HPC Software

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Software Guides

Abaqus Guide - How to use Abaqus FEA 6.12
CAMx Guide - How to use CAMx with MPI and OMP
Comsol Guide - How to use COMSOL on the HPC Cluster
DXA Guide - How to use Dislocation Extraction Algorithm
Fluent Guide - How to use Fluent of ANSYS
GPU Mathematica Guide - How to run Wolfram Mathematica with GPU acceleration
Grace Guide - How to run grace / xmgrace with GUI
Hadoop Guide - How to use hadoop software
Intel SDK Guide - How to use Intel Cluster Studio XE 2013 (in progress)
LAMMPS Guide - How to use LAMMPS
LS-Dyna Guide - How to use LS-DYNA
MAPLE Guide - How to use MAPLE on the HPC Cluster
MATLAB Guide - How to submit MATLAB jobs
Modules Guide - How to manage and load environment modules
Motif Guide - How to use Motif on the HPC Cluster
MPI Guide - A Quick Guide to Programming with MPI
MPJ Guide - MPJ (Java MPI)
MPICH2 Guide - How to use MPICH2 on the HPC Cluster
MVAPICH2 Guide - How to use MVAPICH2 on the HPC Cluster
NAMD Guide - How to use NAMD on the HPC Cluster
OpenACC Guide - How to use OpenACC on the HPC Cluster
OpenMp Usage - how to use OpenMp on the HPC Cluster
OpenMPI Guide - How to use OpenMPI on the HPC Cluster
phpbb - How to use phpbb
Python virtualenv Guide - How to use virtualenv for python
Qiime Guide - How to use Qiime on the HPC Cluster (in progress)
R Guide - How to use GNU R on HPC Cluster
R-LINE Guide - How to use R-LINE on HPC Cluster
Screenie Guide - How to use Screenie / GNU Screen
StarCCM Guide - How to use StarCCM (in progress)
Trinity Guide - How to use the Trinity RNA Sequence Assembler (in progress)
VASP Guide - How to use VASP
WINE Guide - How to use WINE on HPC Cluster
Tensorflow Guide - How to use Tensorflow on HPC Cluster

Other Software Guidelines


BWA has been compiled to run on the Westmere nodes. When using sbatch, specify --partition=Westmere

$ module load bwa/0.7.5a


On Westmere nodes which refer to cn01 to cn64.

$ module load gcc/4.7.1

on Sandy Bridge nodes which refer to cn65 to cn104.

$ module load gcc/4.8.2


$ module load intelics/2012.0.032 zlib/1.2.3-ics hdf5/1.8.9-ics netcdf/4.2-ics geos-chem/v9-02


For 4.6.5 with plumed on the Westmere nodes. The order of modulefiles should follow this command.

$ module load gcc/4.7.1 intelcis/2013.1.039-full gromacs/4.6.5-plumed

For 5.1.4-plumed-gsl (the default "gromacs" module), the order of modulefiles should follow thiscommand:

$ module load gcc/5.4.0-alt plumed/2-gnu boost/1.61.0-gcc-mpi mpi/openmpi/2.1.0 zlib/1.2.8 fftw/3.3.6-gcc540a gsl gromacs


$ module load gaussian/g09d01


$ module load igraph/0.6.5


$ module load gcc/4.7.1 trinityrnaseq/2013.08.14