The Research Software Library (RSWL)
The Research Software Library (RSWL) is a collection of software packages installed and maintained by the DIT HPC staff for use by researchers on the various UMD HPC clusters. The library is carefully curated to try to ensure that packages are generally compatible with each other (within the same toolchain).
Due to the complexities in many of the software packages, packages built with one toolchain are typically not compatible with packages built with other toolchains; this is especially true with codes depending on MPI libraries or C++ or modern Fortran code bases.
Because of these and similar incompatibilities, the software in the Research Software Library is not enabled by default. Instead you need to use the module command to setup the environment for the package(s) you wish to use. The advantage of this is that you can somewhat easily switch between different package versions and/or toolchains. Using the module command, you can specify which of the installed versions of the package you wish to use. If you do not specify a version, the module command will attempt to load the latest version found compatible with the toolchain being used (as determined by any compiler, MPI library and similar packages you have previously loaded with the module command.
Software Packages in the Research Software Library
The following sections list the various packages available in the Research Software Library. We have attempted to organize the lists of packages by field of research, etc. for which they might be used, however the HPC team generally is not familiar with the use of these packages, and there might be omissions and other errors in this organization. If you do not find a specific package in the category for the applicable field of research, please try looking for it in the uncategorized list (and if appropriate submit a ticket to HPC staff with the suggested correction).
For each list, you can click on the name of the package to bring up a page with more information about the package, including what versions of the package are available by cluster and CPU, basic usage, and any help or tips we have specific to the use of that package. Note that not all packages (much less all versions of any package) are necessarily available on all clusters or for all CPU types and/or support GPUs. So it behooves you to verify that the required version is available for the cluster and nodes you intend to use..
Packages by category
Aeronautics
This section lists various software packages related to Aeronautics, Aviation, Aerospace Sciences and related fields (Astronautics, Hypersonics, Aerothermodynamics, etc.)
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| dplr | Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | No |
| fun3d | FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | No |
| us3d | Aeordynamic and Aerothermodynamic Simulations Software | skylake_avx512 | No |
Astronomy
This section lists various software packages related to Astronomy and related fields.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| cfitsio | Libraries for Flexible Image Transport System (FITS) data format | icelake, x86_64, zen, zen2 | No |
Biology
This section lists various software packages related to Biology, Bioinformatics and other related fields. See also Genomics.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| hemocell | Framework for simulation of blood and other dense deformable capsule suspensions | zen2 | Yes |
| openstructure | Open-source computational structural biology framework | zen2 | No |
Computional Fluid Dynamics
This section lists various software packages related to Computational Fluid Dynamics (CFD).
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| cgns | CFD General notation system | icelake, x86_64, zen2 | Yes |
| dplr | Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | No |
| fds | Fire Dynamics Simulator | x86_64 | No |
| fun3d | FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | No |
| openfoam | Opensource C++ CFD toolbox | zen, zen2 | Yes |
| smokeview | Visualization tool for FDS and CFAST output | x86_64 | No |
| tecplot360 | CFD visualization software | x86_64 | No |
Chemistry
This section lists various software packages related to Chemistry, Computational Chemistry, Quantum Chemistry, etc. See also MolecularDynamics and MaterialScience.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| cfour | Software for quantum chemical modeling | x86_64 | No |
| charmm | Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| cp2k | quantum chemistry and solid state physics package | zen2 | No |
| gaussian | Software for electronic structure modeling | x86_64 | No |
| gromacs | Chemical simulation/Molecular dynamics package | icelake, zen, zen2 | Yes |
| lammps | LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | icelake, zen, zen2 | Yes |
| libint | library to evaluate molecular integrals | icelake, x86_64, zen, zen2 | Yes |
| namd | Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| onetep | ONETEP (Order-N Electronic Total Energy Package) | zen2 | No |
| openmm | A high-performance toolkit for molecular simulation. | icelake, zen2 | Yes |
| orca | Ab initio quantum chemistry package | x86_64 | No |
| plumed | plugin for molecular dynamics | icelake, zen, zen2 | Yes |
| qmd-progress | PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen | Yes |
| sirius | domain specific library for electronic structure calculations | zen | No |
| vasp | VASP: Vienna Ab-initio Simulation Package | zen2 | No |
| vmd | Visual Molecular Dynamics | x86_64 | No |
Computer Vision
This section lists various software packages related to Computer Vision and related fields. You might also want to look at the section on packages related to Machine Learning.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| caffe | Deep learning framework | icelake, x86_64, zen, zen2 | No |
| opencv | Open-source Computer Vision Library | zen2 | No |
| pytorch | Open-source machine learning library | icelake, zen2 | Yes |
| tensorflow | Open-source software library for machine intelligence | icelake, zen, zen2 | Yes |
Data Compression
This section lists various software packages related to Data Compression. Basically libraries and binaries for compressing and uncompressing data to/from various compressed formats and/or compression algorithms.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| bzip2 | patent-free high quality data compression libraries | icelake, x86_64, zen, zen2 | No |
| c-blosc | A blocking, shuffling, and loss-less compression library | icelake, x86_64, zen, zen2 | No |
| lz4 | Lossless compression utility and library | icelake, x86_64, zen, zen2 | No |
| sz | Error-bounded Lossy Compressor for HPC Data | icelake, x86_64, zen, zen2 | Yes |
| xerces-c | validating XML parser in C++ | icelake, x86_64, zen, zen2 | No |
| xz | Lossless compression utility and library | icelake, x86_64, zen, zen2 | No |
| zfp | Library for lossy compression of multidimensional arrays | icelake, x86_64, zen, zen2 | No |
| zlib | General purpose, patent-free compression ibrary | icelake, x86_64, zen, zen2 | No |
| zstd | Fast, lossless compression algorithm | icelake, x86_64, zen, zen2 | No |
Data Formats
This section lists various software packages related to various scientific or other data formats, including libraries and binaries for reading, writing, and manipulating data in specific formats.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| adios2 | The Adapatble Input/Output System, version 2 | icelake, x86_64, zen, zen2 | Yes |
| bamtools | Command line toolkit for dealing with BAM files | icelake, x86_64, zen, zen2 | No |
| cdo | Climate Data Operators | zen2 | Yes |
| cfitsio | Libraries for Flexible Image Transport System (FITS) data format | icelake, x86_64, zen, zen2 | No |
| eccodes | Libraries for encoding/decoding weather related data formats | icelake, x86_64, zen, zen2 | Yes |
| h5utils | Utilities for visualization/conversion of HDF5 data | zen2 | Yes |
| hdf-eos2 | HDF for Earth Observing System (hdf4) | icelake, x86_64, zen, zen2 | No |
| hdf-eos5 | HDF for Earth Observing System (hdf5) | icelake, x86_64, zen2 | Yes |
| hdf4 | Libraries for Hierarchical Data Format v4 | icelake, x86_64, zen, zen2 | No |
| hdf5 | Libraries for Hierarchical Data Format v5 | icelake, x86_64, zen, zen2 | Yes |
| ioapi | Models-3/EDSS Input/Output Applications Programming Interface | zen2 | Yes |
| matio | MATLAB MAT file I/O library | icelake, x86_64, zen, zen2 | Yes |
| nco | Toolkits for manipulating data in NetCDF formats | icelake, x86_64, zen, zen2 | Yes |
| ncview | Viewer for NetCDF files | zen2 | Yes |
| netcdf | C Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-cxx | C++ Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-fortran | Fortran Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| parallel-netcdf | Parallel I/O library for NetCDF file format | icelake, x86_64, zen, zen2 | Yes |
| silo | libraries for reading/writing a variety of scientific data | icelake, x86_64, zen, zen2 | Yes |
Earth Sciences
This section lists various software packages related to various Earth sciences. See also Meteorology.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| esmf | The Earth System Modeling Framework | icelake, x86_64, zen, zen2 | Yes |
| gdal | Geospatial Data Abstraction Library | icelake, zen2 | Yes |
| geos | C++ Geometry Engine Open Source | icelake, x86_64, zen2 | No |
| grads | Grid Analysis and Display System | zen2 | No |
| gssha | Gridded Surface/Subsurface Hydrologic Analysis | x86_64 | No |
| hdf-eos2 | HDF for Earth Observing System (hdf4) | icelake, x86_64, zen, zen2 | No |
| hdf-eos5 | HDF for Earth Observing System (hdf5) | icelake, x86_64, zen2 | Yes |
| proj | Generic Coordinate Transformation package | icelake, zen, zen2 | No |
Engineering
This section lists various software packages related to various Engineering fields.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| abaqus | Finite-element analysis/Computer-aided engineering software | x86_64 | No |
| ansys | Computer-aided engineering software | x86_64 | No |
| ansys-em | Computer-aided engineering software for electromagnetic systems | x86_64 | No |
| comsol | General-purpose simulation software | x86_64 | No |
| edem | Simulation using Discrete Element Method | x86_64 | No |
| lumerical | Photonic simulation software | x86_64 | No |
| petsc | PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | No |
| rocky | ANSYS Rocky DEM | x86_64 | No |
| trilinos | Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 | No |
Genomics and Genetics
This section lists various software packages related to Genomics, Genetics, and related fields.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| adapterremoval | Tool for removing remnant adapter sequences from sequencing data | icelake, x86_64, zen2 | No |
| angsd | Program for analyzing NGS data | zen2 | No |
| bamtools | Command line toolkit for dealing with BAM files | icelake, x86_64, zen, zen2 | No |
| bcftools | BCFtools is a set of utilities that manipulate variant calls | zen2 | Yes |
| bedtools2 | swiss-army knife of genomics analysis tasks | zen2 | No |
| blast-plus | Basic Local Alignment Search Tool | icelake, x86_64, zen, zen2 | No |
| bowtie | ultrafast sequence aligner | zen2 | No |
| bowtie2 | ultrafast sequence aligner | zen2 | No |
| bwa | Burrows-Wheeler Aligner | zen2 | No |
| exonerate | generic tool for pairwise sequence comparison | zen2 | No |
| fastqc | quality control tool for high throughput sequence data. | zen2 | No |
| freebayes | Haplotype-based variant detector | zen2 | No |
| gatk | Genome Analysis Tool Kit | icelake, x86_64, zen2 | No |
| hmmer | biosequence analyser using profile hidden Markov models | icelake, x86_64, zen, zen2 | Yes |
| htslib | Library for accessing high-throughput sequencing data formats | icelake, x86_64, zen, zen2 | No |
| igv | Integrative Genomics Viewer | zen2 | No |
| impute2 | genotype imputatin and haplotype phasing tool | icelake, x86_64, zen2 | No |
| jellyfish | JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | icelake, x86_64, zen, zen2 | No |
| kallisto | Program for RNA-sequence quantification | zen2 | No |
| mothur | Bioinformatics tool for microbial ecology | icelake, x86_64, zen2 | No |
| picard | Command line tools for manipulation sequencing data | zen2 | No |
| plink | genome association analysis toolset | zen2 | No |
| popoolation2 | PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. | zen2 | No |
| samtools | SAM (Sequence/Alignment Mapping) Tools | icelake, x86_64, zen, zen2 | No |
| shapeit4 | estimation of haplotypes for sequencing data. | icelake, x86_64, zen2 | Yes |
| snpeff | Genomic variant annotation and functional effect prediction | icelake, x86_64, zen2 | No |
| stacks | pipeline for building loci from short-read sequences | zen2 | No |
| tophat | Spliced read mapper for RNA-Seq | x86_64 | No |
| usearch | Ultra-fast sequence analysis tool | x86_64 | No |
| vcftools | VCFtools is a set of utilities for working with VCF files | zen2 | No |
Image/Video Processing
This section lists various software packages related to the processing/editting/manipulation/etc of image or video files.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| embree | High performance ray tracing kernels | x86_64 | No |
| ffmpeg | icelake, x86_64, zen, zen2 | No | |
| jasper | Library for manipulating JPEG-2000 images | icelake, x86_64, zen2 | No |
| libpng | libpng is the official PNG reference library | icelake, x86_64, zen, zen2 | No |
| libtiff | Library for TIFF (Tag Image File Format) image format | icelake, x86_64, zen, zen2 | No |
Machine Learning
This section lists various software packages related to Machine Learning, Deep Learning, Neural Nets and related fields. You might also wish to look at the section on Computer Vision
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| caffe | Deep learning framework | icelake, x86_64, zen, zen2 | No |
| cudnn | Library of deep learning/neural network primitives for GPUs | icelake, zen, zen2 | Yes |
| gloo | Gloo collective communications package | icelake, zen2 | Yes |
| libxsmm | library for specialized dense and sparse matrix operations | icelake, x86_64, zen, zen2 | No |
| opencv | Open-source Computer Vision Library | zen2 | No |
| pyray | Framework for scaling AI and Python applications | zen2 | No |
| pytorch | Open-source machine learning library | icelake, zen2 | Yes |
| tensorflow | Open-source software library for machine intelligence | icelake, zen, zen2 | Yes |
Material Science
This section lists various software packages related to Material Science and related fields. See also Chemistry and SolidStatePhysics.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| cp2k | quantum chemistry and solid state physics package | zen2 | No |
| spglib | C library for finding and handling crystal symmetries | icelake, x86_64, zen, zen2 | No |
| vasp | VASP: Vienna Ab-initio Simulation Package | zen2 | No |
Meteorology
This section lists various software packages related to Meteorology, Weather, Atmospheric and Oceanographic Sciences and related fields. See also Earth Sciences
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| cdo | Climate Data Operators | zen2 | Yes |
| eccodes | Libraries for encoding/decoding weather related data formats | icelake, x86_64, zen, zen2 | Yes |
| magics | meteorological plotting software | icelake, zen2 | Yes |
| ufs-weather-model | Unified Forecast System Weather Model | zen2 | Yes |
Miscellaneous
Miscellaneous packages. Libraries and other stuff which we need a modulefile for but do not belong anywhere else and do not merit there own category.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| binutils | GNU Binary utilities | icelake, x86_64, zen, zen2 | No |
| freetype | freely available software library to render fonts | icelake, x86_64, zen, zen2 | No |
| fribidi | Unicode Bidirectional Algorithm implementation | icelake, x86_64, zen, zen2 | No |
| harfbuzz | Text shaping library | icelake, x86_64, zen, zen2 | No |
Molecular Dynamics
This section lists various software packages related to Molecular Dynamics and related fields. See also Chemistry and Material Science.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| charmm | Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| gromacs | Chemical simulation/Molecular dynamics package | icelake, zen, zen2 | Yes |
| lammps | LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | icelake, zen, zen2 | Yes |
| latte | Open source density functional tight binding molecular dynamics. | icelake, x86_64, zen, zen2 | Yes |
| libint | library to evaluate molecular integrals | icelake, x86_64, zen, zen2 | Yes |
| libvdwxc | library for vdW-DF exchange-correlation functionals | x86_64, zen, zen2 | Yes |
| namd | Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| openmm | A high-performance toolkit for molecular simulation. | icelake, zen2 | Yes |
| openstructure | Open-source computational structural biology framework | zen2 | No |
| plumed | plugin for molecular dynamics | icelake, zen, zen2 | Yes |
| qmd-progress | PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen | Yes |
| quantum-espresso | Electronic-structure calculations at the nanoscale. | zen2 | Yes |
| sirius | domain specific library for electronic structure calculations | zen | No |
| spglib | C library for finding and handling crystal symmetries | icelake, x86_64, zen, zen2 | No |
| vmd | Visual Molecular Dynamics | x86_64 | No |
| wannier90 | tool to calculate maximally-localized Wannier functions | icelake, x86_64, zen, zen2 | Yes |
| xssp | Secondary structure assignments for entries in the Protein Data Bank | zen | No |
Multiphysics
This section lists various software packages related to Multiphysics.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| petsc | PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | No |
| trilinos | Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 | No |
Neuroscience
This section lists various software packages related to Neuroscience and related fields liek brain imaging, etc.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| afni | AFNI (Analysis of Functional NeuroImages) | x86_64 | No |
| fsl | FSL - FMRIB Software Library | x86_64 | No |
Numerical Methods
This section lists various software packages related to Numerical Methods and Computational Mathematics. It includes both underlying numerical libraries as well as advanced computational (and often GUI) environments. These packages are generally useful across a wide range of disciplines.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| alphafold | AlphaFold Protein Structure Database and Software | icelake, x86_64 | No |
| alphafold3 | AlphaFold Protein Structure Database and Software V3 | x86_64 | No |
| amber | Amber is a suite of biomolecular simulation programs. | x86_64 | No |
| amdblis | AMD Optimized BLAS libraries | zen2 | No |
| amdfftw | AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | AMD Optimized BLAS libraries | zen2 | No |
| amdlibm | AMD Optimized BLAS libraries | zen2 | No |
| amdscalapack | AMD Optimized Scalable linear algebra package | zen2 | Yes |
| aocl-sparse | Suite of Sparse Matrix algorithms | zen2 | No |
| arpack-ng | Fortran77 subroutines designed to solve large scale eigenvalue problems | icelake, x86_64, zen, zen2 | Yes |
| bml | Basic Matrix Library | icelake, x86_64, zen, zen2 | Yes |
| cgal | Computations Geometry Algorithms Library | icelake, x86_64, zen, zen2 | Yes |
| cminpack | Library for solving nonlinear equations and nonlinear least squares problems | icelake, x86_64, zen, zen2 | No |
| cosma | Distributed Communication-Optimal Matrix-Matrix Multiplication Library | icelake, x86_64, zen2 | Yes |
| eigen | C++ template library for matrix and vector operations, | icelake, x86_64, zen, zen2 | No |
| elpa | Eigenvalue solvers for Petaflop Applications | zen2 | No |
| envi | ENVI software for processing and analyzing geospatial data | x86_64 | No |
| fftw | Discrete Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| freesurfer | FreeSurfer is a brain imaging software package | x86_64 | No |
| gmp | GNU Multiple Precision Arithmetic Library | icelake, x86_64, zen, zen2 | No |
| gsl | GNU Scientific Library | icelake, x86_64, zen, zen2 | No |
| gurobi | Gurobi Optimizer for numerical programming | x86_64 | No |
| hypre | Scalable Linear Solvers and Multigrid Methods | icelake, x86_64, zen2 | Yes |
| jags | JAGS Gibbs Sampler | icelake, x86_64, zen2 | No |
| kahip | Karlsruhe High Quality Graph Partitioning Framework | icelake, x86_64, zen, zen2 | Yes |
| magma | Matrix Algebra on GPU and Multicore Architectures | icelake, zen2 | Yes |
| magma-computer-algebra | MAGMA is a computational algebra package. | x86_64_v3 | Yes |
| materials-studio | Materials Studio for simulating and modeling materials | x86_64 | No |
| mathematica | Mathematica symbolic and computational mathematics package. | x86_64 | No |
| matio | MATLAB MAT file I/O library | icelake, x86_64, zen, zen2 | Yes |
| matlab | Matlab numerical computing environment | x86_64 | No |
| metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mgridgen | Multilevel Serial & Parallel Coarse Grid Construction Library | icelake, x86_64, zen, zen2 | Yes |
| mpfr | GNU Multiple-precision Floating point library | icelake, x86_64, zen, zen2 | No |
| mt-metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mumps | MUltifrontal Massively Parallel sparse direct Solver | icelake, x86_64, zen, zen2 | Yes |
| ncl | NCAR Command Language | icelake, x86_64, zen2 | Yes |
| netlogo | NetLogo is a programming language and an IDE for agent-based modeling. | x86_64 | No |
| openblas | Optimized BLAS libraries | icelake, x86_64, zen, zen2 | No |
| pari-gp | computer algebra system for computations in number theory | zen2 | Yes |
| parmetis | Parallel Metis | icelake, x86_64, zen, zen2 | Yes |
| parmgridgen | Multilevel Serial & Parallel Coarse Grid Construction Library | icelake, x86_64, zen, zen2 | Yes |
| pexsi | electronic structure calculation based on Kohn-Sham density functional theory | icelake, x86_64, zen, zen2 | Yes |
| pfft | Parallel Fast Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| pytorch | Open-source machine learning library | icelake, zen2 | Yes |
| scalapack | Scalable linear algebra package | icelake, x86_64, zen, zen2 | Yes |
| scotch | Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | icelake, x86_64, zen, zen2 | Yes |
| slepc | Scalable Library for Eigenvalue Problem Computations | zen2 | No |
| spfft | 3D FFT library for sparse frequency domain data | icelake, x86_64, zen, zen2 | No |
| star-ccm | CFD based simulation software from Siemens | x86_64 | No |
| suite-sparse | Suite of Sparse Matrix algorithms | icelake, x86_64, zen, zen2 | No |
| superlu | Sparse Linear system solver (sequential) | icelake, x86_64, zen, zen2 | No |
| superlu-dist | Sparse Linear system solver (distributed mem/MPI) | icelake, x86_64, zen, zen2 | No |
| superlu-mt | Sparse Linear system solver (multithreaded) | icelake, x86_64, zen, zen2 | No |
| tensorflow | Open-source software library for machine intelligence | icelake, zen, zen2 | Yes |
| voropp | library for 3D computations of the Voronoi tessellation | icelake, x86_64, zen, zen2 | No |
| zoltan | Toolkit for parallel combinatorial algorithms | icelake, x86_64, zen, zen2 | Yes |
Software Development
This section lists various software packages related to the development and optimization, etc. of software and codes. It includes compilers, debuggers, profiling tools, as well as relatively low level libraries. It also includes various scripting languages.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| alphafold | AlphaFold Protein Structure Database and Software | icelake, x86_64 | No |
| alphafold3 | AlphaFold Protein Structure Database and Software V3 | x86_64 | No |
| amdblis | AMD Optimized BLAS libraries | zen2 | No |
| amdfftw | AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | AMD Optimized BLAS libraries | zen2 | No |
| amdlibm | AMD Optimized BLAS libraries | zen2 | No |
| amdscalapack | AMD Optimized Scalable linear algebra package | zen2 | Yes |
| aocc | AMD Optimizing Compiler Suite | x86_64 | No |
| aocl-sparse | Suite of Sparse Matrix algorithms | zen2 | No |
| apptainer | Apptainer Container System | x86_64 | No |
| armadillo | Linear algebra library for C++ | icelake, x86_64, zen2 | Yes |
| bml | Basic Matrix Library | icelake, x86_64, zen, zen2 | Yes |
| boost | free, portable C++ source libraries | icelake, x86_64, zen, zen2 | Yes |
| cgal | Computations Geometry Algorithms Library | icelake, x86_64, zen, zen2 | Yes |
| charm4py | distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmpp | parallel programming framework in C++ | icelake, x86_64, zen, zen2 | No |
| cmake | cross-platform, open-source build system | icelake, x86_64, zen, zen2 | No |
| cmdstan | command line interface to Stan | icelake, x86_64, zen2 | Yes |
| cminpack | Library for solving nonlinear equations and nonlinear least squares problems | icelake, x86_64, zen, zen2 | No |
| cosma | Distributed Communication-Optimal Matrix-Matrix Multiplication Library | icelake, x86_64, zen2 | Yes |
| cube | Performance report explorer for Scalasca and Score-P | zen2 | No |
| cubelib | C++ library and tools for cube | zen2 | No |
| cubew | High performance C writer library for cube | zen2 | No |
| cuda | parallel computing platform/programming model for NVIDIA GPUs | icelake, x86_64, zen, zen2 | No |
| cuda-compatibility | CUDA Toolkit Compatibility package | x86_64 | No |
| cudnn | Library of deep learning/neural network primitives for GPUs | icelake, zen, zen2 | Yes |
| cython | Compiler for writing C extensions for Python | icelake, x86_64, zen, zen2 | No |
| dmtcp | Distributed Multithreaded Checkpointing | icelake, x86_64, zen, zen2 | No |
| dyninst | API for dynamic binary instrumentation | icelake, zen, zen2 | Yes |
| eccodes | Libraries for encoding/decoding weather related data formats | icelake, x86_64, zen, zen2 | Yes |
| eigen | C++ template library for matrix and vector operations, | icelake, x86_64, zen, zen2 | No |
| elpa | Eigenvalue solvers for Petaflop Applications | zen2 | No |
| envi | ENVI software for processing and analyzing geospatial data | x86_64 | No |
| esmf | The Earth System Modeling Framework | icelake, x86_64, zen, zen2 | Yes |
| ffmpeg | icelake, x86_64, zen, zen2 | No | |
| fftw | Discrete Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| gcc | GNU Compiler Suite | x86_64 | Yes |
| gdal | Geospatial Data Abstraction Library | icelake, zen2 | Yes |
| geos | C++ Geometry Engine Open Source | icelake, x86_64, zen2 | No |
| gloo | Gloo collective communications package | icelake, zen2 | Yes |
| go | Go programming language | icelake, x86_64, zen2 | No |
| gsl | GNU Scientific Library | icelake, x86_64, zen, zen2 | No |
| gurobi | Gurobi Optimizer for numerical programming | x86_64 | No |
| hdf4 | Libraries for Hierarchical Data Format v4 | icelake, x86_64, zen, zen2 | No |
| hdf5 | Libraries for Hierarchical Data Format v5 | icelake, x86_64, zen, zen2 | Yes |
| hip | Heterogeneous Interface for Portability (HIP) | zen2 | Yes |
| hpctoolkit | toolkit for performance measurement and analysis | zen2 | Yes |
| hpl | High Performance Computing Linpack Benchmark | icelake, x86_64, zen2 | Yes |
| hpx | C++ runtime for parallel and distributed applications | zen, zen2 | No |
| hypre | Scalable Linear Solvers and Multigrid Methods | icelake, x86_64, zen2 | Yes |
| icu4c | Libraries for unicode and globalization support | icelake, x86_64, zen, zen2 | No |
| intel | Intel OneAPI Classic compilers | x86_64 | No |
| intel-advisor | Intel advisor performance analysis tool | zen2 | No |
| intel-dal | Intel Data Analytics Library (DAL) | zen2 | No |
| intel-dnn | Intel Deep Neural Network Library | zen2 | No |
| intel-dpl | Intel Data Parallel C++ Library (DPL) | zen2 | No |
| intel-inspector | Intel Inspector memory, thread checking and debugging tool | zen2 | No |
| intel-ipp | Intel Integrated Performance Primitives (IPP) | zen2 | No |
| intel-ippcp | Intel Integrated Performance Primitives Cryptography (IPP Crypto) | zen2 | No |
| intel-mkl | Intel Math Kernel Library (MKL/oneMKL) | icelake, x86_64, zen2 | Yes |
| intel-mpi | Intel Message Passing Interface (MPI) Library | zen2 | No |
| intel-mpi-benchmarks | MPI benchmarks from Intel | zen2 | Yes |
| intel-tbb | Intel Threaded Building Blocks | icelake, x86_64, zen, zen2 | Yes |
| intel-vpl | Intel Video Processing Library (oneVPL) | zen2 | No |
| intel-vtune | Intel oneAPI VTune Profiler | zen2 | No |
| ioapi | Models-3/EDSS Input/Output Applications Programming Interface | zen2 | Yes |
| ior | Parallel IO benchmark | icelake, x86_64, zen2 | Yes |
| jags | JAGS Gibbs Sampler | icelake, x86_64, zen2 | No |
| jasper | Library for manipulating JPEG-2000 images | icelake, x86_64, zen2 | No |
| json-c | JSON library implemented in C | icelake, x86_64, zen2 | No |
| jsoncpp | JSON library implemented in C++ | icelake, zen, zen2 | No |
| julia | Julia programming language: A fresh approach to technical computing | x86_64 | No |
| kahip | Karlsruhe High Quality Graph Partitioning Framework | icelake, x86_64, zen, zen2 | Yes |
| libiconv | Functions for internationalization/character set conversion | icelake, x86_64, zen, zen2 | No |
| libpng | libpng is the official PNG reference library | icelake, x86_64, zen, zen2 | No |
| libtiff | Library for TIFF (Tag Image File Format) image format | icelake, x86_64, zen, zen2 | No |
| libxsmm | library for specialized dense and sparse matrix operations | icelake, x86_64, zen, zen2 | No |
| libzmq | ZeroMQ networking/concurrency library and core API | icelake, x86_64, zen, zen2 | No |
| llvm | LLVM collection of compiler and toolchain modules | icelake, zen, zen2 | No |
| magma | Matrix Algebra on GPU and Multicore Architectures | icelake, zen2 | Yes |
| magma-computer-algebra | MAGMA is a computational algebra package. | x86_64_v3 | Yes |
| mathematica | Mathematica symbolic and computational mathematics package. | x86_64 | No |
| matio | MATLAB MAT file I/O library | icelake, x86_64, zen, zen2 | Yes |
| matlab | Matlab numerical computing environment | x86_64 | No |
| mesa | Mesa is an open-source OpenGL graphics library | icelake, x86_64, zen, zen2 | No |
| metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mgridgen | Multilevel Serial & Parallel Coarse Grid Construction Library | icelake, x86_64, zen, zen2 | Yes |
| mpfr | GNU Multiple-precision Floating point library | icelake, x86_64, zen, zen2 | No |
| mt-metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mumps | MUltifrontal Massively Parallel sparse direct Solver | icelake, x86_64, zen, zen2 | Yes |
| nccl | NVIDIA Collective Communication Library | icelake, zen2 | Yes |
| ncl | NCAR Command Language | icelake, x86_64, zen2 | Yes |
| nco | Toolkits for manipulating data in NetCDF formats | icelake, x86_64, zen, zen2 | Yes |
| netcdf | C Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-cxx | C++ Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-fortran | Fortran Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netlogo | NetLogo is a programming language and an IDE for agent-based modeling. | x86_64 | No |
| nvhpc | Nvidia HPC SDK Compiler suite | x86_64 | No |
| nvmpi | MPI libraries from the Nvidia HPC SDK Compiler suite | x86_64 | No |
| oneapi | Intel OneAPI new compilers | x86_64 | No |
| openblas | Optimized BLAS libraries | icelake, x86_64, zen, zen2 | No |
| opencv | Open-source Computer Vision Library | zen2 | No |
| openjdk | Open-source implementation of Java | icelake, x86_64, zen, zen2 | No |
| openmpi | OpenMPI implementation of Message Passing Interface | icelake, x86_64, zen, zen2 | Yes |
| osu-micro-benchmarks | Microbenchmarks for MPI | icelake, x86_64, zen, zen2 | No |
| parallel | GNU parallel tool for executing jobs in parallel | zen2 | No |
| parallel-netcdf | Parallel I/O library for NetCDF file format | icelake, x86_64, zen, zen2 | Yes |
| parmetis | Parallel Metis | icelake, x86_64, zen, zen2 | Yes |
| perl | Perl scripting language | icelake, x86_64, zen, zen2 | No |
| pfft | Parallel Fast Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| python | Python scripting language | icelake, x86_64, zen2 | Yes |
| qt | cross-platform application development framework for GUIs | icelake, x86_64, zen, zen2 | No |
| r | R statistical computing scripting language | icelake, x86_64, zen2 | No |
| rdma-core | RDMA Core userspace libraries and drivers | zen2 | No |
| rust | Rust programming language | icelake, x86_64, zen, zen2 | No |
| scalapack | Scalable linear algebra package | icelake, x86_64, zen, zen2 | Yes |
| scons | SCons open-source software construction tool | icelake, x86_64, zen2 | No |
| scorep | suite for profiling, event tracing, and analysis of HPC applications | zen2 | Yes |
| scotch | Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | icelake, x86_64, zen, zen2 | Yes |
| silo | libraries for reading/writing a variety of scientific data | icelake, x86_64, zen, zen2 | Yes |
| singularity | Singularity container utilities | x86_64 | No |
| sox | Sound eXchange, the Swiss Army knife of sound processing | icelake, x86_64, zen2 | No |
| sqlite | Library for lossy compression of multidimensional arrays | icelake, x86_64, zen, zen2 | No |
| star-ccm | CFD based simulation software from Siemens | x86_64 | No |
| suite-sparse | Suite of Sparse Matrix algorithms | icelake, x86_64, zen, zen2 | No |
| superlu | Sparse Linear system solver (sequential) | icelake, x86_64, zen, zen2 | No |
| superlu-dist | Sparse Linear system solver (distributed mem/MPI) | icelake, x86_64, zen, zen2 | No |
| superlu-mt | Sparse Linear system solver (multithreaded) | icelake, x86_64, zen, zen2 | No |
| swig | compiler to interface C/C++ libraries to Perl, Python, etc | icelake, x86_64, zen, zen2 | No |
| toolchain/aocc | AOCC Compiler Toolchains | x86_64 | No |
| toolchain/gcc | GNU Compiler Toolchains | x86_64 | No |
| toolchain/intel | Intel Classic Compiler Toolchains | x86_64 | No |
| udunits | The UDUNITS package supports units of physical quantities. | icelake, x86_64, zen, zen2 | No |
| umd-examples/hello-umd | Simple Hello world binary | icelake, x86_64, zen, zen2 | Yes |
| zlib | General purpose, patent-free compression ibrary | icelake, x86_64, zen, zen2 | No |
| zoltan | Toolkit for parallel combinatorial algorithms | icelake, x86_64, zen, zen2 | Yes |
Basic Utilities
This section lists various utility software packages, etc. This is sort of a catch-all category for packages which are useful across a wide range of disciplines but do not really fall into any discipline. These are often just newer versions of utilities supplied by the OS.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| apptainer | Apptainer Container System | x86_64 | No |
| coreutils-progress-viewer | command line tool for monitoring progress of core utilities | zen2 | No |
| curl | command line tool for transferring data | icelake, x86_64, zen, zen2 | No |
| dmtcp | Distributed Multithreaded Checkpointing | icelake, x86_64, zen, zen2 | No |
| git-lfs | command line tool for managing cloud storage | icelake, x86_64, zen2 | No |
| hpcc | Default env setting for the various clusters | x86_64 | No |
| jupyter | The Jupyter Notebook application | icelake, x86_64, zen, zen2 | No |
| mercurial | Mercurial source control management system | icelake, x86_64, zen2 | No |
| rclone | command line tool for managing cloud storage | zen2 | No |
| singularity | Singularity container utilities | x86_64 | No |
| sox | Sound eXchange, the Swiss Army knife of sound processing | icelake, x86_64, zen2 | No |
Visualization and Graphics
This section lists various software packages related to Visualization; basically packages to assist in visualizing data generated from other packages/codes. It includes both basic graphics libraries and high end (GUI) visualization platforms.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| colmap | Image-based 3D reconstruction pipeline | zen2 | Yes |
| envi | ENVI software for processing and analyzing geospatial data | x86_64 | No |
| gnuplot | command-line driven graphing utility | icelake, x86_64, zen, zen2 | No |
| grads | Grid Analysis and Display System | zen2 | No |
| graphviz | Graph Visualization Software | icelake, x86_64, zen2 | Yes |
| magics | meteorological plotting software | icelake, zen2 | Yes |
| mesa | Mesa is an open-source OpenGL graphics library | icelake, x86_64, zen, zen2 | No |
| ncl | NCAR Command Language | icelake, x86_64, zen2 | Yes |
| paraview | data analysis and visualization application | zen, zen2 | No |
| paraview-headless | data analysis and visualization application (headless version) | zen2 | No |
| pgplot | PGPLOT Graphics Subroutine Library | icelake, x86_64, zen2 | No |
| plplot | Cross-platform software for creating scientific plots | zen2 | No |
| povray | Persistence of Vision Ray tracer | icelake, x86_64, zen, zen2 | No |
| tecplot360 | CFD visualization software | x86_64 | No |
| virtualgl | Toolkit to allow remote display to run OpenGL applications with full hardware acceleration | icelake, x86_64, zen, zen2 | No |
| visit | interactive, scalable, visualization, animation and analysis tool | zen2 | Yes |
| vmd | Visual Molecular Dynamics | x86_64 | No |
| vtk | 3D computer graphics, image processing and visualization library | icelake, zen, zen2 | Yes |
All packages (unsorted by field)
This section list all installed research software, unsorted by field of research/category/etc.
| Package Name | Description | CPUS optimized for | GPU ready? |
|---|---|---|---|
| abaqus | Finite-element analysis/Computer-aided engineering software | x86_64 | No |
| adapterremoval | Tool for removing remnant adapter sequences from sequencing data | icelake, x86_64, zen2 | No |
| adios2 | The Adapatble Input/Output System, version 2 | icelake, x86_64, zen, zen2 | Yes |
| afni | AFNI (Analysis of Functional NeuroImages) | x86_64 | No |
| alphafold | AlphaFold Protein Structure Database and Software | icelake, x86_64 | No |
| alphafold3 | AlphaFold Protein Structure Database and Software V3 | x86_64 | No |
| amber | Amber is a suite of biomolecular simulation programs. | x86_64 | No |
| amdblis | AMD Optimized BLAS libraries | zen2 | No |
| amdfftw | AMD Discrete Fourier Transform library | zen2 | Yes |
| amdlibflame | AMD Optimized BLAS libraries | zen2 | No |
| amdlibm | AMD Optimized BLAS libraries | zen2 | No |
| amdscalapack | AMD Optimized Scalable linear algebra package | zen2 | Yes |
| angsd | Program for analyzing NGS data | zen2 | No |
| ansys | Computer-aided engineering software | x86_64 | No |
| ansys-em | Computer-aided engineering software for electromagnetic systems | x86_64 | No |
| aocc | AMD Optimizing Compiler Suite | x86_64 | No |
| aocl-sparse | Suite of Sparse Matrix algorithms | zen2 | No |
| apptainer | Apptainer Container System | x86_64 | No |
| armadillo | Linear algebra library for C++ | icelake, x86_64, zen2 | Yes |
| arpack-ng | Fortran77 subroutines designed to solve large scale eigenvalue problems | icelake, x86_64, zen, zen2 | Yes |
| bamtools | Command line toolkit for dealing with BAM files | icelake, x86_64, zen, zen2 | No |
| bcftools | BCFtools is a set of utilities that manipulate variant calls | zen2 | Yes |
| bedtools2 | swiss-army knife of genomics analysis tasks | zen2 | No |
| binutils | GNU Binary utilities | icelake, x86_64, zen, zen2 | No |
| blast-plus | Basic Local Alignment Search Tool | icelake, x86_64, zen, zen2 | No |
| bml | Basic Matrix Library | icelake, x86_64, zen, zen2 | Yes |
| boost | free, portable C++ source libraries | icelake, x86_64, zen, zen2 | Yes |
| bowtie | ultrafast sequence aligner | zen2 | No |
| bowtie2 | ultrafast sequence aligner | zen2 | No |
| bwa | Burrows-Wheeler Aligner | zen2 | No |
| bzip2 | patent-free high quality data compression libraries | icelake, x86_64, zen, zen2 | No |
| c-blosc | A blocking, shuffling, and loss-less compression library | icelake, x86_64, zen, zen2 | No |
| caffe | Deep learning framework | icelake, x86_64, zen, zen2 | No |
| cdo | Climate Data Operators | zen2 | Yes |
| cfitsio | Libraries for Flexible Image Transport System (FITS) data format | icelake, x86_64, zen, zen2 | No |
| cfour | Software for quantum chemical modeling | x86_64 | No |
| cgal | Computations Geometry Algorithms Library | icelake, x86_64, zen, zen2 | Yes |
| cgns | CFD General notation system | icelake, x86_64, zen2 | Yes |
| charm4py | distributed/parallel programing framework for Python | zen, zen2 | Yes |
| charmm | Chemistry at HARvard Macromolecular Mechanics. | zen2 | Yes |
| charmpp | parallel programming framework in C++ | icelake, x86_64, zen, zen2 | No |
| cmake | cross-platform, open-source build system | icelake, x86_64, zen, zen2 | No |
| cmdstan | command line interface to Stan | icelake, x86_64, zen2 | Yes |
| cminpack | Library for solving nonlinear equations and nonlinear least squares problems | icelake, x86_64, zen, zen2 | No |
| colmap | Image-based 3D reconstruction pipeline | zen2 | Yes |
| comsol | General-purpose simulation software | x86_64 | No |
| coreutils-progress-viewer | command line tool for monitoring progress of core utilities | zen2 | No |
| cosma | Distributed Communication-Optimal Matrix-Matrix Multiplication Library | icelake, x86_64, zen2 | Yes |
| cp2k | quantum chemistry and solid state physics package | zen2 | No |
| cube | Performance report explorer for Scalasca and Score-P | zen2 | No |
| cubelib | C++ library and tools for cube | zen2 | No |
| cubew | High performance C writer library for cube | zen2 | No |
| cuda | parallel computing platform/programming model for NVIDIA GPUs | icelake, x86_64, zen, zen2 | No |
| cuda-compatibility | CUDA Toolkit Compatibility package | x86_64 | No |
| cudnn | Library of deep learning/neural network primitives for GPUs | icelake, zen, zen2 | Yes |
| cupy | a Python array library accelerated with NVIDIA CUDA | zen2 | Yes |
| curl | command line tool for transferring data | icelake, x86_64, zen, zen2 | No |
| cython | Compiler for writing C extensions for Python | icelake, x86_64, zen, zen2 | No |
| dmtcp | Distributed Multithreaded Checkpointing | icelake, x86_64, zen, zen2 | No |
| dplr | Hypersonic Continuum CFD Code | skylake_avx512, x86_64 | No |
| dyninst | API for dynamic binary instrumentation | icelake, zen, zen2 | Yes |
| eccodes | Libraries for encoding/decoding weather related data formats | icelake, x86_64, zen, zen2 | Yes |
| edem | Simulation using Discrete Element Method | x86_64 | No |
| eigen | C++ template library for matrix and vector operations, | icelake, x86_64, zen, zen2 | No |
| elpa | Eigenvalue solvers for Petaflop Applications | zen2 | No |
| embree | High performance ray tracing kernels | x86_64 | No |
| envi | ENVI software for processing and analyzing geospatial data | x86_64 | No |
| esmf | The Earth System Modeling Framework | icelake, x86_64, zen, zen2 | Yes |
| exonerate | generic tool for pairwise sequence comparison | zen2 | No |
| fastqc | quality control tool for high throughput sequence data. | zen2 | No |
| fds | Fire Dynamics Simulator | x86_64 | No |
| ffmpeg | icelake, x86_64, zen, zen2 | No | |
| fftw | Discrete Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| freebayes | Haplotype-based variant detector | zen2 | No |
| freesurfer | FreeSurfer is a brain imaging software package | x86_64 | No |
| freetype | freely available software library to render fonts | icelake, x86_64, zen, zen2 | No |
| fribidi | Unicode Bidirectional Algorithm implementation | icelake, x86_64, zen, zen2 | No |
| fsl | FSL - FMRIB Software Library | x86_64 | No |
| fun3d | FUN3d (Fully Unstructured Navier-Stokes) CFD suite | skylake_avx512 | No |
| gatk | Genome Analysis Tool Kit | icelake, x86_64, zen2 | No |
| gaussian | Software for electronic structure modeling | x86_64 | No |
| gcc | GNU Compiler Suite | x86_64 | Yes |
| gdal | Geospatial Data Abstraction Library | icelake, zen2 | Yes |
| geos | C++ Geometry Engine Open Source | icelake, x86_64, zen2 | No |
| git-lfs | command line tool for managing cloud storage | icelake, x86_64, zen2 | No |
| gloo | Gloo collective communications package | icelake, zen2 | Yes |
| gmp | GNU Multiple Precision Arithmetic Library | icelake, x86_64, zen, zen2 | No |
| gnuplot | command-line driven graphing utility | icelake, x86_64, zen, zen2 | No |
| go | Go programming language | icelake, x86_64, zen2 | No |
| grads | Grid Analysis and Display System | zen2 | No |
| graphviz | Graph Visualization Software | icelake, x86_64, zen2 | Yes |
| gromacs | Chemical simulation/Molecular dynamics package | icelake, zen, zen2 | Yes |
| gsl | GNU Scientific Library | icelake, x86_64, zen, zen2 | No |
| gssha | Gridded Surface/Subsurface Hydrologic Analysis | x86_64 | No |
| gurobi | Gurobi Optimizer for numerical programming | x86_64 | No |
| h5utils | Utilities for visualization/conversion of HDF5 data | zen2 | Yes |
| harfbuzz | Text shaping library | icelake, x86_64, zen, zen2 | No |
| hdf-eos2 | HDF for Earth Observing System (hdf4) | icelake, x86_64, zen, zen2 | No |
| hdf-eos5 | HDF for Earth Observing System (hdf5) | icelake, x86_64, zen2 | Yes |
| hdf4 | Libraries for Hierarchical Data Format v4 | icelake, x86_64, zen, zen2 | No |
| hdf5 | Libraries for Hierarchical Data Format v5 | icelake, x86_64, zen, zen2 | Yes |
| hemocell | Framework for simulation of blood and other dense deformable capsule suspensions | zen2 | Yes |
| hip | Heterogeneous Interface for Portability (HIP) | zen2 | Yes |
| hmmer | biosequence analyser using profile hidden Markov models | icelake, x86_64, zen, zen2 | Yes |
| hpcc | Default env setting for the various clusters | x86_64 | No |
| hpctoolkit | toolkit for performance measurement and analysis | zen2 | Yes |
| hpl | High Performance Computing Linpack Benchmark | icelake, x86_64, zen2 | Yes |
| hpx | C++ runtime for parallel and distributed applications | zen, zen2 | No |
| htslib | Library for accessing high-throughput sequencing data formats | icelake, x86_64, zen, zen2 | No |
| hypre | Scalable Linear Solvers and Multigrid Methods | icelake, x86_64, zen2 | Yes |
| icu4c | Libraries for unicode and globalization support | icelake, x86_64, zen, zen2 | No |
| igv | Integrative Genomics Viewer | zen2 | No |
| impute2 | genotype imputatin and haplotype phasing tool | icelake, x86_64, zen2 | No |
| intel | Intel OneAPI Classic compilers | x86_64 | No |
| intel-advisor | Intel advisor performance analysis tool | zen2 | No |
| intel-dal | Intel Data Analytics Library (DAL) | zen2 | No |
| intel-dnn | Intel Deep Neural Network Library | zen2 | No |
| intel-dpl | Intel Data Parallel C++ Library (DPL) | zen2 | No |
| intel-inspector | Intel Inspector memory, thread checking and debugging tool | zen2 | No |
| intel-ipp | Intel Integrated Performance Primitives (IPP) | zen2 | No |
| intel-ippcp | Intel Integrated Performance Primitives Cryptography (IPP Crypto) | zen2 | No |
| intel-mkl | Intel Math Kernel Library (MKL/oneMKL) | icelake, x86_64, zen2 | Yes |
| intel-mpi | Intel Message Passing Interface (MPI) Library | zen2 | No |
| intel-mpi-benchmarks | MPI benchmarks from Intel | zen2 | Yes |
| intel-tbb | Intel Threaded Building Blocks | icelake, x86_64, zen, zen2 | Yes |
| intel-vpl | Intel Video Processing Library (oneVPL) | zen2 | No |
| intel-vtune | Intel oneAPI VTune Profiler | zen2 | No |
| ioapi | Models-3/EDSS Input/Output Applications Programming Interface | zen2 | Yes |
| ior | Parallel IO benchmark | icelake, x86_64, zen2 | Yes |
| jags | JAGS Gibbs Sampler | icelake, x86_64, zen2 | No |
| jasper | Library for manipulating JPEG-2000 images | icelake, x86_64, zen2 | No |
| jellyfish | JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | icelake, x86_64, zen, zen2 | No |
| json-c | JSON library implemented in C | icelake, x86_64, zen2 | No |
| jsoncpp | JSON library implemented in C++ | icelake, zen, zen2 | No |
| julia | Julia programming language: A fresh approach to technical computing | x86_64 | No |
| jupyter | The Jupyter Notebook application | icelake, x86_64, zen, zen2 | No |
| kahip | Karlsruhe High Quality Graph Partitioning Framework | icelake, x86_64, zen, zen2 | Yes |
| kallisto | Program for RNA-sequence quantification | zen2 | No |
| lammps | LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator | icelake, zen, zen2 | Yes |
| latte | Open source density functional tight binding molecular dynamics. | icelake, x86_64, zen, zen2 | Yes |
| libiconv | Functions for internationalization/character set conversion | icelake, x86_64, zen, zen2 | No |
| libint | library to evaluate molecular integrals | icelake, x86_64, zen, zen2 | Yes |
| libpng | libpng is the official PNG reference library | icelake, x86_64, zen, zen2 | No |
| libtiff | Library for TIFF (Tag Image File Format) image format | icelake, x86_64, zen, zen2 | No |
| libvdwxc | library for vdW-DF exchange-correlation functionals | x86_64, zen, zen2 | Yes |
| libxsmm | library for specialized dense and sparse matrix operations | icelake, x86_64, zen, zen2 | No |
| libzmq | ZeroMQ networking/concurrency library and core API | icelake, x86_64, zen, zen2 | No |
| llvm | LLVM collection of compiler and toolchain modules | icelake, zen, zen2 | No |
| lumerical | Photonic simulation software | x86_64 | No |
| lz4 | Lossless compression utility and library | icelake, x86_64, zen, zen2 | No |
| magics | meteorological plotting software | icelake, zen2 | Yes |
| magma | Matrix Algebra on GPU and Multicore Architectures | icelake, zen2 | Yes |
| magma-computer-algebra | MAGMA is a computational algebra package. | x86_64_v3 | Yes |
| materials-studio | Materials Studio for simulating and modeling materials | x86_64 | No |
| mathematica | Mathematica symbolic and computational mathematics package. | x86_64 | No |
| matio | MATLAB MAT file I/O library | icelake, x86_64, zen, zen2 | Yes |
| matlab | Matlab numerical computing environment | x86_64 | No |
| mercurial | Mercurial source control management system | icelake, x86_64, zen2 | No |
| mesa | Mesa is an open-source OpenGL graphics library | icelake, x86_64, zen, zen2 | No |
| metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mgridgen | Multilevel Serial & Parallel Coarse Grid Construction Library | icelake, x86_64, zen, zen2 | Yes |
| mothur | Bioinformatics tool for microbial ecology | icelake, x86_64, zen2 | No |
| mpfr | GNU Multiple-precision Floating point library | icelake, x86_64, zen, zen2 | No |
| mt-metis | Metis unstructured graph partitioner | icelake, x86_64, zen, zen2 | No |
| mumps | MUltifrontal Massively Parallel sparse direct Solver | icelake, x86_64, zen, zen2 | Yes |
| namd | Nanoscale Molecular Dynamics | zen, zen2 | Yes |
| nccl | NVIDIA Collective Communication Library | icelake, zen2 | Yes |
| ncl | NCAR Command Language | icelake, x86_64, zen2 | Yes |
| nco | Toolkits for manipulating data in NetCDF formats | icelake, x86_64, zen, zen2 | Yes |
| ncview | Viewer for NetCDF files | zen2 | Yes |
| netcdf | C Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-cxx | C++ Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netcdf-fortran | Fortran Libraries for NetCDF data format | icelake, x86_64, zen, zen2 | Yes |
| netlogo | NetLogo is a programming language and an IDE for agent-based modeling. | x86_64 | No |
| nvhpc | Nvidia HPC SDK Compiler suite | x86_64 | No |
| nvmpi | MPI libraries from the Nvidia HPC SDK Compiler suite | x86_64 | No |
| oneapi | Intel OneAPI new compilers | x86_64 | No |
| onetep | ONETEP (Order-N Electronic Total Energy Package) | zen2 | No |
| openblas | Optimized BLAS libraries | icelake, x86_64, zen, zen2 | No |
| opencv | Open-source Computer Vision Library | zen2 | No |
| openfoam | Opensource C++ CFD toolbox | zen, zen2 | Yes |
| openjdk | Open-source implementation of Java | icelake, x86_64, zen, zen2 | No |
| openmm | A high-performance toolkit for molecular simulation. | icelake, zen2 | Yes |
| openmpi | OpenMPI implementation of Message Passing Interface | icelake, x86_64, zen, zen2 | Yes |
| openstructure | Open-source computational structural biology framework | zen2 | No |
| orca | Ab initio quantum chemistry package | x86_64 | No |
| osu-micro-benchmarks | Microbenchmarks for MPI | icelake, x86_64, zen, zen2 | No |
| parallel | GNU parallel tool for executing jobs in parallel | zen2 | No |
| parallel-netcdf | Parallel I/O library for NetCDF file format | icelake, x86_64, zen, zen2 | Yes |
| paraview | data analysis and visualization application | zen, zen2 | No |
| paraview-headless | data analysis and visualization application (headless version) | zen2 | No |
| pari-gp | computer algebra system for computations in number theory | zen2 | Yes |
| parmetis | Parallel Metis | icelake, x86_64, zen, zen2 | Yes |
| parmgridgen | Multilevel Serial & Parallel Coarse Grid Construction Library | icelake, x86_64, zen, zen2 | Yes |
| perl | Perl scripting language | icelake, x86_64, zen, zen2 | No |
| petsc | PETSc (Portable, Extensible Toolkit for Scientific Computation) | zen2 | No |
| pexsi | electronic structure calculation based on Kohn-Sham density functional theory | icelake, x86_64, zen, zen2 | Yes |
| pfft | Parallel Fast Fourier Transform library | icelake, x86_64, zen, zen2 | Yes |
| pgplot | PGPLOT Graphics Subroutine Library | icelake, x86_64, zen2 | No |
| picard | Command line tools for manipulation sequencing data | zen2 | No |
| plink | genome association analysis toolset | zen2 | No |
| plplot | Cross-platform software for creating scientific plots | zen2 | No |
| plumed | plugin for molecular dynamics | icelake, zen, zen2 | Yes |
| popoolation2 | PoPoolation2 allows to compare allele frequencies for single-nucleotide polymorphisms. | zen2 | No |
| povray | Persistence of Vision Ray tracer | icelake, x86_64, zen, zen2 | No |
| proj | Generic Coordinate Transformation package | icelake, zen, zen2 | No |
| pyray | Framework for scaling AI and Python applications | zen2 | No |
| python | Python scripting language | icelake, x86_64, zen2 | Yes |
| pytorch | Open-source machine learning library | icelake, zen2 | Yes |
| qmd-progress | PROGRESS: Parallel, Rapid O(N) and Graph-based Recursive Electronic Structure Solver | zen | Yes |
| qt | cross-platform application development framework for GUIs | icelake, x86_64, zen, zen2 | No |
| quantum-espresso | Electronic-structure calculations at the nanoscale. | zen2 | Yes |
| r | R statistical computing scripting language | icelake, x86_64, zen2 | No |
| rclone | command line tool for managing cloud storage | zen2 | No |
| rdma-core | RDMA Core userspace libraries and drivers | zen2 | No |
| rocky | ANSYS Rocky DEM | x86_64 | No |
| rust | Rust programming language | icelake, x86_64, zen, zen2 | No |
| samtools | SAM (Sequence/Alignment Mapping) Tools | icelake, x86_64, zen, zen2 | No |
| scalapack | Scalable linear algebra package | icelake, x86_64, zen, zen2 | Yes |
| scons | SCons open-source software construction tool | icelake, x86_64, zen2 | No |
| scorep | suite for profiling, event tracing, and analysis of HPC applications | zen2 | Yes |
| scotch | Package for graph and mesh partitioning, graph clustering, and sparse matrix ordering | icelake, x86_64, zen, zen2 | Yes |
| shapeit4 | estimation of haplotypes for sequencing data. | icelake, x86_64, zen2 | Yes |
| silo | libraries for reading/writing a variety of scientific data | icelake, x86_64, zen, zen2 | Yes |
| singularity | Singularity container utilities | x86_64 | No |
| sirius | domain specific library for electronic structure calculations | zen | No |
| slepc | Scalable Library for Eigenvalue Problem Computations | zen2 | No |
| smokeview | Visualization tool for FDS and CFAST output | x86_64 | No |
| snpeff | Genomic variant annotation and functional effect prediction | icelake, x86_64, zen2 | No |
| sox | Sound eXchange, the Swiss Army knife of sound processing | icelake, x86_64, zen2 | No |
| spfft | 3D FFT library for sparse frequency domain data | icelake, x86_64, zen, zen2 | No |
| spglib | C library for finding and handling crystal symmetries | icelake, x86_64, zen, zen2 | No |
| sqlite | Library for lossy compression of multidimensional arrays | icelake, x86_64, zen, zen2 | No |
| stacks | pipeline for building loci from short-read sequences | zen2 | No |
| star-ccm | CFD based simulation software from Siemens | x86_64 | No |
| suite-sparse | Suite of Sparse Matrix algorithms | icelake, x86_64, zen, zen2 | No |
| superlu | Sparse Linear system solver (sequential) | icelake, x86_64, zen, zen2 | No |
| superlu-dist | Sparse Linear system solver (distributed mem/MPI) | icelake, x86_64, zen, zen2 | No |
| superlu-mt | Sparse Linear system solver (multithreaded) | icelake, x86_64, zen, zen2 | No |
| swig | compiler to interface C/C++ libraries to Perl, Python, etc | icelake, x86_64, zen, zen2 | No |
| sz | Error-bounded Lossy Compressor for HPC Data | icelake, x86_64, zen, zen2 | Yes |
| tecplot360 | CFD visualization software | x86_64 | No |
| tensorflow | Open-source software library for machine intelligence | icelake, zen, zen2 | Yes |
| toolchain/aocc | AOCC Compiler Toolchains | x86_64 | No |
| toolchain/gcc | GNU Compiler Toolchains | x86_64 | No |
| toolchain/intel | Intel Classic Compiler Toolchains | x86_64 | No |
| tophat | Spliced read mapper for RNA-Seq | x86_64 | No |
| trilinos | Solvers collection including linear, non-linear, optimization, and transient solvers | zen2 | No |
| udunits | The UDUNITS package supports units of physical quantities. | icelake, x86_64, zen, zen2 | No |
| ufs-weather-model | Unified Forecast System Weather Model | zen2 | Yes |
| umd-examples/hello-umd | Simple Hello world binary | icelake, x86_64, zen, zen2 | Yes |
| us3d | Aeordynamic and Aerothermodynamic Simulations Software | skylake_avx512 | No |
| usearch | Ultra-fast sequence analysis tool | x86_64 | No |
| vasp | VASP: Vienna Ab-initio Simulation Package | zen2 | No |
| vcftools | VCFtools is a set of utilities for working with VCF files | zen2 | No |
| virtualgl | Toolkit to allow remote display to run OpenGL applications with full hardware acceleration | icelake, x86_64, zen, zen2 | No |
| visit | interactive, scalable, visualization, animation and analysis tool | zen2 | Yes |
| vmd | Visual Molecular Dynamics | x86_64 | No |
| voropp | library for 3D computations of the Voronoi tessellation | icelake, x86_64, zen, zen2 | No |
| vtk | 3D computer graphics, image processing and visualization library | icelake, zen, zen2 | Yes |
| wannier90 | tool to calculate maximally-localized Wannier functions | icelake, x86_64, zen, zen2 | Yes |
| xerces-c | validating XML parser in C++ | icelake, x86_64, zen, zen2 | No |
| xssp | Secondary structure assignments for entries in the Protein Data Bank | zen | No |
| xz | Lossless compression utility and library | icelake, x86_64, zen, zen2 | No |
| zfp | Library for lossy compression of multidimensional arrays | icelake, x86_64, zen, zen2 | No |
| zlib | General purpose, patent-free compression ibrary | icelake, x86_64, zen, zen2 | No |
| zoltan | Toolkit for parallel combinatorial algorithms | icelake, x86_64, zen, zen2 | Yes |
| zstd | Fast, lossless compression algorithm | icelake, x86_64, zen, zen2 | No |