jjgoings / yalehpc

submission scripts for use on HPCs with Yale CRC

YaleHPC

Gaussian 16 or Q-Chem submission scripts for use on HPCs (primarily Grace) with Yale CRC

Note: you need to be given access to either G16 or Q-Chem before use

Installation

To use submit, easiest way is to put it into $HOME/bin (or otherwise add to $PATH).

To make it executable, just

chmod +x submit 

Usage

The script will automatically detect what type of job you want to run based on the extension. Q-Chem is .in or .inp and G16 is .com or .gjf. The script will gently scream at you if the file does not exist or is badly named, and will give you advice on how to fix it.

Anyway.

Say you want to run a G16 job called gaussian16-job.com. Just navigate to your job and

submit gaussian16-job.com

which will generate the submit script gaussian16-job.sh, which you can then

sbatch gaussian16-job.sh

Command-line options

Aside from the required input file, you can also

Set number of CPU threads (defaults to 16)

submit -nt <NUMBER_THREADS>

Set time to run (default is 24 hours)

submit -t <TIME_IN_HOURS>

Set partition (defaults to pi_hammes_schiffer,day,week, so it should give the most available partition)

submit -p <PARTITION>

The script should check if the walltime requested makes sense given the partitions requested, e.g. you cannot run a job for 48 hours on the day partition.

Help

If you run into issues, just submit --help which will give you all the nice command-line options!

user@grace:~$ submit --help
usage: submit [-h] [-nt N] [-p P] [-t T] infile

Prepare Gaussian 16 or Q-Chem submit script on Grace.

positional arguments:
  infile               Gaussian 16 or Q-Chem input file

optional arguments:
  -h, --help           show this help message and exit
  -nt N, --nthreads N  CPUs-per-node
  -p P, --partition P  partition
  -t T, --time T       time (hours)

Feel free to modify the submit script afterward to your liking, since not all the options you may wish to use (such as email on completetion) are not included by default.

Happy computing!