auto_slurm
The purpose of this repo is to simplify setup and submission of SLURM jobs. This script is currently designed to run SLURM jobs doing gaussian or gamess calculations. If you are interested in how the scripts work, see the README in the scripts section.
Installing the script
- Login to the server used to submit SLURM jobs.
- Clone this repo using the following command:
git clone https://github.com/CurtisColwell/auto_slurm.git
Running the script
For gaussian, simply place gaussian input (.com) files in the auto_slurm/gaussian/input/
directory and run the script using the following command.
bash auto_slurm/gaussian/scripts/submit_gaussian.bash
A test input file of a hydrogen molecule is included. Run this first to ensure everything is working properly. Output, checkpoint and formatted checkpoint files will be generated in the output directory. A log showing the steps performed by the script will be available in the log directory.
Running gamess
Follow the instructions for gaussian, but replace every mention of "gaussian" with "gamess". Gamess does not generate checkpoint, formatted checkpoint, or log files. The text normally generated in the log file for gaussian submissions instead appears at the beginning and end of the output file.
Running orca
Follow the instructions for gaussian, but replace every mention of "gaussian" with "orca". Orca generates a gbw file, property file, and property text file with the output file.
Running on different nodes
If your job needs more time, you can run on a different node. The default node is 'short' which has a 24 h time limit. Switching to 'long' changes the time limit to 2 weeks. A full list of nodes can be found here. To run on a different node add the name of the node at the end of the submission command. For example to run on a long node run the following command:
bash auto_slurm/scripts/submit_gaussian.bash long
Note about input files
Do not place %Chk= directives at the top of the input file. Checkpoint files
are handled automatically by the script.
Limit input filenames to 8 characters. Otherwise, the script will resubmit jobs that are already running.