From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Feb 14 2022 - 07:44:07 CST
This sounds like a slurm problem that you need to work out with your
cluster's sysadmin.
Best,
Peter
On Mon, Feb 14, 2022 at 8:43 AM İmren Bayıl <
ib57001_at_student.gaziantep.edu.tr> wrote:
> #!/bin/bash
> #SBATCH -A ibayil
> #SBATCH -J namd-multicore-test
> #SBATCH -N 2
> #SBATCH -n 16
> #SBATCH --time=15-00:00:00
> #SBATCH --workdir=/truba_scratch/ibayil/amber
> #SBATCH --output=out_slurm/slurm-%j.out
> #SBATCH --error=error_slurm/slurm-%j.err
>
> export OMP_NUM_THREADS=2
> export
> LD_LIBRARY_PATH=/truba/sw/centos7.3/app/namd/2017-11-10-multicore/lib:$LD_LIBRARY_PATH
> export PATH=/truba/sw/centos7.3/app/namd/2017-11-10-multicore/bin:$PATH
>
> echo "SLURM_NODELIST $SLURM_NODELIST"
> echo "NUMBER OF CORES $SLURM_NTASKS"
>
> wdir=/truba_scratch/ibayil/amber #Uygulama için çalıştırılacak dosyaların
> adresleri.
> cd $wdir
>
> infile=$wdir/water.namd #Uygulamanın çalışması için gerekli input ve
> output dosyaların adları.
> outfile=$wdir/job.log
>
> #tum kuyruklar icin
> module load centos7.3/app/namd/2017-11-10-multicore
>
> #cuda kuyrugu icin
> #module load centos7.3/app/namd/2017-11-10-multicore-cuda
>
> mpirun /truba/sw/centos7.3/app/namd/2017-11-10-multicore/namd2 <$infile>
> $outfile
>
> #$NAMD_DIR/namd2 +p $SLURM_NTASKS +idlepoll water.namd > job.log
>
> when I run sbatch namd_slurm.bash,I am getting this error sbatch: error:
> Batch job submission failed: Unspecified error how to fix it
>
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST