HPC Software

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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/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