Looking for desktop software? This catalog covers the module system on the HPC clusters. DoIT licenses additional programs for faculty and staff — including SAS and SPSS — for on-campus use, off-campus download, and through the Virtual SINC Site. See the DoIT software catalog.
Category
Availability shown is for SeaWulf. Module availability and versions on NVwulf and ClinWulf vary — run module avail <name> on your cluster, or ask HPC support.
| Software | Category | Available on |
|---|---|---|
| GCC A popular open-source compiler for C, C++, and other languages. | Compilers | SeaWulf |
| Intel oneAPI A unified programming model with support for Intel CPUs, GPUs, and FPGAs. | Compilers | SeaWulf |
| AOCC AMD's Optimizing C Compiler, designed for high performance on AMD architectures. | Compilers | SeaWulf |
| NVHPC NVIDIA's HPC compiler suite optimized for performance on NVIDIA GPUs. | Compilers | SeaWulf |
| LLVM A collection of modular and reusable compiler and toolchain technologies. | Compilers | SeaWulf |
| Intel MPI A high-performance, production-quality MPI implementation for Intel architectures. | MPI implementations | SeaWulf |
| MVAPICH A high-performance MPI implementation for modern interconnects. | MPI implementations | SeaWulf |
| OpenMPI An open-source MPI implementation that supports a wide range of protocols. | MPI implementations | SeaWulf |
| mpi4py A Python interface for MPI-based parallel computing. | MPI implementations | SeaWulf |
| Bowtie2 A fast, memory-efficient tool for aligning sequencing reads to long reference sequences. | Bioinformatics | SeaWulf |
| bioconvert A tool for converting bioinformatics data between various formats. | Bioinformatics | SeaWulf |
| diffexp A tool for differential expression analysis in bioinformatics datasets. | Bioinformatics | SeaWulf |
| genome_assembly Software tools for assembling genomes from short sequencing reads. | Bioinformatics | SeaWulf |
| genome_annotation Tools for annotating genomes with genes, regulatory elements, and other features. | Bioinformatics | SeaWulf |
| GWAS Tools for performing Genome-Wide Association Studies to identify genetic variants. | Bioinformatics | SeaWulf |
| hts A set of tools for working with high-throughput sequencing data. | Bioinformatics | SeaWulf |
| metagenomics Tools for analyzing metagenomic data to study microbial communities. | Bioinformatics | SeaWulf |
| popgen Tools for population genetics analysis, including allele frequency and diversity. | Bioinformatics | SeaWulf |
| phylo Software for constructing and analyzing phylogenetic trees. | Bioinformatics | SeaWulf |
| singlecell Tools for analyzing single-cell RNA-seq and other single-cell omics datasets. | Bioinformatics | SeaWulf |
| structural-variant Tools for detecting and analyzing structural variations in genomes. | Bioinformatics | SeaWulf |
| QIIME A powerful software package for analyzing and visualizing microbiome data. | Bioinformatics | SeaWulf |
| Freesurfer A suite for the analysis and visualization of structural and functional neuroimaging data. | Neuroimaging | SeaWulf |
| FSL A comprehensive library of analysis tools for FMRI, MRI, and DTI data. | Neuroimaging | SeaWulf |
| NAMD A parallel molecular dynamics code for high-performance simulation of large biomolecular systems. | Molecular dynamics & chemistry | SeaWulf |
| GROMACS A versatile, efficient package for performing molecular dynamics simulations. | Molecular dynamics & chemistry | SeaWulf |
| LAMMPS A molecular dynamics simulator widely used for materials science and molecular simulation. | Molecular dynamics & chemistry | SeaWulf |
| AmberMD A suite of biomolecular simulation programs focusing on molecular dynamics and free energy. | Molecular dynamics & chemistry | SeaWulf |
| VASP A software package for atomic-scale materials modeling using quantum mechanical simulations. | Molecular dynamics & chemistry | SeaWulf |
| MATLAB A high-performance language for technical computing, data analysis, and algorithm development. | Mathematics & statistics | SeaWulf |
| Mathematica A computational software system used across scientific, engineering, and mathematical fields. | Mathematics & statistics | SeaWulf |
| MPFR A C library for multiple-precision floating-point computation with correct rounding. | Mathematics & statistics | SeaWulf |
| PETSc A suite of data structures and routines for scalable solution of PDE-modeled problems. | Mathematics & statistics | SeaWulf |
| OpenBLAS An open-source implementation of the BLAS library for linear algebra operations. | Mathematics & statistics | SeaWulf |
| Intel MKL A set of highly optimized routines for scientific, engineering, and financial applications. | Mathematics & statistics | SeaWulf |
| AOCL AMD's collection of optimized math libraries for scientific workloads on AMD CPUs. | Mathematics & statistics | SeaWulf |
| TensorFlow An open-source machine learning library for deep learning and AI applications. | Machine learning & AI | SeaWulf |
| PyTorch An open-source machine learning framework used for computer vision and NLP. | Machine learning & AI | SeaWulf |
| Scikit-learn A Python module for machine learning built on NumPy, SciPy, and matplotlib. | Machine learning & AI | SeaWulf |
| Ollama An AI tool for building and deploying natural language processing models. | Machine learning & AI | SeaWulf |
| ParaView An open-source data analysis and visualization application for scientific data. | Visualization & analysis | SeaWulf |
| VMD A molecular visualization program for displaying and analyzing large biomolecular systems. | Visualization & analysis | SeaWulf |
| Matplotlib A Python plotting library for static, animated, and interactive visualizations. | Visualization & analysis | SeaWulf |
| Jupyter A web-based interactive computing environment supporting many languages, especially Python. | Visualization & analysis | SeaWulf |
| HDF5 A file format and set of tools for managing large and complex data sets. | Data processing | SeaWulf |
| NetCDF Libraries and machine-independent formats for array-oriented scientific data. | Data processing | SeaWulf |
| FFTW3 A C library for computing discrete Fourier transforms in one or more dimensions. | Data processing | SeaWulf |
| Anaconda A free, open-source distribution of Python and R for scientific computing. | Development | SeaWulf |
| Git A free, open-source version control system for tracking changes in source code. | Development | SeaWulf |
| CMake An open-source build system generator for managing the build process of projects. | Development | SeaWulf |
| Singularity An open-source container platform for executing applications in isolated environments. | Development | SeaWulf |
| GNU Parallel A shell tool for executing jobs in parallel using one or more computers. | Development | SeaWulf |
| Valgrind An instrumentation framework for building dynamic analysis tools for debugging and profiling. | Monitoring & debugging | SeaWulf |
| Linaro Forge A platform providing tools for optimizing and debugging HPC and ARM-based systems. | Monitoring & debugging | SeaWulf |
| htop An interactive process viewer for Unix systems with a user-friendly interface. | Monitoring & debugging | SeaWulf |
| Python A high-level programming language widely used for general-purpose and AI applications. | Programming languages | SeaWulf |
| R A programming language and environment for statistical computing and graphics. | Programming languages | SeaWulf |
Live catalog: rci.stonybrook.edu/HPC/software. In the Drupal build each package is a node with a category taxonomy term and a per-cluster availability field; this table is a View.