.. _Installed Software: Installed Software ================== .. code-block:: julia ABINIT: ABINIT/9.6.2 ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ANSYS_CFD: ANSYS_CFD/2021R1, ANSYS_CFD/2022R2 ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX. ANTLR: ANTLR/2.7.7-Java-11 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. ASE: ASE/3.22.1 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/2.36.0, ATK/2.38.0 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. AmberTools: AmberTools/21, AmberTools/22.3 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Anaconda3: Anaconda3/2022.05 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. Arrow: Arrow/6.0.0, Arrow/8.0.0 Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. ArviZ: ArviZ/0.11.4, ArviZ/0.12.1 Exploratory analysis of Bayesian models with Python Autoconf: Autoconf/2.69, Autoconf/2.71 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/1.16.1, Automake/1.16.4, Automake/1.16.5 Automake: GNU Standards-compliant Makefile generator Autotools: Autotools/20180311, Autotools/20210726, Autotools/20220317 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool BDBag: BDBag/1.6.3 The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles. BEDTools: BEDTools/2.30.0 BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. BLIS: BLIS/0.8.1, BLIS/0.9.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. BamTools: BamTools/2.5.2 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Bambi: Bambi/0.7.1, Bambi/0.10.0 Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines. Bazel: Bazel/4.2.2, Bazel/5.1.1 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. BeautifulSoup: BeautifulSoup/4.10.0 Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. Biopython: Biopython/1.79 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/3.5.3, Bison/3.7.6, Bison/3.8.2 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. Boost: Boost/1.77.0, Boost/1.79.0 Boost provides free peer-reviewed portable C++ source libraries. Brotli: Brotli/1.0.9 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. CGAL: CGAL/4.14.3 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. CMake: CMake/3.16.4, CMake/3.21.1, CMake/3.22.1, CMake/3.23.1, CMake/3.24.3 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. CP2K: CP2K/8.2 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. CapnProto: CapnProto/0.9.1 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. CheMPS2: CheMPS2/1.8.11, CheMPS2/1.8.12 CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. CubeLib: CubeLib/4.4.4, CubeLib/4.8 Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools. CubeWriter: CubeWriter/4.4.3, CubeWriter/4.8 Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. DB: DB/18.1.32, DB/18.1.40 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. DBus: DBus/1.13.18, DBus/1.14.0 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. DFT-D3: DFT-D3/3.2.0 DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. Dalton: Dalton/2020.0 The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html. DendroPy: DendroPy/4.5.2 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. Doxygen: Doxygen/1.8.17, Doxygen/1.9.1, Doxygen/1.9.4 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: ELPA/2021.05.001, ELPA/2021.11.001 Eigenvalue SoLvers for Petaflop-Applications . ESMF: ESMF/8.2.0, ESMF/8.3.0 The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Eigen: Eigen/3.3.9, Eigen/3.4.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. FDS: FDS/6.7.7, FDS/6.7.9 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. FFTW: FFTW/3.3.8, FFTW/3.3.10 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.MPI/3.3.10 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: FFmpeg/4.3.2, FFmpeg/4.4.2 A complete, cross-platform solution to record, convert and stream audio and video. FLAC: FLAC/1.3.3, FLAC/1.3.4 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. FMS: FMS/2022.02 The Flexible Modeling System (FMS) is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models. FastANI: FastANI/1.33 FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. FastQC: FastQC/0.11.9-Java-11 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. FastTree: FastTree/2.1.11 FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Flask: Flask/2.0.2, Flask/2.2.2 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/3.0.4, FlexiBLAS/3.2.0 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Flye: Flye/2.9, Flye/2.9.1 Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. FriBidi: FriBidi/1.0.10, FriBidi/1.0.12 The Free Implementation of the Unicode Bidirectional Algorithm. GATK: GATK/4.2.6.1-Java-11 The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. GCC: GCC/9.3.0, GCC/11.2.0, GCC/11.3.0 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: GCCcore/9.3.0, GCCcore/11.2.0, GCCcore/11.3.0 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/3.3.2, GDAL/3.5.0 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. GEOS: GEOS/3.9.1, GEOS/3.10.3 GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) GLPK: GLPK/5.0 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/2.69.1, GLib/2.72.1 GLib is one of the base libraries of the GTK+ project GMP: GMP/6.2.0, GMP/6.2.1 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. GObject-Introspection: GObject-Introspection/1.68.0, GObject-Introspection/1.72.0 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. GPAW: GPAW/22.8.0 GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. GPAW-setups: GPAW-setups/0.9.20000 PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. GROMACS: GROMACS/2021.5-PLUMED-2.8.0, GROMACS/2021.5-PLUMED-2.8.1, GROMACS/2021.5 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 CPU only 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: GSL/2.7 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: GST-plugins-bad/1.20.2 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: GST-plugins-base/1.20.2 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/1.20.2 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. GTDB-Tk: GTDB-Tk/2.0.0 A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTK2: GTK2/2.24.33 The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. GTK3: GTK3/3.24.31 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: GTK4/4.7.0 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: Gdk-Pixbuf/2.42.6, Gdk-Pixbuf/2.42.8 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/9.54.0, Ghostscript/9.56.1 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. GitPython: GitPython/3.1.24, GitPython/3.1.27 GitPython is a python library used to interact with Git repositories GlobalArrays: GlobalArrays/5.8.1 Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model Graphene: Graphene/1.10.8 Graphene is a thin layer of types for graphic libraries HDF: HDF/4.2.15 HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. HDF5: HDF5/1.10.6, HDF5/1.12.1, HDF5/1.12.2 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. HMMER: HMMER/3.3.2 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. HPL: HPL/2.3 HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. HarfBuzz: HarfBuzz/2.8.2, HarfBuzz/4.2.1 HarfBuzz is an OpenType text shaping engine. Hypre: Hypre/2.24.0, Hypre/2.25.0 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/69.1, ICU/71.1 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. IMB: IMB/2021.3 The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes IPython: IPython/7.26.0, IPython/8.5.0 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: ISA-L/2.30.0 Intelligent Storage Acceleration Library ImageMagick: ImageMagick/7.1.0-4, ImageMagick/7.1.0-37 ImageMagick is a software suite to create, edit, compose, or convert bitmap images Imath: Imath/3.1.5 Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics JasPer: JasPer/2.0.33 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/11.0.16 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. JsonCpp: JsonCpp/1.9.4, JsonCpp/1.9.5 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/1.8.5-linux-x86_64 Julia is a high-level, high-performance dynamic programming language for numerical computing KaHIP: KaHIP/3.14 The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. LAME: LAME/3.100 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. LAMMPS: LAMMPS/23Jun2022-kokkos 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. LAPACK: LAPACK/3.10.1 LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. LLVM: LLVM/12.0.1, LLVM/14.0.3 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/0.9.29 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. LMfit: LMfit/1.0.3 Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python LibTIFF: LibTIFF/4.3.0 tiff: Library and tools for reading and writing TIFF data files Libint: Libint/2.6.0-lmax-6-cp2k 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: LittleCMS/2.12, LittleCMS/2.13.1 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Lua: Lua/5.4.3, Lua/5.4.4 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: M4/1.4.18, M4/1.4.19 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. MDAnalysis: MDAnalysis/2.0.0, MDAnalysis/2.2.0 MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. MDTraj: MDTraj/1.9.7 Read, write and analyze MD trajectories with only a few lines of Python code. METIS: METIS/5.1.0 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. MPFR: MPFR/4.1.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPICH: MPICH/3.4.2 MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MUMPS: MUMPS/5.4.1-metis, MUMPS/5.5.1-metis A parallel sparse direct solver Mako: Mako/1.1.4, Mako/1.2.0 A super-fast templating language that borrows the best ideas from the existing templating languages Mash: Mash/2.3 Fast genome and metagenome distance estimation using MinHash Mesa: Mesa/21.1.7, Mesa/22.0.3 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Meson: Meson/0.55.1-Python-3.8.2, Meson/0.58.2, Meson/0.62.1 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. MultiQC: MultiQC/1.12 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. NASM: NASM/2.15.05 NASM: General-purpose x86 assembler NCO: NCO/5.0.3, NCO/5.1.0 The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. NLopt: NLopt/2.7.0, NLopt/2.7.1 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: NSPR/4.32, NSPR/4.34 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. NSS: NSS/3.69, NSS/3.79 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. NWChem: NWChem/7.0.2 NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Ninja: Ninja/1.10.0, Ninja/1.10.2 Ninja is a small build system with a focus on speed. OPARI2: OPARI2/2.0.5, OPARI2/2.0.7 OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. ORCA: ORCA/5.0.3 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. OSU-Micro-Benchmarks: OSU-Micro-Benchmarks/5.6.3, OSU-Micro-Benchmarks/5.7.1, ... OSU Micro-Benchmarks OTF2: OTF2/2.2, OTF2/3.0.2 The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. OpenBLAS: OpenBLAS/0.3.9, OpenBLAS/0.3.18, OpenBLAS/0.3.20 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. OpenCV: OpenCV/4.5.5-contrib, OpenCV/4.6.0-contrib 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/3.1.1, OpenEXR/3.1.5 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications OpenFOAM: OpenFOAM/v2112, OpenFOAM/v2206 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. OpenJPEG: OpenJPEG/2.5.0 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. OpenMPI: OpenMPI/4.0.3, OpenMPI/4.1.1, OpenMPI/4.1.4, OpenMPI/4.1.5 The Open MPI Project is an open source MPI-3 implementation. OpenMolcas: OpenMolcas/22.10 OpenMolcas is a quantum chemistry software package. OpenPGM: OpenPGM/5.2.122 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. 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: OpenSSL/1.1 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. PAPI: PAPI/6.0.0, PAPI/7.0.0 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 opportunites across the hardware and software stack. PCRE: PCRE/8.45 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE2: PCRE2/10.37, PCRE2/10.40 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PDT: PDT/3.25.1 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. PLUMED: PLUMED/2.8.0, PLUMED/2.8.1 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: PMIx/3.1.5, PMIx/4.1.0, PMIx/4.1.2 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. PROJ: PROJ/8.1.0, PROJ/9.0.0 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates PSolver: PSolver/1.8.3 Interpolating scaling function Poisson Solver Library Pango: Pango/1.48.8, Pango/1.50.7 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/4.0.3 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/5.9.1-mpi, ParaView/5.10.1-mpi ParaView is a scientific parallel visualizer. Perl: Perl/5.30.2-minimal, Perl/5.30.2, Perl/5.34.0-minimal, Perl/5.34.0, Perl/5.34.1-minimal, ... Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies. Pillow: Pillow/8.3.2, Pillow/9.1.1 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-SIMD/9.2.0 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. PnetCDF: PnetCDF/1.12.1, PnetCDF/1.12.3 Parallel netCDF: A Parallel I/O Library for NetCDF File Access PyCairo: PyCairo/1.21.0 Python bindings for the cairo library PyGObject: PyGObject/3.42.1 PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. PyMC3: PyMC3/3.11.1 Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano PyTorch: PyTorch/1.12.1 Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. PyYAML: PyYAML/5.4.1, PyYAML/6.0 PyYAML is a YAML parser and emitter for the Python programming language. Pysam: Pysam/0.17.0, Pysam/0.19.1 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/2.7.18-bare, Python/3.8.2, Python/3.9.6-bare, Python/3.9.6, Python/3.10.4-bare, ... Python is a programming language that lets you work more quickly and integrate your systems more effectively. Qhull: Qhull/2020.2 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: Qt5/5.15.2, Qt5/5.15.5 Qt is a comprehensive cross-platform C++ application framework. QuantumESPRESSO: QuantumESPRESSO/7.0, QuantumESPRESSO/7.1 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). R: R/4.2.0, R/4.2.1 R is a free software environment for statistical computing and graphics. R-bundle-Bioconductor: R-bundle-Bioconductor/3.15-R-4.2.0, R-bundle-Bioconductor/3.15-R-4.2.1 Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. RE2: RE2/2022-02-01, RE2/2022-06-01 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. RapidJSON: RapidJSON/1.1.0 A fast JSON parser/generator for C++ with both SAX/DOM style API Rust: Rust/1.54.0, Rust/1.60.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. SAMtools: SAMtools/1.16.1 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: SCOTCH/6.0.9, SCOTCH/6.1.2, SCOTCH/7.0.1 Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. SIONlib: SIONlib/1.7.6-tools, SIONlib/1.7.7-tools SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. SISSO: SISSO/3.1-20220324 A data-driven method combining symbolic regression and compressed sensing toward accurate & interpretable models. SPOTPY: SPOTPY/1.5.14 SPOTPY is a Python framework that enables the use of Computational optimization techniques for calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model. SQLite: SQLite/3.31.1, SQLite/3.36, SQLite/3.38.3 SQLite: SQL Database Engine in a C Library STAR: STAR/2.7.9a STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. SUNDIALS: SUNDIALS/6.3.0 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers ScaFaCoS: ScaFaCoS/1.0.1 ScaFaCoS is a library of scalable fast coulomb solvers. ScaLAPACK: ScaLAPACK/2.1.0-fb, ScaLAPACK/2.1.0, ScaLAPACK/2.2.0-fb The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. SciPy-bundle: SciPy-bundle/2021.10, SciPy-bundle/2022.05 Bundle of Python packages for scientific software Score-P: Score-P/6.0, Score-P/8.0 The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. Siesta: Siesta/4.1.5 SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SimPEG: SimPEG/0.18.1 An open source Python package for simulation and gradient based parameter estimation in geophysical applications. SuiteSparse: SuiteSparse/5.10.1-METIS-5.1.0, SuiteSparse/5.13.0-METIS-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices. SuperLU: SuperLU/5.3.0 SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Szip: Szip/2.1.1 Szip compression software, providing lossless compression of scientific data TELEMAC-MASCARET: TELEMAC-MASCARET/8p3r1 TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field. Tcl: Tcl/8.6.10, Tcl/8.6.11, Tcl/8.6.12 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: TensorFlow/2.8.4 An open-source software library for Machine Intelligence Theano: Theano/1.1.2-PyMC Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Tk: Tk/8.6.11, Tk/8.6.12 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/3.9.6, Tkinter/3.10.4 Tkinter module, built with the Python buildsystem Togl: Togl/2.0 A Tcl/Tk widget for OpenGL rendering. UCC: UCC/1.0.0 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. UCX: UCX/1.8.0, UCX/1.11.2, UCX/1.12.1 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications UDUNITS: UDUNITS/2.2.26, UDUNITS/2.2.28 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/6.0 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. VTK: VTK/9.1.0, VTK/9.2.2 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. Valgrind: Valgrind/3.16.1, Valgrind/3.18.1, Valgrind/3.20.0 Valgrind: Debugging and profiling tools Voro++: Voro++/0.4.6 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. Wannier90: Wannier90/3.1.0 A tool for obtaining maximally-localised Wannier functions Wayland: Wayland/1.20.0 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. X11: X11/20200222, X11/20210802, X11/20220504 The X Window System (X11) is a windowing system for bitmap displays XCrySDen: XCrySDen/1.6.2 XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. XZ: XZ/5.2.5 xz: XZ utilities Xvfb: Xvfb/1.20.13, Xvfb/21.1.3 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. YAXT: YAXT/0.9.2 Yet Another eXchange Tool Yasm: Yasm/1.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license ZeroMQ: ZeroMQ/4.3.4 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/3.0 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 ant: ant/1.10.11-Java-11, ant/1.10.12-Java-11 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: archspec/0.1.3, archspec/0.1.4 A library for detecting, labeling, and reasoning about microarchitectures arpack-ng: arpack-ng/3.8.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. arrow-R: arrow-R/6.0.0.2-R-4.2.0, arrow-R/8.0.0-R-4.2.1 R interface to the Apache Arrow C++ library astropy: astropy/5.0.4, astropy/5.1.1 The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. at-spi2-atk: at-spi2-atk/2.38.0 AT-SPI 2 toolkit bridge at-spi2-core: at-spi2-core/2.40.3, at-spi2-core/2.44.1 Assistive Technology Service Provider Interface. attr: attr/2.5.1 Commands for Manipulating Filesystem Extended Attributes binutils: binutils/2.34, binutils/2.37, binutils/2.38 binutils: GNU binary utilities buildenv: buildenv/default This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show bwidget: bwidget/1.9.15 The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. bzip2: bzip2/1.0.8 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: cURL/7.69.1, cURL/7.78.0, cURL/7.83.0 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/1.16.0, cairo/1.17.4 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 cppy: cppy/1.1.0, cppy/1.2.1 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. cutadapt: cutadapt/3.5 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. dill: dill/0.3.4 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. double-conversion: double-conversion/3.1.5, double-conversion/3.2.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. ecCodes: ecCodes/2.24.2, ecCodes/2.27.0 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). elfutils: elfutils/0.187 The elfutils project provides libraries and tools for ELF files and DWARF data. expat: expat/2.2.9, expat/2.4.1, expat/2.4.8 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: expecttest/0.1.3 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. flatbuffers: flatbuffers/2.0.0 FlatBuffers: Memory Efficient Serialization Library flatbuffers-python: flatbuffers-python/2.0 Python Flatbuffers runtime library. flex: flex/2.6.4 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/2.13.92, fontconfig/2.13.94, fontconfig/2.14.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access. foss: foss/2020a, foss/2021b, foss/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. freetype: freetype/2.10.1, freetype/2.11.0, freetype/2.12.1 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. futile: futile/1.8.3 The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code. gettext: gettext/0.20.1, gettext/0.21 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 giflib: giflib/5.2.1 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/2.23.0-nodocs, git/2.33.1-nodocs, git/2.36.0-nodocs 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. gnuplot: gnuplot/5.4.2, gnuplot/5.4.4 Portable interactive, function plotting utility gompi: gompi/2020a, gompi/2021b, gompi/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. googletest: googletest/1.11.0 Google's framework for writing C++ tests on a variety of platforms gperf: gperf/3.1 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. graphite2: graphite2/1.3.14 Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. groff: groff/1.22.4 Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. gzip: gzip/1.10, gzip/1.12 gzip (GNU zip) is a popular data compression program as a replacement for compress h5py: h5py/3.6.0, h5py/3.7.0 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/1.47.12, help2man/1.48.3, help2man/1.49.2 help2man produces simple manual pages from the '--help' and '--version' output of other commands. hwloc: hwloc/2.2.0, hwloc/2.5.0, hwloc/2.7.1 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/6.14.6, hypothesis/6.46.7 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: iimpi/2021b, iimpi/2022a Intel C/C++ and Fortran compilers, alongside Intel MPI. imkl: imkl/2021.4.0, imkl/2022.1.0 Intel oneAPI Math Kernel Library imkl-FFTW: imkl-FFTW/2021.4.0, imkl-FFTW/2022.1.0 FFTW interfaces using Intel oneAPI Math Kernel Library impi: impi/2021.4.0, impi/2021.6.0 Intel MPI Library, compatible with MPICH ABI intel: intel/2021b, intel/2022a Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). intel-compilers: intel-compilers/2021.4.0, intel-compilers/2022.1.0 Intel C, C++ & Fortran compilers (classic and oneAPI) intltool: intltool/0.51.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iompi: iompi/2021b Intel C/C++ and Fortran compilers, alongside Open MPI. jbigkit: jbigkit/2.1 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. kim-api: kim-api/2.3.0 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. libGLU: libGLU/9.0.2 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. libGridXC: libGridXC/0.9.6 A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems. libaec: libaec/1.0.6 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: libarchive/3.5.1, libarchive/3.6.1 Multi-format archive and compression library libcerf: libcerf/1.17, libcerf/2.1 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: libdap/3.20.8, libdap/3.20.11 A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. libdeflate: libdeflate/1.10 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. libdrm: libdrm/2.4.107, libdrm/2.4.110 Direct Rendering Manager runtime library. libepoxy: libepoxy/1.5.8, libepoxy/1.5.10 Epoxy is a library for handling OpenGL function pointer management for you libevent: libevent/2.1.11, libevent/2.1.12 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/1.11.0, libfabric/1.13.2, libfabric/1.15.1 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: libffi/3.3, libffi/3.4.2 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: libgd/2.3.3 GD is an open source code library for the dynamic creation of images by programmers. libgeotiff: libgeotiff/1.7.0, libgeotiff/1.7.1 Library for reading and writing coordinate system information from/to GeoTIFF files libgit2: libgit2/1.1.1, libgit2/1.4.3 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/1.3.3, libglvnd/1.4.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. libiconv: libiconv/1.16, libiconv/1.17 Libiconv converts from one character encoding to another through Unicode conversion libjpeg-turbo: libjpeg-turbo/2.0.6, libjpeg-turbo/2.1.3 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: libogg/1.3.5 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. libopus: libopus/1.3.1 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: libpciaccess/0.16 Generic PCI access library. libpng: libpng/1.6.37 libpng is the official PNG reference library libreadline: libreadline/8.0, libreadline/8.1, libreadline/8.1.2 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. libsndfile: libsndfile/1.0.31, libsndfile/1.1.0 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: libsodium/1.0.18 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libtirpc: libtirpc/1.3.2 Libtirpc is a port of Suns Transport-Independent RPC library to Linux. libtool: libtool/2.4.6, libtool/2.4.7 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunwind: libunwind/1.3.1, libunwind/1.5.0, libunwind/1.6.2 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 libvdwxc: libvdwxc/0.4.0 libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. libvorbis: libvorbis/1.3.7 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format libwebp: libwebp/1.2.0, libwebp/1.2.4 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/4.3.4, libxc/5.1.6, libxc/5.2.3 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: libxml2/2.9.10, libxml2/2.9.13 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). libxslt: libxslt/1.1.34 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). libxsmm: libxsmm/1.17 LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). libyaml: libyaml/0.2.5 LibYAML is a YAML parser and emitter written in C. lmod: lmod Lmod: An Environment Module System loompy: loompy/3.0.7 Python implementation of the Loom file format, an efficient file format for large omics datasets lxml: lxml/4.9.1 The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. lz4: lz4/1.9.3 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. make: make/4.3 GNU version of make utility makeinfo: makeinfo/6.7-minimal 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/3.4.3, matplotlib/3.5.2 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. mkl-service: mkl-service/2.3.0 Python hooks for Intel(R) Math Kernel Library runtime control settings. ncurses: ncurses/6.1, ncurses/6.2, ncurses/6.3 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. ncview: ncview/2.1.8 Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. netCDF: netCDF/4.7.4, netCDF/4.8.1, netCDF/4.9.0 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-C++4/4.3.1 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-Fortran/4.5.2, netCDF-Fortran/4.5.3, netCDF-Fortran/4.6.0 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: netcdf4-python/1.5.7, netcdf4-python/1.6.1 Python/numpy interface to netCDF. nettle: nettle/3.7.3, nettle/3.8 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/2.6.3, networkx/2.8.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. nlohmann_json: nlohmann_json/3.10.5 JSON for Modern C++ nodejs: nodejs/14.17.6, nodejs/16.15.1 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/1.24.0, nsync/1.25.0 nsync is a C library that exports various synchronization primitives, such as mutexes numactl: numactl/2.0.13, numactl/2.0.14 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/0.54.1, numba/0.56.4 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. pigz: pigz/2.6 pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. pixman: pixman/0.40.0 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/0.29.2 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/1.8.0 pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. pkgconfig: pkgconfig/1.5.5-python pkgconfig is a Python module to interface with the pkg-config command line tool pmi: pmi/pmix-x86_64 pplacer: pplacer/1.1.alpha19 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. prodigal: prodigal/2.6.3 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. protobuf: protobuf/3.17.3, protobuf/3.19.4 Google Protocol Buffers protobuf-python: protobuf-python/3.17.3, protobuf-python/3.19.4 Python Protocol Buffers runtime library. pybedtools: pybedtools/0.8.2, pybedtools/0.9.0 pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. pybind11: pybind11/2.7.1, pybind11/2.9.2 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. python-isal: python-isal/0.11.1 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. re2c: re2c/2.2 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. scikit-bio: scikit-bio/0.5.7 scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. scikit-build: scikit-build/0.11.1, scikit-build/0.15.0 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. scikit-learn: scikit-learn/1.0.1, scikit-learn/1.0.2, scikit-learn/1.1.2 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: settarg The settarg module provides a way to connect the loaded modules with your build system by setting environment variables. snakemake: snakemake/6.10.0, snakemake/7.22.0 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snappy: snappy/1.1.9 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. spglib-python: spglib-python/1.16.3, spglib-python/2.0.0 Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. statsmodels: statsmodels/0.13.1 Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. tbb: tbb/2020.3, tbb/2021.5.0 Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. torchsampler: torchsampler/0.1.2 A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones. torchvision: torchvision/0.13.1 Datasets, Transforms and Models specific to Computer Vision tqdm: tqdm/4.62.3, tqdm/4.64.0 A fast, extensible progress bar for Python and CLI typing-extensions: typing-extensions/3.10.0.2, typing-extensions/4.3.0 Typing Extensions – Backported and Experimental Type Hints for Python utf8proc: utf8proc/2.6.1, utf8proc/2.7.0 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: util-linux/2.35, util-linux/2.37, util-linux/2.38 Set of Linux utilities worker: worker/1.6.12, worker/1.6.13 The Worker framework has been developed to help deal with parameter exploration experiments that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework. x264: x264/20210613, x264/20220620 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: x265/3.5 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/0.20.1, xarray/2022.6.0, xarray/2022.9.0 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. xmlf90: xmlf90/1.5.4 xmlf90 is a basic XML parsing library written in Fortran. xorg-macros: xorg-macros/1.19.2, xorg-macros/1.19.3 X.org macros utilities. xxd: xxd/8.2.4220 xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files. zlib: zlib/1.2.11, zlib/1.2.12 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: zstd/1.5.0, zstd/1.5.2 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.