| Table of Contents |
|---|
...
Usage
Installation
| No Format |
|---|
mountTo -ouse 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 |
Module load instructions
| No Format |
|---|
To use g03, simply do this:
module load gaussian/g03
If using g09, do this:
module load gaussian/g09
If you want to swap between g03 and g09, do this:
module swap gaussian/g03 gaussian/g09
|
Sample PBS script
Gaussian can be executed by typing
g03 < input > output &
OR:
g03 < input
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 load gaussian/g16legacy
OR
module load gaussian/g03 |
Gaussian 03
Installation
| No Format |
|---|
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
|
Module load instructions
| No Format |
|---|
To use g03, simply do this:
module load gaussian/g03
If using g09, do this:
module load gaussian/g09
If you want to swap between g03 and g09, do this:
module swap gaussian/g03 gaussian/g09
|
Sample PBS script
Gaussian can be executed by typing
g03 < input > output &
OR:
g03 < input
Users are reminded to keep an eye on interactive jobs and that interactive jobs shouldn't be left to run more than 15 minutes. Jobs longer than this should be considered Production Jobs and run through PBS batching system.
...
| No Format |
|---|
#!/bin/bash #PBS -N gaussian1 #PBS -m abe #PBS -M YourEmail@griffith.edu.au #PBS -l select=21:ncpus=21:mem=12gb ,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> |
...
| No Format |
|---|
#!/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 <<... > $PBS_O_WORKDIR/pinene_2.com.out
%mem=3GB
%NProcshared=2
%nproc=2
%chk=pinene_2.com.chk
#P rb3lyp/6-31G* FREQ iop1=timestamp
Alpha-pinene
0,1
C,-0.1273692137,-0.6462988969,-0.7524944873
C,-1.4477041451,-0.2794851567,-0.0867213008
C,-2.5860464422,-1.2583783257,-0.1391304784
C,1.0856948669,-0.3322068693,0.2126188526
C,0.3211006941,0.5905762449,-1.5895340172
C,0.8727653221,1.1569894555,-0.2509716145
C,-0.2877726915,1.8205854739,0.5169186751
C,-1.509519224,0.9249157767,0.4994348271
C,0.9712833239,-0.6726944381,1.7005672426
C,2.4084796519,-0.9186471116,-0.3075889933
H,1.7573199543,1.8050219581,-0.2835783694
H,-0.4737704686,1.1570136799,-2.0846350548
H,1.105915281,0.3652327996,-2.3144053682
H,-0.1543420805,-1.63041802,-1.2341302178
H,1.0392245646,-1.7580982696,1.8515590322
H,1.7984173899,-0.2160067783,2.2599213205
H,0.0329682418,-0.3341838975,2.1448183521
H,2.426925411,-2.0066150881,-0.1652518889
H,3.256078334,-0.5002639995,0.2504468316
H,2.5858549208,-0.7228031753,-1.3687192518
H,-3.4806519207,-0.867446541,0.3570936649
H,-2.8519928168,-1.5058157478,-1.1766371331
H,-2.315284857,-2.2072614785,0.345418714
H,-2.4208684094,1.2742596113,0.9831044354
H,-0.5214551923,2.7956708978,0.0624986118
H,0.0101887933,2.0395771319,1.5539040849
...
|
...
| No Format |
|---|
diff /sw/Gaussian/g03.D01/bsd/g03.profile /sw/Gaussian/g03.D01/bsd/g03.profile.old 15,17c15,17 < GAUSS_EXEDIR="$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
| No Format |
|---|
Readme file that came with the CD
...
| No Format |
|---|
#!/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 .......
|
...
| No Format |
|---|
#!/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 ,-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 |
Sample PBS file for g16
| No Format |
|---|
#!/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
| No Format |
|---|
#!/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
| No Format |
|---|
#!/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
| No Format |
|---|
%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