Difference between revisions of "HPC Software"

Revision as of 11:18, 15 October 2014

List of software installed on the HORNET cluster

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 Hornet Cluster

DXA Guide - How to use Dislocation Extraction Algorithm

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)

LS-Dyna Guide - How to use LS-DYNA

MAPLE Guide - How to use MAPLE on Hornet cluster

MATLAB Guide - How to submit MATLAB jobs

Modules Guide - How to manage and load environment modules

MPI Guide - A Quick Guide to Programming with MPI

MPJ Guide - MPJ (Java MPI)

MPICH2 Guide - How to use MPICH2 on the Hornet cluster

MVAPICH2 Guide - How to use MVAPICH2 on the Hornet cluster

NAMD Guide - How to use NAMD on the Hornet cluster

OpenACC Guide - How to use OpenACC on the Hornet cluster

OpenMp Usage - how to use OpenMp on the Hornet cluster

OpenMPI Guide - How to use OpenMPI on the Hornet cluster

phpbb - How to use phpbb

Python virtualenv Guide - How to use virtualenv for python

Qiime Guide - How to use Qiime on the Hornet cluster (in progress)

R Guide - How to use GNU R on Hornet 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

Other Software Guidelines

BWA

BWA is only available in the Westmere nodes. i.e. hornet-login1.engr.uconn.edu and hornet.engr.uconn.edu

$ module load bwa/0.7.5a

fluent

First load the fluent module

module load fluent/version

For example, to load fluent-v14.0:

module load fluent/14.0

Next, with an input script foo.txt, run

bsub fluent 3d -g -i foo.txt

foo.txt must refer to a .cas input file. 3d is one of

2d    2ddp_host  2d_host  3d	3ddp_host  3d_host
2ddp  2ddp_node  2d_node  3ddp	3ddp_node  3d_node

To run with mpi, try

bsub -n $np fluent 2ddp -t$np -pnmpi -ssh -g -i foo.txt -lsf

Replace $np with the number of cores you need.

GCC

On Westmere nodes which refer to cn01 to cn64. Login node: hornet.engr.uconn.edu or hronet-login1.engr.uconn.edu

$ module load gcc/4.7.1

on Sandy Bridge nodes which refer to cn65 to cn104. Login node: hornet-login1.engr.uconn.edu

$ module load gcc/4.8.2

GEOS-Chem

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

Gromacs

For 4.6.5 with plumed on the Westmere nodes (hornet.engr.uconn.edu). The order of modulefiles should follow this command.

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

Gaussian

$ module load gaussian/g09d01

igraph

$ module load igraph/0.6.5

LAMMPS

$ module load lammps/28Jun14

motif

$ module load motif/2.3.4

R-LINE

$ module load rline/1.2

Then run:

$ RLINE

TrinityRNASeq

$ module load gcc/4.7.1 trinityrnaseq/2013.08.14

WINE

WINE is used to execute windows application on linux, but we do not recommend user to do so. You can send email to hpchelp@engr.uconn.edu to request installation of software in linux for help.

To load WINE,

$ module load wine/1.1.27-withoutX