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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
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 send an e-mail to “oit_help at help dot ncsu dot edu”.

 

Applications

Name Obsolete 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		 Installed
12.6.3		 Linear, Mixed-integer and Quadratic solvers 
http://www.ilog.com/products/cplex/
CPMD   Installed 
3.13.2
Ab initio molecular dynamics 
CUDA-GPU Installed 
6.0,7.5		   NVIDIA library for using GPUs
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 (qe)   Installed
6.2.0,5.4.0		 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
Grass GIS   Installed
grass-7.2.0		 Geographical Information System
GenomeTools   Installed
1.5.5		 Genome informatics tools
GROMACS   Installed
5.1.1		 Molecular dynamics 
biochemicals and polymers 
InterProScan   Installed
5.3-46.0		 scans protein and nucleic sequences for signatures
Java   Installed  See the Howto for access to some newer versions 
Julia   Installed 
0.5.2		 Efficient language for matrix computations
KmerGenie   Installed
19Mar14		 aids in de novo genome assembly
LAMMPS   Installed
9Dec14
5Mar13		 Molecular dynamics
MAKER   Installed
2.10, 2.31		 Genome annotation pipeline
Mathematica   Installed 
11.2		 Commercial language for symbolic computations
Matlab   Installed 
2014a,2016a,2017a		 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
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
MOOSE Installed Nov. 1, 2018 Finite-element Multiphysics
DOE parallel package		 Idea to Solution in Hours? 
NAMD Molecular Dynamics   versions 2.7 and 2.9 http://www.ks.uiuc.edu/Research/namd/ 
NCAR Graphics   6.1.2 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
Perl   Installed
v5.16.3		 General Purpose Scripting Language 
PETSc DOE software 
package to enable parallel computations		 Installed 
3.8.0		 Portable, Extensible, Toolkit for Scientific Computation
PLINK   Installed
1.07		 Whole genome association analysis
PSPP Installed
0.8.0-g13bf3f		   Tool for statistical analysis of sampled data
Python   Installed
2.7.13, 3.4.0		 2.7.13 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
3.3.0
3.4.2		 Open Source Statistics Package
RAxML   Installed
8.1.17		 Phylogenetic Analysis 
RepeatModeler 1-0-7   de novo repeat (genomic) family identification and modeling 
SageMath   Installed
7.4		 Sage variable precision and symbolic computations 
SAMtools   Installed
1.12		 SAM (Sequence Alignment/Map) tools
SAS   Installed
9.3		 Commerical Statistical Analysis Package 
Siesta   Installed
3.2,4.0.1		 Open Source Pseudo Potential 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/ 
       

 

Libraries

Name Status
Out of Date		 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
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
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: December 12 2017 14:58:38.

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