From 29afdeac014d3f43c8d02166d248bf015df6988d Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 29 Jul 2013 16:32:19 +0000
Subject: [PATCH] [ENSCORESW-550]. Made the pipeline run on the new farm
infrastructure by editting memory requirements.
The original version had memory requirements in KB. New farm infrastructure says we
specify in MB. This is good so now all memory requirement params are all in the
same order of magnitude. The final collection job now specifies its memory
requirements. This is a good thing again. Currently this is set to 5MB.
---
.../xref_mapping/XrefMapper/Methods/ExonerateBasic.pm | 6 +++---
misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index 8432418f37..79c33667f2 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 $usage = '-M 1500000 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" -J "'.$unique_name.'" -q '.$queue;
+ my $usage = '-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" -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 $queue ".'-M 1500000 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e '.$prefix.'.%J-%I.err';
+ my $usage = "-q $queue ".'-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" '.'-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;
@@ -301,7 +301,7 @@ EON
}
else{
# write details of job to database
- my $command = "$exonerate_path $query $target --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo ".
+ 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 | grep ".'"'."^xref".'"'." > $root_dir/$output";
my $sth = $mapper->xref->dbc->prepare("insert into process_status (status, date) values('mapping_submitted',now())");
diff --git a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
index 81c75211fb..2e24b1e455 100644
--- a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
@@ -1033,8 +1033,8 @@ sub submit_depend_job {
# push @depend_bsub, ('-q', $queue, '-o', "$root_dir/depend.out", '-e', "$root_dir/depend.err");
my $jobid = 0;
-
- my $com = "bsub -K -q ".$queue." -o $root_dir/depend.out -e $root_dir/depend.err $ended_str /bin/true";
+ my $memory_resources = q{-M 5 -R"select[mem>5] rusage[mem=5]"}
+ my $com = "bsub -K -q $queue $memory_resources -o $root_dir/depend.out -e $root_dir/depend.err $ended_str /bin/true";
my $line = `$com`;
--
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