Gaussian 09

Gaussian is a general purpose suite of electronic structure programs. Version g09d01 is installed. It is available as binaries only. The source code is not available on the CSF.

If you want information about Gaussian 16 on the CSF please see our G16 docs.

Restrictions on use – G09 ONLY

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.

The procedure for getting access on the CSF is as follows (please read carefully):

  1. Print out and complete the University’s gaussian paperwork. Note – you must sign the appropriate section(s) in ink (anything else will be rejected). PLEASE NOTE: the PDF is only available if on campus or running GlobalProtect. If you cannot access the PDF please email its-ri-team@manchester.ac.uk and we will send you a copy.)
  2. Scan in the entire document (yes, even the pages you didn’t sign) and email its-ri-team@manchester.ac.uk (please send to the its-ri-team address rather than gaussian@manchester.ac.uk) to request being added to the g09 gaussian group on CSF, attaching a scanned copy of the completed paperwork (the whole document). Anything other than the entire document will be rejected and lead to a delay in your access to Gaussian.
  3. We will add your paperwork to the ITS database of Gaussian users, add you to the appropriate group on the CSF and then send a confirmation to you.

Please ensure you follow the above instructions carefully. We are required by the University License Manager to follow the above procedure. Failure to supply the requested information correctly will delay your access to the software.

This paperwork does not enable access to Gaussian 16. Please see the CSF gaussian 16 webpage for more info.

Set up procedure

After being added to the relevant unix group, you will be able to access the executables by loading the modulefile

For g09:

module load apps/binapps/gaussian/g09d01_em64t

We recommend you do this in your jobscript, see examples below (not on the command line before job submission as per the previous CSF2).

Gaussian MUST ONLY be run in batch. Please DO NOT run g09 on the login nodes. Computational work found to be running on the login nodes will be killed WITHOUT WARNING.

Gaussian Scratch

Gaussian uses an environment variable $GAUSS_SCRDIR to specify a directory path for where to write scratch (temporary) files (two-electron integral files, integral derivative files and a read-write file for temporary workings). It is set to your scratch directory (~/scratch) 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.

A faster, but smaller, local /tmp on each compute node is available should users prefer to use that. It can be more efficient if you have a need to create lots of small files, but space is limited. The minimum /tmp on intel compute nodes is 800GB, the largest is 3.5TB.

Gaussian should delete scratch files automatically when a job completes successfully or dies cleanly. However, it often fails to do this. Scratch files are also not 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 whether you have a lot of temporary Gaussian files that can be deleted.

Using a Scratch Directory per Job

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 job within your scratch area. It is also then easy to delete the entire directory if Gaussian has left unwanted scratch files behind.

The example jobscripts below show how to use this method (it is simple – just two extra lines in your jobscript).

Very large Gaussian scratch files

Occasionally some jobs create .rwf 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 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 file be split into multiple files. For example to split the file into two 3TB files:

%rwf=/scratch/$USER/myjob/one.rwf,3000GB,/scratch/$USER/myjob/two.rwf,3000GB

Serial batch job

Example job submission

  • It is recommended you run from within your scratch area and use one directory per job: 
    cd ~/scratch
mkdir job1
cd job1
  • Create a job script, for example: 
    #!/bin/bash --login
#$ -cwd                       # Run job in directory you submitted from

# Load g09
module load apps/binapps/gaussian/g09d01_em64t

# We recommend using a Gaussian scratch directory per job
export GAUSS_SCRDIR=/scratch/$USER/gau_temp_$JOB_ID
mkdir -p $GAUSS_SCRDIR

$g09root/g09/g09 < file.inp > file.out
  • Submit with the command: 
    qsub scriptname

    where scriptname is the name of your job script.

  • When the job has finished check whether Gaussian has left behind unwanted scratch files (you’ll need to know the job id). For example, assuming your job id was 456789: 
    cd ~/scratch/gau_temp_456789
ls
Gau-21738.inp  Gau-21738.chk  Gau-21738.d2e  Gau-21738.int  Gau-21738.scr

# Example: Remove a specific scratch file
rm Gau-21738.scr

# Example: Remove all files in the directory (use with caution)
rm Gau*

# Example: go up and remove the empty directory
cd ..
rmdir gau_temp_456789

Parallel batch job

On the CSF Gaussian is a multi-threaded application (shared memory) only, so a job can not run across multiple compute nodes. Hence you are limited to a maximum of 32 cores. This means that you must run in smp.pe to confine your job to a single node.

Follow the steps below to submit a parallel Gaussian job.

Important Information About Requesting cores

You MUST declare the number of cores for your job twice – via the pe request in you jobscript and using a Gaussian specific variable, also set in the jobscript. See below for further details.

Old method: We used to advise setting the number of cores to use for a job in the Gaussian input file using %NProcsShared or %nprocs. But this can easily lead to mistakes – if you change the number of cores in the jobscript but forget to also change it in the Gaussian input file you will either use too few cores (some of the cores your job requested are sat idle) or too many cores (your job is trying to use cores it shouldn’t, possibly trampling on another user’s job).

New recommended method: We now advise setting the GAUSS_PDEF environment variable in your jobscript (set it to $NSLOTS) so that it always tells Gaussian the correct number of cores to use. This also means you don’t have to keep editing your Gaussian input file each time you want to run the input deck with a different number of cores.

For example, depending which shell you use (look at the first line of your jobscript to find out):

# If using CSH (the 'traditional' shell used by chemistry users):
setenv GAUSS_PDEF $NSLOTS

# If using BASH (the default shell used by most CSF users):
export GAUSS_PDEF=$NSLOTS

Remember that $NSLOTS is automatically set by the batch system to the number of cores you requested on the #$ -pe smp.pe line in the jobscript. Hence there is only one number-of-cores to change if you want to run the job with a different number of cores.

Note: %NProcShared= in the input file takes precedence over GAUSS_PDEF, so one could override the latter by setting %NProcShared in the input file.

Example job submission

You MUST declare the number of cores for your job twice – via the pe request in your jobscript and using a Gaussian specific variable, also set in the jobscript. See the above explanation for further details.
  • It is recommended you run from within your scratch area and use one directory per job: 
    cd ~/scratch
mkdir job1
cd job1
  • Create a job script, for example: 
    #!/bin/bash --login
#$ -cwd                       # Run job in directory you submitted from
#$ -pe smp.pe 12              # Run in SMP parallel environment with e.g. 12 cores
                              # Maximum 32

# Load g09
module load apps/binapps/gaussian/g09d01_em64t                         

# We now recommend using a scratch directory per job
export GAUSS_SCRDIR=/scratch/$USER/gau_temp_$JOB_ID
mkdir -p $GAUSS_SCRDIR

# Ensure correct no. of cores used. No longer done in the input file.
export GAUSS_PDEF=$NSLOTS

$g09root/g09/g09 < file.inp > file.out
  • Submit with the command: 
    qsub scriptname

    where scriptname is the name of your job script.

  • See the serial job information for how to tidy up your scratch directory if Gaussian leaves scratch files behind once the job has finished.

Further info

Last modified on January 25, 2022 at 4:25 pm by Pen Richardson