Software
Contents
- Staff maintained software — Officially supported applications and libraries
- Sponsored software — Bioinformatics, AI/ML tools, atmospheric and climate modeling
- User maintained software — Installing your own software
- General guidance for installing software
- Setting the compute environment
- Creating custom modules
- Installing software with Conda
HPC has a very small team of computational scientists that are responsible for everything related to helping users run their applications on the Hazel cluster. Hazel has thousands of users in very different fields of expertise, each using different types of software. Additionally, there are a huge number of permutations of possible ways to install that software (versions, dependencies, options, etc.). This is why the core set of software that is officially supported by staff must remain small. HPC staff will help all users with any problems in installing user maintained software, but users are asked to first look at the documentation and make efforts to do installs themselves as much as feasible. 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, 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.
Quota
There is a quota for each HPC Project at /usr/local/usrapps/$GROUP. To check the quota, issue the command:
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... | Benchmarks |
|---|---|---|---|---|---|
| Abaqus | 2024.HF4 | module load abaqus | Commercial finite element package | Abaqus | Slurm | Abaqus benchmarks |
| Amber (Request access) | Amber25 | module load amber | Parallel molecular dynamics | Amber | Slurm | |
| ANSYS (Request access) | 25.2 | module load ansys | Commercial finite element package | ANSYS | Slurm | ANSYS benchmarks |
| Apptainer (Singularity) | 1.4.2-1 | module load apptainer | Apptainer (formerly Singularity) is a secure, portable, and easy-to-use container system | Apptainer | Slurm | |
| BLAST+ | 2.17.0 | module load blast | Basic Local Alignment Search Tool | BLAST+ | Slurm | |
| CMake | 3.20.4 | module load cmake | Build, test, and package software | CMake | Slurm | |
| Conda | 24.5.0 | module load conda | Package manager for installing software | Conda | Slurm | |
| Gaussian (Request access) | 16 (A.03) | module load gaussian | Commercial quantum chemistry code | Gaussian | Slurm | Gaussian benchmarks |
| Gurobi | 8.1 | module load gurobi | Commercial optimzation solver | Gurobi | Slurm | |
| Julia | 1.7.0 | module load julia | High performance scripting language | Julia | Slurm | |
| Jupyter | 24.5.0 | conda activate (your_conda_notebook_env) | Interactive computing IDE | Jupyter | Slurm | |
| LAMMPS | 2022Jun23 | module load lammps/2022Jun23/intel/cpu | Molecular dynamics simulator | LAMMPS | Slurm | LAMMPS benchmarks |
| MAKER | 2.31.10 | module load maker | Genome annotation pipeline | MAKER | Slurm | |
| Maple | 2021 | module load maple | Symbolic and numeric computing | Maple | Slurm | |
| Mathematica | 12.0.0 | module load mathematica | Technical computing | Mathematica | Slurm | |
| MATLAB | R2023a | module load matlab | Commercial language for matrix computations | MATLAB | Slurm | MATLAB benchmarks |
| ParaView | 5.6.0 | module load paraview | Open source parallel application for visualization and analysis | ParaView | Slurm | |
| Perl | 5.16.3 5.28.0 |
[none required] module load perl |
General purpose scripting language | Perl | Slurm | |
| Python | 2.7.53.9.213.12.2 | [none required] module load conda |
Interpreted programming language | Python | Slurm | |
| R | 4.4.0 | module load R | Open source statistics package | R | Slurm | R benchmarks |
| RStudio | 4.4.0 | Access via Open OnDemand | IDE for R, an open source statistics package | RStudio | Slurm | |
| SAS | 9.4 | module load sas | Commercial statistical analysis package | SAS | Slurm | |
| Stata (UNCG Users only) | 17.0 | module load stata | Commercial statistical analysis package | Stata | Slurm | |
| VASP (Request access) | 5.4.1 | module load vasp | Vienna Ab initio Simulation Package | VASP | Slurm | |
| VMD | 1.9.3 | module load vmd | Software package for visualizing molecules | VMD | Slurm |
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 | 12.0 | 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.
Bioinformatics tools
- How to request access and instructions for use | Slurm
| 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
- How to request access and instructions for use | Slurm
| Application Type | Description | Includes: |
|---|---|---|
| Geospatial tools | Geospatial, GIS (Geographic Information System), and OSGeo tools | GRASS GIS, PDAL, GDAL, PROJ |
Machine learning, neural network frameworks
- Self-installation guidelines | Slurm
| Application Type | Description | Includes: |
|---|---|---|
| Machine learning, neural network frameworks | Conda environments for TensorFlow and PyTorch | TensorFlow, PyTorch |
Marine, earth, and atmospheric modeling tools
- How to request access and instructions for use | Slurm
| 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 | Slurm |
| GenomeTools | 1.5.5 | /usr/local/apps/genometools | Genome informatics tools | GenomeTools | Slurm |
| GROMACS | 2016 | /usr/local/apps/gromacs | Molecular dynamics of biochemicals and polymers | GROMACS | Slurm |
| Java | 1.8.0 | module load java | Programming language | Java | Slurm |
| MAPS | 4.1.0 | /usr/local/apps/scienomics | Software package for material modeling, simulation and analysis | MAPS | Slurm |
| NAMD | 2.10 | /usr/local/apps/NAMD | Parallel molecular dynamics package | NAMD | Slurm |
| SIESTA | 4.0.1 | /usr/local/apps/siesta | Open Source Pseudo Potential Package | SIESTA | Slurm |
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-
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. Globus and HPC-VCL cannot write to this space either.
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.
-
The Project PI, or a group member with the Project PI cc'ed, should 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 licenses purchased by our group. For licenses purchased by our group, we will maintain proper file and directory permissions to comply with the license. 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.
There is a quota for each HPC Project at /usr/local/usrapps/$GROUP.
To check the quota, issue the command:
quota_display
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