Difference between revisions of "NAMD Guide"
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You need following modules: | You need following modules: | ||
| − | module load namd/2. | + | module load namd/2.10-ibverbs mpi/openmpi/1.6.5-gcc |
The script for submission will be: | The script for submission will be: | ||
#!/bin/tcsh -f | #!/bin/tcsh -f | ||
Revision as of 18:12, 9 March 2021
You need following modules:
module load namd/2.10-ibverbs mpi/openmpi/1.6.5-gcc
The script for submission will be:
#!/bin/tcsh -f
#SBATCH -J fhvtest2 # job name
#SBATCH -o fhvtest.o%j # output and error file name (%j expands to jobID)
#SBATCH -n 40 # total number of mpi tasks requested
#SBATCH --ntasks-per-node=20 # Ivy Bridge: 20, SandyBridge: 16, Westmere: 12
#SBATCH -p IvyBridge # queue (partition) -- SandyBridge, Westmere, etc.
charmrun +p$SLURM_NTASKS ++mpiexec ++remote-shell \
"srun --mpi=pmi2 --resv-port" /apps/namd/2.9-ibverbs/namd2 \
$workdir/namd_pentamer_equil.conf > quil.out # use srun command instead of mpirun.
