...
| No Format |
|---|
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 $mntpnt/tar/*.taz | zcat | tar xvf - mv g03 g03.D01 chgrp -R gaussian g03.D01/ ln -s g03.D01 g03 cd g03 ./bsd/install Add the user in /etc/group gaussian:x:20000:username |
...
| No Format |
|---|
diff /sw/Gaussian/g03.D01/bsd/g03.profile /sw/Gaussian/g03.D01/bsd/g03.profile.old 15,17c15,17 < GAUSS_EXEDIR="$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 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 |
...
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 -j oe #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 |
Troubleshooting
line 9: /sw/Gaussian/g03.D01/bsd/g03.profile: Permission denied
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
If you get this error "line 9: /sw/Gaussian/g03.D01/bsd/g03.profile: Permission denied", Or: "g03: command not found", please ask the system administrator to add you into the gaussian group (/etc/group) on the cluster.
...
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