openblasOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
tensorflowOpen source software library for numerical computation
theanoOptimizing compiler for evaluating mathematical expressions on CPUs and GPUs
caffe-bvlcFast open framework for deep learning (BVLC upstream)
caffe-ibmFast open framework for deep learning (BVLC upstream) with optimizations made by IBM
digitsDeep Learning GPU Training System
caffe-nvFast open framework for deep learning (NVIDIA's fork)
anaconda2Anaconda 2 python distribution
cudaNVIDIA CUDA Toolkit (C, C++, cuda-gdb, cuda-memcheck, gpu accel)
chainerA flexible framework of neural networks for deep learning
gccGNU Compiler Collection (C, C++, Fortran), GNU Compiler Collection (C, C++, Fortran, Go)
mpichOSU MPI
spectrummpiIBM spectrum MPI for power8
torchTorch 7 | Scientific computing framework for LuaJIT
ncclNVIDIA Collectives Communication Library (NCCL) Runtime
jdkJava Development Kit
geosGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS).
pigzParallel implimentation of gzip
nvbioGPU-accelerated C++ framework for High-Throughput Sequence Analysis
ls-dynaLS-DYNA general-purpose finite element simulation software.
mysqlMySQL: a very fast and reliable SQL database server
libjpeg-turbolibjpeg-turbo is a JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems.
ansysEngineering simulation software
iperfiPerf - The ultimate speed test tool for TCP, UDP and SCTP
pgiPGI Compilers (C, C++, Fortran)
hisat2HiSat2 Fast and Sensitive Read Alignment
trinityrnaseqRNA-Seq De novo Assembly Using Trinity
cufflinksTranscriptome assembly and differential expression analysis for RNA-Seq.
seqtkToolkit for processing sequences in FASTA/Q formats
hdf5Tool suite for managing very large and complex data collections
cddlibCDD library for fundamental polyhedral computations
CLAPACKLAPACK linear algebra routines in C
openmpiOpen MPI
boost-mpiBOOST template libraries
glmOpenGL Mathematics
p7zipp7zip is a quick port of 7z
udunitsUDUNITS units package
mvapich2OSU MPI
parallel-netcdfParallel Network Common Data Form
p4estParallel adaptive mesh refinement on forests of octrees
AnacondaAnaconda python distribution
ensightCSM and CFD Post processing
eigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
apbs-staticAdaptive Poisson Boltzmann Solver
projRPROJ.4 (or proj) is a library for performing conversions between cartographic projections.
intelIntel Compilers (C, C++, Fortran)
netcdfNetwork Common Data Form
diamondSequence Alignment Tool
gslGNU Scientific Library
flintFast Library for Number Theory
discovarnew genome assembler
matplotlibmatplotlib is a library for making 2D plots of arrays in Python.
noseNose is open-source testing software for python.
numpyNumPy is the fundamental package for scientific computing in Python
mklIntel MKL Library
pycudaPython wrapper for Nvidia CUDA
RR For Statistical Computing
gmap-gsnapGMAP/GSNAP 2017-01-10
metisMultilevel Partitioning Algorithms
scipySciPy is open-source software for mathematics, science, and engineering.
singularComputer algebra system for polynomial computations
boostBOOST template libraries
fftwFastest Fourier Transform in the West
scalapackScalable Linear Algebra PACKage
hplHigh-Performance Linpack
parmetisMultilevel Partitioning Algorithms
phdf5Tool suite for managing very large and complex data collections
mpiblastBLAST sequence alignment
mpe2MPI Parallel Environment
lammpsLarge-scale Atomic/Molecular Massively Parallel Simulator
trilinosObject-oriented software framework for multiphysics applications
R-gpuGPU packages for R
abinitABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
R-parallelParallel packages for R
espressonanoscale material modeling
vaspThe Vienna Ab initio Simulation Package
mvapich2-testOSU MPI
valgrindValgrind Tool Suite
netcdf-cNetwork Common Data Form
openmpi-testOpen MPI
discovardenovonew genome assembler
occaOpen Concurrent Compute Abstraction
sparsehashAn extremely memory-efficient hash_map implementation
allpathslgAssembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
impiIntel MPI
octaveGNU Octave
vtuneIntel VTune Performance Profiler
sconsOpen source software construction / build tool
zlibZlib compression software
starccm+Engineering simulation software
cmakeCross Platform Makefile Generator
parallelGNU Parallel
cudnncuDNN | GPU-accelerated library for deep neural networks
tecplotScientific Visualization
gnuplotGNU Plot
stataStatistical software
ifs_psmPSM library from Intel Omni-Path Fabric Host Software (IFS) 10.6, PSM library from Intel Omni-Path Fabric Host Software (IFS) 10.5
patranFEA Modeling Solution
fastx_toolkitFastX toolkit for working with fastxx files
igvThe Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
miniagenome assembler
FLASHFLASh - Fast Length Adjustment of Short reads
CGALThe Computational Geometry Algorithms Library is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry.
atlasATLAS Tuned Linear Algebra (includes LAPACK)
picardPicard: A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats
spadesgenome assembler
autodocksuiteAutomated molecule docking tool
trimmomaticTrimmomatic: A flexible read trimming tool for Illumina NGS data
extraeInstrumentation framework to generate execution traces of the most used parallel runtimes.
ea-utilsEA-utils are command line tools for processing biological sequencing data.
RSEMRSEM is a RNASeq utility
miraMIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects
lsoptLS-OPT is a standalone package with an interface to LS-DYNA.