Difference between revisions of "HPC Software"

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(Remove broken link)
(Changed instances of Hornet to HPC Cluster, removed login node specification)
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:[[Abaqus Guide]] - How to use Abaqus FEA 6.12
 
:[[Abaqus Guide]] - How to use Abaqus FEA 6.12
 
:[[CAMx Guide]] - How to use CAMx with MPI and OMP
 
:[[CAMx Guide]] - How to use CAMx with MPI and OMP
:[[Comsol Guide]] - How to use COMSOL on Hornet Cluster
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:[[Comsol Guide]] - How to use COMSOL on the HPC Cluster
 
:[[DXA Guide]] - How to use Dislocation Extraction Algorithm
 
:[[DXA Guide]] - How to use Dislocation Extraction Algorithm
 
:[[Fluent Guide]] - How to use Fluent of ANSYS
 
:[[Fluent Guide]] - How to use Fluent of ANSYS
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:[[LAMMPS Guide]] - How to use LAMMPS
 
:[[LAMMPS Guide]] - How to use LAMMPS
 
:[[LS-Dyna Guide]] - How to use LS-DYNA
 
:[[LS-Dyna Guide]] - How to use LS-DYNA
:[[MAPLE Guide]] - How to use MAPLE on Hornet cluster
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:[[MAPLE Guide]] - How to use MAPLE on the HPC Cluster
 
:[[MATLAB Guide]] - How to submit MATLAB jobs
 
:[[MATLAB Guide]] - How to submit MATLAB jobs
 
:[[Modules Guide]] - How to manage and load environment modules
 
:[[Modules Guide]] - How to manage and load environment modules
:[[Motif Guide]] - How to use Motif on Hornet cluster
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:[[Motif Guide]] - How to use Motif on the HPC Cluster
 
:[[MPI Guide]] - A Quick Guide to Programming with MPI
 
:[[MPI Guide]] - A Quick Guide to Programming with MPI
 
:[[MPJ Guide]] - MPJ (Java MPI)
 
:[[MPJ Guide]] - MPJ (Java MPI)
:[[MPICH2 Guide]] - How to use MPICH2 on the Hornet cluster
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:[[MPICH2 Guide]] - How to use MPICH2 on the HPC Cluster
:[[MVAPICH2 Guide]] - How to use MVAPICH2 on the Hornet cluster
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:[[MVAPICH2 Guide]] - How to use MVAPICH2 on the HPC Cluster
:[[NAMD Guide]] - How to use NAMD on the Hornet cluster
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:[[NAMD Guide]] - How to use NAMD on the HPC Cluster
:[[OpenACC Guide]] - How to use OpenACC on the Hornet cluster
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:[[OpenACC Guide]] - How to use OpenACC on the HPC Cluster
:[[OpenMp Usage]] - how to use OpenMp on the Hornet cluster
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:[[OpenMp Usage]] - how to use OpenMp on the HPC Cluster
:[[OpenMPI Guide]] - How to use OpenMPI on the Hornet cluster
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:[[OpenMPI Guide]] - How to use OpenMPI on the HPC Cluster
 
:[[phpbb]] - How to use phpbb
 
:[[phpbb]] - How to use phpbb
 
:[[Python virtualenv Guide]] - How to use virtualenv for python
 
:[[Python virtualenv Guide]] - How to use virtualenv for python
:[[Qiime Guide]] - How to use Qiime on the Hornet cluster (in progress)
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:[[Qiime Guide]] - How to use Qiime on the HPC Cluster (in progress)
:[[R Guide]] - How to use GNU R on Hornet cluster
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:[[R Guide]] - How to use GNU R on HPC Cluster
:[[R-LINE Guide]] - How to use R-LINE on Hornet cluster
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:[[R-LINE Guide]] - How to use R-LINE on HPC Cluster
 
:[[Screenie | Screenie Guide]] - How to use Screenie / GNU Screen
 
:[[Screenie | Screenie Guide]] - How to use Screenie / GNU Screen
 
:[[StarCCM Guide]] - How to use StarCCM (in progress)
 
:[[StarCCM Guide]] - How to use StarCCM (in progress)
 
:[[Trinity Guide]] - How to use the Trinity RNA Sequence Assembler (in progress)
 
:[[Trinity Guide]] - How to use the Trinity RNA Sequence Assembler (in progress)
 
:[[VASP Guide]] - How to use VASP
 
:[[VASP Guide]] - How to use VASP
:[[WINE Guide]] - How to use WINE on Hornet cluster
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:[[WINE Guide]] - How to use WINE on HPC Cluster
  
 
== Other Software Guidelines ==
 
== Other Software Guidelines ==
 
===BWA===
 
===BWA===
BWA is only available in the Westmere nodes. i.e. hornet-login1.engr.uconn.edu and hornet.engr.uconn.edu
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BWA has been compiled to run on the Westmere nodes. When using sbatch, specify --partition=Westmere
 
  $ module load bwa/0.7.5a
 
  $ module load bwa/0.7.5a
 
===GCC===
 
===GCC===
On Westmere nodes which refer to cn01 to cn64. Login node: hornet.engr.uconn.edu or hronet-login1.engr.uconn.edu
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On Westmere nodes which refer to cn01 to cn64.
 
  $ module load gcc/4.7.1
 
  $ module load gcc/4.7.1
on Sandy Bridge nodes which refer to cn65 to cn104. Login node: hornet-login1.engr.uconn.edu
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on Sandy Bridge nodes which refer to cn65 to cn104.
 
  $ module load gcc/4.8.2
 
  $ module load gcc/4.8.2
  
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  $ module load intelics/2012.0.032 zlib/1.2.3-ics hdf5/1.8.9-ics netcdf/4.2-ics geos-chem/v9-02
 
  $ 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 ===
 
=== Gromacs ===
For 4.6.5 with plumed on the Westmere nodes (hornet.engr.uconn.edu). The order of modulefiles should follow this command.
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For 4.6.5 with plumed on the Westmere nodes. The order of modulefiles should follow this command.
 
  $ module load gcc/4.7.1 intelcis/2013.1.039-full gromacs/4.6.5-plumed
 
  $ module load gcc/4.7.1 intelcis/2013.1.039-full gromacs/4.6.5-plumed
  

Revision as of 17:15, 19 February 2016

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 the HPC Cluster
DXA Guide - How to use Dislocation Extraction Algorithm
Fluent Guide - How to use Fluent of ANSYS
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)
LAMMPS Guide - How to use LAMMPS
LS-Dyna Guide - How to use LS-DYNA
MAPLE Guide - How to use MAPLE on the HPC Cluster
MATLAB Guide - How to submit MATLAB jobs
Modules Guide - How to manage and load environment modules
Motif Guide - How to use Motif on the HPC Cluster
MPI Guide - A Quick Guide to Programming with MPI
MPJ Guide - MPJ (Java MPI)
MPICH2 Guide - How to use MPICH2 on the HPC Cluster
MVAPICH2 Guide - How to use MVAPICH2 on the HPC Cluster
NAMD Guide - How to use NAMD on the HPC Cluster
OpenACC Guide - How to use OpenACC on the HPC Cluster
OpenMp Usage - how to use OpenMp on the HPC Cluster
OpenMPI Guide - How to use OpenMPI on the HPC Cluster
phpbb - How to use phpbb
Python virtualenv Guide - How to use virtualenv for python
Qiime Guide - How to use Qiime on the HPC Cluster (in progress)
R Guide - How to use GNU R on HPC Cluster
R-LINE Guide - How to use R-LINE on HPC 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
WINE Guide - How to use WINE on HPC Cluster

Other Software Guidelines

BWA

BWA has been compiled to run on the Westmere nodes. When using sbatch, specify --partition=Westmere

$ module load bwa/0.7.5a

GCC

On Westmere nodes which refer to cn01 to cn64.

$ module load gcc/4.7.1

on Sandy Bridge nodes which refer to cn65 to cn104.

$ 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. 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

TrinityRNASeq

$ module load gcc/4.7.1 trinityrnaseq/2013.08.14