Gaussian
Gaussian is a computational chemistry software package which works on electronic structure. This section illustrates how to submit a small Gaussian job to a Slurm queue. This Gaussian example runs the Fletcher-Powell multivariable optimization.
Prepare a Gaussian input file with an appropriate filename, here named myjob.com. The final blank line is necessary:
#P TEST OPT=FP STO-3G OPTCYC=2
STO-3G FLETCHER-POWELL OPTIMIZATION OF WATER
0 1
O
H 1 R
H 1 R 2 A
R 0.96
A 104.
To submit this job, load Gaussian then run the provided script, named subg16. This job uses one compute node with 20 processor cores:
module load gaussian16
subg16 myjob -N 1 -n 20
View job status:
squeue -u myusername
View results in the file for Gaussian output, here named myjob.log. Only the first and last few lines appear here:
Entering Gaussian System, Link 0=/apps/cent7/gaussian/g16-A.03/g16-haswell/g16/g16
Initial command:
/apps/cent7/gaussian/g16-A.03/g16-haswell/g16/l1.exe /scratch/scholar/myusername/gaussian/Gau-7781.inp -scrdir=/scratch/scholar/myusername/gaussian/
Entering Link 1 = /apps/cent7/gaussian/g16-A.03/g16-haswell/g16/l1.exe PID= 7782.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016,
Gaussian, Inc. All Rights Reserved.
.
.
.
Job cpu time: 0 days 0 hours 3 minutes 28.2 seconds.
Elapsed time: 0 days 0 hours 0 minutes 12.9 seconds.
File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 2 Scr= 2
Normal termination of Gaussian 16 at Tue May 1 17:12:00 2018.
real 13.85
user 202.05
sys 6.12
Machine:
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
scholar-a012.rcac.purdue.edu
Link to section 'Examples of Gaussian SLURM Job Submissions' of 'Gaussian' Examples of Gaussian SLURM Job Submissions
Submit job using 20 processor cores on a single node:
subg16 myjob -N 1 -n 20 -t 200:00:00 -A myqueuename
Submit job using 20 processor cores on each of 2 nodes:
subg16 myjob -N 2 --ntasks-per-node=20 -t 200:00:00 -A myqueuename
To submit a bash job, a submit script sample looks like:
#!/bin/bash
#SBATCH -A myqueuename # Queue name(use 'slist' command to find queues' name)
#SBATCH --nodes=1 # Total # of nodes
#SBATCH --ntasks=64 # Total # of MPI tasks
#SBATCH --time=1:00:00 # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
module load gaussian16
g16 < myjob.com
For more information about Gaussian: