NAMD

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NAMD v2.13

This is the NAMD version 2.13 Scalable Molecular Dynamics package. NAMD_2.13_Linux-x86_64-ibverbs-smp.tar.gz binary tarball from TCBG.

It was built directly on top of ibverbs, plus smp, 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=00:15:00
#SBATCH --job-name namdtest

module load namd/2.13

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

# Generate NAMD nodelist
for n in `echo $SLURM_NODELIST | scontrol show hostnames`; do
  echo "host $n" >> nodelist.$SLURM_JOBID
done

NODELIST=nodelist.$SLURM_JOBID
cat $NODELIST

# Calculate total processes (P) and procs per node (PPN)
PPN=2
P=$(($SLURM_NTASKS * 2))

charmrun ++verbose +p $P ++ppn $PPN ++nodelist $NODELIST $SCINET_NAMD_ROOT/bin/namd2 input.namd

# Cleaning
rm $NODELIST

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

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=00:15:00
#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

# Generate NAMD nodelist
for n in `echo $SLURM_NODELIST | scontrol show hostnames`; do
  echo "host $n" >> nodelist.$SLURM_JOBID
done

NODELIST=nodelist.$SLURM_JOBID
cat $NODELIST

# Calculate total processes (P) and procs per node (PPN)
PPN=4
P=$(($SLURM_NTASKS * 2))

charmrun ++verbose +p $P ++ppn $PPN ++nodelist $NODELIST $SCINET_NAMD_ROOT/bin/namd2 input.namd

# Cleaning
rm $NODELIST

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