Non-Comprehensive List of Software on the SeaWulf Cluster
The SeaWulf High Performance Computing cluster provides a wide range of software to support computational research across multiple disciplines.
Note: Software on SeaWulf is managed using the module system.
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Compilers
GCC
A popular open-source compiler for C, C++, and other languages.
Intel oneAPI
A unified programming model that provides support for Intel CPUs, GPUs, and FPGAs.
AOCC
AMD's Optimizing C Compiler, designed for high performance on AMD architectures.
NVHPC
NVIDIA's HPC compiler suite optimized for performance on NVIDIA GPUs.
LLVM
A collection of modular and reusable compiler and toolchain technologies.
MPI Implementations
Bioinformatics
Bowtie2
A fast and memory-efficient tool for aligning sequencing reads to long reference sequences.
bioconvert
A tool for converting bioinformatics data between various formats.
diffexp
A tool for differential expression analysis in bioinformatics datasets.
genome_assembly
Software tools for assembling genomes from short sequencing reads.
genome_annotation
Tools for annotating genomes with genes, regulatory elements, and other features.
GWAS
Tools for performing Genome-Wide Association Studies (GWAS) to identify genetic variants.
hts
A set of tools for working with high-throughput sequencing (HTS) data.
metagenomics
Tools for analyzing metagenomic data to study microbial communities.
popgen
Tools for population genetics analysis, including allele frequency and genetic diversity.
phylo
Software for constructing and analyzing phylogenetic trees.
singlecell
Tools for analyzing single-cell RNA-seq data and other single-cell omics datasets.
structural-variant
Tools for detecting and analyzing structural variations in genomes.
QIIME
QIIME is a powerful software package for analyzing and visualizing microbiome data.
Neuroimaging
Freesurfer
A suite of software tools for the analysis and visualization of structural and functional neuroimaging data.
FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI data.
Molecular Dynamics and Computational Chemistry
NAMD
A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
GROMACS
GROMACS is a versatile and efficient package for performing molecular dynamics simulations.
LAMMPS
LAMMPS is a molecular dynamics simulation software widely used for materials science and molecular simulation.
AmberMD
Amber is a suite of biomolecular simulation programs, focusing on molecular dynamics and free energy calculations.
VASP
VASP is a software package for atomic scale materials modeling, primarily used for quantum mechanical simulations.
Mathematics and Statistics
MATLAB
MATLAB is a high-performance language for technical computing, used in areas such as data analysis and algorithm development.
Mathematica
Mathematica is a computational software system used in scientific, engineering, mathematical, and computing fields.
MPFR
MPFR is a C library for multiple-precision floating-point computation with correct rounding.
PETSc
PETSc is a suite of data structures and routines for the scalable solution of scientific problems modeled by partial differential equations.
OpenBLAS
OpenBLAS is an open-source implementation of the BLAS library for linear algebra operations.
Intel MKL
Intel MKL (Math Kernel Library) is a set of highly optimized routines for scientific, engineering, and financial applications.
AOCL
AMD AOCL (Optimizing CPU Libraries) is a collection of optimized math libraries for scientific and engineering workloads on AMD CPUs.
Machine Learning and AI
TensorFlow
TensorFlow is an open-source machine learning library developed by Google for deep learning and AI applications.
PyTorch
PyTorch is an open-source machine learning library based on the Torch library, used for applications such as computer vision and NLP.
Scikit-learn
Scikit-learn is a Python module for machine learning built on top of NumPy, SciPy, and matplotlib.
Ollama
Ollama is an AI tool for building and deploying natural language processing models.
Visualization and Analysis
ParaView
ParaView is an open-source data analysis and visualization application for scientific data.
VMD
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems.
Matplotlib
Matplotlib is a Python plotting library for creating static, animated, and interactive visualizations.
Jupyter
Jupyter is a web-based interactive computing environment that supports various programming languages, especially Python.
Data Processing
HDF5
HDF5 is a file format and set of tools for managing large and complex data sets.
NetCDF
NetCDF is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented data.
FFTW3
FFTW3 is a C library for computing discrete Fourier transforms (DFTs) in one or more dimensions.
Development
Anaconda
Anaconda is a free and open-source distribution of Python and R programming languages for scientific computing.
Git
Git is a free and open-source version control system for tracking changes in source code during software development.
CMake
CMake is an open-source build system generator for managing the build process of software projects.
Singularity
Singularity is an open-source container platform designed to execute applications in isolated environments.
GNU Parallel
GNU Parallel is a shell tool for executing jobs in parallel using one or more computers.
Monitoring and Debugging
Valgrind
Valgrind is an instrumentation framework for building dynamic analysis tools, often used for debugging and profiling.
Linaro Forge
Linaro Forge is a web-based platform providing tools for optimizing and debugging ARM-based systems.
htop
htop is an interactive process viewer for Unix systems, providing a more user-friendly interface than the traditional top command.