Gaussian

Gaussian 16 is the latest version of the Gaussian series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Gaussian 16 provides a wide-ranging suite of the most advanced modeling capabilities available. You can use it to investigate the real-world chemical problems that interest you, in all of their complexity, even on modest computer hardware.

Official website : https://gaussian.com/g16main/

update : 12 Dec 2024

Available version
1. Input files
- 1.1 CPU
- 1.2 GPU
2. Job submission script
- 2.1 Run Gaussian on CPU node
- 2.2 Run Gaussian on GPU node
3. Job submission

Available version

Currently, only Gaussian version 16.C.02 is available on Lanta. This Gaussian module can be used for running on both CPU node and GPU node. Gaussian on Lanta does not support parallelization across nodes (can only request a single node per job)

Version	Processing unit	Module name

Version	Processing unit	Module name
16.C.02	CPU	Gaussian/16.C.02-AVX2
16.C.02	GPU	Gaussian/16.C.02-AVX2

1. Input files

The basic input files for running Gaussian on Lanta are gaussian input file (.gjf or .com) and job submission script. The Gaussian input file for CPU and GPU node is slightly different for the Link 0 command section.

1.1 CPU

Example of gaussian input file for running on CPU

%Chk=react                      
%Mem = 10GB
%Nproc = 64
# opt freq APFD/6-311+g(2d,p) geom=connectivity Int=(UltraFine,Acc2E=12)

(CH3)2CH-N=N=N Reactant Opt Freq

0 1
 C                 -1.83177831   -0.66472886    2.11461257
 C                 -0.34820496   -0.85131460    1.74610765
 H                 -0.27347155   -1.22969857    0.74803927
 H                 -2.28349687    0.02809460    1.43575618
 H                 -2.33612081   -1.60629555    2.05143972
 H                 -1.90651173   -0.28634489    3.11268095
 C                  0.30193203   -1.84846238    2.72315330
 H                  1.33272650   -1.97810312    2.46711416
 H                  0.22719861   -1.47007841    3.72122168
 H                 -0.20241047   -2.79002907    2.65998044
 N                  0.34467679    0.44223964    1.83289652
 N                  0.37818431    1.05254766    2.90258123
 N                  0.41169183    1.66285567    3.97226594

 1 2 1.0 4 1.0 5 1.0 6 1.0
 2 7 1.0 3 1.0 11 1.0
 3
 4
 5
 6
 7 8 1.0 9 1.0 10 1.0
 8
 9
 10
 11 12 2.0
 12 13 2.0
 13

Here, %Chk locate and name scratch files, %Mem sets the amount of dynamic memory to use, %CPU contains a list of processor/core numbers for shared memory parallel processing. In this example, the total CPU cores is 64. For further information, please visit https://gaussian.com/link0/.

Note 1.1 : %CPU = 0-63 can replace %Nproc = 64, but it need to specify #SBATCH --exclusive in job submission script

1.2 GPU

Example of gaussian input file for running on GPU. The extra tag is %GPUCPU=gpu-list=core-list. In this example %GPUCPU=0-3=0-3, the job uses 4 GPUs (id 0-3) and assigns CPU no. 0-3 to control these GPUs, respectively.

%Chk=react                      
%Mem = 10GB
%CPU = 0-63
%GPUCPU=0-3=0-3
# opt freq APFD/6-311+g(2d,p) geom=connectivity Int=(UltraFine,Acc2E=12)

(CH3)2CH-N=N=N Reactant Opt Freq

0 1
 C                 -1.83177831   -0.66472886    2.11461257
 C                 -0.34820496   -0.85131460    1.74610765
 H                 -0.27347155   -1.22969857    0.74803927
 H                 -2.28349687    0.02809460    1.43575618
 H                 -2.33612081   -1.60629555    2.05143972
 H                 -1.90651173   -0.28634489    3.11268095
 C                  0.30193203   -1.84846238    2.72315330
 H                  1.33272650   -1.97810312    2.46711416
 H                  0.22719861   -1.47007841    3.72122168
 H                 -0.20241047   -2.79002907    2.65998044
 N                  0.34467679    0.44223964    1.83289652
 N                  0.37818431    1.05254766    2.90258123
 N                  0.41169183    1.66285567    3.97226594

 1 2 1.0 4 1.0 5 1.0 6 1.0
 2 7 1.0 3 1.0 11 1.0
 3
 4
 5
 6
 7 8 1.0 9 1.0 10 1.0
 8
 9
 10
 11 12 2.0
 12 13 2.0
 13

2. Job submission script

create a script using vi submit.sh command and specify the following details depending on computational resources you want to use.

2.1 Run Gaussian on CPU node

#!/bin/bash -l
#SBATCH -p compute                 	#specify partition
#SBATCH -N 1                        #specify number of nodes
#SBATCH --cpus-per-task=64   	    #specify number of cpus
#SBATCH -t 2:00:00                  #job time limit <hr:min:sec>
#SBATCH -J react            	    #job name
#SBATCH -A ltXXXXXX                 #project account

#module purge                            #purge all module
module load Gaussian/16.C.02-AVX2      	#load gaussian version16

FILENAME=react                    # please change the FILENAME
WORKDIR=$SLURM_SUBMIT_DIR
#################################

#create temporary scratch directory
mkdir -p /scratch/lantaXXXXXX-Y/$USER/$SLURM_JOB_ID

#export gaussain scratch directory to this one
export GAUSS_SCRDIR=/scratch/lantaXXXXXX-Y/$USER/$SLURM_JOB_ID

g16 < $FILENAME.gjf > $WORKDIR/$FILENAME.log

The script above request for compute partition (-p compute), 1 node (-N 1) with 64 CPU cores per task (--cpus-per-task=64). The wall-time limit is set to 2 hours 2:00:00 (the maximum time limit is 5 days -t 5-00:00:00) . The account is set to ltXXXXXX (-A ltXXXXXX) that is subjected to change to your own account. The job name is set to react (-J react ). For Gaussian, #SBATCH --exclusive might be needed if %CPU in gaussian input file is used instead of %Nproc (see the note in section 1.1)

Total cores per LANTA Compute node is 128

Please change FILENAME to you own input file and change the GAUSS_SCRDIR to your own project scratch directory ( The path format is /scratch/[projID-shortname] )

2.2 Run Gaussian on GPU node

The script above request for GPU partition (-p gpu), 1 node (-N 1) and 4 GPUs cards --gpus-per-node=4 , and the total CPU cores = 64 (--cpus-per-task=64)

3. Job submission

using sbatch submit.sh command to submit the job to the queuing system.