Difference between revisions of "NAMD"

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(Created page with "====NAMD v2.9==== This is the NAMD version 2.9 Scalable Molecular Dynamics package. It was built directly on top of ibverbs, so it will only run on InfiniBand nodes. Here...")
 
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====NAMD v2.9====
+
====NAMD v2.12====
  
This is the NAMD version 2.9 Scalable Molecular Dynamics package.   
+
This is the NAMD version 2.12 Scalable Molecular Dynamics package.   
 
 
It was built directly on top of ibverbs, so it will only run on InfiniBand nodes.  Here is a sample run script:
 
  
 +
It was built directly on top of ibverbs, so it will run on InfiniBand nodes.  Here is a sample run script:
  
 
<source lang="bash">
 
<source lang="bash">
 
#!/bin/bash
 
#!/bin/bash
# MOAB/Torque submission script for SciNet GPC (InfiniBand)
 
 
#
 
#
#PBS -l nodes=2:ppn=8,walltime=1:00:00,os=centos6computeA
+
#SBATCH --nodes=2
#PBS -N namdtest
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#SBATCH --ntasks-per-node=40
 +
#SBATCH --time=11:00:00
 +
#SBATCH --job-name namdtest
  
module purge
+
# Note that the module will likely be taken out of experimental mode at some point.
module load gcc openmpi/1.4.4-gcc-v4.6.1 namd/2.9-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 - $PBS_O_WORKDIR is directory job was submitted from
cd $PBS_O_WORKDIR
+
cd $SLURM_SUBMIT_DIR
  
 
# EXECUTION COMMAND; -np = nodes*ppn
 
# EXECUTION COMMAND; -np = nodes*ppn
$SCINET_NAMD_HOME/charmrun ++verbose ++p 16 ++mpiexec ++remote-shell $SCINET_NAMD_HOME/namdmpiexec $SCINET_NAMD_HOME/namd2 water-salt.conf >& o/WATER_SALT.log
+
charmrun ++p 80 namd2 +idlepoll input.namd
 
</source>
 
</source>
  
The above script requests 2 nodes with ib interconnect, and runs namd on 16 processors.
+
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 17:57, 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 - $PBS_O_WORKDIR 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/