Difference between revisions of "HPC Software"

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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.
 
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,
 
To load WINE,
$ module load wine/1.1.27-withoutX
+
$ module load wine/1.1.27-withoutX

Revision as of 15:42, 21 July 2014

List of software installed on the HORNET cluster

Software Guides

Abaqus Guide - How to use Abaqus FEA 6.12
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
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
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

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

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/23Sep13

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