User maintained software
Users must install and maintain custom software.

Staff cannot install and maintain custom software for each of Henry2's many users, so users must install their own packages. For executables that are too large for a home directory, users may request space for custom software:

Space for user maintained executables

Acceptable use
    The directory /usr/local/usrapps provides space for user installed and maintained applications.
    Directories in /usr/local/usrapps may not to be used for data or as a working space from which to execute jobs.
    Applications must be maintained/patched to minimize potential security vulnerabilities.
    Access should be managed via Linux group permissions to comply with license restrictions.
    Applications that require root access to install are not permitted.
Procedure to request space under /usr/local/usrapps
    Submit a request via email to including the following information:
    • Name of HPC Project that will be responsible for the application
    • Name of the application to be installed
    • Statement that the group is authorized to install the application on the HPC Linux cluster
    A directory will be created with group read/write access for the requesting project.
    The project group will be responsible for installing and maintaining the application.

HPC maintained software
The list of supported software is under construction. The tables below contain both supported and obsolete software.

The following tables show the status of software that has been requested and/or installed on HPC systems for general use. Many of the applications require group membership for access. If you encounter a permission denied error for one of the packages, please contact and, license permitting, we will add you to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access and agree to the licensing terms using the button provided below. For Gaussian, a license acknowledgement needs to be signed and returned to obtain access.

Officially Supported Applications

These applications have been approved as HPC Maintained Applications - the application review is NOT complete; all other applications are currently under review.

Name Default Version Load Environment Description How to Use
Abaqus 2018 module load abaqus Commercial finite element package View
Amber Amber18 module load amber Parallel molecular dynamics View
    Commercial finite element package View
    Commercial fluid dynamics package View
cmake 3.12.3 module load cmake Build, test, and package software View
    Commercial quantum chemistry code View
Java 1.8.0 module load java Programming language View
Julia 1.0.0 module load julia Efficient language for matrix computations View
LAMMPS Molecular dynamics simulator View
MAKER 2.31.10 module load maker Genome annotation pipeline View
MATLAB R2018b module load matlab Commercial language for matrix computations
Perl 5.28.0 [none required] General purpose scripting language
Python 2.7.15
module load python2
module load python3
Interpreted programming language View
R 3.5.1 module load R Open source statistics package
SAS 9.4 module load sas Commercial statistical analysis package View
Tecplot 360 2018 R2 module load tecplot Commerial application for CFD visualization and analysis View
VMD 1.9.3 module load vmd Software package for visualizing molecules View

Officially Supported Libraries

These libraries have been approved as HPC Maintained Applications - the library review is NOT complete; all other libraries are currently under review.

Name Default Version Load Environment Description How to Use
CUDA 9.0 module load cuda NVIDIA library for using GPUs View

Other Applications

These applications are under review for adding to either the Officially Supported or Obselete lists.

Name Latest Installed Version Location Notes
Abinit 7.10.2 /usr/local/abinit An ab initio quantum chemistry package
BAMTools 2.30 /usr/local/apps/bam Manipulate BAM (genetic sequence) files
Bowtie2 2.2.5 /usr/local/bowtie2 Fast aligner for short DNA sequences
CHARMM 35b3 /usr/local/apps/c35b3 A molecular dynamics program
CPLEX 12.6.3 /usr/local/apps/cplex Linear, Mixed-integer and Quadratic solvers
Cufflinks 2.2.1 /usr/local/apps/cufflinks Analysis of RNA-Seq samples
EggLib 2.1.9 /usr/local/apps/egglib Evolutionary genetics and genomics
Elmer 8.0 /usr/local/apps/elmer Open Source Finite Element Software for Multiphysics Problems
ESPRESSO 5.4.0 /usr/local/apps/espresso Electronic-structure calculations and materials modeling package (including PWscf, PHONON, CP90, FPMD, Wannier)
Falcon 0.5 /usr/local/apps/falcon Hierarchical Sequencing
FastQC 0.10.1 /usr/local/apps/FastQC Quality control for high throughput sequence data
fastStructure 1.0-4 /usr/local/apps/fastStructure An algorithm for inferring population structure from large SNP genotype data
FASTX-Toolkit 0.0.14 /usr/local/apps/fastx_toolkit FASTQ/A short-reads pre-processing
Gamess 2013 /usr/local/apps/GAMESS ab initio quantum chemistry
Grass GIS 7.2.0 /usr/local/apps/grass Open Source Geographical Information System
GDB x86_64-redhat-linux-gnu System installed GDB Debugger
GenomeTools 1.5.5 /usr/local/apps/genometools Genome informatics tools
5.1.1 /usr/local/apps/gromacs Molecular dynamics of biochemicals and polymers
InterProScan 5.3-46.0 /usr/local/apps/interproscan Scans protein and nucleic sequences for signatures
KmerGenie 2014 /usr/local/apps/kmergenie Aids in de novo genome assembly
MAPS 4.1.0 /usr/local/apps/scienomics Software package for material modeling, simulation and analysis
Mathematica 11.2 /usr/local/apps/mathematica Commercial language for symbolic computations
mrFAST /usr/local/apps/mrfast Micro read fast alignment search tool
MOOSE /usr/local/moose Finite-element Multiphysics DOE parallel package
NAMD Molecular Dynamics 2.10 /usr/local/apps/NAMD
Oases 0.2.08 /usr/local/apps/oases De novo transcriptome assembler for very short reads
Octave 3.8.2 System installed Interpreted language for matrix computations
OpenFOAM v1706 /usr/local/apps/OpenFOAM Open Source Finite Element Software
PETSc 3.8.4 /usr/local/apps/PETSc DOE software
package to enable parallel computations
PLINK 1.07 /usr/local/apps/plink Whole genome association analysis
SageMath 7.4 /usr/local/apps/sage Sage variable precision and symbolic computations
SAMtools 0.1.7.a /usr/local/apps/samtools SAM (Sequence Alignment/Map) tools
SeaDAS 7.5 /usr/local/apps/seadas-7.5 For the processing, display, analysis, and quality control of ocean color data or satellite-based earth science data analyses
Siesta 4.0.1 /usr/local/apps/siesta Open Source Pseudo Potential Package
SOAPdenovo2 2.04 /usr/local/apps/SOAPdenovo2 short-read method for de novo assembly of genomes
Stata UNCG Users only Commercial statistical analysis package
Tophat 2.0.14 /usr/local/apps/tophat Splice junction mapper for RNA-Seq reads
TotalView 8.4.1-4 /usr/local/apps/totalview Parallel debugger with GUI interface
VariationHunter 0.04 /usr/local/apps/variationhunter Find individual genomic structural variation
Velvet 1.2.10 /usr/local/apps/velvet de novo genomic assembler

Other Libraries

These libraries are under review for adding to either the Officially Supported or Obselete lists.

Name Latest Installed Version Location or
Load Environment
ACML 4.3.0 /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.
BLAS Part of the AMD and mkl libraries
fftw 3.3.4 /usr/local/apps/fftw Fast Fourier Transforms -- includes parallel versions
hdf 1.8.16 /usr/local/apps/hdf-centos7
Intel MKL 2017 module load mkl Intel math kernel libraries
LAPACK Part of the AMD and mkl libraries
NetCDF 4.4.0 /usr/local/apps/netcdf-centos7
ScaLAPACK 2017 module load mkl Distributed memory dense dense linear algebra
Trilinos   Parallel numeric library from Sandia
Other packages, likely unsupported, may be found in the subdirectories of /usr/local/apps.