Difference between revisions of "NAMD"

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(NAMD v2.12)
(NAMD v2.12)
Line 10: Line 10:
 
#SBATCH --nodes=2
 
#SBATCH --nodes=2
 
#SBATCH --ntasks-per-node=40
 
#SBATCH --ntasks-per-node=40
#SBATCH --time=11:00:00
+
#SBATCH --time=00:15:00
 
#SBATCH --job-name namdtest
 
#SBATCH --job-name namdtest
  
Line 19: Line 19:
 
cd $SLURM_SUBMIT_DIR
 
cd $SLURM_SUBMIT_DIR
  
# EXECUTION COMMAND; -np = nodes*ppn
+
# Generate NAMD nodelist
charmrun ++p 80 namd2 +idlepoll input.namd
+
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
 
</source>
 
</source>
 
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/
 
Full documentation for NAMD is available on their website:  http://www.ks.uiuc.edu/Research/namd/

Revision as of 16:11, 19 September 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=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/