| The CSF2 has been replaced by the CSF3 - please use that system! This documentation may be out of date. Please read the CSF3 documentation instead. To display this old CSF2 page click here. |
NWChem
Overview
NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.
Available versions:
- 6.3 (compiled with gcc 4.7.1)
- 6.6 (compiled with gcc 4.9.0 using
-march=westmere -mtune=haswell, appears to be compatible with all CSF Intel CPUs)
Restrictions on use
All CSF users may access the software which is open source under the Educational Community License version 2.0. Information on how to cite your usage of the software is available on the NWChem website.
Set up procedure
To access the software you must first load the relevant modulefile. For running a serial job or on up to 24 Intel cores (single node, no infiniband):
module load apps/gcc/nwchem/6.6 module load apps/gcc/nwchem/6.3
To run on more than one Intel node with infiniband (job must be 48+ cores and a multiple of 24):
module load apps/gcc/nwchem/6.6-ib module load apps/gcc/nwchem/6.3-ib
The first time you use the software you need to make a copy of a configuration file to your home directory using this command:
cp $NWCHEM_HOME/default.nwchemrc .nwchemrc
Note: The contents of the file differs depending on which version you wish to run. It must be called .nwchemrc .
Running the application
Please do not run NWChem on the login node. Jobs should be submitted to the compute nodes via batch.
Please note that nwchem does not run on the AMD nodes.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd ### The above uses the current directory where you should have all relevant files #$ -V ### The above inherits your user environment from the login node i.e. so it can find commands nwchem myinput.nw >& myoutput.$JOB_ID
Submit the jobscript using:
qsub scriptname
Parallel batch job submission
Make sure you have the relevant modulefile loaded then create a batch submission script.
#!/bin/bash #$ -S /bin/bash #$ -cwd ### The above uses the current directory where you should have all relevant files #$ -V ### The above inherits your user environment from the login node i.e. so it can find commands #$ -pe smp.pe 12 ### The above ensures the job uses a parallel environment which has nodes setup for multi-core work. mpirun -n $NSLOTS nwchem myinput.nw >& myoutput.$JOB_ID
The variable $NSLOTS automatically picks up the number requested in the parallel environment (pe). This means if you wish to submit a job of a different size you only need to change the number on the pe line.
Submit your job with:
qsub scriptname
#!/bin/bash #$ -S /bin/bash #$ -cwd ### The above uses the current directory where you should have all relevant files #$ -V ### The above inherits your user environment from the login node i.e. so it can find commands #$ -pe orte-24-ib.pe 48 ### The above ensures the job uses the parallel environment specifically setup to do multi-node work. mpirun -n $NSLOTS nwchem myinput.nw >& myoutput.$JOB_ID
The variable $NSLOTS automatically picks up the number requested in the parallel environment (pe). This means if you wish to submit a job of a different size you only need to change the number on the pe line.
Submit your job with:
qsub scriptname
Further info
Updates
Jan 2016 – 6.6 installed.