github container size built at description
GITHUB abi-dumper 76MB 2021-11-17 20:52:00 +0000 ABI Dumper is a tool to dump ABI of an ELF object containing DWARF debug info.
GITHUB abyss 80MB 2021-11-17 15:49:37 +0000 ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.
GITHUB accumulo 273MB 2021-08-26 08:06:29 +0000 Apache Accumulo is a sorted, distributed key/value store that provides robust, scalable data storage and retrieval.
GITHUB addrwatch 31MB 2021-05-26 02:58:32 +0000 A tool similar to arpwatch for IPv4/IPv6 and ethernet address pairing monitoring.
GITHUB adios 61MB 2021-11-17 15:48:48 +0000 The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
GITHUB adios2 61MB 2021-11-17 15:49:08 +0000 The Adaptable Input Output System version 2, developed in the Exascale Computing Program
GITHUB admixtools 58MB 2021-10-29 14:57:04 +0000 The ADMIXTOOLS package implements 5 methods described in Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper..
GITHUB advancecomp 27MB 2021-10-29 14:57:11 +0000 AdvanceCOMP contains recompression utilities for your .zip archives, .png images, .mng video clips and .gz files.
GITHUB alan 26MB 2021-09-15 23:27:31 +0000 Alignment viewer for linux terminal
GITHUB alps 260MB 2021-11-17 15:55:54 +0000 Algorithms for Physics Simulations Tags: Condensed Matter Physics, Computational Physics
GITHUB amrex 54MB 2021-11-02 14:51:01 +0000 AMReX is a publicly available software framework designed for building massively parallel block- structured adaptive mesh refinement (AMR) applications.
GITHUB angsd 281MB 2021-11-17 15:49:41 +0000 Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
GITHUB ant 220MB 2021-09-15 23:29:01 +0000 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other
GITHUB ants 563MB 2021-06-18 02:03:07 +0000 ANTs extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.
GITHUB apr-util 36MB 2021-10-19 07:13:41 +0000 Apache Portable Runtime Utility
GITHUB apr 30MB 2021-08-25 05:20:13 +0000 Apache portable runtime.
GITHUB arborx 53MB 2021-11-17 15:48:17 +0000 ArborX is a performance-portable library for geometric search
GITHUB argobots 27MB 2021-10-29 14:56:04 +0000 Argobots, which was developed as a part of the Argo project, is a lightweight runtime system that supports integrated computation and data movement with massive concurrency. It will directly leverage the lowest-level constructs in the hardware and OS: lightweight notification mechanisms, data movement engines, memory mapping, and data placement strategies. It consists of an execution model and a memory model.
GITHUB aria2 43MB 2021-10-19 07:15:40 +0000 An ultra fast download utility
GITHUB ascent 114MB 2021-11-04 16:02:30 +0000 Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.
GITHUB astral 220MB 2021-10-19 07:14:55 +0000 ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.
GITHUB autodock-vina 45MB 2021-11-17 15:48:13 +0000 AutoDock Vina is an open-source program for doing molecular docking
GITHUB bart 154MB 2021-09-15 23:36:58 +0000 BART: Toolbox for Computational Magnetic Resonance Imaging
GITHUB bbmap 231MB 2021-08-27 17:29:04 +0000 Short read aligner for DNA and RNA-seq data.
GITHUB bcftools 155MB 2021-11-18 19:10:53 +0000 BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
GITHUB beast2 227MB 2021-10-19 07:13:53 +0000 BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
GITHUB bedops 30MB 2021-10-04 15:30:18 +0000 BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
GITHUB bedtools2 28MB 2021-11-17 15:47:20 +0000 Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
GITHUB benchmark 27MB 2021-11-17 15:47:33 +0000 A microbenchmark support library
GITHUB binutils 54MB 2021-10-29 14:57:32 +0000 GNU binutils, which contain the linker, assembler, objdump and others
GITHUB bismark 110MB 2021-11-18 19:08:52 +0000 A tool to map bisulfite converted sequence reads and determine cytosine methylation states
GITHUB bolt 27MB 2021-10-29 14:57:27 +0000 BOLT targets a high-performing OpenMP implementation, especially specialized for fine-grain parallelism. Unlike other OpenMP implementations, BOLT utilizes a lightweight threading model for its underlying threading mechanism. It currently adopts Argobots, a new holistic, low-level threading and tasking runtime, in order to overcome shortcomings of conventional OS-level threads. The current BOLT implementation is based on the OpenMP runtime in LLVM, and thus it can be used with LLVM/Clang, Intel OpenMP compiler, and GCC.
GITHUB boost 48MB 2021-11-17 15:48:12 +0000 Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
GITHUB bowtie2 105MB 2021-11-17 15:48:52 +0000 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
GITHUB bracken 102MB 2021-11-17 15:48:55 +0000 Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
GITHUB buildsi-mpich 607MB 2021-05-27 20:49:43 +0000
GITHUB bwa 27MB 2021-09-15 23:32:08 +0000 Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
GITHUB bzip2 26MB 2021-06-23 18:00:01 +0000 bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
GITHUB cabana 53MB 2021-11-17 15:48:25 +0000 The Exascale Co-Design Center for Particle Applications Toolkit
GITHUB caliper 72MB 2021-11-17 15:49:06 +0000 Caliper is a program instrumentation and performance measurement framework. It is designed as a performance analysis toolbox in a library, allowing one to bake performance analysis capabilities directly into applications and activate them at runtime.
GITHUB cantera 127MB 2021-11-17 15:51:08 +0000 Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.
GITHUB cctools 113MB 2021-11-17 15:49:16 +0000 The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.
GITHUB cdo 126MB 2021-11-17 15:55:00 +0000 CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
GITHUB cfitsio 33MB 2021-11-17 15:50:33 +0000 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
GITHUB circos 126MB 2021-10-19 07:24:32 +0000 Circos is a software package for visualizing data and information.
GITHUB clhep 29MB 2021-11-17 15:52:13 +0000 CLHEP is a C++ Class Library for High Energy Physics.
GITHUB clingo-bootstrap 87MB 2021-11-17 15:54:53 +0000 Clingo with some options used for bootstrapping
GITHUB clingo 88MB 2021-11-17 18:25:19 +0000 Clingo: A grounder and solver for logic programs Clingo is part of the Potassco project for Answer Set Programming (ASP). ASP offers a simple and powerful modeling language to describe combinatorial problems as logic programs. The clingo system then takes such a logic program and computes answer sets representing solutions to the given problem.
GITHUB cloc 48MB 2021-10-19 07:20:41 +0000 Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.
GITHUB cmake 54MB 2021-11-17 15:53:00 +0000 A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
GITHUB conduit 71MB 2021-11-02 14:50:46 +0000 Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.
GITHUB corset 27MB 2021-08-26 08:09:09 +0000 Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.
GITHUB cowsay 48MB 2021-10-19 07:21:01 +0000 A program that generates ASCII pictures of a cow with a message.
GITHUB cufflinks 32MB 2021-09-15 23:36:56 +0000 Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
GITHUB curl 31MB 2021-11-17 15:52:27 +0000 cURL is an open source command line tool and library for transferring data with URL syntax
GITHUB dakota 162MB 2021-11-17 15:56:45 +0000 The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods. Dakota contains algorithms for: - optimization with gradient and non gradient-based methods; - uncertainty quantification with sampling, reliability, stochastic - expansion, and epistemic methods; - parameter estimation with nonlinear least squares methods; - sensitivity/variance analysis with design of experiments and - parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.
GITHUB datatransferkit 128MB 2021-10-04 00:31:12 +0000 DataTransferKit is an open-source software library of parallel solution transfer services for multiphysics simulations
GITHUB diamond 29MB 2021-10-26 04:22:29 +0000 DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
GITHUB dyninst 70MB 2021-10-19 07:24:58 +0000 API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.
GITHUB eagle 35MB 2021-11-17 15:52:40 +0000 EAGLE: Explicit Alternative Genome Likelihood Evaluator
GITHUB ed 27MB 2021-06-22 20:01:05 +0000 GNU ed is a line-oriented text editor. It is used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts.
GITHUB elfutils 43MB 2021-11-17 15:52:51 +0000 elfutils is a collection of various binary tools such as eu-objdump, eu-readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.
GITHUB emacs 83MB 2021-11-12 16:02:04 +0000 The Emacs programmable text editor.
GITHUB faodel 75MB 2021-11-17 15:54:58 +0000 Flexible, Asynchronous, Object Data-Exchange Libraries
GITHUB fastqc 249MB 2021-10-19 07:25:26 +0000 A quality control tool for high throughput sequence data.
GITHUB ffmpeg 50MB 2021-10-19 07:23:22 +0000 FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.
GITHUB flit 86MB 2021-11-17 15:55:42 +0000 Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for detecting variability in floating-point code caused by variations in compiler code generation, hardware and execution environments.
GITHUB fraggenescan 66MB 2021-11-12 05:02:26 +0000 FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
GITHUB gasnet 30MB 2021-10-19 07:23:31 +0000 GASNet is a language-independent, networking middleware layer that provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). It has been used to implement parallel programming models and libraries such as UPC, UPC++, Co-Array Fortran, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. ***NOTICE***: The GASNet library built by this Spack package is ONLY intended for unit-testing purposes, and is generally UNSUITABLE FOR PRODUCTION USE. The RECOMMENDED way to build GASNet is as an embedded library as configured by the higher-level client runtime package (UPC++, Legion, etc), including system-specific configuration.
GITHUB gatk 643MB 2021-11-17 15:56:24 +0000 Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data
GITHUB gawk 47MB 2021-10-29 14:57:55 +0000 If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time-consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
GITHUB gcc 142MB 2021-11-12 16:04:23 +0000 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.
GITHUB gdal 56MB 2021-11-17 15:56:04 +0000 GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.
GITHUB geant4 1139MB 2021-11-17 16:04:27 +0000 Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
GITHUB geos 28MB 2021-11-17 15:54:19 +0000 GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.
GITHUB ginkgo 32MB 2021-11-17 15:54:37 +0000 High-performance linear algebra library for manycore systems, with a focus on sparse solution of linear systems.
GITHUB git 300MB 2021-11-17 15:59:18 +0000 Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
GITHUB glpk 27MB 2021-10-29 14:56:24 +0000 The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
GITHUB gmp 27MB 2021-10-29 15:10:19 +0000 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.
GITHUB gnuplot 28MB 2021-10-07 01:40:29 +0000 Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986
GITHUB go 296MB 2021-11-17 16:00:11 +0000 The golang compiler and build environment
GITHUB gotcha 26MB 2021-10-03 23:38:18 +0000 C software library for shared library function wrapping, enables tools to intercept calls into shared libraries
GITHUB graphviz 31MB 2021-11-17 15:59:04 +0000 Graph Visualization Software
GITHUB grass 151MB 2021-11-17 16:00:45 +0000 GRASS GIS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.
GITHUB gromacs 66MB 2021-11-17 15:57:58 +0000 GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.
GITHUB gsl 29MB 2021-10-29 14:59:43 +0000 The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
GITHUB hdf5 85MB 2021-11-17 15:58:06 +0000 .format(version=str(spec.version.up_to(3))) with open("check.c", 'w
GITHUB heaptrack 65MB 2021-11-17 15:57:51 +0000 Heaptrack is a heap memory profiler that traces all memory allocations and annotates these events with stack traces.
GITHUB hisat2 32MB 2021-05-26 06:18:27 +0000 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).
GITHUB hmmer 59MB 2021-10-29 15:02:04 +0000 HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
GITHUB hpctoolkit 382MB 2021-11-17 16:03:45 +0000 HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.
GITHUB hpx 122MB 2021-11-17 16:02:29 +0000 C++ runtime system for parallel and distributed applications.
GITHUB htop 29MB 2021-11-17 15:58:39 +0000 htop is an interactive text-mode process viewer for Unix systems.
GITHUB htslib 34MB 2021-11-17 15:58:35 +0000 C library for high-throughput sequencing data formats.
GITHUB hypre 77MB 2021-10-19 07:32:29 +0000 Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.
GITHUB igraph 34MB 2021-10-19 07:30:24 +0000 igraph is a library for creating and manipulating graphs.
GITHUB intel-mkl 1091MB 2021-11-16 19:48:07 +0000 Intel Math Kernel Library.
GITHUB ior 52MB 2021-11-17 15:59:32 +0000 The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.
GITHUB iq-tree 53MB 2021-11-17 16:00:03 +0000 IQ-TREE Efficient software for phylogenomic inference
GITHUB jags 51MB 2021-11-02 14:50:21 +0000 JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS
GITHUB jasper 28MB 2021-11-17 15:59:20 +0000 Library for manipulating JPEG-2000 images
GITHUB julia 110MB 2021-11-17 16:27:04 +0000 The Julia Language: A fresh approach to technical computing
GITHUB kallisto 86MB 2021-11-17 16:01:04 +0000 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.
GITHUB kraken2 56MB 2021-11-17 16:00:24 +0000 Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
GITHUB lammps 91MB 2021-11-17 16:03:33 +0000 LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See for a detailed discussion.
GITHUB legion 32MB 2021-11-17 16:00:35 +0000 Legion is a data-centric parallel programming system for writing portable high performance programs targeted at distributed heterogeneous architectures. Legion presents abstractions which allow programmers to describe properties of program data (e.g. independence, locality). By making the Legion programming system aware of the structure of program data, it can automate many of the tedious tasks programmers currently face, including correctly extracting task- and data-level parallelism and moving data around complex memory hierarchies. A novel mapping interface provides explicit programmer controlled placement of data in the memory hierarchy and assignment of tasks to processors in a way that is orthogonal to correctness, thereby enabling easy porting and tuning of Legion applications to new architectures.
GITHUB libnrm 51MB 2021-11-17 16:04:16 +0000 Libnrm, the application instrumentation library for the Node Resource Manager(NRM).
GITHUB libpng 27MB 2021-09-15 23:51:39 +0000 libpng is the official PNG reference library.
GITHUB libquo 52MB 2021-10-29 15:03:45 +0000 QUO (as in "status
GITHUB libtiff 27MB 2021-10-20 03:32:00 +0000 LibTIFF - Tag Image File Format (TIFF) Library and Utilities.
GITHUB libunwind 27MB 2021-10-29 15:02:03 +0000 A portable and efficient C programming interface (API) to determine the call-chain of a program.
GITHUB libxpm 46MB 2021-08-27 18:11:47 +0000 libXpm - X Pixmap (XPM) image file format library.
GITHUB llvm 1961MB 2021-11-18 19:51:31 +0000 homepage = "
GITHUB lmod 45MB 2021-11-17 19:44:51 +0000 homepage = '
GITHUB loki 27MB 2021-10-03 22:30:40 +0000 Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.
GITHUB lp-solve 27MB 2021-05-26 06:30:38 +0000 lp_solve is a Mixed Integer Linear Programming (MILP) solver.
GITHUB mafft 34MB 2021-09-15 23:55:17 +0000 MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.
GITHUB meme 138MB 2021-11-17 16:06:28 +0000 The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
GITHUB mercurial 94MB 2021-11-17 16:03:12 +0000 Mercurial is a free, distributed source control management tool.
GITHUB mercury 49MB 2021-11-17 16:03:22 +0000 Mercury is a C library for implementing RPC, optimized for HPC
GITHUB metall 48MB 2021-11-17 16:03:12 +0000 A Persistent Memory Allocator For Data-Centric Analytics
GITHUB mfem 87MB 2021-11-03 15:46:05 +0000 Free, lightweight, scalable C++ library for finite element methods.
GITHUB migrate 27MB 2021-10-03 22:41:33 +0000 Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes
GITHUB mono 146MB 2021-11-17 16:14:43 +0000 Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
GITHUB mothur 73MB 2021-11-17 16:04:27 +0000 This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
GITHUB mpc 30MB 2021-10-29 15:04:25 +0000 Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.
GITHUB mpfr 30MB 2021-10-29 15:05:45 +0000 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
GITHUB mpich-debug 594MB 2021-05-26 00:02:27 +0000
GITHUB mpich 49MB 2021-11-17 16:04:07 +0000 MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
GITHUB mummer 177MB 2021-10-19 07:46:32 +0000 MUMmer is a system for rapidly aligning entire genomes.
GITHUB muscle 27MB 2021-09-15 23:57:22 +0000 MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.
GITHUB nco 88MB 2021-10-29 15:11:18 +0000 The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats
GITHUB ninja 27MB 2021-11-17 16:04:12 +0000 Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.
GITHUB node-js 56MB 2021-11-17 16:05:58 +0000 Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine.
GITHUB octave 74MB 2021-11-18 19:09:28 +0000 GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
GITHUB omega-h 110MB 2021-11-05 15:12:39 +0000 Omega_h is a C++11 library providing data structures and algorithms for adaptive discretizations. Its specialty is anisotropic triangle and tetrahedral mesh adaptation. It runs efficiently on most modern HPC hardware including GPUs.
GITHUB openbabel 198MB 2021-11-18 17:04:01 +0000 Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
GITHUB opencv 30MB 2021-11-17 16:05:08 +0000 OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
GITHUB openjdk 218MB 2021-10-19 07:41:35 +0000 The free and opensource java implementation
GITHUB openmpi 51MB 2021-11-12 05:03:47 +0000 An open source Message Passing Interface implementation. The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
GITHUB pandaseq 28MB 2021-10-29 15:05:39 +0000 PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
GITHUB papi 35MB 2021-10-19 07:41:18 +0000 PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunities across the hardware and software stack.
GITHUB papyrus 52MB 2021-10-19 07:44:02 +0000 Parallel Aggregate Persistent Storage
GITHUB parallel-netcdf 54MB 2021-10-29 15:07:54 +0000 PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5.
GITHUB pcre 28MB 2021-09-16 00:00:15 +0000 The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.
GITHUB pdt 81MB 2021-10-19 07:43:10 +0000 Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
GITHUB perl 47MB 2021-10-19 07:44:19 +0000 Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.
GITHUB petsc 136MB 2021-11-17 16:09:18 +0000 PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
GITHUB phist 77MB 2021-10-19 07:46:53 +0000 The Pipelined, Hybrid-parallel Iterative Solver Toolkit provides implementations of and interfaces to block iterative solvers for sparse linear and eigenvalue problems. In contrast to other libraries we support multiple backends (e.g. Trilinos, PETSc and our own optimized kernels), and interfaces in multiple languages such as C, C++, Fortran 2003 and Python. PHIST has a clear focus on portability and hardware performance: in particular support row-major storage of block vectors and using GPUs (via the ghost library or Trilinos/Tpetra).
GITHUB picard 234MB 2021-11-12 15:57:40 +0000 Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
GITHUB plasma 52MB 2021-10-19 07:45:51 +0000 Parallel Linear Algebra Software for Multicore Architectures, PLASMA is a software package for solving problems in dense linear algebra using multicore processors and Xeon Phi coprocessors. PLASMA provides implementations of state-of-the-art algorithms using cutting-edge task scheduling techniques. PLASMA currently offers a collection of routines for solving linear systems of equations, least squares problems, eigenvalue problems, and singular value problems.
GITHUB plink 30MB 2021-05-26 06:54:09 +0000 PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
GITHUB poppler 77MB 2021-11-17 16:08:42 +0000 Poppler is a PDF rendering library based on the xpdf-3.0 code base.
GITHUB povray 1145MB 2021-08-28 02:05:56 +0000 The Persistence of Vision Raytracer creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file. Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.
GITHUB precice 161MB 2021-11-17 16:12:09 +0000 preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation.
GITHUB prodigal 27MB 2021-05-26 06:56:08 +0000 Fast, reliable protein-coding gene prediction for prokaryotic genomes.
GITHUB proj 42MB 2021-11-17 16:07:32 +0000 PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations.
GITHUB protobuf 30MB 2021-11-17 16:07:31 +0000 Google's data interchange format.
GITHUB psi4 185MB 2021-07-21 00:16:41 +0000 Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.
GITHUB pumi 76MB 2021-11-17 16:09:42 +0000 SCOREC RPI's Parallel Unstructured Mesh Infrastructure (PUMI). An efficient distributed mesh data structure and methods to support parallel adaptive analysis including general mesh-based operations, such as mesh entity creation/deletion, adjacency and geometric classification, iterators, arbitrary (field) data attachable to mesh entities, efficient communication involving entities duplicated across multiple tasks, migration of mesh entities between tasks, and dynamic load balancing.
GITHUB py-libensemble 118MB 2021-11-17 16:12:04 +0000 Library for managing ensemble-like collections of computations.
GITHUB py-petsc4py 195MB 2021-11-17 16:14:02 +0000 This package provides Python bindings for the PETSc package.
GITHUB py-scipy 144MB 2021-11-17 16:12:12 +0000 SciPy (pronounced "Sigh
GITHUB python 84MB 2021-11-17 16:09:15 +0000 The Python programming language.
GITHUB qhull 29MB 2021-11-17 16:08:11 +0000 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.
GITHUB r-seqlogo 273MB 2021-05-26 07:47:14 +0000 Sequence logos for DNA sequence alignments seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).
GITHUB r 273MB 2021-06-23 19:06:56 +0000 SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes
GITHUB raja 65MB 2021-10-19 07:50:38 +0000 RAJA Parallel Framework.
GITHUB raxml 55MB 2021-09-17 06:35:52 +0000 RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
GITHUB rclone 46MB 2021-11-17 16:11:57 +0000 Rclone is a command line program to sync files and directories to and from various cloud storage providers
GITHUB rempi 52MB 2021-10-19 07:51:40 +0000 ReMPI is a record-and-replay tool for MPI applications.
GITHUB restic 33MB 2021-11-17 19:00:31 +0000 Fast, secure, efficient backup program.
GITHUB rsync 34MB 2021-09-16 00:11:46 +0000 An open source utility that provides fast incremental file transfer.
GITHUB ruby 44MB 2021-10-19 07:50:48 +0000 A dynamic, open source programming language with a focus on simplicity and productivity.
GITHUB rust 255MB 2021-11-17 16:14:47 +0000 .format( cargo=join_path(boot_bin, 'cargo
GITHUB salmon 60MB 2021-11-17 16:11:52 +0000 Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
GITHUB samtools 106MB 2021-11-18 19:07:55 +0000 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
GITHUB scons 87MB 2021-11-17 16:12:32 +0000 SCons is a software construction tool
GITHUB scr 138MB 2021-10-22 14:47:48 +0000 SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes
GITHUB siesta 119MB 2021-10-19 07:55:20 +0000 SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
GITHUB singularity 348MB 2021-09-20 04:48:42 +0000
GITHUB slate 80MB 2021-10-03 22:56:20 +0000 The Software for Linear Algebra Targeting Exascale (SLATE) project is to provide fundamental dense linear algebra capabilities to the US Department of Energy and to the high-performance computing (HPC) community at large. To this end, SLATE will provide basic dense matrix operations (e.g., matrix multiplication, rank-k update, triangular solve), linear systems solvers, least square solvers, singular value and eigenvalue solvers.
GITHUB slepc 143MB 2021-11-17 16:17:01 +0000 Scalable Library for Eigenvalue Problem Computations.
GITHUB snappy 26MB 2021-08-25 06:16:43 +0000 A fast compressor/decompressor:
GITHUB spades 103MB 2021-11-17 16:14:01 +0000 SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
GITHUB sparse 26MB 2021-05-26 07:22:17 +0000 An open source sparse linear equation solver.
GITHUB sparsehash 27MB 2021-09-17 06:33:45 +0000 Sparse and dense hash-tables for C++ by Google
GITHUB sqlite 32MB 2021-10-03 20:51:37 +0000 SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without running a separate RDBMS process.
GITHUB stc 269MB 2021-11-17 16:18:00 +0000 STC: The Swift-Turbine Compiler
GITHUB stringtie 106MB 2021-11-18 19:09:11 +0000 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
GITHUB sundials 78MB 2021-11-13 19:08:20 +0000 SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers
GITHUB superlu 51MB 2021-11-17 16:15:34 +0000 SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU is designed for sequential machines.
GITHUB swig 29MB 2021-10-19 07:54:59 +0000 SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application.
GITHUB sz 28MB 2021-11-17 16:15:09 +0000 Error-bounded Lossy Compressor for HPC Data
GITHUB tasmanian 55MB 2021-11-17 16:15:58 +0000 The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN is a robust library for high dimensional integration and interpolation as well as parameter calibration.
GITHUB tau 158MB 2021-11-12 16:11:32 +0000 A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.
GITHUB tcsh 29MB 2021-09-16 00:16:13 +0000 Tcsh is an enhanced but completely compatible version of csh, the C shell. Tcsh is a command language interpreter which can be used both as an interactive login shell and as a shell script command processor. Tcsh includes a command line editor, programmable word completion, spelling correction, a history mechanism, job control and a C language like syntax.
GITHUB trilinos 108MB 2021-11-08 14:51:07 +0000 The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
GITHUB turbine 71MB 2021-11-17 16:17:43 +0000 Turbine: The Swift/T runtime
GITHUB udunits 27MB 2021-05-26 07:25:09 +0000 Automated units conversion
GITHUB umap 27MB 2021-10-03 22:08:27 +0000 Umap is a library that provides an mmap()-like interface to a simple, user-space page fault handler based on the userfaultfd Linux feature (starting with 4.3 linux kernel).
GITHUB unifyfs 79MB 2021-11-17 16:17:50 +0000 User level file system that enables applications to use node-local storage as burst buffers for shared files. Supports scalable and efficient aggregation of I/O bandwidth from burst buffers while having the same life cycle as a batch-submitted job. UnifyFS is designed to support common I/O workloads, including checkpoint/restart. While primarily designed for N-N write/read, UnifyFS compliments its functionality with the support for N-1 write/read.
GITHUB unixodbc 28MB 2021-05-26 07:27:37 +0000 ODBC is an open specification for providing application developers with a predictable API with which to access Data Sources. Data Sources include SQL Servers and any Data Source with an ODBC Driver.
GITHUB upcxx 93MB 2021-11-17 16:16:36 +0000 UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, CUDA and AMTs. It leverages GASNet-EX to deliver low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC).
GITHUB valgrind 97MB 2021-05-26 08:22:47 +0000 ) depends_on('mpi', when='+mpi') depends_on('boost', when='+boost') depends_on("autoconf", type='build', when='@develop') depends_on("automake", type='build', when='@develop') depends_on("libtool", type='build', when='@develop') # Apply the patch suggested here: # patch('valgrind_3_12_0_osx.patch', when='@3.12.0 platform=darwin
GITHUB veloc 74MB 2021-11-17 16:19:15 +0000 Very-Low Overhead Checkpointing System. VELOC is a multi-level checkpoint-restart runtime for HPC supercomputing infrastructures
GITHUB viennarna 128MB 2021-11-17 16:17:02 +0000 The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
GITHUB wget 33MB 2021-11-17 16:16:41 +0000 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
GITHUB xnnpack 28MB 2021-11-17 16:18:19 +0000 High-efficiency floating-point neural network inference operators for mobile, server, and Web
GITHUB xrootd 46MB 2021-11-17 16:18:57 +0000 The XROOTD project aims at giving high performance, scalable fault tolerant access to data repositories of many kinds.
GITHUB xz 27MB 2021-09-16 00:20:11 +0000 XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.
GITHUB zfp 27MB 2021-11-17 16:17:21 +0000 zfp is a compressed number format for multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays.
GITHUB zlib 26MB 2021-09-16 00:20:46 +0000 A free, general-purpose, legally unencumbered lossless data-compression library.