Gaussian is a general purpose suite of electronic structure programs. Two versions are currently available on the system:<\/p>\n
Both are binary installs only. The source code is not available on the CSF.<\/p>\n
The University of Manchester site license allows access for all staff and students of the university, however strict licensing restrictions require that all users who wish to use the software must complete some paperwork and be in a restricted unix group. There are two separate unix groups – one for g09 and one for g03. The procedure for getting access on the CSF is as follows:<\/p>\n
After being added to the relevant unix group, you will be able to access the executables loading one<\/em> of the appropriate modulefiles:<\/p>\n For g09:<\/p>\n For g03 (by default we no longer grant access to this version unless it is essential to the work being undertaken):<\/p>\n Gaussian uses an environment variable A faster, but smaller, local Gaussian should<\/em> delete scratch files automatically when a job completes successfully or dies cleanly. However, it often fails to do this. Scratch files are also not<\/em> deleted when a job is killed externally or terminates abnormally so that you can use the scratch files to restart the job (if possible). Consequently, leftover files may accumulate in the scratch directory, and it is your responsibility to delete these files. Please check periodically<\/strong> whether you have a lot of temporary Gaussian files that can be deleted.<\/p>\n Update:<\/strong> We now recommend using a different scratch directory for each job. This improves file access times if you run many jobs – writing 1000s of scratch files to a single directory can slow down your jobs. It is much better to create a directory for each<\/em> job within your The example jobscripts below show how to use this method (it is simple – just two extra lines in your jobscript).<\/p>\n Occasionally some jobs create where scriptname<\/em> is the name of your job script.<\/li>\n Gaussian is a multi-threaded application (shared memory) so a job can not run across nodes, and you are limited to a maximum of 24 processors. This means that you must<\/em> run in module load apps\/binapps\/gaussian\/g09d01_em64t\r\n\r\nmodule load apps\/binapps\/gaussian\/g09b01_em64t\r\n<\/pre>\n
module load apps\/binapps\/gaussian03\/g03d01_em64t_amd\r\n<\/pre>\n
Gaussian Scratch<\/h2>\n
$GAUSS_SCRDIR<\/code> to specify a directory path for where to write scratch<\/em> (temporary) files (two-electron integral files, integral derivative files and a read-write<\/em> file for temporary workings). It is set to your scratch<\/em> directory (~\/scratch<\/code>) when you load the modulefile. This is a Lustre filesystem which provides good I\/O performance. Do not be tempted to use your home directory for Gaussian scratch files – the files can be huge making the home area at risk of going over quota. We also recommend using a directory-per-job in your scratch area. See below for how to do this.<\/p>\n\/tmp<\/code> on each compute node is available should users prefer to use that. It can be more efficient if you have to a need to create lots of small files, but space is limited. The minimum \/tmp<\/code> on intel compute nodes is 800GB, the largest is 3.5TB.<\/p>\nUsing a Scratch Directory per Job<\/h3>\n
scratch<\/code> area. It is also then easy to delete the entire directory if Gaussian has left unwanted scratch files behind.<\/p>\nVery large Gaussian scratch files<\/h3>\n
.rwf<\/code> files which are very large (several TB). The batch system will not permit a job to create files bigger than 4TB. If your gaussian job fails and the .rwf<\/code> file is 4TB then it may be that this limit has prevented your job from completing. You should re-run the job and in your input file request that the .rwf<\/code> file be split into multiple files. For example to split the file into two 3TB files:<\/p>\n\r\n%rwf=\/scratch\/$USER\/myjob\/one.rwf,3000GB,\/scratch\/$USER\/myjob\/two.rwf,3000GB\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job<\/h3>\n
\n
scratch<\/code> area:\ncd ~\/scratch\r\n<\/pre>\n<\/li>\n
#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Run job in directory you submitted from\r\n#$ -V # Use current environment settings, e.g. from \r\n # loaded modulefiles, when the job runs.\r\n\r\n# We now recommend using a scratch directory per job\r\nexport GAUSS_SCRDIR=\/scratch\/$USER\/gau_temp_$JOB_ID\r\nmkdir -p $GAUSS_SCRDIR\r\n\r\n$g09root\/g09\/g09 < file.inp > file.out\r\n<\/pre>\n<\/li>\n
qsub scriptname<\/em><\/pre>\n
cd ~\/scratch\/gau_temp_456789\r\nls\r\nGau-21738.inp Gau-21738.chk Gau-21738.d2e Gau-21738.int Gau-21738.scr\r\n\r\n# Example: Remove a specific scratch file\r\nrm Gau-21738.scr\r\n\r\n# Example: Remove all files in the directory (use with caution)\r\nrm Gau*\r\n\r\n# Example: go up and remove the empty directory\r\ncd ..\r\nrmdir gau_temp_456789\r\n<\/pre>\n<\/li>\n<\/ol>\n
Parallel batch job<\/h3>\n
smp.pe<\/code> to confine your job to a single node. Follow the steps below to submit a parallel Gaussian job.<\/p>\n