High Performance Computing

Software

The following tables show the status of software that has been requested and/or installed on HPC systems for general use. Tables are divided between Compilers, Applications, and Libraries. Many of the applications require group membership for access. If you encounter a "permission denied" error for one of the packages, please contact "oit_hpc at help dot ncsu dot edu" and we will (if the software license permits), add you to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access using the button provided below (you have to agree to some software licensing terms). For Gaussian a license acknowledgement needs to be signed and returned to obtain access.

Compilers

Name Status
centos5
cluster
Status
henry2
cluster
Notes
Intel   2013, 2016 Intel Linux Compilers Web Site
Intel MPI   Installed
openmpi-2013,2016
mvapich2-2016
intelmpi2016
Portland
Group
MPI
  Installed
14.3,15.1
http://www.pgroup.com/
Portland
Group
 
OpenMPI 14.3
http://www.pgroup.com/

The following list of applications is not complete. If you look in subdirectories of /usr/local/apps, you'll see many other packages. If you need an application you think would be appropriate for general use, or a more up-to-date version of an existing package, please sent an e-mail to "oit_help at help dot ncsu dot edu".

Applications

--->
Name Centos 5 Status henry2 cluster Notes
Abinit   Installed
7.2.1
An ab initio quantum chemistry package
ABAQUS Installed
6.16
http://www.abaqus.com/
Commercial Finite Element Package
AMBER Installed
12 14
http://amber.scripps.edu/
Parallel Molecular Dynamics
ANSYS Installed
170
http://www.ansys.com/
Commercial Finite Elment Package
ANSYS
CFX
  Installed
170
http://www.ansys.com/cfx
Commercial Fluid Dyaamics Package
BAMTools   Installed
2.30
Manipulate BAM (genetic sequence) files
bioperl Installed
1.6.1
  Perl modules for DNA sequence analysis
mpiBLAST Installed   A parallel version of the NCBI program BLAST
Bowtie2   Installed
2.2.5
Fast aligner for short DNA sequences
CHARMM Installed
c35b3
  A molecular dynamics program
CPLEX Installed
11.2, 12.1
  Linear, Mixed-integer and Quadratic solvers
http://www.ilog.com/products/cplex/
CPMD  Installed
3.13.2
Ab initio molecular dynamics
Cufflinks   Installed
2.2.1
Analysis of RNA-Seq samples
Cutadapt Installed
1.0.0
  Remove adapter sequences from high-throughput data
DL_POLY_4   Installed
4.07
Molecular dynamics simulation
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
EggLib   Installed
2.1.9
Evolutionary genetics and genomics
Elmer  Installed
8.0
Open Source Finite Element Software for Multiphysical Problems
http://www.csc.fi/english/pages/elmer
ESPRESSO   Installed
5.1.1
Electronic-structure calculations and materials modeling package (including PWscf, PHONON, CP90, FPMD, Wannier)
FastQC Installed
0.10.1
  Quality control for high throughput sequence data
fastStructure   Installed
1.0-4
An algorithm for inferring population structure from large SNP genotype data
FASTX-Toolkit   Installed
0.0.14
FASTQ/A short-reads pre-processing
Gamess Installed
18Apr20013
  ab initio quantum chemistry
http://www.msg.ameslab.gov/GAMESS/
Gaussian
  Installed
g09
Commerical quantum chemistry code
http://gaussian.com
GenomeTools   Installed
1.5.5
Genome informatics tools
GROMACS
  Installed
5.1.1
Molecular dynamics
biochemicals and polymers
Java Installed
See the Howto for access to some newer versions
InterProScan
Installed
5.3-46.0
scans protein and nucleic sequences for signatures
KmerGenie
Installed
19Mar14
aids in de novo genome assembly
LAMMPS Installed
9Dec14
5Mar13
Molecular dynamics
MAKER   Installed
2.10, 2.31
Genome annotation pipeline
Matlab Installed
2013a,2014a
Commercial language for matrix computations
MITE-Hunter   Installed
Version of November 2011
Find transposable elements in DNA datasets
Mobyle Workbench   Updated Feb. 2014 A portal with many genetic analysis programs
Mr Bayes Installed
Installed
3.1.1
3.1.2
Construct evolutionary trees from genetic sequences
http://mrbayes.csit.fsu.edu
mrFAST   Installed
2.6.0.1
Micro read fast alignment search tool
NAMD Molecular Dynamics  versions 2.7 and 2.9 http://www.ks.uiuc.edu/Research/namd/
NCAR Graphics Installed Visualization of scientific data
http://ngwww.ucar.edu/ng4.3/
NCBI Toolbox Installed Includes BLAST, SEQUIN, FA2HTGS, ENTREZ, and CN3D
NWChem   Scalably parallel computational chemistry
www.emsl.pnl.gov/docs/nwchem/doc/user/index.html
Oases   Installed
0.2.06
De novo transcriptome assembler for very short reads
Octave Installed
3.6.3
Interpreted language for matrix computations
OpenFOAM Installed
2.2.2
  Open Source Finite Element Software
http://www.opencfd.co.uk/openfoam/doc/tutorials.html
PBJelly Installed
14.1.14
  Aligns long sequencing reads to high-confidence draft assembles
PLINK   Installed
1.07
Whole genome association analysis
PSPP Installed
0.8.0-g13bf3f
  Tool for statistical analysis of sampled data
Python Installed
2.7.9, 3.4.0
2.7.9 includes numpy, scipy, and some additional modules, 3.4.0 has somewhat fewer modules.
Qiime centos7
under python2.7.9

R Installed
3.1.2
Open Source Statistics Package
RAxML  Installed
8.1.17
Phylogenetic Analysis
RepeatModeler 1-0-7
  de novo repeat (genomic) family identification and modeling
SAMtools   Installed
1.12
SAM (Sequence Alignment/Map) tools
SAS Installed
9.3
Commerical Statistical Analysis Package
SOAPdenovo2   240 short-read method for de novo assembly of genomes
STACKS Installed
1.08
  Building loci from short-read sequences
Stata Installed (UNCG Users only) Commercial statistical analyis package
Tophat   Installed
2.0.14
Splice junction mapper for RNA-Seq reads
TotalView Installed
8.4.1-4
http://www.etnus.com/
Another full-featured parallel debugger
is the pgdbg debugger for codes compiled
with the Portland Group compilers.
VariationHunter   Installed
0.04
Find individual genomic structural varation
VASP Installed
5.2
Commercial molecular dynamics code
Velvet   Installed
1.2.10
de novo genomic assembler
VMD   Installed
1.9.1
A Package for visualizing molecules
http://www.ks.uiuc.edu/Research/vmd/
WRF   Weather Research and Forecasting
Forecasting Lab Guide to Using WRF

Libraries

Name Status
centos 5
cluster
Status
henry2
cluster
Notes
ACML Installed
3.6.0
3.6.1
4.3.0
subdirectories of /usr/local/apps/acml
Numerical libraries provided by AMD (64 bit only). Versions for pgi, intel, and gnu compilers. Separate directories for 64 bit integer and multithreaded versions.
http://developer.amd.com/cpu/Libraries/acml/Pages/default.aspx
BLAS   Installed Part of the AMD and mkl libraries
fftw Installed
2.1.5
3.3.4
subdirectories of /usr/local/apps/fftw
Fast Fourier Transforms -- includes parallel versions
hdf   Installed
hdf5-1.8.14
hdf5-1.8.16
subdirectories of
/usr/local/apps/hdf-centos7
Intel MKL   Installed
2013,2016
mklXXX subdirectores of /usr/local/apps/intel
http://software.intel.com/en-us/articles/intel-math-kernel-library-documentation/
LAPACK Installed Part of the AMD and mkl libraries
NetCDF Installed
4.3.3
4.4.0
subdirectories of
/usr/local/apps/netcdf-centos7
ScaLAPACK   Installed
MKL 2013,2016
Distributed memory dense dense linear algebra
www.netlib.org/scalapack/
Trilinos   Installed http://software.sandia.gov/trilinos/
Parallel numeric library from Sandia
Last modified: May 17 2016 12:36:49.