From: Susmita Ghosh (g.susmita6_at_gmail.com)
Date: Tue May 09 2017 - 05:39:23 CDT
Dear Zeki,
If you are using single job on mutiple node, then I think you should use
"export OMP_NUM_THREADS=1". I have given an example in the following SBATCH
script:
#!/bin/sh
#BATCH -A Name
#SBATCH -N 4
#SBATCH --ntasks-per-node=24
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out
#SBATCH --time=1-02:00:00
module load slurm
### To launch mpi job through srun user have to export the below library
file##
export I_MPI_PMI_LIBRARY=/cm/shared/apps/slurm/15.08.13/lib64/libpmi.so
export LD_LIBRARY_PATH=/home/cdac/jpeg/lib:$LD_LIBRARY_PATH
#export PATH=/home/cdac/lammps_10oct2014/bin:$PATH
export OMP_NUM_THREADS=1
time srun -n 96 namd2 eq_NVT_run1.conf > eq_NVT_run1.log
Susmita Ghosh,
Research Scholar,
Department of Physics,
IIT Guwahati, India.
On Tue, May 9, 2017 at 3:38 PM, Zeki Zeybek <zeki.zeybek_at_bilgiedu.net>
wrote:
> Hi!
>
>
> 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 ?
>
>
> #!/bin/bash
> #SBATCH --clusters=AA
> #SBATCH --account=AA
> #SBATCH --partition=AA
> #SBATCH --job-name=AA
> #SBATCH --nodes=4
> #SBATCH --ntasks=1
> #SBATCH --cpus-per-task=80
> #SBATCH --time=120:00:00
>
> source /truba/sw/centos6.4/comp/intel/bin/compilervars.sh intel6i4
> source /truba/sw/centos6.4/lib/impi/4.1.1.036/bin64/mpivars.sh
> module load centos6.4/app/namd/2.9-multicore
> module load centos6.4/lib/impi/4.1.1
>
> export OMP_NUM_THREADS=20
> 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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