Difference between revisions of "HPC Software"

Revision as of 13:01, 13 February 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

GCC

On Westmere nodes

$ module load gcc/4.7.1

on Sandy Bridge nodes

$ 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

Grace

$ module load intelics/2013.1.039-compiler libjpeg-turbo libpng zlib/1.2.8-ics motif grace/5.1.23

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

Trouble Shooting

Module Load

If the 'module load' command returns the following errors:

$ module load <Module1>
<Module1>(4):ERROR:150: Module '<Module1>' conflicts with the currently loaded module(s) '<Module2>'
<Module1>(4):ERROR:102: Tcl command execution failed: conflict <Module_Group>

This means that the module you want to load conflicts with the currently loaded module, <Module2>. To fix it, please unload <Module2> and then load <Module1> again:

$ module unload <Module2>
$ module load <Module1>

Or

$ module switch <Module2> <Module1>

If the 'module load' command returns the following errors:

$ module load <Module1>
<Module1>(9):ERROR:151: Module '<Module1>' depends on one of the module(s) '<Module2>'
<Module1>(9):ERROR:102: Tcl command execution failed: prereq <Modle2>

This means that the module you want to load depends on the module <Module2>. To fix it, pleas load <Module2> prior to <Module1>:

$ module load <Module2> <Module1>

You may encounter the above errors many times. Please load/unload the requested/conflicted modules and try again.

Intel SDK and MPIs

If you got the following errors while using both Intel SDK and one of the mpi modules:

/apps/intelics/2013.1.039/composer_xe_2013_sp1.0.080/mpirt/bin/intel64/mpirun: line 96: 
/apps/intelics/2013.1.039/composer_xe_2013_sp1.0.080/mpirt/bin/intel64/mpivars.sh: No such file or directory

please unload the intelics and mpi modules and reload them in the order. Make sure that the intelics module is prior to the mpi module:

$ module list
1) modules                                      3) intelics/<version>
2) mpi/<software>/<version>
$ module unload intelics mpi
$ module load intelics/<version> mpi/<software>/<version>
$ module list
1) modules                                      3) mpi/<software>/<version>
2) intelics/<version>