From: Fidan Sumbul (fidansumbul_at_gmail.com)
Date: Tue Sep 18 2018 - 06:00:36 CDT
Dear NAMD users,
I'm trying to run NAMD in a HPCC that i have access which has multiple nodes connected by OFED, possible usage of CUDA, support for MPI.
I'm having difficulties to use NAMD in the server.
I've tried different versions of pre-compiled NAMD, by basically downloading and untar'ing them but i got the following error messages.
Error messages with multicore-CUDA
/scratch/xxx/NAMD_2.13b1_Linux-x86_64-multicore-CUDA/charmrun: line 34: /scratch/xxx/xxx/xxx/charmlist: Permission denied
/scratch/xxx/NAMD_2.13b1_Linux-x86_64-multicore-CUDA/charmrun: line 34: exec: /scratch/xxx/xxx/xxx/charmlist: cannot execute: Permission denied
Error message of ibverbs
Charmrun> charmrun started...
Charmrun> mpiexec started
Charmrun> node programs all started
Charmrun> node programs all connected
------------- Processor 9 Exiting: Called CmiAbort ------------
Reason:
Length mismatch!!
I already found some information on the web that they were saying the “length mismatch” error means you are not using the correct version.
Which version should i use?
Thanks a lot for your help. Please find the sh script below.
Best,
#!/bin/sh
# number of nodes
#SBATCH -N 2
# number of tasks / node, keep at 12 !
#SBATCH --ntasks-per-node 32
#SBATCH -n 64
# name of job, optional
#SBATCH -J trial_job
#SBATCH -p xxx
#SBATCH -A xxx
# time. max 7 days #SBATCH -t JJ-HH:MM:SS
#SBATCH -t 2:00:00
# name of output file, optional
#SBATCH -o slurm_trial.out
#SBATCH -e slurm_trial.err
# mail recipient, optional
#SBATCH --mail-user=xxx_at_gmail.com
# should mail be sent ? optional
#SBATCH --mail-type=ALL
# source /share/apps/scripts/env_vars.sh
module purge
module load userspace/all
module load openmpi/2.1.2/2018
#export NAMD_DIR=/softs/NAMD_2.12_Linux-x86_64-multicore-CUDA
export NAMD_DIR=/scratch/fsumbul/NAMD_2.13b1_Linux-x86_64-ibverbs
export PATH=$PATH:$NAMD_DIR
echo "Running on: $SLURM_NODELIST"
srun -s hostname > $PWD/charmlist
charmrun ++verbose ++nodelist $PWD/charmlist ++p $SLURM_NPROCS ++mpiexec $NAMD_DIR/namd2 $PWD/xxx.conf > $PWD/xxx.log
--- Fidan Sumbul, PhD Postdoctoral Researcher Force microscopy group <https://sites.google.com/view/fm4b-lab/> @LAI U1067 Aix-Marseille Université / Inserm / CNRS 163, Av. de Luminy, Bât TPR2 bloc 5, case 909 13288 Marseille Cedex 9, France fidan.sumbul_at_inserm.fr fidansumbul_at_gmail.com
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