Connecting Infrastructure, Connecting Research

Gulp

Description

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. See the Gulp web site for more details.
Site	Version (Latest: v3.4)	Notes
ngs.rl.ac.uk	v3.1	serial only (64 bit)

License
Running Gulp
Compilation Information
Further Information

License

The following license conditions are taken from the GULP web site. Please check that site for up to date license conditions.

GULP is available free of charge to academics provided you accept the following conditions of use:

1. The program is not to be distributed to anyone else without the express permission of the author.
2. The program is not to be used for commercial research. For any commercial use of the program a license must be obtained from Accelrys Inc, including contract research.
3. The program is supplied on an "as is" basis with no implied guarantee or support.

To download GULP you must register here. https://www.ivec.org/GULP/register.cgi then contact the NGS helpdesk to access the software on the NGS.

Running Gulp on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS. The examples below use the test input file:

gsiftp://ngs.rl.ac.uk:2811/apps/gulp/3.1/Examples/example2.gin

However there are many other example benchmark input and output files that can be found in that directory, if required.

Submission Using the UI/WMS

To submit a Gulp job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

glite-wms-job-submit -o jobIDs -a gulp.jdl

Type = "Job";
JobType = "normal";
Executable = "/usr/ngs/GULP";
StdInput = "example2.gin";
StdOutput = "example2.gout";
StdError = "example2.gerr";
InputSandbox = {"example2.gin"};
InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/gulp";
OutputSandbox = {"example2.gout","example2.gerr"};
OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/gulp/outputs";
MyProxyServer = "myproxy.ngs.ac.uk";
Requirements = (
     member("NGS-UEE-GULP", other.GlueHostApplicationSoftwareRunTimeEnvironment)
);
Rank = other.GlueCEStateFreeCPUs;
ShallowRetryCount = -1;

This runs the default version at a site. To run specifically 3.1 for example, use GULP_3_1 instead of GULP, in the Executable and Requirements lines.
The directory /home/ngsxxxx/gulp/outputs must exist on the UI before the job is submitted.

NGS Web Portal Submission

After logging in to the NGS Portal, select the "Gulp" template under the " Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

Submission Using Globus
The string 'xxx' in the subsequent commands is to be replaced with your id on NGS. You can also create a directory within your home directory (named gulp in the following examples) which will be the working directory.

Any input files required should be copied onto the NGS (using gsiscp or gsisftp) in the appropriate directory (/home/ngsxxx/gulp in our example).

Currently only the serial version of Gulp3 is installed on ngs.rl.ac.uk. The parallel version is not available yet.
- Example run of the Example2 Gulp3 benchmark on the NGS:

Compilation Information for ngs.rl.ac.uk

If you need information on how this application was compiled please contact the NGS support centre.

Further Information

The online gulp manuals can be found on the Gulp web site here :

Gulp Manual: https://www.ivec.org/GULP/help/manuals.html

There are available the example test input files, above, and others at

ngs.rl.ac.uk:/apps/gulp/3.1/Examples

Applications Support

The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.

Acknowledgements

Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.

Primary links