threads = $argument2; - } elsif ($switch =~ m/^--/) { # Config options - # Convert CLI option to variable name - # by removing '--' from the switch and replacing any - # '-' with a '_' - $switch =~ s/^--//; - $switch =~ s/-/_/g; - $cli_options{$switch} = $argument; - } else { # Other qsub options - passed as is - $qsub_opts .= "$switch $argument "; - } - } - } - if ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+):(\d+)$/) { # e.g. JOB=1:20 - $array_job = 1; - $jobname = $1; - $jobstart = $2; - $jobend = $3; - shift; - if ($jobstart > $jobend) { - die "queue.pl: invalid job range $ARGV[0]"; - } - if ($jobstart <= 0) { - die "run.pl: invalid job range $ARGV[0], start must be strictly positive (this is a GridEngine limitation)."; - } - } elsif ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+)$/) { # e.g. JOB=1. - $array_job = 1; - $jobname = $1; - $jobstart = $2; - $jobend = $2; - shift; - } elsif ($ARGV[0] =~ m/.+\=.*\:.*$/) { - print STDERR "Warning: suspicious first argument to queue.pl: $ARGV[0]\n"; - } -} - -if (@ARGV < 2) { - print_usage(); -} - -if (exists $cli_options{"config"}) { - $config = $cli_options{"config"}; -} - -my $default_config_file = <<'EOF'; -# Default configuration -command qsub -v PATH -cwd -S /bin/bash -j y -l arch=*64* -option mem=* -l mem_free=$0,ram_free=$0 -option mem=0 # Do not add anything to qsub_opts -option num_threads=* -pe smp $0 -option num_threads=1 # Do not add anything to qsub_opts -option max_jobs_run=* -tc $0 -default gpu=0 -option gpu=0 -option gpu=* -l gpu=$0 -q g.q -EOF - -# Here the configuration options specified by the user on the command line -# (e.g. --mem 2G) are converted to options to the qsub system as defined in -# the config file. (e.g. if the config file has the line -# "option mem=* -l ram_free=$0,mem_free=$0" -# and the user has specified '--mem 2G' on the command line, the options -# passed to queue system would be "-l ram_free=2G,mem_free=2G -# A more detailed description of the ways the options would be handled is at -# the top of this file. - -my $opened_config_file = 1; - -open CONFIG, "<$config" or $opened_config_file = 0; - -my %cli_config_options = (); -my %cli_default_options = (); - -if ($opened_config_file == 0 && exists($cli_options{"config"})) { - print STDERR "Could not open config file $config\n"; - exit(1); -} elsif ($opened_config_file == 0 && !exists($cli_options{"config"})) { - # Open the default config file instead - open (CONFIG, "echo '$default_config_file' |") or die "Unable to open pipe\n"; - $config = "Default config"; -} - -my $qsub_cmd = ""; -my $read_command = 0; - -while(<CONFIG>) { - chomp; - my $line = $_; - $_ =~ s/\s*#.*//g; - if ($_ eq "") { next; } - if ($_ =~ /^command (.+)/) { - $read_command = 1; - $qsub_cmd = $1 . " "; - } elsif ($_ =~ m/^option ([^=]+)=\* (.+)$/) { - # Config option that needs replacement with parameter value read from CLI - # e.g.: option mem=* -l mem_free=$0,ram_free=$0 - my $option = $1; # mem - my $arg= $2; # -l mem_free=$0,ram_free=$0 - if ($arg !~ m:\$0:) { - die "Unable to parse line '$line' in config file ($config)\n"; - } - if (exists $cli_options{$option}) { - # Replace $0 with the argument read from command line. - # e.g. "-l mem_free=$0,ram_free=$0" -> "-l mem_free=2G,ram_free=2G" - $arg =~ s/\$0/$cli_options{$option}/g; - $cli_config_options{$option} = $arg; - } - } elsif ($_ =~ m/^option ([^=]+)=(\S+)\s?(.*)$/) { - # Config option that does not need replacement - # e.g. option gpu=0 -q all.q - my $option = $1; # gpu - my $value = $2; # 0 - my $arg = $3; # -q all.q - if (exists $cli_options{$option}) { - $cli_default_options{($option,$value)} = $arg; - } - } elsif ($_ =~ m/^default (\S+)=(\S+)/) { - # Default options. Used for setting default values to options i.e. when - # the user does not specify the option on the command line - # e.g. default gpu=0 - my $option = $1; # gpu - my $value = $2; # 0 - if (!exists $cli_options{$option}) { - # If the user has specified this option on the command line, then we - # don't have to do anything - $cli_options{$option} = $value; - } - } else { - print STDERR "queue.pl: unable to parse line '$line' in config file ($config)\n"; - exit(1); - } -} - -close(CONFIG); - -if ($read_command != 1) { - print STDERR "queue.pl: config file ($config) does not contain the line \"command .*\"\n"; - exit(1); -} - -for my $option (keys %cli_options) { - if ($option eq "config") { next; } - if ($option eq "max_jobs_run" && $array_job != 1) { next; } - my $value = $cli_options{$option}; - - if (exists $cli_default_options{($option,$value)}) { - $qsub_opts .= "$cli_default_options{($option,$value)} "; - } elsif (exists $cli_config_options{$option}) { - $qsub_opts .= "$cli_config_options{$option} "; - } else { - if ($opened_config_file == 0) { $config = "default config file"; } - die "queue.pl: Command line option $option not described in $config (or value '$value' not allowed)\n"; - } -} - -my $cwd = getcwd(); -my $logfile = shift @ARGV; - -if ($array_job == 1 && $logfile !~ m/$jobname/ - && $jobend > $jobstart) { - print STDERR "queue.pl: you are trying to run a parallel job but " - . "you are putting the output into just one log file ($logfile)\n"; - exit(1); -} - -# -# Work out the command; quote escaping is done here. -# Note: the rules for escaping stuff are worked out pretty -# arbitrarily, based on what we want it to do. Some things that -# we pass as arguments to queue.pl, such as "|", we want to be -# interpreted by bash, so we don't escape them. Other things, -# such as archive specifiers like 'ark:gunzip -c foo.gz|', we want -# to be passed, in quotes, to the Kaldi program. Our heuristic -# is that stuff with spaces in should be quoted. This doesn't -# always work. -# -my $cmd = ""; - -foreach my $x (@ARGV) { - if ($x =~ m/^\S+$/) { $cmd .= $x . " "; } # If string contains no spaces, take - # as-is. - elsif ($x =~ m:\":) { $cmd .= "'$x' "; } # else if no dbl-quotes, use single - else { $cmd .= "\"$x\" "; } # else use double. -} - -# -# Work out the location of the script file, and open it for writing. -# -my $dir = dirname($logfile); -my $base = basename($logfile); -my $qdir = "$dir/q"; -$qdir =~ s:/(log|LOG)/*q:/q:; # If qdir ends in .../log/q, make it just .../q. -my $queue_logfile = "$qdir/$base"; - -if (!-d $dir) { system "mkdir -p $dir 2>/dev/null"; } # another job may be doing this... -if (!-d $dir) { die "Cannot make the directory $dir\n"; } -# make a directory called "q", -# where we will put the log created by qsub... normally this doesn't contain -# anything interesting, evertyhing goes to $logfile. -if (! -d "$qdir") { - system "mkdir $qdir 2>/dev/null"; - sleep(5); ## This is to fix an issue we encountered in denominator lattice creation, - ## where if e.g. the exp/tri2b_denlats/log/15/q directory had just been - ## created and the job immediately ran, it would die with an error because nfs - ## had not yet synced. I'm also decreasing the acdirmin and acdirmax in our - ## NFS settings to something like 5 seconds. -} - -my $queue_array_opt = ""; -if ($array_job == 1) { # It's an array job. - $queue_array_opt = "-t $jobstart:$jobend"; - $logfile =~ s/$jobname/\$SGE_TASK_ID/g; # This variable will get - # replaced by qsub, in each job, with the job-id. - $cmd =~ s/$jobname/\$\{SGE_TASK_ID\}/g; # same for the command... - $queue_logfile =~ s/\.?$jobname//; # the log file in the q/ subdirectory - # is for the queue to put its log, and this doesn't need the task array subscript - # so we remove it. -} - -# queue_scriptfile is as $queue_logfile [e.g. dir/q/foo.log] but -# with the suffix .sh. -my $queue_scriptfile = $queue_logfile; -($queue_scriptfile =~ s/\.[a-zA-Z]{1,5}$/.sh/) || ($queue_scriptfile .= ".sh"); -if ($queue_scriptfile !~ m:^/:) { - $queue_scriptfile = $cwd . "/" . $queue_scriptfile; # just in case. -} - -# We'll write to the standard input of "qsub" (the file-handle Q), -# the job that we want it to execute. -# Also keep our current PATH around, just in case there was something -# in it that we need (although we also source ./path.sh) - -my $syncfile = "$qdir/done.$$"; - -system("rm $queue_logfile $syncfile 2>/dev/null"); -# -# Write to the script file, and then close it. -# -open(Q, ">$queue_scriptfile") || die "Failed to write to $queue_scriptfile"; - -print Q "#!/bin/bash\n"; -print Q "cd $cwd\n"; -print Q ". ./path.sh\n"; -print Q "( echo '#' Running on \`hostname\`\n"; -print Q " echo '#' Started at \`date\`\n"; -print Q " echo -n '# '; cat <<EOF\n"; -print Q "$cmd\n"; # this is a way of echoing the command into a comment in the log file, -print Q "EOF\n"; # without having to escape things like "|" and quote characters. -print Q ") >$logfile\n"; -print Q "time1=\`date +\"%s\"\`\n"; -print Q " ( $cmd ) 2>>$logfile >>$logfile\n"; -print Q "ret=\$?\n"; -print Q "time2=\`date +\"%s\"\`\n"; -print Q "echo '#' Accounting: time=\$((\$time2-\$time1)) threads=$num_threads >>$logfile\n"; -print Q "echo '#' Finished at \`date\` with status \$ret >>$logfile\n"; -print Q "[ \$ret -eq 137 ] && exit 100;\n"; # If process was killed (e.g. oom) it will exit with status 137; - # let the script return with status 100 which will put it to E state; more easily rerunnable. -if ($array_job == 0) { # not an array job - print Q "touch $syncfile\n"; # so we know it's done. -} else { - print Q "touch $syncfile.\$SGE_TASK_ID\n"; # touch a bunch of sync-files. -} -print Q "exit \$[\$ret ? 1 : 0]\n"; # avoid status 100 which grid-engine -print Q "## submitted with:\n"; # treats specially. -$qsub_cmd .= "-o $queue_logfile $qsub_opts $queue_array_opt $queue_scriptfile >>$queue_logfile 2>&1"; -print Q "# $qsub_cmd\n"; -if (!close(Q)) { # close was not successful... || die "Could not close script file $shfile"; - die "Failed to close the script file (full disk?)"; -} - -my $ret = system ($qsub_cmd); -if ($ret != 0) { - if ($sync && $ret == 256) { # this is the exit status when a job failed (bad exit status) - if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/*/g; } - print STDERR "queue.pl: job writing to $logfile failed\n"; - } else { - print STDERR "queue.pl: error submitting jobs to queue (return status was $ret)\n"; - print STDERR "queue log file is $queue_logfile, command was $qsub_cmd\n"; - print STDERR `tail $queue_logfile`; - } - exit(1); -} - -my $sge_job_id; -if (! $sync) { # We're not submitting with -sync y, so we - # need to wait for the jobs to finish. We wait for the - # sync-files we "touched" in the script to exist. - my @syncfiles = (); - if (!defined $jobname) { # not an array job. - push @syncfiles, $syncfile; - } else { - for (my $jobid = $jobstart; $jobid <= $jobend; $jobid++) { - push @syncfiles, "$syncfile.$jobid"; - } - } - # We will need the sge_job_id, to check that job still exists - { # Get the SGE job-id from the log file in q/ - open(L, "<$queue_logfile") || die "Error opening log file $queue_logfile"; - undef $sge_job_id; - while (<L>) { - if (m/Your job\S* (\d+)[. ].+ has been submitted/) { - if (defined $sge_job_id) { - die "Error: your job was submitted more than once (see $queue_logfile)"; - } else { - $sge_job_id = $1; - } - } - } - close(L); - if (!defined $sge_job_id) { - die "Error: log file $queue_logfile does not specify the SGE job-id."; - } - } - my $check_sge_job_ctr=1; - # - my $wait = 0.1; - my $counter = 0; - foreach my $f (@syncfiles) { - # wait for them to finish one by one. - while (! -f $f) { - sleep($wait); - $wait *= 1.2; - if ($wait > 3.0) { - $wait = 3.0; # never wait more than 3 seconds. - # the following (.kick) commands are basically workarounds for NFS bugs. - if (rand() < 0.25) { # don't do this every time... - if (rand() > 0.5) { - system("touch $qdir/.kick"); - } else { - system("rm $qdir/.kick 2>/dev/null"); - } - } - if ($counter++ % 10 == 0) { - # This seems to kick NFS in the teeth to cause it to refresh the - # directory. I've seen cases where it would indefinitely fail to get - # updated, even though the file exists on the server. - # Only do this every 10 waits (every 30 seconds) though, or if there - # are many jobs waiting they can overwhelm the file server. - system("ls $qdir >/dev/null"); - } - } - - # Check that the job exists in SGE. Job can be killed if duration - # exceeds some hard limit, or in case of a machine shutdown. - if (($check_sge_job_ctr++ % 10) == 0) { # Don't run qstat too often, avoid stress on SGE. - if ( -f $f ) { next; }; #syncfile appeared: OK. - $ret = system("qstat -j $sge_job_id >/dev/null 2>/dev/null"); - # system(...) : To get the actual exit value, shift $ret right by eight bits. - if ($ret>>8 == 1) { # Job does not seem to exist - # Don't consider immediately missing job as error, first wait some - # time to make sure it is not just delayed creation of the syncfile. - - sleep(3); - # Sometimes NFS gets confused and thinks it's transmitted the directory - # but it hasn't, due to timestamp issues. Changing something in the - # directory will usually fix that. - system("touch $qdir/.kick"); - system("rm $qdir/.kick 2>/dev/null"); - if ( -f $f ) { next; } #syncfile appeared, ok - sleep(7); - system("touch $qdir/.kick"); - sleep(1); - system("rm $qdir/.kick 2>/dev/null"); - if ( -f $f ) { next; } #syncfile appeared, ok - sleep(60); - system("touch $qdir/.kick"); - sleep(1); - system("rm $qdir/.kick 2>/dev/null"); - if ( -f $f ) { next; } #syncfile appeared, ok - $f =~ m/\.(\d+)$/ || die "Bad sync-file name $f"; - my $job_id = $1; - if (defined $jobname) { - $logfile =~ s/\$SGE_TASK_ID/$job_id/g; - } - my $last_line = `tail -n 1 $logfile`; - if ($last_line =~ m/status 0$/ && (-M $logfile) < 0) { - # if the last line of $logfile ended with "status 0" and - # $logfile is newer than this program [(-M $logfile) gives the - # time elapsed between file modification and the start of this - # program], then we assume the program really finished OK, - # and maybe something is up with the file system. - print STDERR "**queue.pl: syncfile $f was not created but job seems\n" . - "**to have finished OK. Probably your file-system has problems.\n" . - "**This is just a warning.\n"; - last; - } else { - chop $last_line; - print STDERR "queue.pl: Error, unfinished job no " . - "longer exists, log is in $logfile, last line is '$last_line', " . - "syncfile is $f, return status of qstat was $ret\n" . - "Possible reasons: a) Exceeded time limit? -> Use more jobs!" . - " b) Shutdown/Frozen machine? -> Run again!\n"; - exit(1); - } - } elsif ($ret != 0) { - print STDERR "queue.pl: Warning: qstat command returned status $ret (qstat -j $sge_job_id,$!)\n"; - } - } - } - } - my $all_syncfiles = join(" ", @syncfiles); - system("rm $all_syncfiles 2>/dev/null"); -} - -# OK, at this point we are synced; we know the job is done. -# But we don't know about its exit status. We'll look at $logfile for this. -# First work out an array @logfiles of file-locations we need to -# read (just one, unless it's an array job). -my @logfiles = (); -if (!defined $jobname) { # not an array job. - push @logfiles, $logfile; -} else { - for (my $jobid = $jobstart; $jobid <= $jobend; $jobid++) { - my $l = $logfile; - $l =~ s/\$SGE_TASK_ID/$jobid/g; - push @logfiles, $l; - } -} - -my $num_failed = 0; -my $status = 1; -foreach my $l (@logfiles) { - my @wait_times = (0.1, 0.2, 0.2, 0.3, 0.5, 0.5, 1.0, 2.0, 5.0, 5.0, 5.0, 10.0, 25.0); - for (my $iter = 0; $iter <= @wait_times; $iter++) { - my $line = `tail -10 $l 2>/dev/null`; # Note: although this line should be the last - # line of the file, I've seen cases where it was not quite the last line because - # of delayed output by the process that was running, or processes it had called. - # so tail -10 gives it a little leeway. - if ($line =~ m/with status (\d+)/) { - $status = $1; - last; - } else { - if ($iter < @wait_times) { - sleep($wait_times[$iter]); - } else { - if (! -f $l) { - print STDERR "Log-file $l does not exist.\n"; - } else { - print STDERR "The last line of log-file $l does not seem to indicate the " - . "return status as expected\n"; - } - exit(1); # Something went wrong with the queue, or the - # machine it was running on, probably. - } - } - } - # OK, now we have $status, which is the return-status of - # the command in the job. - if ($status != 0) { $num_failed++; } -} -if ($num_failed == 0) { exit(0); } -else { # we failed. - if (@logfiles == 1) { - if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/$jobstart/g; } - print STDERR "queue.pl: job failed with status $status, log is in $logfile\n"; - if ($logfile =~ m/JOB/) { - print STDERR "queue.pl: probably you forgot to put JOB=1:\$nj in your script.\n"; - } - } else { - if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/*/g; } - my $numjobs = 1 + $jobend - $jobstart; - print STDERR "queue.pl: $num_failed / $numjobs failed, log is in $logfile\n"; - } - exit(1); -} |