From d28b985fd78689475f5e18b492c4b839863d97a8 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Tue, 10 Apr 2012 16:26:52 +0000
Subject: [PATCH] extended memory limit for exonerate jobs
---
.../xref_mapping/XrefMapper/Methods/ExonerateBasic.pm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index 6c9797af0d..b671688b31 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
@@ -123,7 +123,7 @@ sub resubmit_exonerate {
my $queue = $self->mapper->farm_queue || 'long';
- my $usage = '-R "select[linux] rusage[tmp='.$disk_space_needed.']" -J "'.$unique_name.'" -q '.$queue;
+ my $usage = '-M 1500000 -R"select[mem>1500] rusage[mem=1500:tmp='.$disk_space_needed.']" -J "'.$unique_name.'" -q '.$queue;
my $com = "bsub $usage -o $root_dir/$outfile -e $root_dir/$errfile ".$exe_file;
@@ -265,7 +265,7 @@ EON
my $queue = $self->mapper->farm_queue || 'long';
- my $usage = "-q $queue ".'-R "-rusage[tmp='.$disk_space_needed.']" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e '.$prefix.'.%J-%I.err';
+ my $usage = "-q $queue ".'-M 1500000 -R"select[mem>1500] rusage[mem=1500:tmp='.$disk_space_needed.']" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e '.$prefix.'.%J-%I.err';
my $command = $exe." ".$query." ".$target.' --querychunkid $LSB_JOBINDEX --querychunktotal '.$num_jobs.' --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" '.$options_str;
--
GitLab