Difference between revisions of "NAMD"

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module load namd/.experimental-2.12-ibverbs-smp
 
module load namd/.experimental-2.12-ibverbs-smp
  
# DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
+
# DIRECTORY TO RUN - $SLURM_SUBMIT_DIR is directory job was submitted from
 
cd $SLURM_SUBMIT_DIR
 
cd $SLURM_SUBMIT_DIR
  

Revision as of 19:33, 13 August 2018

NAMD v2.12

This is the NAMD version 2.12 Scalable Molecular Dynamics package.

It was built directly on top of ibverbs, so it will run on InfiniBand nodes. Here is a sample run script:

#!/bin/bash
#
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40
#SBATCH --time=11:00:00
#SBATCH --job-name namdtest

# Note that the module will likely be taken out of experimental mode at some point.
module load namd/.experimental-2.12-ibverbs-smp

# DIRECTORY TO RUN - $SLURM_SUBMIT_DIR is directory job was submitted from
cd $SLURM_SUBMIT_DIR

# EXECUTION COMMAND; -np = nodes*ppn
charmrun ++p 80 namd2 +idlepoll input.namd

The above script requests 2 nodes and runs namd on 80 processors.

Full documentation for NAMD is available on their website: http://www.ks.uiuc.edu/Research/namd/