Software Modules on the Aces Cluster

ACES Software Modules FASTER Software Modules Grace Software Modules Terra Software Modules

Last Updated: Aug 7 12:04:43 CDT

The available software for the ACES cluster is listed in the table. Click on any software package name to get more information such as the available versions, additional documentation if available, etc.

Name Description
ACTC'ACTC converts independent triangles into triangle strips or fans.'
ANTLR'ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.'
AOCC'AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0'
APR'Apache Portable Runtime (APR) libraries.'
APR-util'Apache Portable Runtime (APR) util libraries.'
ASE'ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.'
ATK'ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. '
Abseil'Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.'
AlphaFold'AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold contains patches for ColabFold.'
Anaconda3'Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. '
Armadillo'Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.'
Arrow'Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.'
Autoconf'Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.'
Automake'Automake: GNU Standards-compliant Makefile generator'
Autotools'This bundle collect the standard GNU build tools: Autoconf, Automake and libtool '
BLAST+'Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.'
BLIS'BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.'
BWA'Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. '
BamTools'BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.'
Bazel'Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.'
BeautifulSoup'Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.'
Biopython'Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. '
Bison'Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.'
Blender'Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.'
Boost'Boost provides free peer-reviewed portable C++ source libraries.'
Boost.MPI'Boost provides free peer-reviewed portable C++ source libraries.'
Boost.Python'Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.'
Brotli'Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.'
Brotli-python'Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.'
Brunsli'Brunsli is a lossless JPEG repacking library.'
CDO'CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.'
CESM-deps'CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.'
CFITSIO'CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.'
CGAL'The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.'
CLIP'CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.'
CMake'CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. '
CP2K'CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. '
CUDA'CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.'
CUDAcore'CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.'
Check'Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.'
ChimeraX'UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.'
Clang'C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.'
CliMetLab'CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats. It is mostly intended to be used in Jupyter notebooks, and be interoperable with all popular data analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.'
ColabFold'Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine.'
CoordgenLibs'Schrodinger-developed 2D Coordinate Generation'
CuPy'CuPy is an open-source array library accelerated with NVIDIA CUDA.'
Cython'Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). '
DB'Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.'
DBus'D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. '
DCMTK'DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.'
Doxygen'Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. '
ELPA'Eigenvalue SoLvers for Petaflop-Applications.'
ESMF'The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.'
EasyBuild'EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.'
EasyBuild-aces'EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on'
EasyBuild-aces-SCRATCH'User EasyBuild environment for in $SCRATCH/eb'
EasyBuild-aces-myeb'User EasyBuild environment for in $SCRATCH/eb'
EasyBuild-aces-tmp'EasyBuild environment variables for building in /tmp and installing in /sw/eb on'
Eigen'Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.'
FFTW'FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.'
FFTW.MPI'FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.'
FFmpeg'A complete, cross-platform solution to record, convert and stream audio and video.'
FLAC'FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.'
FLTK'FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.'
FastQC'FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.'
Firefox'Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.'
Flask'Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors'
FlexiBLAS'FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.'
FriBidi'The Free Implementation of the Unicode Bidirectional Algorithm. '
GCC'The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).'
GCCcore'The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).'
GDAL'GDAL is a translator library for raster 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 abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.'
GDRCopy'A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.'
GEOS'GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)'
GL2PS'GL2PS: an OpenGL to PostScript printing library'
GLFW'GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop'
GLM'OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.'
GLPK'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.'
GLib'GLib is one of the base libraries of the GTK+ project'
GMP'GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. '
GObject-Introspection'GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.'
GROMACS'GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds for both single and double precision. It also contains the gmxapi extension for the single precision MPI build next to PLUMED.'
GSL'The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.'
GST-plugins-bad'GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.'
GST-plugins-base'GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.'
GStreamer'GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.'
GTK2'The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. '
GTK3'GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. '
GTK4'GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. '
Gdk-Pixbuf'The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. '
Ghostscript'Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.'
Go'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.'
Graphene'Graphene is a thin layer of types for graphic libraries'
GraphicsMagick'GraphicsMagick is the swiss army knife of image processing.'
Greenlet'The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. '
HDF'HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. '
HDF5'HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.'
HH-suite'The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).'
HMMER'HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.'
HTSlib'A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix'
HarfBuzz'HarfBuzz is an OpenType text shaping engine.'
Highway'Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'.'
Horovod'Horovod is a distributed training framework for TensorFlow.'
Hyperopt'hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.'
Hypre'Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.'
ICU'ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.'
IPython'IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.'
ISA-L'Intelligent Storage Acceleration Library'
ITK'Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.'
ImageJ'Image Processing and Analysis in Java'
ImageMagick'ImageMagick is a software suite to create, edit, compose, or convert bitmap images'
Imath'Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics '
JasPer'The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. '
Java'Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.'
JsonCpp'JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. '
Julia'Julia is a high-level, high-performance dynamic programming language for numerical computing'
KaHIP'The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.'
Kalign'Kalign is a fast multiple sequence alignment program for biological sequences.'
LAME'LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.'
LAMMPS'LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. '
LASSO-Python'This python library is designed for general purpose usage in the field of Computer Aided Engineering (CAE). It's name originates from the original initiator and donator of the project Lasso GmbH. The library is now maintained by an open-source community.'
LERC'LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).'
LLVM'The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.'
LMDB'LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.'
Leptonica'Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.'
LibTIFF'tiff: Library and tools for reading and writing TIFF data files'
Libint'Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.'
LittleCMS'Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. '
Lua'Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.'
M4'GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.'
MATIO'matio is an C library for reading and writing Matlab MAT files.'
METIS'METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. '
MONAI'MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. '
MPFR'The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. '
MUMPS'A parallel sparse direct solver'
Magics'Magics is ECMWF's meteorological plotting software and can be either accessed directly through its Python or Fortran interfaces or by using Metview.'
Mako'A super-fast templating language that borrows the best ideas from the existing templating languages'
MemoryViewer'MemoryViewer software gives system administrators comprehensive insight into the physical memory topology as well as the application memory utilization.'
Mesa'Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.'
Meson'Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.'
Miniconda3'Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.'
NASM'NASM: General-purpose x86 assembler'
NCCL'The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.'
NCO'The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.'
NLopt'NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. '
NSPR'Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.'
NSS'Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.'
NVHPC'C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)'
NVSHMEM'NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams. '
NiBabel'NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.'
Ninja'Ninja is a small build system with a focus on speed.'
OpenBLAS'OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.'
OpenBabel'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.'
OpenCV'OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository.'
OpenEXR'OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications'
OpenFOAM'OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.'
OpenFold'A faithful PyTorch reproduction of DeepMind's AlphaFold 2'
OpenJPEG'OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.'
OpenMM'OpenMM is a toolkit for molecular simulation.'
OpenMPI'The Open MPI Project is an open source MPI-3 implementation.'
OpenPGM'OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. '
OpenSSL'The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. '
OpenSceneGraph'The OpenSceneGraph is an open source high performance 3D graphics toolkit, used by application developers in fields such as visual simulation, games, virtual reality, scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating systems. The OpenSceneGraph is now well established as the world leading scene graph technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual reality industries.'
Optuna'Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters.'
PCRE'The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. '
PCRE2'The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. '
PETSc'PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.'
PLUMED'PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. '
PMIx'Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. '
POV-Ray'The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.'
PROJ'Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates'
PYTHIA'PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a general purpose Monte Carlo event generator.'
Pango'Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.'
ParMETIS'ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.'
ParaView'ParaView is a scientific parallel visualizer.'
Parabricks'Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing DNA and RNA data.'
Perl'Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. '
Pillow'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.'
Pillow-SIMD'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.'
PnetCDF'Parallel netCDF: A Parallel I/O Library for NetCDF File Access'
PyCUDA'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.'
PyCairo'Python bindings for the cairo library'
PyGObject'PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.'
PyTorch'Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.'
PyTorch-Geometric'PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.'
PyTorch-Lightning'PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.'
PyYAML'PyYAML is a YAML parser and emitter for the Python programming language.'
Pysam'Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.'
Python'Python is a programming language that lets you work more quickly and integrate your systems more effectively.'
Qhull'Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-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. '
Qt5'Qt is a comprehensive cross-platform C++ application framework.'
R'R is a free software environment for statistical computing and graphics.'
RDFlib'RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.'
RDKit'RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.'
RE2'RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. '
ROOT'The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.'
RapidJSON'A fast JSON parser/generator for C++ with both SAX/DOM style API'
ReFrame'ReFrame is a framework for writing regression tests for HPC systems.'
Redis'Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.'
Rust'Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.'
SAMtools'SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.'
SCOTCH'Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.'
SCons'SCons is a software construction tool.'
SDL2'SDL: Simple DirectMedia Layer, a cross-platform multimedia library'
SHAP'SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions.'
SLEPc'SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.'
SQLite'SQLite: SQL Database Engine in a C Library'
SRA-Toolkit'The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format'
SUNDIALS'SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers'
SWIG'SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.'
ScaFaCoS'ScaFaCoS is a library of scalable fast coulomb solvers.'
ScaLAPACK'The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.'
SciPy-bundle'Bundle of Python packages for scientific software'
SentencePiece'Unsupervised text tokenizer for Neural Network-based text generation.'
Serf'The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library'
Subversion'Subversion is an open source version control system.'
SuiteSparse'SuiteSparse is a collection of libraries manipulate sparse matrices.'
SuperLU_DIST'SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.'
Szip'Szip compression software, providing lossless compression of scientific data '
Tcl'Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. '
TensorFlow'An open-source software library for Machine Intelligence'
TensorRT'An SDK for high-performance deep learning inference, includes a deep learning inference optimizer and runtime that delivers low latency and high throughput for inference applications.'
Theano'Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.'
Tk'Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.'
Tkinter'Tkinter module, built with the Python buildsystem'
Trilinos'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.'
UCC'UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. '
UCC-CUDA'UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support. '
UCX'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications '
UCX-CUDA'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. '
UDUNITS'UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.'
UnZip'UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality.'
VMD'VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.'
VTK'The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.'
VTune'Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.'
Voro++'Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.'
WRF'The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.'
Wayland'Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. '
WebProxy'WebProxy module sets up web proxy environment variables, http_proxy and https_proxy, for internet acceess from the compute nodes. Wiki page:'
X11'The X Window System (X11) is a windowing system for bitmap displays'
XGBoost'XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.'
XML-LibXML'Perl binding for libxml2'
XZ'xz: XZ utilities'
Xerces-C++'Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.'
Xvfb'Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.'
YACS'YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These "configurations" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.'
Yasm'Yasm: Complete rewrite of the NASM assembler with BSD license'
Z3'Z3 is a theorem prover from Microsoft Research. '
ZeroMQ'ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.'
Zip'Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality'
aiohttp'Asynchronous HTTP client/server framework for asyncio and Python.'
ant'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. The main known usage of Ant is the build of Java applications.'
archspec'A library for detecting, labeling, and reasoning about microarchitectures'
arpack-ng'ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.'
at-spi2-atk'AT-SPI 2 toolkit bridge'
at-spi2-core'Assistive Technology Service Provider Interface. '
binutils'binutils: GNU binary utilities'
bokeh'Statistical and novel interactive HTML plots for Python'
bzip2'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. '
cURL'libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. '
cairo'Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB'
captum'Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.'
ccache'Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again'
cdsapi'Climate Data Store API'
charliecloud'Charliecloud provides user-defined software stacks (UDSS) for high-performance computing (HPC) centers.'
chemprop'Message Passing Neural Networks for Molecule Property Prediction'
cisTEM'cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.'
cppy'A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.'
cuDF'Built based on the Apache Arrow columnar memory format, cuDF is a GPU DataFrame library for loading, joining, aggregating, filtering, and otherwise manipulating data.'
cuDNN'The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.'
cuTENSOR'The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.'
cython-blis'Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension. '
dask'Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.'
deepdiff'DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.'
dill'dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.'
dm-tree'dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.'
dorado'Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.'
double-conversion'Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.'
ecBuild'A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems '
ecCodes'ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).'
einops'Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.'
elfutils'The elfutils project provides libraries and tools for ELF files and DWARF data. '
expat'Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).'
expecttest'This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.'
fastai'The fastai deep learning library.'
ffnvcodec'FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).'
file'The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.'
flatbuffers'FlatBuffers: Memory Efficient Serialization Library Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. '
flatbuffers-python'Python Flatbuffers runtime library.'
flex'Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. '
fontconfig'Fontconfig is a library designed to provide system-wide font configuration, customization and application access. '
foss'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
fosscuda'GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
freeglut'freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.'
freetype'FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. '
gcccuda'GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.'
gettext'GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation'
gfbf'GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.'
giflib'giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.'
git'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.'
git-lfs'Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like'
gnuplot'Portable interactive, function plotting utility'
gompi'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.'
gompic'GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.'
googletest'Google's framework for writing C++ tests on a variety of platforms'
gperf'GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. '
gperftools'gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. '
gpustat'A simple command-line utility for querying and monitoring GPU status'
graphite2'Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.'
groff'Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.'
gzip'gzip (GNU zip) is a popular data compression program as a replacement for compress'
h5py'HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.'
help2man'help2man produces simple manual pages from the '--help' and '--version' output of other commands.'
hiredis'Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.'
hwloc'The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. '
hypothesis'Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.'
iimpi'Intel C/C++ and Fortran compilers, alongside Intel MPI.'
imageio'Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.'
imbalanced-learn'imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.'
imkl'Intel oneAPI Math Kernel Library'
imkl-FFTW'FFTW interfaces using Intel oneAPI Math Kernel Library'
impi'Intel MPI Library, compatible with MPICH ABI'
intel'Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).'
intel-compilers'Intel C, C++ & Fortran compilers (classic and oneAPI)'
intltool'intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.'
jax'Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more'
jbigkit'JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.'
json-c'JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.'
kim-api'Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. '
kineto'A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters'
libGLU'The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. '
libaec'Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.'
libarchive'Multi-format archive and compression library '
libcerf'libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. '
libdap'A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.'
libdeflate'Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.'
libdrm'Direct Rendering Manager runtime library.'
libepoxy'Epoxy is a library for handling OpenGL function pointer management for you'
libevent'The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. '
libfabric'Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. '
libffi'The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.'
libgd'GD is an open source code library for the dynamic creation of images by programmers.'
libgeotiff'Library for reading and writing coordinate system information from/to GeoTIFF files'
libgit2'libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.'
libglvnd'libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.'
libgpuarray'Library to manipulate tensors on the GPU.'
libiconv'Libiconv converts from one character encoding to another through Unicode conversion'
libjpeg-turbo'libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. '
libogg'Ogg is a multimedia container format, and the native file and stream format for the multimedia codecs.'
libopus'Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.'
libpciaccess'Generic PCI access library.'
libpng'libpng is the official PNG reference library'
libreadline'The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. '
librsvg'Librsvg is a library to render SVG files using cairo.'
libsndfile'Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.'
libsodium'Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. '
libtirpc'Libtirpc is a port of Suns Transport-Independent RPC library to Linux.'
libtool'GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. '
libunwind'The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications'
libvorbis'Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format'
libvori'C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.'
libwebp'WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.'
libxc'Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.'
libxml2'Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). '
libxslt'Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).'
libxsmm'LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).'
libyaml'LibYAML is a YAML parser and emitter written in C.'
lifelines'lifelines is a complete survival analysis library, written in pure Python.'
lmod'Lmod: An Environment Module System'
lxml'The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.'
lz4'LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.'
maeparser'maeparser is a parser for Schrodinger Maestro files.'
magma'The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.'
make'GNU version of make utility'
makeinfo'makeinfo is part of the Texinfo project, the official documentation format of the GNU project. This is a minimal build with very basic functionality. Should only be used for build dependencies. '
matplotlib'matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.'
motif'Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.'
mpi4py'MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.'
ncbi-vdb'The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.'
ncurses'The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. '
netCDF'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netCDF-C++4'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netCDF-Fortran'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netcdf4-python'Python/numpy interface to netCDF.'
nettle'Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.'
networkx'NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.'
nlohmann_json'JSON for Modern C++'
nodejs'Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.'
nsync'nsync is a C library that exports various synchronization primitives, such as mutexes'
numactl'The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. '
numba'Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.'
nvidia-container-cli'NVIDIA container command line tools provides a list of locally installed libraries that Charliecloud needs to interface to the local NVIDIA GPUs.'
physics-tenpy'TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks.'
pixman'Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. '
pkg-config'pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). '
pkgconf'pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from'
pkgconfig'pkgconfig is a Python module to interface with the pkg-config command line tool''An open-source, interactive graphing library for Python'
pocl'Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard'
poppler'Poppler is a PDF rendering library'
protobuf'Google Protocol Buffers'
protobuf-python'Python Protocol Buffers runtime library.'
py3Dmol'A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook.'
pybind11'pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.'
pydantic'Data validation and settings management using Python type hinting.'
pydicom'Pure python package for DICOM medical file reading and writing.'
pytesseract'Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and "read" the text embedded in images. Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, Python-tesseract will print the recognized text instead of writing it to a file.'
pytest'The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.'
pytest-xdist'xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.'
re2c're2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.'
redis-py'The Python interface to the Redis key-value store.'
rising'Provides everything needed for high performance data loading and augmentation in PyTorch.'
scikit-build'Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.'
scikit-cuda'SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIA's CUDA Programming Toolkit.'
scikit-image'scikit-image is a collection of algorithms for image processing.'
scikit-learn'Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.'
settarg'The settarg module provides a way to connect the loaded modules with your build system by setting environment variables. '
snappy'Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.'
spaCy'Industrial-strength Natural Language Processing (NLP) in Python.'
spglib'Spglib is a C library for finding and handling crystal symmetries.'
spglib-python'Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.'
spython'Singularity Python is a Python API to work with the Singularity open source software. '
statsmodels'Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.'
synthcity'A library for generating and evaluating synthetic tabular data.'
tcsh'Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.'
tensorboard'TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.'
tensorboardX'Tensorboard for PyTorch.'
tesseract'Tesseract is an optical character recognition engine'
time'The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.'
tmux'tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.'
torchsampler'A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones.'
torchtext'Data loaders and abstractions for text and NLP'
torchvision'Datasets, Transforms and Models specific to Computer Vision'
tqdm'A fast, extensible progress bar for Python and CLI'
typing-extensions'Typing Extensions – Backported and Experimental Type Hints for Python'
utf8proc'utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.'
util-linux'Set of Linux utilities'
wxWidgets'wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.'
x264'x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. '
x265'x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. '
xarray'xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.'
xorg-macros' macros utilities.'
xprop'The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.'
xxd'xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.'
zarr'Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.'
zlib'zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.'
zstd'Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.'