[Swift-commit] r6074 - in trunk: . bin

[wilde at ci.uchicago.edu]

Author: wilde
Date: 2012-11-21 17:38:43 -0600 (Wed, 21 Nov 2012)
New Revision: 6074

Modified:
   trunk/bin/slurm-qsub
   trunk/bin/slurm-qsub-emulator
   trunk/build.xml
Log:
Corrections to SLURM support: add local copy of qsub emulator to bin/ in build.xml; correct error in pbslog file naming; merge -l options on qsub line into one arg, as qsub emulator only handles one correctly; and remove #PBS lines from submit script, as these seem to be getting picked up by sbatch, causing contradictory settings.

Modified: trunk/bin/slurm-qsub
===================================================================
--- trunk/bin/slurm-qsub	2012-11-21 21:01:21 UTC (rev 6073)
+++ trunk/bin/slurm-qsub	2012-11-21 23:38:43 UTC (rev 6074)
@@ -7,7 +7,7 @@
 script=$1.slurm
 echo '#! /bin/sh' >$script
 # echo 'export PBS_NODELIST=SLURM_NODELIST'' >>$script  # FIXME: convert SLURM_NODELIST to PBS_NODEFILE here...
-cat $1 >>$script
+cat $1 | grep -v '^#PBS' >>$script
 chmod +x $script
 
 srunargs=$(awk <$1 '
@@ -29,7 +29,7 @@
 
 #   printf("-S %s -N %s -m %s -l nodes=%s:ppn=%s -l walltime=%s -q %s -o %s -e %s",
 #            shell, jobname, m, nodes, ppn, walltime, queue, sofile, sefile);
-   printf("-N %s -m %s -l nodes=%s:ppn=%s -l walltime=%s -q %s -o %s -e %s",
+   printf("-N %s -m %s -l nodes=%s:ppn=%s,walltime=%s -q %s -o %s -e %s",
              jobname, m, nodes, ppn, walltime, queue, sofile, sefile);
 
 }')

Modified: trunk/bin/slurm-qsub-emulator
===================================================================
--- trunk/bin/slurm-qsub-emulator	2012-11-21 21:01:21 UTC (rev 6073)
+++ trunk/bin/slurm-qsub-emulator	2012-11-21 23:38:43 UTC (rev 6074)
@@ -81,7 +81,6 @@
 
 my $sbatch = "sbatch";
 my $salloc = "salloc";
-my $srun = "$srun";
 
 GetOptions('a=s'      => \$start_time,
 	   'A=s'      => \$account,
@@ -215,7 +214,7 @@
 
 $command .= " $script";
 
-system("(echo; echo $command; echo) >> $HOME/pbslog");
+system("(echo; echo $command; echo) >> \$HOME/pbslog");
 
 system($command);
 

Modified: trunk/build.xml
===================================================================
--- trunk/build.xml	2012-11-21 21:01:21 UTC (rev 6073)
+++ trunk/build.xml	2012-11-21 23:38:43 UTC (rev 6074)
@@ -113,6 +113,7 @@
 				<include name="worker.sh"/>
 				<include name="workers.ranger.sh"/>
                                 <include name="slurm-qsub"/>
+                                <include name="slurm-qsub-emulator"/>
   				<include name="slurm-qdel"/>
 				<include name="slurm-qstat"/>
 			</fileset>