Difference between revisions of "HPC Software"

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(GCC)
(Intel SDK and MPIs)
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  /apps/intelics/2013.1.039/composer_xe_2013_sp1.0.080/mpirt/bin/intel64/mpivars.sh: No such file or directory
 
  /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:
+
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. For example,
 
  $ module list
 
  $ module list
 
  1) modules                                      3) intelics/<version>
 
  1) modules                                      3) intelics/<version>

Revision as of 15:38, 3 March 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 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

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 Conflict

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>

Module Prereq

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, please 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. For example,

$ 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>