NAMD

NAMD v2.14

This is the NAMD version 2.14 Scalable Molecular Dynamics package. NAMD_2.14_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:

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#!/bin/bash # #SBATCH --nodes=2 #SBATCH --ntasks-per-node=40 #SBATCH --time=00:15:00 #SBATCH --job-name namdtest   module load namd/2.14   # 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:

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#!/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/