Henry2 has a mixture of staff maintained software and user maintained software.

The list of supported software below is currently under construction.

User maintained 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. A compute node cannot write to /usr/local/usrapps.
    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 HPC Support 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 - (e.g. what type of license does the application have and does your group qualify under this license to install and use the application on a shared 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 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 a permission denied error is encountered for one of the packages, please contact HPC Support to be added, license permitting, to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access and agree to the licensing terms using the Reqest Access links 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.

Application Name Default Version Load Environment Description How to Use...
Abaqus 2018 module load abaqus Commercial finite element package Abaqus
Amber Amber18 module load amber Parallel molecular dynamics Amber
ANSYS (Request Access)     Commercial finite element package ANSYS
ANSYS CFD (Request Access)     Commercial fluid dynamics package ANSYS CFD
CMake 3.12.3 module load cmake Build, test, and package software CMake
Gaussian (Request Access)     Commercial quantum chemistry code Gaussian
Java 1.8.0 module load java Programming language Java
Julia 1.0.0 module load julia Efficient language for matrix computations Julia
LAMMPS Molecular dynamics simulator LAMMPS
MAKER 2.31.10 module load maker Genome annotation pipeline MAKER
MATLAB R2018b module load matlab Commercial language for matrix computations
ParaView 5.6.0 module load paraview Open source parallel application for visualization and analysis ParaView
Perl 5.16.3
[none required]
module load perl
General purpose scripting language Perl
Python 2.7.5
[none required]
module load python2
module load python3
Interpreted programming language Python
R 3.5.1 module load R Open source statistics package
SAS 9.4 module load sas Commercial statistical analysis package SAS
Tecplot 360 2018 R2 module load tecplot Commerial application for CFD visualization and analysis Tecplot 360
VMD 1.9.3 module load vmd Software package for visualizing molecules VMD

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.

Library Name Default Version Load Environment Description How to Use...
CUDA 9.0 module load cuda NVIDIA library and compiler for using GPUs CUDA
HDF5 1.10.5 (GNU)
1.10.2 (Intel)
module load hdf5/1.10.5-gcc4.8.5
module load hdf5/1.10.2-intel2017
Hierarchical Data Format HDF5
Intel MKL 2017 module load mkl (GNU)
module load PrgEnv-intel (Intel)
Intel math kernel libraries, including BLAS, LAPACK, and ScaLAPACK Intel MKL
NetCDF 4.6.3 (GNU)
4.6.1 (Intel)
module load netcdf/4.6.3-gcc4.8.5
module load netcdf/4.6.1-intel2017
Self-describing, machine-independent data formats NetCDF
OpenMPI 4.0.0 module load openmpi-gcc Open source Message Passing Interface implementation

Other Applications

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

Name Latest Installed Version Location Description How to Use...
ABINIT 7.10.2 /usr/local/abinit An ab initio quantum chemistry package ABINIT
BamTools 2.30 /usr/local/apps/bam Manipulate BAM (genetic sequence) files BamTools
Bowtie 2 2.2.5 /usr/local/bowtie2 Fast aligner for short DNA sequences Bowtie 2
CHARMM 35b3 /usr/local/apps/c35b3 A molecular dynamics program CHARMM
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 Cufflinks
EggLib 2.1.9 /usr/local/apps/egglib Evolutionary genetics and genomics EggLib
Elmer 8.0 /usr/local/apps/elmer Open Source Finite Element Software for Multiphysics Problems Elmer
ESPResSo 5.4.0 /usr/local/apps/espresso Electronic-structure calculations and materials modeling package ESPResSo
FALCON 0.5 /usr/local/apps/falcon Hierarchical Sequencing FALCON
FastQC 0.10.1 /usr/local/apps/FastQC Quality control for high throughput sequence data FastQC
fastStructure 1.0-4 /usr/local/apps/fastStructure An algorithm for inferring population structure from large SNP genotype data fastStructure
FASTX-Toolkit 0.0.14 /usr/local/apps/fastx_toolkit FASTQ/A short-reads pre-processing FASTX-Toolkit
GAMESS 2013 /usr/local/apps/GAMESS ab initio quantum chemistry GAMESS
Grass GIS 7.2.0 /usr/local/apps/grass Open Source Geographical Information System
GDB x86_64-redhat-linux-gnu System installed GDB Debugger GDB
GenomeTools 1.5.5 /usr/local/apps/genometools Genome informatics tools GenomeTools
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 InterProScan
KmerGenie 2014 /usr/local/apps/kmergenie Aids in de novo genome assembly KmerGenie
MAPS 4.1.0 /usr/local/apps/scienomics Software package for material modeling, simulation and analysis MAPS
Mathematica 11.2 /usr/local/apps/mathematica Commercial language for symbolic computations Mathematica
mrFAST /usr/local/apps/mrfast Micro read fast alignment search tool mrFAST
MOOSE /usr/local/moose Finite-element Multiphysics DOE parallel package MOOSE
NAMD 2.10 /usr/local/apps/NAMD NAMD
Oases 0.2.08 /usr/local/apps/oases De novo transcriptome assembler for very short reads Oases
Octave 3.8.2 System installed Interpreted language for matrix computations Octave
OpenFOAM v1706 /usr/local/apps/OpenFOAM Open Source Finite Element Software OpenFOAM
PETSc 3.8.4 /usr/local/apps/PETSc DOE software package to enable parallel computations PETSc
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 Samtools
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 TopHat
TotalView 8.4.1-4 /usr/local/apps/totalview Parallel debugger with GUI interface TotalView
VariationHunter 0.04 /usr/local/apps/variationhunter Find individual genomic structural variation VariationHunter
Velvet 1.2.10 /usr/local/apps/velvet Sequence assembler for very short reads

Other packages, likely unsupported, may be found in the subdirectories of /usr/local/apps.