8000 Add SLURM control arguments by outpaddling · Pull Request #1033 · marbl/canu · GitHub
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Add SLURM control arguments #1033

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Add SLURM control arguments #1033

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0e75be7
Additional Slurm grid parameters
halfwayBraindead Jul 31, 2018
2dac298
Execution.pm: Restore getInstallDirectory()
Jul 31, 2018
1d769a8
Merge branch 'master' of https://github.com/marbl/canu
Aug 8, 2018
c30d9ec
Clean up useless diffs
Aug 8, 2018
afa08fa
Clean up useless diffs
Aug 8, 2018
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10 changes: 10 additions & 0 deletions src/pipelines/canu/Defaults.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -832,6 +832,16 @@ sub setDefaults () {
setDefault("gridEngineArraySubmitID", undef, "Grid engine configuration, not documented");
setDefault("gridEngineJobID", undef, "Grid engine configuration, not documented");

##### Slurm-specific parameters for controlling the number of
##### cores / tasks dispatched per step or globally (WIP)

setDefault( 'slurmCormhapCoreLimit', undef, 'Maximum number of cores allocated for MHAP pre-computing and alignment within the correction phase' );
setDefault( 'slurmOvbCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore bucketizing step within the trimming phase' );
setDefault( 'slurmOvsCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore sorting step within the trimming phase' );
setDefault( 'slurmRedCoreLimit', undef, 'Maximum number of cores allocated for read error detection within the unitigging phase' );
setDefault( 'slurmArrayTaskLimit', undef, 'Maximum number of tasks permitted for each step throughout assembly' );
setDefault( 'slurmArrayCoreLimit', undef, 'Maximum number of cores allocated for each step throughout assembly' );

##### Grid Engine Pipeline

setDefault("useGrid", 1, "If 'true', enable grid-based execution; if 'false', run all jobs on the local machine; if 'remote', create jobs for grid execution but do not submit; default 'true'");
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44 changes: 39 additions & 5 deletions src/pipelines/canu/Execution.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -773,8 +773,8 @@ sub submitScript ($$) {



sub buildGridArray ($$$$) {
my ($name, $bgn, $end, $opt) = @_;
sub buildGridArray (@) {
my ( $name, $bgn, $end, $opt, $thr ) = @_;
my $off = 0;

# In some grids (SGE) this is the maximum size of an array job.
Expand Down Expand Up @@ -812,8 +812,42 @@ sub buildGridArray ($$$$) {
$off = "-F \"$off\"";
}

$opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
$opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
if( $opt =~ m/(ARRAY_NAME)/ )
{
$opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
}
elsif( $opt =~ m/(ARRAY_JOBS)/ )
{
$opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'

if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
{
if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
{
$opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
}
elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
{
$opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
}
elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
{
$opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
}
elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
{
$opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
}
elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
{
$opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
}
elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
{
$opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
}
}
}

return($opt, $off);
}
Expand Down Expand Up @@ -962,7 +996,7 @@ sub buildGridJob ($$$$$$$$$) {
my $jobNameT = makeUniqueJobName($jobType, $asm);

my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"), $thr);

my $outputOption = buildOutputOption($path, $script);

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