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POLSF issue with large scale runs
 

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  1. POLSF issue with large scale runs
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    <p>On our cluster, when I submit jobs requesting more than (including) 40 nodes or 640 cores, the $LSB_HOSTS gets empty and so the job stops. I use this variable to generate a nodelist file which I use with the mpirun command line as the following:</p> <pre><code>#BSUB -q cpu #BSUB -J gromacs #BSUB -o job.out #BSUB -e job.err #BSUB -n 640 ##################################################### ##################################################### INPUT=test184000atoms_verlet.tpr echo "" echo "----------------------- INTIALIZATIONS -----------------------------" echo "" source /lustre/utility/intel/composer_xe_2013.3.163/bin/compilervars.sh intel64 source /lustre/utility/intel/mkl/bin/intel64/mklvars_intel64.sh source /lustre/utility/intel/impi/4.1.1.036/bin64/mpivars.sh MPIRUN=/path/to/intel/impi/4.1.1.036/intel64/bin/mpirun EXE=mdrun_mpi if test ! -x `which $EXE` ; then echo echo "ERROR: `which $EXE` not existent or not executable" echo "Aborting" exit 1 fi CURDIR=$PWD cd $CURDIR rm -f nodelist &gt;&amp; /dev/null touch nodelist for host in `echo $LSB_HOSTS` do echo $host &gt;&gt; nodelist sleep 2 done NP=`cat nodelist |wc -l` NN=`cat nodelist |sort |uniq|tee nodes |wc -l` echo echo "Executable : `which $EXE`" echo "Working directory is $CURDIR" echo "Running on host `hostname`" echo "Directory is `pwd`" echo "This jobs runs on $NN nodes" echo "This job has allocated $NP core(s)" echo ulimit -aH echo ls -al echo "" echo "----------------------- RUN -----------------------------" echo "" date '+RUN STARTED ON %m/%d/%y AT %H:%M:%S' $MPIRUN -np $NN -machinefile nodes $EXE -v -deffnm $INPUT &gt;&amp; $EXE.log date '+RUN ENDED ON %m/%d/%y AT %H:%M:%S' echo "" echo "----------------------- DONE ----------------------------" echo "" ls -al </code></pre> <p>Any hints here?</p> <p>Can you see something wrong with this script?</p> <p>Thanks,</p> <p>Éric.</p>
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    1. COStackoverflow isn't really for this sorts of questions. Are you absolutely sure `LSB_HOSTS` is empty? That would most likely indicate a problem with the batch system. How long are the hostnames?
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    2. COI'm sure because when I echo $LSB_HOSTS nothing is displayed and nodelist file size is zero. hostnames start from node001 to node332.
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    3. COIs there a size or length limit for bash environment variables?
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