Difference between revisions of "NAMD"

Revision as of 14:42, 31 March 2019

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

# The intel and openmpi modules are needed in order to have mpiexec in the path, to use it to launch the processes
module load intel
module load openmpi
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 +p<procs> ++ppn $PPN ++mpiexec  $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/