Using G09 on the Dell Cluster

Using G09 on the Dell Cluster

Introduction Gaussian 09 software can be used only in parallel mode on the Dell Cluster. Environmental setup for Dell Cluster : Gaussian 09 is installed in the directory /home/pkg/lic/g09. To enable the exection of Gaussian 09 jobs, user must set the proper environmental variables depending upon the login shell The variable g09root must be set to the installation directory of gaussian 09: csh:          setenv g09root /home/pkg/lic/g09/em64t bash/ksh:          export g09root=/home/pkg/lic/g09/em64t sh:          g09root=/home/pkg/lic/g09/em64t; export g09root Initialization files to be set up: csh:          source /home/pkg/lic/g09/em64t/g09/bsd/g09.login bash/ksh:          . /home/pkg/lic/g09/em64t/g09/bsd/g09.profile sh:         /home/pkg/lic/g09/em64t/g09/bsd/g09.profile Setting scratch directory for G09 runs using GAUSS_SCRDIR environmental variable. This should be set to the base directory where scratch files are to be stored. csh:          setenv GAUSS_SCRDIR /global/utemp/loginid         or         setenv GAUSS_SCRDIR /home/dell-scratch/loginid bash/ksh:          export GAUSS_SCRDIR= /global/utemp/loginid          or          export GAUSS_SCRDIR= /home/dell-scratch/loginid sh:         GAUSS_SCRDIR= /global/utemp/loginid         export GAUSS_SCRDIR         or         GAUSS_SCRDIR= /home/dell-scratch/loginid         export GAUSS_SCRDIR Here, loginid refers to your login id Note: Once your job is complete remove all temporary files created by your job in GAUSS_SCRDIR scratch directory. Files in /home/dell-scratch/loginid older than 7 days are removed automatically Number of CPUs to be used: The Gaussian 09 on the Dell Cluster, supports parallel processing. You may specify the default number of CPUs to use in the Default. Route file in your current working directory. For example the following command sets the default number of CPUs to 4: -P- 4 To override the default no of CPUs the following command should be used as the first line in your input file. %nproc=8 Where %nproc is equal to the number of CPUs. The above command sets the number of CPUs to be used to 8 Note: Whatever number of CPUs is mentioned in the Default.Route file or using the %nproc directive in the input file, that number should also be specified in the PBS command file using the ncpus directive. Running Gaussian 09 in the PBS Job Scheduler: Example PBS Script for a Single Node Parallel Job #!/bin/csh #PBS -l ncpus=4 #PBS -S /bin/csh #PBS -V setenv g09root /home/pkg/lic/g09/em64t source $g09root/g09/bsd/g09.login setenv GAUSS_SCRDIR /home/dell-scratch/loginid g09<$GAUSS_SCRDIR/benzene.com>$GAUSS_SCRDIR/benzene.log where benzene.com is the input file to Gaussian 09 Also, add the number of CPUs to the top of the input data file using the following format: %nproc = 4 Where %nproc is equal to the number of CPUs. Example PBS Script for Mutli-Node Parallel Job #!/bin/csh #PBS -l nodes=2:ppn=8 #PBS -S /bin/csh #PBS -V setenv g09root /home/pkg/lic/g09/em64t source $g09root/g09/bsd/g09.login setenv GAUSS_SCRDIR /home/dell-scratch/loginid if  $?PBS_NODEFILE    then        foreach node ( `cat $PBS_NODEFILE | sort | uniq` )            if $?GAUSS_LFLAGS    then                  setenv  GAUSS_LFLAGS "${GAUSS_LFLAGS} ${node}"           else              setenv  GAUSS_LFLAGS ${node}           endif        end        setenv  GAUSS_LFLAGS "-nodelist '${GAUSS_LFLAGS}'" endif g09<$GAUSS_SCRDIR/benzene.com>$GAUSS_SCRDIR/benzene.log where benzene.com is the input file to Gaussian 09 Also, add the number of nodes and CPUs to the input data file using the following format: %NProcLinda=2 , %NProcShared=8 Where NProcLinda is equal to the number of nodes and NProcShared is equal to the number of CPUs. Software documentation: Gaussian 09 online help