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Usage
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module displayTo use gaussian on the cluster, one needs to be in the unix group "gaussian". Please contact the HPC admin to request this. module load gaussian/g16 OR module displayload gaussian/g16legacy OR module displayload gaussian/g03 |
Gaussian 03
Installation
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mount -o loop gaussian-3.iso /data1/ISO/mnt3 groupadd -g 20000 gaussian csh setenv mntpnt "/data1/ISO/mnt3" setenv g03root "/sw/Gaussian/" cd $g03root cat $mntpnt/tar/*.taz | zcat | tar xvf - mv g03 g03.D01 chgrp -R gaussian g03.D01/ ln -s g03.D01 g03 cd g03 ./bsd/install Add the user in /etc/group gaussian:x:20000:username |
...
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#!/bin/bash #PBS -N gaussian1 #PBS -m abe #PBS -M YourEmail@griffith.edu.au #PBS -l select=21:ncpus=21:mem=12gb module ,walltime=100:00:00 module load gaussian/g03 source $g03root/bsd/g03.profile source $HOME/.bashrc echo "Starting job: " cd $PBS_O_WORKDIR g03 <<END > $PBS_O_WORKDIR/Myoutput.out <gaussian stuff here> |
...
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#!/bin/bash
#PBS -N gaussian2
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=2:mem=3gb,walltime=100:00:00
module load gaussian/g03
source $g03root/bsd/g03.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
g03 <<... > $PBS_O_WORKDIR/pinene_2.com.out
%mem=3GB
%NProcshared=2
%nproc=2
%chk=pinene_2.com.chk
#P rb3lyp/6-31G* FREQ iop1=timestamp
Alpha-pinene
0,1
C,-0.1273692137,-0.6462988969,-0.7524944873
C,-1.4477041451,-0.2794851567,-0.0867213008
C,-2.5860464422,-1.2583783257,-0.1391304784
C,1.0856948669,-0.3322068693,0.2126188526
C,0.3211006941,0.5905762449,-1.5895340172
C,0.8727653221,1.1569894555,-0.2509716145
C,-0.2877726915,1.8205854739,0.5169186751
C,-1.509519224,0.9249157767,0.4994348271
C,0.9712833239,-0.6726944381,1.7005672426
C,2.4084796519,-0.9186471116,-0.3075889933
H,1.7573199543,1.8050219581,-0.2835783694
H,-0.4737704686,1.1570136799,-2.0846350548
H,1.105915281,0.3652327996,-2.3144053682
H,-0.1543420805,-1.63041802,-1.2341302178
H,1.0392245646,-1.7580982696,1.8515590322
H,1.7984173899,-0.2160067783,2.2599213205
H,0.0329682418,-0.3341838975,2.1448183521
H,2.426925411,-2.0066150881,-0.1652518889
H,3.256078334,-0.5002639995,0.2504468316
H,2.5858549208,-0.7228031753,-1.3687192518
H,-3.4806519207,-0.867446541,0.3570936649
H,-2.8519928168,-1.5058157478,-1.1766371331
H,-2.315284857,-2.2072614785,0.345418714
H,-2.4208684094,1.2742596113,0.9831044354
H,-0.5214551923,2.7956708978,0.0624986118
H,0.0101887933,2.0395771319,1.5539040849
...
|
...
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diff /sw/Gaussian/g03.D01/bsd/g03.profile /sw/Gaussian/g03.D01/bsd/g03.profile.old 15,17c15,17 < GAUSS_EXEDIR="$gr/bsd:$gr/private:$gr/" < GAUSS_LEXEDIR="$gr/linda-exe" < GAUSS_ARCHDIR="$gr/arch" --- > GAUSS_EXEDIR="$gr/g03/bsd:$gr/g03/private:$gr/g03" > GAUSS_LEXEDIR="$gr/g03/linda-exe" > GAUSS_ARCHDIR="$gr/g03/arch" 21c21 < G03BASIS="$gr/basis" --- > G03BASIS="$gr/g03/basis" |
module file
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Readme file that came with the CD
...
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#!/bin/bash
#PBS -N gaussian2
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=2:mem=3gb,walltime=100:00:00
module load gaussian/g09
source $g09root/bsd/g09.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
g09 .......
|
...
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#!/bin/bash
#PBS -N gaussianG09
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=2:mem=3gb,walltime=100:00:00
module load gaussian/g09
source $g09root/bsd/g09.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
g09 <<END > $PBS_O_WORKDIR/pinene_2.com.out
%mem=3GB
%NProcshared=2
%nproc=2
%chk=pinene_2.com.chk
#P rb3lyp/6-31G* FREQ iop1=timestamp
Alpha-pinene
0,1
C,-0.1273692137,-0.6462988969,-0.7524944873
C,-1.4477041451,-0.2794851567,-0.0867213008
C,-2.5860464422,-1.2583783257,-0.1391304784
C,1.0856948669,-0.3322068693,0.2126188526
C,0.3211006941,0.5905762449,-1.5895340172
C,0.8727653221,1.1569894555,-0.2509716145
C,-0.2877726915,1.8205854739,0.5169186751
C,-1.509519224,0.9249157767,0.4994348271
C,0.9712833239,-0.6726944381,1.7005672426
C,2.4084796519,-0.9186471116,-0.3075889933
H,1.7573199543,1.8050219581,-0.2835783694
H,-0.4737704686,1.1570136799,-2.0846350548
H,1.105915281,0.3652327996,-2.3144053682
H,-0.1543420805,-1.63041802,-1.2341302178
H,1.0392245646,-1.7580982696,1.8515590322
H,1.7984173899,-0.2160067783,2.2599213205
H,0.0329682418,-0.3341838975,2.1448183521
H,2.426925411,-2.0066150881,-0.1652518889
H,3.256078334,-0.5002639995,0.2504468316
H,2.5858549208,-0.7228031753,-1.3687192518
H,-3.4806519207,-0.867446541,0.3570936649
H,-2.8519928168,-1.5058157478,-1.1766371331
H,-2.315284857,-2.2072614785,0.345418714
H,-2.4208684094,1.2742596113,0.9831044354
H,-0.5214551923,2.7956708978,0.0624986118
H,0.0101887933,2.0395771319,1.5539040849
END
|
Troubleshooting
...
Sample PBS file for g16
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#!/bin/bash
#PBS -N G16Test
#PBS -m abe
#PBS -M yourEmail@griffithuni.edu.au
#PBS -l select=1:ncpus=1:mem=8gb,walltime=100:00:00
#PBS -l walltime=10:00:00
###module load gaussian/g09
module load gaussian/g16
source $g16root/bsd/g16.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
g16 <PA-opt_freq-conf-1.com> $PBS_O_WORKDIR/PA-opt_freq-conf-1.out |
Another Sample PBS script for G16
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#!/bin/bash
#PBS -N 2CH3P04
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=12:mem=12gb,walltime=1000:00:00
module load gaussian/g16
source $g16root/bsd/g16.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
g16 <<END > $PBS_O_WORKDIR/2CH3PO4_g16.com.out
%NProcShared=12
%chk=2CH3PO4_M06L_dz_O+_ofs.chk
%mem=512MW
#P M06L/gen opt scrf freq=noraman gfinput
Pt triene with Ncp7 core
-1 1
15 0.000019000 0.628091000 -0.000004000
8 0.783576000 1.334578000 1.054520000
8 -0.783436000 1.334707000 -1.054510000
8 0.968875000 -0.418486000 -0.813248000
8 -0.969029000 -0.418328000 0.813247000
6 1.823641000 -1.261367000 -0.059082000
1 1.248954000 -1.984550000 0.532798000
1 2.462299000 -1.806452000 -0.755387000
1 2.451195000 -0.681463000 0.626300000
6 -1.823669000 -1.261333000 0.059077000
1 -2.451063000 -0.681556000 -0.626564000
1 -1.248895000 -1.984678000 -0.532517000
1 -2.462494000 -1.806241000 0.755369000
C H P 0
6-31g(2d,2p)
****
O 0
6-31+g(2d)
****
END |
Using Gaussian with GPU
This is possible on the gpu node n060 and with version g16.avx.c01.
Usage is as follows:
Sample PBS script
cat pbs.01
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#!/bin/bash
#PBS -N GaussianGPUTest
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -q iworkq
#PBS -l select=1:ncpus=4:ngpus=1:mem=12gb,walltime=5:00:00
#PBS -W group_list=deeplearning -A deeplearning
module load gaussian/g16
source $g16root/bsd/g16.profile
source $HOME/.bashrc
echo "Starting job: "
cd $PBS_O_WORKDIR
set echo
set INPUT=methane.com
module load gaussian/g16
g16 < $PBS_O_WORKDIR/methane.input |
Sample input
cat methane.input
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%nproc=4
%mem=8gb
%CPU=0-3
%GPUCPU=0=0
%chk=methane.chk
# hf/6-31g
Title Card Required
0 1
C 0.80597015 -1.20895521 0.00000000
H 1.16262458 -2.21776521 0.00000000
H 1.16264299 -0.70455702 0.87365150
H 1.16264299 -0.70455702 -0.87365150
H -0.26402985 -1.20894202 0.00000000
END |
The above example will utilise CPUs indexed from 0 to 3rd, but 0th CPU is associated with 0th GPU.
Ref: https://www.osc.edu/resources/available_software/software_list/gaussian
Troubleshooting
line 9: /sw/Gaussian/g03.D01/bsd/g03.profile: Permission denied
...
1. https://wiki.ace-net.ca/index.php/GAUSSIAN
2. http://www.lrz.de/services/software/chemie/gaussian/
3. https://www.msi.umn.edu/~cpsosa/ChemApps/QuaChem/gaussian_tech/support/download/ibm_bench_g98.tar
4. http://docs.notur.no/application-support/chemistry-applications/gaussian-1/troubleshooting-gaussian-calculations
5. https://www.osc.edu/resources/available_software/software_list/gaussian