Difference between revisions of "NWChem"

Latest revision as of 19:11, 24 March 2020

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

6.8

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

NWChem requires the following module file to run:

apps/nwchem/6.8

See Modules for more information.

Running NWChem on CIRCE/SC

The NWChem user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

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/6.8/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/6.8/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.

#!/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.

ulimit -l unlimited 

module purge
module load apps/nwchem/6.8

mpirun nwchem input_file.nw

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

Documentation

Home Page, User Guides, and Manuals

NWChem Home Page
- http://www.nwchem-sw.org/index.php/Main_Page
NWChem Documentation
- https://github.com/nwchemgit/nwchem/wiki

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

NWChem Examples
- /apps/nwchem/6.8/examples
NWChem Benchmarks
- http://www.nwchem-sw.org/index.php/Benchmarks

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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

@@ Line 1: / Line 1: @@
 == 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.
+''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 ==
+{{AppStandardHeader|6.8|nwchem}}
-*6.5
+{{AppRunningOnAll}}
-== Authorized Users ==
-*<code>CIRCE</code> account holders
-== Platforms ==
-*<code>CIRCE</code> cluster
-=== Modules ===
-NWChem requires the following module file to run:
-*<code>apps/nwchem/6.5</code><br />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:
-<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
-[user@host ~]$ module load apps/nwchem/6.5
-</pre>
 === 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: <pre style="white-space:pre-wrap; width:50%; border:1px solid lightgrey; background:#000000; color:white;">ln -s /apps/nwchem/6.5/default.nwchemrc $HOME/.nwchemrc</pre>
+Each user will probably need a .nwchemrc file to point to the default data files. A global one is located in /apps/nwchem/6.8/data and a symbolic link can be made in your $HOME directory. Users should issue the following command prior to using NWChem: <pre style="white-space:pre-wrap; width:50%; border:1px solid lightgrey; background:#000000; color:white;">ln -s /apps/nwchem/6.8/default.nwchemrc $HOME/.nwchemrc</pre>
 &nbsp;<br>
-The script below (for testing, name it “nwchem-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our [[SLURM Users|SLURM User’s Guide]]. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
+*The script below (for testing, name it “nwchem-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
 <pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
@@ Line 43: / Line 23: @@
 #SBATCH --time=01:00:00
-#### Slurm 8 processor NWChem test to run for 1 hour.
+#### SLURM 8 processor NWChem test to run for 1 hour.
+ulimit -l unlimited
 module purge
-module load apps/nwchem/6.5
+module load apps/nwchem/6.8
-mpirun nwchem </pre>
+mpirun nwchem input_file.nw</pre>
+&nbsp;<br>
 Next, you can change to your job’s directory, and run the sbatch command to submit the job:
 <pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
 [user@login0 ~]$ cd my/jobdir
-[user@login0 jobdir]$ sbatch ./abinit-test.sh</pre>
+[user@login0 jobdir]$ sbatch ./nwchem-test.sh</pre>
 *You can view the status of your job with the “squeue -u <username>” command
-=== Benchmarks and Tests ===
+{{Documentation}}
+*NWChem Home Page
-The following folders contain input parameters for known NWChem tests:
+**http://www.nwchem-sw.org/index.php/Main_Page
+*NWChem Documentation
-*/apps/nwchem/6.5/examples
+**https://github.com/nwchemgit/nwchem/wiki
-*http://www.nwchem-sw.org/index.php/Benchmarks
-=== Additional Documentation ===
-*NWChem Documentation
+{{BKETOR}}
-**/apps/nwchem/6.5/NWChem6.5_Documentation.pdf
+*NWChem Examples
-**http://www.nwchem-sw.org/index.php/Release65:NWChem_Documentation
+**/apps/nwchem/6.8/examples
+*NWChem Benchmarks
+**http://www.nwchem-sw.org/index.php/Benchmarks
-{{MoreInformation}}
+{{AppStandardFooter}}
-{{ReportingBugs}}