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Running Gaussian on Graham and Cedar
[name@server $] module spider gaussian
For module commands, please see Using modules.
The national clusters use the Slurm scheduler; for details about submitting jobs, see Running jobs.
Besides your input file (in our example name.com), you have to prepare a job script to define the compute resources for the job; both input file and job script must be in the same directory.
There are two options to run your Gaussian job on Graham and Cedar, based on the location of the default runtime files and the job size.
G16 (G09, G03)
This option will save the default runtime files (unnamed .rwf, .inp, .d2e, .int, .skr files) to /scratch/username/jobid/. Those files will stay there when the job is unfinished or failed for whatever reason, you could locate the .rwf file for restart purpose later.
The following example is a G16 job script:
Note that for coherence, we use the same name for each files, changing only the extension (name.sh, name.com, name.log).
#!/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.c01 G16 name.com # G16 command, input: name.com, output: name.log
To use Gaussian 09 or Gaussian 03, simply modify the module load gaussian/g16.b01 to gaussian/g09.e01 or gaussian/g03.d01, and change G16 to G09 or G03. You can modify the --mem, --time, --cpus-per-task to match your job's requirements for compute resources.
g16 (g09, g03)
This option will save the default runtime files (unnamed .rwf, .inp, .d2e, .int, .skr files) temporarily in $SLURM_TMPDIR (/localscratch/username.jobid.0/) on the compute node where the job was scheduled to. The files will be removed by the scheduler when a job is done (successful or not). If you do not expect to use the .rwf file to restart in a later time, you can use this option.
/localscratch is ~800G shared by all jobs running on the same node. If your job files would be bigger than or close to that size range, you would instead use the G16 (G09, G03) option.
The following example is a g16 job script:
#!/bin/bash #SBATCH --mem=16G # memory, roughly 2 times %mem defined in the input name.com file #SBATCH --time=02-00:00 # expect run time (DD-HH:MM) #SBATCH --cpus-per-task=16 # No. of cpus for the job as defined by %nprocs in the name.com file module load gaussian/g16.c01 g16 < name.com # g16 command, input: name.com, output: slurm-<jobid>.out by default
Submit the job
You can run interactive Gaussian job for testing purpose on Graham and Cedar. It's not a good practice to run interactive Gaussian jobs on a login node. You can start an interactive session on a compute node with salloc, the example for an hour, 8 cpus and 10G memory Gaussian job is like Goto the input file directory first, then use salloc command:
[name@server ~]$ salloc --time=1:0:0 --cpus-per-task=8 --mem=10g
Then use either
[name@server ~]$ module load gaussian/g16.c01 [name@server ~]$ G16 g16_test2.com # G16 saves runtime file (.rwf etc.) to /scratch/yourid/93288/
[name@server ~]$ module load gaussian/g16.c01 [name@server ~]$ g16 < g16_test2.com >& g16_test2.log & # g16 saves runtime file to /localscratch/yourid/
Gaussian jobs can always be restarted from the previous rwf file.
The geometry optimization can be restarted from the chk file as usual. The one-step computation, such as Analytic frequency calculations, including properties like ROA and VCD with ONIOM; CCSD and EOM-CCSD calculations; NMR; Polar=OptRot; CID, CISD, CCD, QCISD and BD energies, can be restarted from rwf file.
To restart a job from previous rwf file, you need to know the location of this rwf file from your previous run.
The restart input is simple: first you need to specify %rwf path to the previous rwf file, secondly change the keywords line to be #p restart, then leave a blank line at the end.
A sample restart input is like:
%rwf=/scratch/yourid/jobid/name.rwf %NoSave %chk=name.chk %mem=5000mb %nprocs=16 #p restart (one blank line)
An example input file and the run scripts *.sh can be found in /opt/software/gaussian/version/examples/ where version is either g03.d10, g09.e01, or g16.c01
Some of the error messages produced by Gaussian have been collected, with suggestions for their resolution. See Gaussian error messages.