Gaussian
Gaussian is a computational chemistry application produced by Gaussian, Inc.
License limitations
Compute Canada currently supports Gaussian only on Graham and certain legacy systems.
In order to use Gaussian you must agree to the following:
- You are not a member of a research group developing software competitive to Gaussian.
- You will not copy the Gaussian software, nor make it available to anyone else.
- You will properly acknowledge Gaussian Inc. and Compute Canada in publications.
- You will notify us of any change in the above acknowledgement.
If you do, please send an email with a copy of those conditions, saying that you agree to them, to support@computecanada.ca. We will then grant you access to Gaussian.
Running Gaussian on Graham
Gaussian g09.e01 and g16.a03 are installed on the newest cluster Graham with modules. You can load them using either of
[name@server ~]$ module load gaussian/g16.a03
[name@server ~]$ module load gaussian/g09.e01
Job Submission
Graham uses Slurm scheduler. For details about submitting jobs, see Running jobs.
Besides your input name.com file, you have to prepare a job script in the same input file directory to define the compute resources for the job.
There are Two Options to run your Gaussian job on Graham based on the size of your job files.
g16 (or g09) for regular size jobs
This option will save the unnamed runtime files (.rwf, .inp, .d2e, .int, .skr) to localscratch /localscratch/yourid/ on the compute node where the job was scheduled to. The files on localscratch will be deleted by the scheduler afterwards, usually users do not track the computer node number, those files could be lost easily. If you do not expect to use the .rwf file for restart in a later time, this is the option to go
Example g16 job script, e.g., name.sh is like (simply change g16 to g09 for a g09 job):
#!/bin/bash
#SBATCH --mem=16G # memory, roughly 2 times %mem defined in the input name.com file
#SBATCH --time=02-00:00 # expect run time (DD-HH:MM)
#SBATCH --cpus-per-task=16 # No. of cpus for the job as defined by %nprocs in the name.com file
module load gaussian/g16.a03
g16 < name.com >& name.log & # g16 command, input: name.com, output: name.log
You can modify the script to fit your job's reqirements for compute resources.
G16 (or G09) for large size jobs
localscratch is ~800G shared by any jobs running on the node. If your job files would be bigger than or close to that size range, you would instead use this option to save files to your /scratch. However it's hard for us to define what size of job would be considered as a large job because we could not predict how many jobs will be running on a node at certain time, how many jobs may save files and the size of the files to /localscratch. It's possible to have multiple Gaussian jobs running on the same node sharing the ~800G space.
G16 provides a better way to manage your files as files are within the jobid directory: /scratch/youris/jobid/, and it's easier to locate the .rwf file to restart a job in a later time.
Example G16 job script, name.sh is like (simply change G16 to G09 for a g09 job):
#!/bin/bash
#SBATCH --mem=16G # memory, roughly 2 times %mem defined in the input name.com file
#SBATCH --time=02-00:00 # expect run time (DD-HH:MM)
#SBATCH --cpus-per-task=16 # No. of cpus for the job as defined by %nprocs in the name.com file
module load gaussian/g16.a03
G16 name.com # G16 command, input: name.com, output: name.log by default
Interactive jobs
You can run interactive Gaussian job for testing purpose on Graham. It's not a good practice to run interactive Gaussian jobs on a login node. You can start an interactive session on a compute node with salloc, the example for an hour, 8 cpus and 10G memory Gaussian job is like Goto the input file directory first, then use salloc command:
[name@server ~]$ salloc --time=1:0:0 --cpus-per-task=8 --mem=10g
Then use either
[name@server ~]$ module load gaussian/g16.a03
[name@server ~]$ G16 g16_test2.com # G16 saves runtime file (.rwf etc.) to /scratch/yourid/93288/
or
[name@server ~]$ module load gaussian/g16.a03
[name@server ~]$ g16 < g16_test2.com >& g16_test2.log & # g16 saves runtime file to /localscratch/yourid/