Difference between revisions of "NAMD Guide"

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(Remove BSUB commands)
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You need following modules:
 
You need following modules:
  module load namd/2.9-ibverbs mpi/openmpi/1.6.5-gcc
+
  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.