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 128 processor cores:
module load gaussian16
subg16 myjob -N 1 -n 128
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/negishi/myusername/gaussian/Gau-7781.inp -scrdir=/scratch/negishi/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:
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
a012.negishi.rcac.purdue.edu
Link to section 'Examples of Gaussian SLURM Job Submissions' of 'Gaussian' Examples of Gaussian SLURM Job Submissions
Submit job using 128 processor cores on a single node:
subg16 myjob -N 1 -n 128 -t 200:00:00 -A myqueuename
Submit job using 128 processor cores on each of 2 nodes:
subg16 myjob -N 2 --ntasks-per-node=128 -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: