Lines Matching refs:getGlobal
269 ($stopAfter ne getGlobal("stopAfter")));
276 if (defined(getGlobal("onSuccess"))) {
280 runCommand(getGlobal("onExitDir"), getGlobal("onSuccess") . " " . getGlobal("onExitNam"));
332 my $taskenv = getGlobal('gridEngineTaskID');
423 if (defined(getGlobal("preExec"))) {
426 $string .= getGlobal('preExec') . "\n";
432 my $javaPath = getGlobal("java");
459 $string .= "export CANU_OBJECT_STORE_CLIENT=" . getGlobal("objectStoreClient") . "\n";
460 $string .= "export CANU_OBJECT_STORE_CLIENT_UA=" . getGlobal("objectStoreClientUA") . "\n";
461 $string .= "export CANU_OBJECT_STORE_CLIENT_DA=" . getGlobal("objectStoreClientDA") . "\n";
462 $string .= "export CANU_OBJECT_STORE_NAMESPACE=" . getGlobal("objectStoreNameSpace") . "\n";
463 $string .= "export CANU_OBJECT_STORE_PROJECT=" . getGlobal("objectStoreProject") . "\n";
494 if ((getGlobal("objectStore") eq "TEST") && (defined($ENV{"JOB_ID"}))) {
503 elsif (getGlobal("objectStore") eq "DNANEXUS") {
506 elsif (getGlobal("gridEngine") eq "PBSPRO") {
530 if (getGlobal("objectStore") eq "TEST") {
542 elsif (getGlobal("objectStore") eq "DNANEXUS") {
547 elsif (getGlobal("gridEngine") eq "PBSPRO") {
581 …return("canu_" . $asm . ((defined(getGlobal("gridOptionsJobName"))) ? ("_" . getGlobal("gridOption…
586 …my $jobName = "${jobType}_" . $asm . ((defined(getGlobal("gridOptionsJobName"))) ? ("_" . getGloba…
591 if (uc(getGlobal("gridEngine")) eq "SGE") {
599 if (uc(getGlobal("gridEngine")) eq "PBS") {
602 if (uc(getGlobal("gridEngine")) eq "PBSPro") {
605 if (uc(getGlobal("gridEngine")) eq "LSF") {
608 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
643 return if (getGlobal("useGrid") ne "1"); # If not requested to run on the grid,
644 …return if (getGlobal("gridEngine") eq undef); # or can't run on the grid, don't run on th…
653 return if (($jobHold eq undef) && (exists($ENV{getGlobal("gridEngineJobID")})));
670 print F "#!" . getGlobal("shell") . "\n";
672 …mpt to (re)configure SGE. For unknown reasons, jobs submitted\n" if (getGlobal("gridEngine") eq…
673 …GE, and running under SGE, fail to read the shell init scripts,\n" if (getGlobal("gridEngine") eq…
674 …so they don't set up SGE (or ANY other paths, etc) properly.\n" if (getGlobal("gridEngine") eq…
675 …the record, interactive logins (qlogin) DO set the environment.\n" if (getGlobal("gridEngine") eq…
676 … if (getGlobal("gridEngine") eq…
677 …x\$SGE_ROOT\" != \"x\" -a \\\n" if (getGlobal("gridEngine") eq…
678 … \$SGE_ROOT/\$SGE_CELL/common/settings.sh ]; then\n" if (getGlobal("gridEngine") eq…
679 …GE_ROOT/\$SGE_CELL/common/settings.sh\n" if (getGlobal("gridEngine") eq…
680 … if (getGlobal("gridEngine") eq…
690 …print F "\$bin/" . basename($0) . " " . getCommandLineOptions() . " canuIteration=" . getGlobal("c…
701 my $mem = getGlobal("executiveMemory");
702 my $thr = getGlobal("executiveThreads");
714 if (uc(getGlobal("gridEngine")) eq "LSF") {
715 … $gridOpts .= getGlobal("gridOptionsExecutive") if (defined(getGlobal("gridOptionsExecutive")));
717 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
722 elsif (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
723 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
725 … $gridOpts .= getGlobal("gridOptionsExecutive") if (defined(getGlobal("gridOptionsExecutive")));
731 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
733 … $gridOpts .= getGlobal("gridOptionsExecutive") if (defined(getGlobal("gridOptionsExecutive")));
736 my $submitCommand = getGlobal("gridEngineSubmitCommand");
737 my $nameOption = getGlobal("gridEngineNameOption");
738 my $outputOption = getGlobal("gridEngineOutputOption");
749 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
751 $qcmd .= " -ioutput_folder:string=\"" . getGlobal("objectStoreNamespace") . "\" \\\n";
754 $qcmd .= " -icanu_iteration:int=" . getGlobal("canuIteration") . " \\\n";
755 $qcmd .= " -icanu_iteration_max:int=" . getGlobal("canuIterationMax") . " \\\n";
791 if ($end > getGlobal('gridEngineArrayMaxJobs')) {
802 if (uc(getGlobal("gridEngine")) eq "PBSPRO" || uc(getGlobal("gridEngine")) eq "PBS") {
810 if (uc(getGlobal("gridEngine")) eq "DNANEXUS" && ($bgn == $end) && ($opt =~ m/ARRAY_JOBS/)) {
819 if (uc(getGlobal("gridEngine")) eq "PBS") {
831 if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
833 if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
835 $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
837 elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
839 $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
841 elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
843 $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
845 elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
847 $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
849 elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
851 $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
853 elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
855 $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
885 my $tid = getGlobal("gridEngineArraySubmitID");
886 my $opt = getGlobal("gridEngineOutputOption");
907 $r = getGlobal("gridEngineStageOption");
922 if (getGlobal("canuIteration") > 0) {
923 $m *= 1.25 ** (getGlobal("canuIteration")-1);
928 …if (getGlobal("gridEngineMemoryPerJob") != "1") { # If anything but "1", divide the memory req…
932 …if (uc(getGlobal("gridEngine")) eq "LSF") { # But then reset …
934 …$m = int($m / 1024 + 0.5) if (getGlobal("gridEngineMemoryUnits") =~ m/t/i); # because …
935 …$m = int($m * 1 + 0.5) if (getGlobal("gridEngineMemoryUnits") =~ m/g/i); # enforce …
936 $m = int($m * 1024 + 0.5) if (getGlobal("gridEngineMemoryUnits") =~ m/m/i);
937 $m = int($m * 1024 * 1024 + 0.5) if (getGlobal("gridEngineMemoryUnits") =~ m/k/i);
941 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
954 my $r = getGlobal("gridEngineResourceOption");
999 my $submitCommand = getGlobal("gridEngineSubmitCommand");
1000 my $nameOption = getGlobal("gridEngineNameOption");
1004 …my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArra…
1005 …my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineA…
1011 my $globalOptions = getGlobal("gridOptions");
1012 my $jobOptions = getGlobal("gridOptions$jobType");
1043 if (uc(getGlobal("gridEngine")) eq "PBSPRO") { # PBSpro needs '--' to tell it to
1050 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
1051 print F " -ioutput_folder:string=\"" . getGlobal("objectStoreNamespace") . "\" \\\n";
1127 my $l = getGlobal("gridEngineArrayMaxJobs") - 1;
1190 my $mem = getGlobal("${jobType}Memory");
1191 my $thr = getGlobal("${jobType}Threads");
1192 my $dsk = getGlobal("${jobType}StageSpace");
1205 if (($nJobs * $mem + 0.5 <= getGlobal("executiveMemory")) &&
1206 ($nJobs * $thr <= getGlobal("executiveThreads"))) {
1231 my $iter = getGlobal("canuIteration");
1232 my $max = getGlobal("canuIterationMax");
1253 setGlobal("canuIteration", getGlobal("canuIteration") + 1);
1261 if (defined(getGlobal("gridEngine")) &&
1262 (getGlobal("useGrid") eq "1") &&
1263 (getGlobal("useGrid$jobType") eq "1") &&
1264 (exists($ENV{getGlobal("gridEngineJobID")})) &&
1272 if (getGlobal("showNext")) {
1304 if (uc(getGlobal("gridEngine")) eq "SGE") {
1315 if (uc(getGlobal("gridEngine")) eq "LSF") {
1322 if (uc(getGlobal("gridEngine")) eq "PBS") {
1327 if (uc(getGlobal("gridEngine")) eq "PBSPRO") {
1332 if (uc(getGlobal("gridEngine")) eq "SLURM") {
1347 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
1372 if (uc(getGlobal("gridEngine")) eq "SGE") {
1376 if (uc(getGlobal("gridEngine")) eq "LSF") {
1380 if (uc(getGlobal("gridEngine")) eq "PBS") {
1387 if (uc(getGlobal("gridEngine")) eq "PBSPRO") {
1391 if (uc(getGlobal("gridEngine")) eq "SLURM") {
1395 if (uc(getGlobal("gridEngine")) eq "DNANEXUS") {
1408 if (defined(getGlobal("gridEngine")) &&
1409 (getGlobal("useGrid") ne "0") &&
1410 (getGlobal("useGrid$jobType") eq "1") &&
1411 (! exists($ENV{getGlobal("gridEngineJobID")})) &&
1451 if (getGlobal("showNext")) {
1469 my $nCParallel = getGlobal("${jobType}Concurrency");
1470 …$nCParallel = int(getGlobal("maxThreads") / $thr) if ((!defined($nCParallel)) || ($nCParallel…
1474 my $nMParallel = getGlobal("${jobType}Concurrency");
1475 …$nMParallel = int(getGlobal("maxMemory") / getGlobal("${jobType}Memory")) if ((!defined($nMPara…
1559 if (getGlobal("showNext")) {
1659 my $asm = getGlobal("onExitNam");
1662 my $version = getGlobal("version");
1696 my $fail = getGlobal('onFailure');
1698 runCommandSilently(getGlobal("onExitDir"), "$fail $asm", 0);
1707 my $asm = getGlobal("onExitNam");
1710 my $version = getGlobal("version");
1741 my $fail = getGlobal('onFailure');
1743 runCommandSilently(getGlobal("onExitDir"), "$fail $asm", 0);