support kaldi decoder

1 files changed, 580 insertions, 0 deletions

diff --git a/kaldi_decode/utils/queue.pl b/kaldi_decode/utils/queue.pl
new file mode 100755
index 0000000..1e36de6
--- /dev/null
+++ b/kaldi_decode/utils/queue.pl
@@ -0,0 +1,580 @@
+#!/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);
+}