pc-gamess

License

Firefly is distributed freely for academics provided they register to use the code. You must register your use of the program before requesting access on the NGS. If you have already registered to use the program at your home Institute then you don't need to register again, just contact the NGS helpdesk.

To register with the Firefly developers for the first time, you need download a copy of one of the binary release zip files from their downloads page. Read the included "readme.txt" file and follow the instructions to register. In your email, please specify that you plan to use the Firefly installation on ngs.rl.ac.uk cluster hosted in the eScience centre at RAL, and the ngs.leeds.ac.uk cluster hosted at Leeds University.

Finally email the NGS helpdesk to give you access to the code. Your NGS id will then be added to the pcgamess group so that you can access the program.

Running Firefly on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS

• Submission Using UI/WMS
• NGS Web Portal Submission

Submission Using Globus

The default version of Firefly on ngs.rl.ac.uk is 7.1.G, if you need to run 7.1.F, or 7.1.E replace /usr/ngs/PCGAMESS with /usr/ngs/PCGAMESS_7_1_F or PCGAMESS_7_1_E for example.

All the input files required to run Firefly should be in the working directory. The general input and output files must be given as -i and -o arguments to the program not as stdin and stdout, and the full path names must always be given, as in the following example (the command should be in one line).:

globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
'&(executable=/usr/ngs/PCGAMESS)(jobtype=mpi)(count=8)(maxWallTime=10) \
(arguments= -r -f -p -i /home/ngsxxx/pc-gamess/run/bench11.inp \
-o /home/ngsxxxx/pc-gamess/run/bench11.out -ex /apps/pc-gamess/7.1.11/bin \
-t /tmp/ngsxxxx)(stdout=/home/ngsxxxx/pc-gamess/run/stdout.o) \
(stderr=/home/ngsxxxx/pc-gamess/run/stderr.e)'

The -ex argument should be replaced by the bin directory relevant to your run version. The example above shows the setting for the default version 7.1.11. The example input files (with their benchmark output files) can be copied to your home/working directory from /apps/pc-gamess/<version>/examples .

If you are submitting locally, while logged onto ngs.rl.ac.uk (only), rather than via the grid, you can use the run_pcgamess_lsf script that is in your path to submit the default version (7.1.E) to the local batch system.

[ngs0xxx@ngs]# run_pcgamess_lsf -h
Program usage: run_pcgamess_lsf [-h] [-n x] [-ptile x] -i inputfile.inp -o outputfile.out

It is possible to select other versions by setting the environment variable PCGAMESSVERSION to one of 7.1.4 7.1.9 7.1.C, 7.1.D, 7.1.F before running the script. For example:

[ngs0xxx@ngs]# export PCGAMESSVERSION=7.1.F; run_pcgamess_lsf -n 8
-ptile 4 -i inputfile.inp -o outputfile.out

If you are logged into ngs.leeds.ac.uk, the equivalent command is:

[ngs0xxx@ngs]$ module load pc-gamess/7.1.E
[ngs0xxx@ngs]$ run_pcgamess_pbs -n 8 -ptile 4 -i inputfile.inp -o outputfile.out

Compilation Information

•  PC-GAMESS on ngs.rl.ac.uk has been compiled using Platform MPI (SCALI-MPI)

• PC-GAMESS on ngs.leeds.ac.uk has been compiled using MPICH-MX

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

Further Information 

• Firefly User's Manuals and readme's can be found under /apps/pc-gamess/doc/ on ngs.rl.ac.uk . Or some more details may be found from the Firefly web page.
• Firefly (MSU) Home page
• GAMESS-US Home page