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authorredpony <redpony@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-08-10 20:03:53 +0000
committerredpony <redpony@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-08-10 20:03:53 +0000
commit2cc482a64c687ef9505449e903776a1f1e595343 (patch)
tree57f666d208646824b12a70795dd3c50b9c05f883 /vest
parentf7935125ba51a0f84def04c25e14ccdbdc5fb7b7 (diff)
support for running in multiple environments which are automatically detected
git-svn-id: https://ws10smt.googlecode.com/svn/trunk@501 ec762483-ff6d-05da-a07a-a48fb63a330f
Diffstat (limited to 'vest')
-rwxr-xr-xvest/dist-vest.pl35
-rwxr-xr-xvest/parallelize.pl5
2 files changed, 24 insertions, 16 deletions
diff --git a/vest/dist-vest.pl b/vest/dist-vest.pl
index b66b8e9c..8f7f2053 100755
--- a/vest/dist-vest.pl
+++ b/vest/dist-vest.pl
@@ -3,13 +3,13 @@
use strict;
my @ORIG_ARGV=@ARGV;
use Cwd qw(getcwd);
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR; }
+my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../environment"; }
+use LocalConfig;
use Getopt::Long;
use IPC::Open2;
use strict;
use POSIX ":sys_wait_h";
-#my $QSUB_FLAGS = "-q batch -l pmem=3000mb,walltime=5:00:00";
-my $QSUB_FLAGS = "-l mem_free=9G";
+my $QSUB_CMD = qsub_args(mert_memory());
# Default settings
my $srcFile;
@@ -24,6 +24,8 @@ my $REDUCER = "$bin_dir/mr_vest_reduce";
my $parallelize = "$bin_dir/parallelize.pl";
my $sentserver = "$bin_dir/sentserver";
my $sentclient = "$bin_dir/sentclient";
+my $LocalConfig = "$SCRIPT_DIR/../environment/LocalConfig.pm";
+
my $SCORER = $FAST_SCORE;
die "Can't find $MAPPER" unless -x $MAPPER;
my $cdec = "$bin_dir/../decoder/cdec";
@@ -197,7 +199,7 @@ if ($dryrun){
} else {
-e $dir || mkdir $dir;
mkdir "$dir/hgs";
- modbin("$dir/bin",\$cdec,\$SCORER,\$MAPINPUT,\$MAPPER,\$REDUCER,\$parallelize,\$sentserver,\$sentclient) if $cpbin;
+ modbin("$dir/bin",\$LocalConfig,\$cdec,\$SCORER,\$MAPINPUT,\$MAPPER,\$REDUCER,\$parallelize,\$sentserver,\$sentclient) if $cpbin;
mkdir "$dir/scripts";
my $cmdfile="$dir/rerun-vest.sh";
open CMD,'>',$cmdfile;
@@ -276,6 +278,8 @@ while (1){
print STDERR "ERROR: Parallel decoder returned non-zero exit code $result\n";
die;
}
+ my $num_hgs = `ls $dir/hgs/*.gz | wc -l`;
+ print STDERR "HGs: $num_hgs\n";
my $dec_score = `cat $runFile | $SCORER $refs_comma_sep -l $metric`;
chomp $dec_score;
print STDERR "DECODER SCORE: $dec_score\n";
@@ -343,20 +347,21 @@ while (1){
die "ERROR: mapper returned non-zero exit code $result\n";
}
} else {
- my $script_file = "$dir/scripts/map.$shard";
- open F, ">$script_file" or die "Can't write $script_file: $!";
- print F "$script\n";
- close F;
+ my $script_file = "$dir/scripts/map.$shard";
+ open F, ">$script_file" or die "Can't write $script_file: $!";
+ print F "$script\n";
+ close F;
if ($first_shard) { print STDERR "$script\n"; $first_shard=0; }
$nmappers++;
- my $jobid = `qsub $QSUB_FLAGS -S /bin/bash -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file`;
- die "qsub failed: $!" unless $? == 0;
- chomp $jobid;
+ my $qcmd = "$QSUB_CMD -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file";
+ my $jobid = `$qcmd`;
+ die "qsub failed: $!\nCMD was: $qcmd" unless $? == 0;
+ chomp $jobid;
$jobid =~ s/^(\d+)(.*?)$/\1/g;
- $jobid =~ s/^Your job (\d+) .*$/\1/;
- push(@cleanupcmds, "`qdel $jobid 2> /dev/null`");
- print STDERR " $jobid";
+ $jobid =~ s/^Your job (\d+) .*$/\1/;
+ push(@cleanupcmds, "`qdel $jobid 2> /dev/null`");
+ print STDERR " $jobid";
if ($joblist == "") { $joblist = $jobid; }
else {$joblist = $joblist . "\|" . $jobid; }
}
@@ -368,7 +373,7 @@ while (1){
print STDERR "Waiting for mappers to complete...\n";
while ($nmappers > 0) {
sleep 5;
- my @livejobs = grep(/$joblist/, split(/\n/, `qstat`));
+ my @livejobs = grep(/$joblist/, split(/\n/, `qstat | grep -v ' C '`));
$nmappers = scalar @livejobs;
}
print STDERR "All mappers complete.\n";
diff --git a/vest/parallelize.pl b/vest/parallelize.pl
index a5a40704..daaf9b2f 100755
--- a/vest/parallelize.pl
+++ b/vest/parallelize.pl
@@ -18,6 +18,9 @@
#ANNOYANCE: if input is shorter than -j n lines, or at the very last few lines, repeatedly sleeps. time cut down to 15s from 60s
+my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../environment"; }
+use LocalConfig;
+
use File::Temp qw/ tempfile /;
use Getopt::Long;
use IPC::Open2;
@@ -303,7 +306,7 @@ sub launch_job {
push @errors,$errorfile;
push @outs,$outfile;
}
- my $todo = "qsub -l mem_free=$pmem -N $clientname -o $outfile -e $errorfile";
+ my $todo = qsub_args($pmem) . " -N $clientname -o $outfile -e $errorfile";
push @cmds,$todo;
print STDERR "Running: $todo\n";