NWChem

Description

From the NWChem home page: NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.

Version

• 6.5

Authorized Users

• CIRCE account holders

Platforms

• CIRCE cluster

Modules

NWChem requires the following module file to run:

• apps/nwchem/6.5
  See Modules for more information.

• NOTE: This module MUST be loaded persistently in order for the application to run. In order to properly execute NWChem, use:

[user@host ~]$ module load apps/nwchem/6.5

Submitting a Job

Each user will probably need a .nwchemrc file to point to the default data files. A global one is located in /apps/nwchem/6.5/data and a symbolic link can be made in your $HOME directory. Users should issue the following command prior to using NWChem:

ln -s /apps/nwchem/6.5/default.nwchemrc $HOME/.nwchemrc

 
The script below (for testing, name it “nwchem-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/bin/bash
#
#SBATCH --comment=nwchem-test
#SBATCH --ntasks=8
#SBATCH --job-name=nwchem-test
#SBATCH --export=ARMCI_DEFAULT_SHMMAX=8192
#SBATCH --output=output.%j.nwchem-test
#SBATCH --time=01:00:00

#### Slurm 8 processor NWChem test to run for 1 hour.

module purge
module load apps/nwchem/6.5

mpirun nwchem 

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./nwchem-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Benchmarks and Tests

The following folders contain input parameters for known NWChem tests:

• /apps/nwchem/6.5/examples
• http://www.nwchem-sw.org/index.php/Benchmarks

Additional Documentation

• NWChem Documentation
  • /apps/nwchem/6.5/NWChem6.5_Documentation.pdf
  • http://www.nwchem-sw.org/index.php/Release65:NWChem_Documentation

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

Report bugs with NWChem to the IT Help Desk: rc-help@usf.edu