From: Almeida-Hernández, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Jul 25 2022 - 04:20:55 CDT
Dear all,
I am trying to restart a simulation but it doesn't work anymore. The slurm output file is empty and the NAMD output only writes '
Charmrun> scalable start enabled.
My script is the following and used to work perfectly:
#!/bin/bash
## SLURM options ##
#SBATCH --job-name=S1_comp_3
#SBATCH --exclusive
#SBATCH -N 4
#SBATCH -p MD
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=1
NAMD=$HOME/Softwares/NAMD_2.13_Linux-x86_64-ibverbs-smp
NODELIST=$(pwd)/nodelist.${SLURM_JOBID}
for host in $(scontrol show hostnames); do
echo "host ${host} ++cpus ${SLURM_CPUS_ON_NODE}" >> ${NODELIST}
done
# calculate total processes (P) and procs per node (PPN)
PPN=`expr $SLURM_NTASKS_PER_NODE - 1`
P="$(($PPN * $SLURM_NNODES))"
CHARMRUN="${NAMD}/charmrun ++nodelist ${NODELIST} ++remote-shell ssh ++p ${P} ++ppn ${PPN}"
prod=complex_solv_ion-PROD
## RUNNING...
$CHARMRUN $NAMD/namd2 +setcpuaffinity +isomalloc_sync +idlepoll $prod\-3.conf >> $prod\-3.out;
#END
Any help will be very much appreciated.
Best regards,
Yasser
-- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T03 R01 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de> Phone: +49 201 183 2457<tel:+49%20201%20183%202457>
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