User maintained software

If a /usr/local/usrapps/group_name directory does not exist, see the following requirements for requesting the space:

Space for user maintained executables

Acceptable use
Procedure to request space under /usr/local/usrapps

Where to install?

A space in /usrapps is by default writable by everyone in the project, so all members have permissions to write directly to the /usrapps/$GROUP space. This leads to confusion and potential permissions problems. Users should create their own space within the group directory. Each user should make their own directory to install software and adjust permissions as necessary.

mkdir /usr/local/usrapps/$GROUP/$USER

How to install?

Please see the 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 Request 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+ 2.11.0 module load blast Basic Local Alignment Search Tool BLAST+
CMake 3.20.4 module load cmake Build, test, and package software CMake
Conda 4.11.0 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 1.7.0 module load julia High performance scripting language Julia
LAMMPS 29Sep21u3 module load lammps Molecular dynamics simulator LAMMPS
MAKER 2.31.10 module load maker Genome annotation pipeline MAKER
Maple 2021 module load maple Symbolic and numeric computing
Maple
Mathematica 12.0.0 module load mathematica Technical computing
Mathematica
MATLAB R2020a 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
3.7.7
[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
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

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.

Bioinformatics tools

  • How to request access and instructions for use
  • Application Type Description Includes:
    Bioinformatics tools Various packages available, either as binary installations or Conda environments: Assemblers, Metagenomics, Quality Assessment and Trimming... SPAdes, Canu, Trimmomatic, QIIME2, DADA2, hmmer, metabat, prodigal, sratoolkit, and many others.

Geospatial tools

Machine learning, neural network frameworks

Marine, earth, and atmospheric modeling tools

  • How to request access and instructions for use
  • Application Type Description Includes:
    NetCDF utilities Conda environment with various applications for analyzing NetCDF output CDO, GEOS, NCO, NCL, Ncview, xarray,
    PseudoNetCDF, PyNGL, PyNIO, nccmp,
    Cartopy, MetPy, MONET
    Geophysical numerical modeling and analysis Applications for numerical modeling and analysis MET
    CMAQ dependencies Intel 2018 based software stack for compiling CMAQ. Does not include CMAQ itself, includes a sample configure script and LSF script tested with CMAQ 5.3.2 Benchmark. NetCDF, I/O API
    UFS dependencies Intel 2018 based software stack for compiling Unified Forecasting System. Does not include UFS itself, tested with simple-test-case. NCEP and NCEP-external libs, including NetCDF, JasPer, JPEG, PNG, Wgrib2
    WRF dependencies Intel 2017 based software stack for compiling WRF. Does not include WRF itself, tested with WRF 4.2.2 using compile option 15. HDF5, Perl5, NetCDF, JasPer, GRIB2

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
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