diff options
Diffstat (limited to 'vest/dist-vest.pl')
| -rwxr-xr-x | vest/dist-vest.pl | 22 |
1 files changed, 11 insertions, 11 deletions
diff --git a/vest/dist-vest.pl b/vest/dist-vest.pl index dca2f06b..22d6478a 100755 --- a/vest/dist-vest.pl +++ b/vest/dist-vest.pl @@ -6,6 +6,8 @@ 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"; # Default settings my $srcFile; @@ -17,12 +19,13 @@ die "Can't execute $FAST_SCORE" unless -x $FAST_SCORE; my $MAPINPUT = "$bin_dir/mr_vest_generate_mapper_input"; my $MAPPER = "$bin_dir/mr_vest_map"; my $REDUCER = "$bin_dir/mr_vest_reduce"; +my $parallelize = "$bin_dir/parallelize.pl"; my $SCORER = $FAST_SCORE; die "Can't find $MAPPER" unless -x $MAPPER; my $cdec = "$bin_dir/../decoder/cdec"; die "Can't find decoder in $cdec" unless -x $cdec; +die "Can't find $parallelize" unless -x $parallelize; my $decoder = $cdec; -my $DISCARD_FORESTS = 0; my $lines_per_mapper = 400; my $rand_directions = 15; my $iteration = 1; @@ -157,7 +160,6 @@ $SIG{HUP} = "cleanup"; my $decoderBase = `basename $decoder`; chomp $decoderBase; my $newIniFile = "$dir/$decoderBase.ini"; -my $parallelize = '/chomes/redpony/svn-trunk/sa-utils/parallelize.pl'; my $inputFileName = "$dir/input"; my $user = $ENV{"USER"}; @@ -254,12 +256,8 @@ while (1){ } # run optimizer - print LOGFILE "\nUNION FORESTS\n"; print LOGFILE `date`; my $mergeLog="$logdir/prune-merge.log.$iteration"; - if ($DISCARD_FORESTS) { - `rm -f $dir/hgs/*gz`; - } my $score = 0; my $icc = 0; @@ -314,7 +312,7 @@ while (1){ die; } } else { - my $todo = "qsub -q batch -l pmem=3000mb,walltime=5:00:00 -N $client_name -o /dev/null -e $logdir/$client_name.ER"; + my $todo = "qsub $QSUB_FLAGS -S /bin/bash -N $client_name -o /dev/null -e $logdir/$client_name.ER"; local(*QOUT, *QIN); open2(\*QOUT, \*QIN, $todo); print QIN $script; @@ -323,9 +321,10 @@ while (1){ $nmappers++; while (my $jobid=<QOUT>){ chomp $jobid; - push(@cleanupcmds, "`qdel $jobid 2> /dev/null`"); $jobid =~ s/^(\d+)(.*?)$/\1/g; - print STDERR "short job id $jobid\n"; + $jobid =~ s/^Your job (\d+) .*$/\1/; + push(@cleanupcmds, "`qdel $jobid 2> /dev/null`"); + print LOGFILE " $jobid"; if ($joblist == "") { $joblist = $jobid; } else {$joblist = $joblist . "\|" . $jobid; } } @@ -334,7 +333,8 @@ while (1){ } if ($run_local) { } else { - print LOGFILE "Launched $nmappers mappers.\n"; + print LOGFILE "\nLaunched $nmappers mappers.\n"; + sleep 10; print LOGFILE "Waiting for mappers to complete...\n"; while ($nmappers > 0) { sleep 5; @@ -353,7 +353,7 @@ while (1){ die "$mo: output lines ($olines) doesn't match input lines ($ilines)" unless $olines==$ilines; } print LOGFILE "Results for $tol/$til lines\n"; - print LOGFILE "\nSORTING AND RUNNING FMERT REDUCER\n"; + print LOGFILE "\nSORTING AND RUNNING VEST REDUCER\n"; print LOGFILE `date`; $cmd="sort -t \$'\\t' -k 1 @mapoutputs | $REDUCER -l $metric > $dir/redoutput.$im1"; print LOGFILE "COMMAND:\n$cmd\n"; |