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Gaussian at CHPC

  • NOTE : You should always run your jobs from scratch5

We have two versions of Gaussian 09 installed at CHPC. Here is an example on how to access them:

username@login01:~/scratch5 $ module avail                   ### list available modules
username@login01:~/scratch5 $ module add gaussian/g09.A01    ### load g09 version A01 (older) or
username@login01:~/scratch5 $ module add gaussian/g09.D01    ### load g09 version D01 (new)

Example moab job script for g09.A01

#/bin/csh
#MSUB -l nodes=1:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=2:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /export/home/username/scratch5/log.out
#MSUB -e /export/home/username/scratch5/log.err
#MSUB -d /export/home/username/scratch5
 
source /opt/gridware/applications/gaussian/old/g09/g09setup 
source /etc/profile.d/modules.sh
module add gaussian/g09.A01
g09 < input.com > output.log

Example moab job script for g09.D01

#/bin/csh
#MSUB -l nodes=1:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=2:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /export/home/username/scratch5/log.out
#MSUB -e /export/home/username/scratch5/log.err
#MSUB -d /export/home/username/scratch5
 
   
source /opt/gridware/applications/gaussian/g09/g09setup
source /etc/profile.d/modules.sh
module add gaussian/g09.D01
g09 < input.com > output.log

Both examples above use this example of a gaussian input file:

%nprocshared=12
%nprocl=1
#P HF/6-31G*  IOP(6/33=2,6/41=10,6/42=17) SCF=Tight Pop=MK       
Title Card Required
0 1
 C                 -3.19550100    0.11344600   -0.18511100
 O                 -3.05859100    0.83554400   -1.15941100
 N                 -2.14200500   -0.25446800    0.60848900
 H                 -2.32841200   -0.78506500    1.44398900
 C                 -0.75900100    0.12341400    0.36048900
 C                  0.14379200   -0.42259800    1.48678900
 C                  0.59047400   -1.84630300    1.03238900
 C                  1.59689900    0.10938400    1.28248900
 C                  0.08697100   -2.05959700   -0.42431100
 C                  2.05278100   -1.31402200    0.82788900
 C                 -0.14011000   -0.59319400   -0.87441100
 C                  1.35866600   -2.48501300   -1.17731100
 C                  1.32989700   -0.05621300   -1.07501100
 C                  1.66721100    0.99508300    0.02128900
 C                  2.20428100   -1.28752400   -0.71551100
 C                  0.60162500    2.08159700    0.02358900
 N                 -0.63668200    1.58111300    0.28218900
 O                  0.86964000    3.24909300   -0.21751100
 H                 -1.43757500    2.10622300   -0.04521100
 O                  2.93691800    1.56466600   -0.15981100
 H                  2.76333000    2.51016900   -0.30861100
 H                 -0.28050600   -0.28619200    2.48278900
 H                  0.43696300   -2.68340100    1.71298900
 H                  2.07960500    0.56667700    2.14378900
 H                 -0.78403700   -2.70728500   -0.52611100
 H                  2.86017500   -1.79913300    1.37408900
 H                 -0.75990800   -0.47138600   -1.76101100
 H                  1.22276500   -2.52601100   -2.26181100
 H                  1.75375300   -3.44771800   -0.83891100
 H                  1.50280200    0.34398500   -2.07391100
 H                  3.22968200   -1.22473700   -1.07621100
 C                 -4.55170800   -0.42883700    0.22928900
 H                 -5.23089700    0.41157200    0.38338900
 H                 -4.52881600   -1.04383700    1.13088900
 H                 -4.94951500   -1.02253200   -0.59631100

 

Last Updated on Tuesday, 03 June 2014 14:27

Hits: 1312

DL_poly

DL_Poly_2.18 up to 3.10  (Sun Microsystems)

###These lines are for Moab
#MSUB -l nodes=5:ppn=12
#MSUB -l partition=dell|westmere
#MSUB -l walltime=168:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /lustre/SCRATCH5/users/username/work/stdout.out
#MSUB -e /lustre/SCRATCH5/users/username/work/stderr.err
#MSUB -d /lustre/SCRATCH5/users/username/work
#MSUB -mb
#MSUB -M This email address is being protected from spambots. You need JavaScript enabled to view it.
##### Running commands
exe=/opt/gridware/applications/dlpoly/DLPOLY_3.09.Y
nproc=`cat $PBS_NODEFILE | wc -l`
mpirun -np $nproc $exe

Last Updated on Tuesday, 03 June 2014 14:25

Hits: 1308

Sun Compilers

1. Sun Compilers

To use sun compilers, clustertools and intel compilers, please do the following on the command line:

user@login02:~> module add sunstudio

user@login02:~> module add clustertools

user@login02:~> module add intel-XE/11.1 Or intel-XE/12.0 Or intel-XE/13.0

These will add sun compilers and clustertools (including MPI compiled to run over the infiniband and MPI compiler) to your path.

Path to SUN MPI compilers:

Code Name

Directory

Notes

mpicc

/opt/gridware/sun-hpc-ct-8.2-Linux-sun/bin/mpicc

MPI Sun C compiler

mpicxx

/opt/gridware/sun-hpc-ct-8.2-Linux-sun/bin/mpicxx

MPI Sun C++ compiler

mpif77

/opt/gridware/sun-hpc-ct-8.2-Linux-sun/bin/mpif77

MPI Sun Fotran 77 compiler

mpif90

/opt/gridware/sun-hpc-ct-8.2-Linux-sun/bin/mpif90

MPI Sun Fotran 90 compiler

 

2. GNU Compilers

Path to GNU compilers:

gcc: /usr/bin/gcc

gfortran: /usr/bin/gfortran

Path to GNU MPI compilers:

Code Name

Directory

Notes

mpicc

/opt/gridware/sun-hpc-ct-8.2-Linux-gnu/bin/mpicc

MPI gcc C compiler

mpicxx

/opt/gridware/sun-hpc-ct-8.2-Linux-gnu/bin/mpicxx

MPI g++ C++ compiler

mpif77

/opt/gridware/sun-hpc-ct-8.2-Linux-gnu/bin/mpif77

MPI gfotran Fotran 77 compiler

mpif90

/opt/gridware/sun-hpc-ct-8.2-Linux-gnu/bin/mpif90

MPI gfotran Fotran 90 compiler

 

3. Intel Compilers

Path to Intel MPI compilers:

Code Name

Directory

Notes

mpicc

/opt/gridware/sun-hpc-ct-8.2-Linux-intel/bin/mpicc

MPI icc C compiler

mpicxx

/opt/gridware/sun-hpc-ct-8.2-Linux-intel/bin/mpicxx

MPI ic++ C++ compiler

mpif77

/opt/gridware/sun-hpc-ct-8.2-Linux-intel/bin/mpif77

MPI ifort Fotran 77 compiler

mpif90

/opt/gridware/sun-hpc-ct-8.2-Linux-intel/bin/mpif90

MPI ifort Fotran 90 compiler

 

Last Updated on Tuesday, 03 June 2014 14:48

Hits: 1497

FAQ

SUN Cluster

Q: How do I Login to SUN cluster?
A: Logging in - via Secure Shell

Q: How do I change my password?
A: Logging in - Changing your password

Q: What are the complilers on SUN?
A: Compilers on SUN

Q: How do I Submit/Run Jobs?
A: Submit/Run on Sun

Last Updated on Tuesday, 03 June 2014 14:54

Hits: 1270

Documentation for users:

CHPC Student Cluster Competition 2013

Tsessebe Cluster Available

Graphical Processing Unit Cluster Available

CHPC SAGrid Cluster Available

Dirisa Storage Unit Available

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