#!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# In general, doing
# run.pl some.log a b c is like running the command a b c in
# the bash shell, and putting the standard error and output into some.log.
# To run parallel jobs (backgrounded on the host machine), you can do (e.g.)
# run.pl JOB=1:4 some.JOB.log a b c JOB is like running the command a b c JOB
# and putting it in some.JOB.log, for each one. [Note: JOB can be any identifier].
# If any of the jobs fails, this script will fail.
# A typical example is:
# run.pl some.log my-prog "--opt=foo bar" foo \| other-prog baz
# and run.pl will run something like:
# ( my-prog '--opt=foo bar' foo | other-prog baz ) >& some.log
#
# Basically it takes the command-line arguments, quotes them
# as necessary to preserve spaces, and evaluates them with bash.
# In addition it puts the command line at the top of the log, and
# the start and end times of the command at the beginning and end.
# The reason why this is useful is so that we can create a different
# version of this program that uses a queueing system instead.
# use Data::Dumper;
@ARGV < 2 && die "usage: run.pl log-file command-line arguments...";
$max_jobs_run = -1;
$jobstart = 1;
$jobend = 1;
$ignored_opts = ""; # These will be ignored.
# First parse an option like JOB=1:4, and any
# options that would normally be given to
# queue.pl, which we will just discard.
if (@ARGV > 0) {
while (@ARGV >= 2 && $ARGV[0] =~ m:^-:) { # parse any options
# that would normally go to qsub, but which will be ignored here.
$switch = shift @ARGV;
if ($switch eq "-V") {
$ignored_opts .= "-V ";
} elsif ($switch eq "--max-jobs-run" || $switch eq "-tc") {
# we do support the option --max-jobs-run n, and its GridEngine form -tc n.
$max_jobs_run = shift @ARGV;
if (! ($max_jobs_run > 0)) {
die "run.pl: invalid option --max-jobs-run $max_jobs_run";
}
} else {
$option = shift @ARGV;
if ($switch eq "-sync" && $option =~ m/^[yY]/) {
$ignored_opts .= "-sync "; # Note: in the
# corresponding code in queue.pl it says instead, just "$sync = 1;".
}
$ignored_opts .= "$switch $option ";
if ($switch eq "-pe") { # e.g. -pe smp 5
$option2 = shift @ARGV;
$ignored_opts .= "$option2 ";
}
}
}
if ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+):(\d+)$/) { # e.g. JOB=1:10
$jobname = $1;
$jobstart = $2;
$jobend = $3;
shift;
if ($jobstart > $jobend) {
die "run.pl: invalid job range $ARGV[0]";
}
if ($jobstart <= 0) {
die "run.pl: invalid job range $ARGV[0], start must be strictly positive (this is required for GridEngine compatibility).";
}
} elsif ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+)$/) { # e.g. JOB=1.
$jobname = $1;
$jobstart = $2;
$jobend = $2;
shift;
} elsif ($ARGV[0] =~ m/.+\=.*\:.*$/) {
print STDERR "run.pl: Warning: suspicious first argument to run.pl: $ARGV[0]\n";
}
}
# Users found this message confusing so we are removing it.
# if ($ignored_opts ne "") {
# print STDERR "run.pl: Warning: ignoring options \"$ignored_opts\"\n";
# }
if ($max_jobs_run == -1) { # If --max-jobs-run option not set,
# then work out the number of processors if possible,
# and set it based on that.
$max_jobs_run = 0;
if (open(P, "</proc/cpuinfo")) { # Linux
while (<P>) { if (m/^processor/) { $max_jobs_run++; } }
if ($max_jobs_run == 0) {
print STDERR "run.pl: Warning: failed to detect any processors from /proc/cpuinfo\n";
$max_jobs_run = 10; # reasonable default.
}
close(P);
} elsif (open(P, "sysctl -a |")) { # BSD/Darwin
while (<P>) {
if (m/hw\.ncpu\s*[:=]\s*(\d+)/) { # hw.ncpu = 4, or hw.ncpu: 4
$max_jobs_run = $1;
last;
}
}
close(P);
if ($max_jobs_run == 0) {
print STDERR "run.pl: Warning: failed to detect any processors from sysctl -a\n";
$max_jobs_run = 10; # reasonable default.
}
} else {
# allow at most 32 jobs at once, on non-UNIX systems; change this code
# if you need to change this default.
$max_jobs_run = 32;
}
# The just-computed value of $max_jobs_run is just the number of processors
# (or our best guess); and if it happens that the number of jobs we need to
# run is just slightly above $max_jobs_run, it will make sense to increase
# $max_jobs_run to equal the number of jobs, so we don't have a small number
# of leftover jobs.
$num_jobs = $jobend - $jobstart + 1;
if ($num_jobs > $max_jobs_run && $num_jobs < 1.4 * $max_jobs_run) {
$max_jobs_run = $num_jobs;
}
}
$logfile = shift @ARGV;
if (defined $jobname && $logfile !~ m/$jobname/ &&
$jobend > $jobstart) {
print STDERR "run.pl: you are trying to run a parallel job but "
. "you are putting the output into just one log file ($logfile)\n";
exit(1);
}
$cmd = "";
foreach $x (@ARGV) {
if ($x =~ m/^\S+$/) { $cmd .= $x . " "; }
elsif ($x =~ m:\":) { $cmd .= "'$x' "; }
else { $cmd .= "\"$x\" "; }
}
#$Data::Dumper::Indent=0;
$ret = 0;
$numfail = 0;
%active_pids=();
use POSIX ":sys_wait_h";
for ($jobid = $jobstart; $jobid <= $jobend; $jobid++) {
if (scalar(keys %active_pids) >= $max_jobs_run) {
# Lets wait for a change in any child's status
# Then we have to work out which child finished
$r = waitpid(-1, 0);
$code = $?;
if ($r < 0 ) { die "run.pl: Error waiting for child process"; } # should never happen.
if ( defined $active_pids{$r} ) {
$jid=$active_pids{$r};
$fail[$jid]=$code;
if ($code !=0) { $numfail++;}
delete $active_pids{$r};
# print STDERR "Finished: $r/$jid " . Dumper(\%active_pids) . "\n";
} else {
die "run.pl: Cannot find the PID of the chold process that just finished.";
}
# In theory we could do a non-blocking waitpid over all jobs running just
# to find out if only one or more jobs finished during the previous waitpid()
# However, we just omit this and will reap the next one in the next pass
# through the for(;;) cycle
}
$childpid = fork();
if (!defined $childpid) { die "run.pl: Error forking in run.pl (writing to $logfile)"; }
if ($childpid == 0) { # We're in the child... this branch
# executes the job and returns (possibly with an error status).
if (defined $jobname) {
$cmd =~ s/$jobname/$jobid/g;
$logfile =~ s/$jobname/$jobid/g;
}
system("mkdir -p `dirname $logfile` 2>/dev/null");
open(F, ">$logfile") || die "run.pl: Error opening log file $logfile";
print F "# " . $cmd . "\n";
print F "# Started at " . `date`;
$starttime = `date +'%s'`;
print F "#\n";
close(F);
# Pipe into bash.. make sure we're not using any other shell.
open(B, "|bash") || die "run.pl: Error opening shell command";
print B "( " . $cmd . ") 2>>$logfile >> $logfile";
close(B); # If there was an error, exit status is in $?
$ret = $?;
$lowbits = $ret & 127;
$highbits = $ret >> 8;
if ($lowbits != 0) { $return_str = "code $highbits; signal $lowbits" }
else { $return_str = "code $highbits"; }
$endtime = `date +'%s'`;
open(F, ">>$logfile") || die "run.pl: Error opening log file $logfile (again)";
$enddate = `date`;
chop $enddate;
print F "# Accounting: time=" . ($endtime - $starttime) . " threads=1\n";
print F "# Ended ($return_str) at " . $enddate . ", elapsed time " . ($endtime-$starttime) . " seconds\n";
close(F);
exit($ret == 0 ? 0 : 1);
} else {
$pid[$jobid] = $childpid;
$active_pids{$childpid} = $jobid;
# print STDERR "Queued: " . Dumper(\%active_pids) . "\n";
}
}
# Now we have submitted all the jobs, lets wait until all the jobs finish
foreach $child (keys %active_pids) {
$jobid=$active_pids{$child};
$r = waitpid($pid[$jobid], 0);
$code = $?;
if ($r == -1) { die "run.pl: Error waiting for child process"; } # should never happen.
if ($r != 0) { $fail[$jobid]=$code; $numfail++ if $code!=0; } # Completed successfully
}
# Some sanity checks:
# The $fail array should not contain undefined codes
# The number of non-zeros in that array should be equal to $numfail
# We cannot do foreach() here, as the JOB ids do not necessarily start by zero
$failed_jids=0;
for ($jobid = $jobstart; $jobid <= $jobend; $jobid++) {
$job_return = $fail[$jobid];
if (not defined $job_return ) {
# print Dumper(\@fail);
die "run.pl: Sanity check failed: we have indication that some jobs are running " .
"even after we waited for all jobs to finish" ;
}
if ($job_return != 0 ){ $failed_jids++;}
}
if ($failed_jids != $numfail) {
die "run.pl: Sanity check failed: cannot find out how many jobs failed ($failed_jids x $numfail)."
}
if ($numfail > 0) { $ret = 1; }
if ($ret != 0) {
$njobs = $jobend - $jobstart + 1;
if ($njobs == 1) {
if (defined $jobname) {
$logfile =~ s/$jobname/$jobstart/; # only one numbered job, so replace name with
# that job.
}
print STDERR "run.pl: job failed, log is in $logfile\n";
if ($logfile =~ m/JOB/) {
print STDERR "run.pl: probably you forgot to put JOB=1:\$nj in your script.";
}
}
else {
$logfile =~ s/$jobname/*/g;
print STDERR "run.pl: $numfail / $njobs failed, log is in $logfile\n";
}
}
exit ($ret);