From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Feb 14 2022 - 08:55:00 CST
Three things:
1. This looks like a multicore NAMD installation, which doesn’t need mpirun at all.
2. Multicore builds *cannot* be run across multiple nodes.
3. Without +p argument that matches the number of cores, the default is to assume 1 core, which will run very slowly.
-Josh
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of İmren Bayıl <ib57001_at_student.gaziantep.edu.tr>
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, İmren Bayıl <ib57001_at_student.gaziantep.edu.tr>
Date: Monday, February 14, 2022 at 9:31 AM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Subject: namd-l: /tmp/slurmd/job8440949/slurm_script: line 31: mpirun: command not found
ı wan to run namd slurm but when ı write sbatch namd_slurm.bash it s failed ı am getting this error /tmp/slurmd/job8440949/slurm_script: line 31: mpirun: command not found
actually when the run my local computer it is running but it takes so long but ı want to run slurm so could you help me please
#!/bin/bash
#SBATCH -p sardalya
#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
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