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. Users may request space for custom software for their project group as described here:

Space for user maintained executables

Acceptable use
    The directory /usr/local/usrapps provides space for user installed and maintained applications.
    A project may request a directory in which all group members may install software.
    All new /usrapps directories will be named for the project group unless otherwise requested.
    Directories in /usr/local/usrapps may not 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
    • The following statement: "The HPC group [mygroup] certifies that we will only install appropriately licensed applications on the HPC Linux cluster - e.g., applications where the license is fully open source with no applicable restrictions, applications for which NCSU has approved a clickwrap, or applications with licences purchased by our group. For licenses purchased by our group, we will maintain proper file and directory permissions to comply with the licence. The group will maintain software by installing security patches or upgrades when necessary."
    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.
    Please contact HPC staff with any questions about licensing when installing software.
Here is some general guidance for installing software.

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) 20.1 module load ansys Commercial finite element package ANSYS
ANSYS CFD (Request Access) 20.1 module load ansys Commercial fluid dynamics package ANSYS CFD
BLAST+ 2.10.1 module load blast Basic Local Alignment Search Tool BLAST+
CMake 3.16.3 module load cmake Build, test, and package software CMake
Conda 4.8.4 module load conda Package manager for installing software Conda
Gaussian (Request Access) 16 (A.03) module load gaussian Commercial quantum chemistry code Gaussian
Gurobi (Request access) 8.1 module load gurobi Commercial optimzation solver
Julia 1.3.1 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
Mathematica 12.0.0 module load mathematica Technical computing
Mathematica
MATLAB R2018b module load matlab Commercial language for matrix computations
MATLAB
ParaView 5.6.0 module load paraview Open source parallel application for visualization and analysis ParaView
Perl 5.16.3
5.28.0
[none required]
module load perl
General purpose scripting language Perl
Python 2.7.5
3.7.4
[none required]
module load conda
Interpreted programming language Python
R 4.0.2 module load R Open source statistics package
R
SAS 9.4 module load sas Commercial statistical analysis package SAS
Stata (UNCG Users only) 16.0 module load stata Commercial statistical analysis package Stata
TotalView 2019.2.8 module load totalview Parallel debugger with GUI interface
VASP (Request access) 5.4.1 module load vasp Vienna Ab initio Simulation Package VASP
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

Sponsored Applications

These applications are not officially maintained, that is, HPC does not update this software or provide official support or documentation. Sponsored applications are sponsored by users who have volunteered to share their software installations with users outside of their Project Group and to field basic questions about usage. To access these applications, send an email to HPC requesting access to the Software Group.

Application Type Software Group Request access Description Includes:
Assemblers bioinfo Request access Binary installations of genome assemblers SPAdes, Canu
Geographic Information System tools gis Request access GIS tools QGIS, GRASS
Geophysical numerical modeling and analysis ncdfutil Request access Applications for numerical modeling and analysis MET
Machine Learning, Neural Network frameworks gputools Request access Conda environments for TensorFlow and PyTorch TensorFlow, PyTorch
Metagenomics bioinfo Request access Conda environments for QIIME2 and DATA2 QIIME2, DADA2
NetCDF Utilities ncdfutil Request access Conda environment with various applications for analyzing NetCDF output CDO, GEOS, NCO, NCL, Ncview, xarray,
PseudoNetCDF, PyNGL, PyNIO, nccmp,
Cartopy, MetPy, MONET
Quality Assessment and Trimming bioinfo Request access Binary installations of trimming tools Trimmomatic
Spack installed applications spack Request access These applications are compiled from source using Spack, a package manager for HPC. Click here for a list of available packages and libraries.

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...
FALCON 0.5 /usr/local/apps/falcon Hierarchical Sequencing FALCON
GenomeTools 1.5.5 /usr/local/apps/genometools Genome informatics tools GenomeTools
GROMACS
5.1.1 /usr/local/apps/gromacs Molecular dynamics of biochemicals and polymers GROMACS
Java 1.8.0 module load java Programming language Java
MAPS 4.1.0 /usr/local/apps/scienomics Software package for material modeling, simulation and analysis MAPS
NAMD 2.10 /usr/local/apps/NAMD Parallel molecular dynamics package NAMD
SIESTA 4.0.1 /usr/local/apps/siesta Open Source Pseudo Potential Package SIESTA

Other packages, likely unsupported, may be found in the subdirectories of /usr/local/apps. Here are further instructions on using existing but unsupported packages.