From: Zeki Zeybek (zeki.zeybek_at_bilgiedu.net)
Date: Tue May 09 2017 - 05:08:22 CDT
I am trying to come up with a slurm script file for my simulation but I failed miserably. The point is that in the uni. super computer for a single node there exist 20 cores. What I want to do is for my single job, lets say aaaa.conf, I want to use 80 cores. However to allocate such numbers of cores I need to use 4 nodes (4*20=80). However slurm gives error if I try to run one task on multiple nods. How can I overcome this situation ?
source /truba/sw/centos6.4/comp/intel/bin/compilervars.sh intel6i4
module load centos6.4/app/namd/2.9-multicore
module load centos6.4/lib/impi/4.1.1
echo "SLURM_NODELIST $SLURM_NODELIST"
echo "NUMBER OF CORES $SLURM_NTASKS"
#$NAMD_DIR/namd2 +p$OMP_NUM_THREADS namd_input.conf > namd_multinode_output.log for single node
#$mpirun NAMD_DIR/namd2 +p$OMP_NUM_THREADS namd_input.conf > namd_multinode_output.log for multiple node
THE ABOVE SCRIPT GIVES ERROR as in --ntasks=1 is not valid. However if I make --ntasks=4 and --cpus-per-task=20 it works. But it does not enhance the run speed. (Note: each user can use at most 80 cores in the super computer server)
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