Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision | |||
|
cluster:squidward.che:nbo6 [2015/10/09 18:23] frey |
— (current) | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Using NBO6 on Squidward ====== | ||
| - | |||
| - | As of 2015/10/09, a license for NBO6 was purchased for the Vlachos group. The NBO6 program can be used in a standalone (post-processing) mode, or inline with a Gaussian '09 job. The inline method uses Gaussian ''l612'' to execute an external program -- in this case, ''gaunbo6'' -- that will operate on data contained in several state files (a formatted checkpoint file, etc.) | ||
| - | |||
| - | ===== Standalone ===== | ||
| - | |||
| - | Setup NBO6 in your environment using VALET: | ||
| - | |||
| - | <code bash> | ||
| - | $ vpkg_require nbo/6.0-gcc | ||
| - | </code> | ||
| - | |||
| - | The programs ''nbo6'' and ''gennbo'' will be on your path. In standalone form, the NBO programs are linked against the ACML (AMD Core Math Library) for BLAS/LAPACK support and can function in threaded mode. For lengthy NBO jobs, making use of multiple threads within the linear algebraic manipulations could make a difference in the walltime required. An example job script for running the standalone NBO can be found on Squidward at ''/opt/Templates/nbo.qs''. | ||
| - | |||
| - | ===== Inline with Gaussian '09 ===== | ||
| - | |||
| - | NBO6 requires Gaussian '09 revision D01 or newer for inline mode. This version of Gaussian was installed on Squidward on 2015/10/08 in order to satisfy this dependency. | ||
| - | |||
| - | In order to function properly with Gaussian, NBO6 must be built without using any external BLAS/LAPACK libraries. Thus, an alternate version, ''nbo/6.0-pgi-g09'', was built to match with the Gaussian '09 revision D01 specifications. | ||
| - | |||
| - | ==== Submitting via GQueue ==== | ||
| - | |||
| - | A new pe-type was added to the gqueue configuration on Squidward: ''g09d01''. This is now the default pe-type chosen when users submit jobs using gqueue. | ||
| - | |||
| - | The code underlying this pe-type will check your Gaussian input file for NBO directives; if found, it will load both Gaussian and NBO6 into the job's environment. | ||
| - | |||
| - | So running a Gaussian job that includes NBO6 analysis is as simple as submitting it with gqueue. | ||
| - | |||
| - | ==== From a Job Script ==== | ||
| - | |||
| - | The job script for a Gaussian calculation that includes NBO6 analysis must load both Gaussian '09 revision D01 and the appropriate NBO6 package into the environment: | ||
| - | |||
| - | <code bash> | ||
| - | # Load Gaussian and NBO6: | ||
| - | source /etc/profile.d/valet.sh | ||
| - | vpkg_require gaussian/g09.d01 nbo/6.0-pgi-g09 | ||
| - | </code> | ||
| - | |||
| - | From there, execute ''g09'' on your input file and Gaussian will handle the rest: | ||
| - | |||
| - | <code bash> | ||
| - | # Run the Gaussian + NBO6 computation: | ||
| - | g09 my_molecule.com | ||
| - | </code> | ||