Software Guide


R

We use module system to manage software with multiple versions installed. Currently there are two different versions of R installed, R/3.4.2 and R/2.15.0.  You will need ‘module load R/3.4.2’ in your job script for R 3.4.2. Here is a sample job script for running R 3.4.2 where the last line is the command you want R executed in batch mode with MySin.R file.

#PBS -q hpcc
#PBS -l nodes=2:ppn=16,mem=128GB
#PBS -l walltime=72:00:00
#PBS -M [email protected] -m abe
#PBS -N MySimJob
#PBS -r y
#PBS -j oe
#PBS -k o

echo ""
echo "***Ignore Warnings for access to tty***"
echo ""
echo -n "Changing to directory... "
cd $PBS_O_WORKDIR
echo ""
echo "Our List of nodes:"
echo ""
cat $PBS_NODEFILE
echo ""
echo -n "Loading module mpi/mpich-x86_64....   "
module load mpi/mpich-x86_64
echo -n "Loading module R/3.4.2.... "
module load R/3.4.2
echo "Done!"
echo ""
echo -n "Finished program at: "
date
echo ""
export OMP_NUM_THREADS=1

R CMD BATCH --no-save MySim.R


Matlab MDCS

The MATLAB Distributed Computing Server (MDCS) allows you to extend your MATLAB workflows from your desktop to HPCC without having to learn the details of submitting jobs to the cluster. Before you can use MDCS on your computer, we will need to apply a few integration scripts to each computer that you plan to run MATLAB on and submit jobs via MDCS to the cluster. Please contact [email protected] for more details. Depending on the availability of licenses at the time of your request, you can run up to 96 cores in parallel. The screen shot below shows how and where you get access to MDCS from your desktop MATLAB after applying the integration scripts to MATLAB on your computer.


Mathematica

the commands you want executed in your job submission script where math.infile is your Mathematica file

math < math.infile


MacAulay 2

the commands you want executed in your job submission script ……


IMa2p

the commands you want executed in your job submission script ……


Stata/MP

Here is a sample job script for running Stata/MP where the last line is the command you want stata-mp to run in batch mode and the input do file is MyStataDoFile.do.

#PBS -q hpcc
#PBS -l nodes=1:ppn=12,mem=48GB
#PBS -l walltime=24:00:00
#PBS -M [email protected] -m abe
#PBS -N MyStataDoJob
#PBS -r y
#PBS -j oe
#PBS -k o

echo ""
echo "***Ignore Warnings for access to tty***"
echo ""
echo -n "Changing to directory... "
cd $PBS_O_WORKDIR
echo ""
echo "Our List of nodes:"
echo ""
cat $PBS_NODEFILE
echo ""
echo -n "Loading module mpi/mpich-x86_64....   "
module load mpi/mpich-x86_64
echo "Done!"
echo ""
echo -n "Finished program at: "
date
echo ""

stata-mp -b do MyStataDoFile.do