SeaWulf Software

SeaWulf Software

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. 

module avail <query>
module load <software_name>
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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

Intel MPI

A high-performance, production-quality MPI implementation for Intel architectures.

MVAPICH

A high-performance MPI implementation based on the Open MPI and MPICH frameworks.

OpenMPI

An open-source MPI implementation that supports a wide range of communication protocols.

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.

Programming Languages

Python

Python is a high-level programming language widely used for general-purpose programming and AI applications.

R

R is a programming language and environment for statistical computing and graphics.