See the following for information about applications installed on the Henry2 cluster by HPC staff.
The list of supported software below is currently under construction.
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.
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||4.10.3||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||1.6.1||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|
module load perl
|General purpose scripting language||Perl|
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|
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|
|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|
|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. To access these applications, send an email to HPC requesting access to the software group.
|Application Type||Software group, info and access||Description||Includes:|
|Assemblers||bioinfo||Binary installations of genome assemblers||SPAdes, Canu|
|CMAQ dependencies||ncdfutil||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|
|Geographic Information System tools||gis||GIS tools||QGIS, GRASS|
|Geophysical numerical modeling and analysis||ncdfutil||Applications for numerical modeling and analysis||MET|
|Machine Learning, Neural Network frameworks||gputools||Conda environments for TensorFlow and PyTorch||TensorFlow, PyTorch|
|Metagenomics||bioinfo||Conda environments for QIIME2 and DATA2||QIIME2, DADA2|
|NetCDF Utilities||ncdfutil||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||Binary installations of trimming tools||Trimmomatic|
|Spack installed applications||bioinfo||These applications are compiled from source using Spack, a package manager for HPC.||Click here for a list of available packages and libraries.|
|UFS dependencies||ncdfutil||Intel 2018 based software stack for compiling Unified Forecasting System (UFS). Does not include UFS itself, tested with simple-test-case.)||NCEP and NCEP-external libs, including NetCDF, JasPer, JPEG, PNG, Wgrib2|
|WRF dependencies||ncdfutil||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|
These applications are under review for adding to either the Officially Supported or Obselete lists.
|Name||Latest Installed Version||Location||Description||How to Use...|
|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.