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authorgraehl <graehl@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-06-30 18:14:22 +0000
committergraehl <graehl@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-06-30 18:14:22 +0000
commit2d55061770d01f74a2c70042bc378e5f11d84868 (patch)
treee7b9ac01df765affddc6f990ee1845027e59f114 /vest
parent719b607539a9f76e1968314c11db06e85f459338 (diff)
par: abspath for -e dir, dir creation works, -e may be omitted safely (qsub -o /dev/null was bad)
git-svn-id: https://ws10smt.googlecode.com/svn/trunk@80 ec762483-ff6d-05da-a07a-a48fb63a330f
Diffstat (limited to 'vest')
-rwxr-xr-xvest/parallelize.pl82
1 files changed, 53 insertions, 29 deletions
diff --git a/vest/parallelize.pl b/vest/parallelize.pl
index 0b7ffaa2..66d54d02 100755
--- a/vest/parallelize.pl
+++ b/vest/parallelize.pl
@@ -14,6 +14,10 @@
# return it to the output *without* buffering
# multiple lines.
+#TODO: if -j 1, run immediately, not via sentserver? possible differences in environment might make debugging harder
+
+#BUG: if input is short, nothing ever gets to clients. bug in sentserver or in this Perl?
+
use Getopt::Long;
use IPC::Open2;
use strict;
@@ -26,8 +30,7 @@ my $joblist = "";
my $errordir="";
my $multiline;
my @files_to_stage;
-my $verbose = 1;
-my $numnodes;
+my $numnodes = 8;
my $user = $ENV{"USER"};
my $pmem = "9g";
my $basep=50300;
@@ -37,10 +40,17 @@ my $no_which;
my $no_cd;
my $DEBUG=$ENV{DEBUG};
+print STDERR "DEBUG=$DEBUG output enabled.\n" if $DEBUG;
+my $verbose = 1;
+sub verbose {
+ if ($verbose) {
+ print STDERR @_,"\n";
+ }
+}
sub debug {
if ($DEBUG) {
my ($package, $filename, $line) = caller;
- print STDERR "$filename($line): ",join(' ',@_);
+ print STDERR "DEBUG: $filename($line): ",join(' ',@_),"\n";
}
}
sub abspath($) {
@@ -63,12 +73,12 @@ sub escape_shell {
}
my $tailn=5;
sub preview_files {
- my $n=shift;
+ my ($l,$skipempty,$n)=@_;
$n=$tailn unless defined $n;
- my $fn=join(' ',map {escape_shell($_)} @_);
+ my @f=grep { ! ($skipempty && -z $_) } @$l;
+ my $fn=join(' ',map {escape_shell($_)} @f);
my $cmd="tail -n $n $fn";
my $text=`$cmd`;
- debug($cmd,$text);
$text
}
sub prefix_dirname($) {
@@ -81,6 +91,10 @@ sub prefix_dirname($) {
$_ ? $_ : '';
}
}
+sub ensure_final_slash($) {
+ local ($_)=@_;
+ m#/$# ? $_ : ($_."/");
+}
sub extend_path($$;$$) {
my ($base,$ext,$mkdir,$baseisdir)=@_;
if (-d $base) {
@@ -93,7 +107,8 @@ sub extend_path($$;$$) {
} else {
$dir=prefix_dirname($base);
}
- system("/bin/mkdir","-p",$dir) if $mkdir;
+ my @cmd=("/bin/mkdir","-p",$dir);
+ system(@cmd) if $mkdir;
}
return $base.$ext;
}
@@ -133,10 +148,33 @@ if ($no_which) {
for my $arg (@ARGV) {
$cmd .= " ".escape_shell($arg);
}
-
die "Please specify a command to parallelize\n" if $cmd eq '';
-if ($verbose){ print STDERR "Parallelizing: $cmd\n\n"; }
+my $cdcmd=$no_cd ? '' : ("cd ".escape_shell($abscwd)."\n");
+
+my $executable = $cmd;
+$executable =~ s/^\s*(\S+)($|\s.*)/$1/;
+$executable=`basename $executable`;
+chomp $executable;
+
+
+if ($verbose){ print STDERR "Parallelizing ($numnodes ways): $cmd\n\n"; }
+
+# create -e dir and save .sh
+use File::Temp qw/tempdir/;
+unless ($errordir) {
+ $errordir=tempdir("$executable.XXXXXX",CLEANUP=>1);
+}
+if ($errordir) {
+ my $scriptfile=extend_path("$errordir/","$executable.sh",1,1);
+ -d $errordir || die "should have created -e dir $errordir";
+ open SF,">",$scriptfile || die;
+ print SF "$cdcmd$cmd\n";
+ close SF;
+ chmod 0755,$scriptfile;
+ $errordir=abspath($errordir);
+ &verbose("-e dir: $errordir");
+}
# set cleanup handler
my @cleanup_cmds;
@@ -158,10 +196,6 @@ my $sentclient = "$mydir/sentclient";
my $host = `hostname`;
chomp $host;
-my $executable = $cmd;
-$executable =~ s/^\s*(\S+)($|\s.*)/$1/;
-$executable=`basename $executable`;
-chomp $executable;
# find open port
srand;
@@ -196,11 +230,10 @@ if ($stay_alive){ $stay_alive_flag = "--stay-alive"; print STDERR "staying alive
my %node_count;
my $script = "";
-my $cdcmd=$no_cd ? '' : "cd '$abscwd'\n";
# fork == one thread runs the sentserver, while the
# other spawns the sentclient commands.
if (my $pid = fork){
- sleep 2; # give other thread time to start sentserver
+ sleep 4; # give other thread time to start sentserver
$script =
qq{wait
$cdcmd$sentclient $host:$port:$key $cmd
@@ -219,13 +252,13 @@ $cdcmd$sentclient $host:$port:$key $cmd
while (1) {
$ret = waitpid($pid, WNOHANG);
#print STDERR "waitpid $pid ret = $ret \n";
- if ($ret != 0) {last; } # break
+ last if ($ret != 0);
$livejobs = numof_live_jobs();
- if ($numnodes >= $livejobs ) { # a client terminated
+ if ($numnodes >= $livejobs ) { # a client terminated, OR # lines of input was less than -j
print STDERR "num of requested nodes = $numnodes; num of currently live jobs = $livejobs; Client terminated - launching another.\n";
launch_job_on_node(1); # TODO: support named nodes
} else {
- sleep (60);
+ sleep 15;
}
}
}
@@ -246,14 +279,6 @@ sub numof_live_jobs {
return ($#livejobs + 1);
}
my (@errors,@outs,@cmds);
-if ($errordir) {
- my $scriptfile=extend_path("$errordir","$executable.sh",1,1);
- -d $errordir || die "should have created -e dir $errordir";
- open SF,">",$scriptfile || die;
- print SF "$cdcmd$cmd\n";
- close SF;
- chmod 0755,$scriptfile;
-}
sub launch_job_on_node {
my $node = $_[0];
@@ -288,7 +313,6 @@ sub launch_job_on_node {
$jobid =~ s/^Your job (\d+) .*$/\1/;
print STDERR " short job id $jobid\n";
if ($verbose){
- print STDERR "-e dir: $errordir\n" if $errordir;
print STDERR "cd: $abscwd\n";
print STDERR "cmd: $cmd\n";
}
@@ -312,8 +336,8 @@ sub cleanup {
if ($verbose){ print STDERR " $cmd\n"; }
eval $cmd;
}
- print STDERR "outputs:\n",preview_files(undef,@outs),"\n";
- print STDERR "errors:\n",preview_files(undef,@errors),"\n";
+ print STDERR "outputs:\n",preview_files(\@outs,1),"\n";
+ print STDERR "errors:\n",preview_files(\@errors,1),"\n";
print STDERR "cmd:\n",$cmd,"\n";
if ($verbose){ print STDERR "Cleanup finished.\n"; }
}