Skip to content

Available Karolina Modules

Base

Module Description

Bio

Module Description
AlphaFold AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
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.
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.
Cordax CORDAX is an aggregation propensity predictor based on predicted packing energies.
FoldX FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
GATK 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.
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.
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.
Kalign Kalign is a fast multiple sequence alignment program for biological sequences.
MaSuRCA MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).
picard A set of tools (in Java) for working with next generation sequencing data in the BAM format.
snpEff SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
Tango N/A
Waltz N/A

Cae

Module Description
DualSPHysics DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems.
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.

Chem

Module Description
ABINIT 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.
Amber Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
BEEF BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
CheMPS2 CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
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.
dftd3-lib This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 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.
libGridXC A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC.
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.
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.
Molden Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
Molpro Molpro is a local_complete system of ab initio programs for molecular electronic structure calculations.
NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Newton-X ACTC converts independent triangles into triangle strips or fans.
NWChem 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.
Octopus Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.
OpenMolcas OpenMolcas is a quantum chemistry software package
ORCA 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.
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.
PSI4 PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform local_computations with more than 2500 basis functions running serially or in parallel.
pymatgen Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.
QuantumESPRESSO 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).
Schrodinger Schrödinger aims to provide integrated software solutions and services that truly meet its customers▒~@~Y needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced local_computational techniques that transform the way chemists design local_compounds and materials.
spglib-python Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
TURBOMOLE TURBOMOLE is a quantum chemical program package, initially developed in the group of Prof. Dr. Reinhart Ahlrichs at the University of Karlsruhe and at the Forschungszentrum Karlsruhe. Until 2007 the main development of the program was conducted by students and postdoctoral researchers in the group of Ahlrichs, who usually changed their field of work after leaving the group. Therefore, the code was well localized at and, consequently, owned by the University of Karlsruhe. However, since 2007 the situation has changed. Several people, who started their work with TURBOMOLE in Karlsruhe, still make significant contributions and feel responsible for the program, but do no longer reside in Karlsruhe. It was thus necessary to arrange the development of TURBOMOLE in a different manner, namely as a company.
Wannier90 A tool for obtaining maximally-localised Wannier functions

Compiler

Module Description
AOCC AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0
AOMP AMD fork of LLVM, setup for OpenMP offloading to Accelerators
Clang C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
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,...).
Go Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
hipSYCL hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP
icc Intel C and C++ compilers
iccifort Intel C, C++ & Fortran compilers
ifort Intel Fortran compiler
intel-compilers Intel C, C++ & Fortran compilers (classic and oneAPI)
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 local_compiler) to use LLVM as an optimizer and code generator.
NVHPC C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

Data

Module Description
FLAC Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
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.
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.
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 unique technology suite that makes possible the management of extremely large and local_complex data collections.
LAME LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
libPSML A library to handle PSML, the pseudopotential markup language.
mkl-service Python hooks for Intel(R) Math Kernel Library runtime control settings.
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-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.
PnetCDF Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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.
SoX Sound eXchange, the Swiss Army knife of audio manipulation
xmlf90 xmlf90 is a basic XML parsing library written in Fortran.

Debugger

Module Description
Forge Allinea Forge is the local_complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to local_complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
TotalView TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with local_complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.
Valgrind Valgrind: Debugging and profiling tools

Devel

Module Description
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.
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
Bazel Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
Boost Boost provides free peer-reviewed portable C++ source libraries.
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
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.
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.
flatbuffers FlatBuffers: Memory Efficient Serialization Library
flatbuffers-python Python Flatbuffers runtime library.
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.
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.
guile Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
hipify-clang Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced.
HyperQueue HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated notes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.
intltool intltool is a set of tools to centralize translation of many different file formats using GNU gettext-local_compatible PO 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.
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.
make GNU version of make utility
makeinfo makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
Mako A super-fast templating language that borrows the best ideas from the existing templating languages
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.
nsync nsync is a C library that exports various synchronization primitives, such as mutexes
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.
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 freedesktop.org.
pkgconfig pkgconfig is a Python module to interface with the pkg-config command line tool
protobuf Google Protocol Buffers
protobuf-python Python Protocol Buffers runtime library.
PyTorch Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
Qt5 Qt is a comprehensive cross-platform C++ application framework.
rocm-cuda2hip ROCm-HIPIFY : Tools to translate CUDA source code into portable HIP C++ automatically.
Spack Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
SQLite SQLite: SQL Database Engine in a C Library
squashfs-tools Squashfs is a local_compressed read-only filesystem for Linux.
SWIG SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
texinfo Texinfo is the official documentation format of the GNU project.
texlive TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
typing-extensions Typing Extensions – Backported and Experimental Type Hints for Python
xorg-macros X.org macros utilities.

Geo

Module Description
PROJ_4 PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.

Lang

Module Description
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.
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.
byacc Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular local_compiler.
Cython Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
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.
FriBidi The Free Implementation of the Unicode Bidirectional Algorithm.
Guile Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.
Java Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Julia Julia is a high-level, high-performance dynamic programming language for numerical computing
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.
Mono An open source, cross-platform, implementation of C# and the CLR that is binary local_compatible with Microsoft.NET.
NASM NASM: General-purpose x86 assembler
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.
OpenCL-runtime OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal local_computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.
OpenCL-sdk OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal local_computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.
Perl Larry Wall's Practical Extraction and Report Language
Python Python is a programming language that lets you work more quickly and integrate your systems more effectively.
R R is a free software environment for statistical computing and graphics.
Ruby Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Rust Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SciPy-bundle Bundle of Python packages for scientific software
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.
Tkinter Tkinter module, built with the Python buildsystem
Yasm Yasm: Complete rewrite of the NASM assembler with BSD license

Lib

Module Description
ACTC ACTC converts independent triangles into triangle strips or fans.
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.
c-ares c-ares is a C library for asynchronous DNS requests (including name resolves)
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.
double-conversion Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
elfutils The elfutils project provides libraries and tools for ELF files and DWARF data.
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.
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.
gc The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
GDRCopy A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
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.
GlobalArrays Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
graphite2 Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.
ICU ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
IOTK The input/output tool kit (IOTK) is a Fortran90 library intended to provide a simplified access to tagged files formatted using some specific rule.
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.
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
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 local_compression and delocal_compression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libmatheval GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
libogg Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
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.
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.
LibTIFF tiff: Library and tools for reading and writing TIFF data files
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.
libunistring This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
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
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.
libxml2 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libyaml LibYAML is a YAML parser and emitter written in C.
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.
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.
magic python-magic is a Python interface to the libmagic file type identification library. libmagic identifies file types by checking their headers according to a predefined list of file types. This functionality is exposed to the command line by the Unix command file.
NCCL The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
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.
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.
PLASMA PLASMA is a software package for solving problems in dense linear algebra using multicore processors and Xeon Phi coprocessors. PLASMA provides implementations of state-of-the-art algorithms using cutting-edge task scheduling techniques. PLASMA currently offers a collection of routines for solving linear systems of equations, least squares problems, eigenvalue problems, and singular value problems.
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.
PROJ Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
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.
pytest Simple powerful testing with Python
PyYAML PyYAML is a YAML parser and emitter for the Python programming language.
scikit-build Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
SDL2 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SIONlib 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.
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.
tbb 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.
TensorFlow An open-source software library for Machine Intelligence
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.
zlib zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-local_compression library for use on virtually any local_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.

Math

Module Description
Dakota The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models.
Eigen Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
ELPA Eigenvalue SoLvers for Petaflop-Applications .
ELSI ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
GEOS GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GMP GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gmpy2 GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x
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.
libxsmm LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
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.
MATLAB MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
MCR The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
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.
MPC Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPS A parallel sparse direct solver
Octave GNU Octave is a high-level interpreted language, primarily intended for numerical local_computations.
ParMETIS ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for local_computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR local_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.
SCOTCH Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
sympy SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
Theano Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

Mpi

Module Description
impi Intel MPI Library, compatible with MPICH ABI
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.
MPICH MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).
OpenCoarrays OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran.
OpenMPI The Open MPI Project is an open source MPI-2 implementation.

Numlib

Module Description
AOCL AMD provides a free set of thoroughly optimized and threaded math routines for HPC, scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more.
arpack-ng ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
BLIS AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
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.
cuDNN The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
FFTW FFTW is a C subroutine library for local_computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and local_complex data.
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.
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.
imkl Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
imkl-FFTW FFTW interfaces using Intel oneAPI Math Kernel Library
LAPACK 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.
libFLAME libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.
mkl Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
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.
OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
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.
ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SuiteSparse SuiteSparse is a collection of libraries manipulate sparse matrices.

Perf

Module Description
Advisor Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
Cube 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.
CubeGUI 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 graphical report explorer.
CubeLib 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 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.
ipp Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
OPARI2 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.
OTF2 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.
PAPI 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.
PDT 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.
Scalasca Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.
Score-P 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.
Vampir The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very local_complex performance monitoring data.

Phys

Module Description
COMSOL COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.
DFTB+ DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.
Gaussian Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
MedeA Materials Design, Inc. announces the release of MedeA® version 2.22 software environment for atomistic materials modeling and simulation.
phono3py This software calculates phonon-phonon interaction related properties
phonopy This software calculates phonon-phonon interaction related properties
QMCPACK QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense.
ReSpect ReSpect is a computer simulation program enabling the prediction and understanding of molecular and material properties from advanced first-principle relativistic DFT calculations.
Siesta 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.
TB2J Python is a programming language that lets you work more quickly and integrate your systems more effectively.
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.
VASP The Vienna Ab initio Simulation Package (VASP) is a local_computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.
Yambo Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.

Python

Module Description
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.

System

Module Description
CUDA CUDA (formerly Compute Unified Device Architecture) is a parallel local_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 local_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.
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.
libpciaccess Generic PCI access library.
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.

Toolchain

Module Description
foss GNU Compiler Collection (GCC) based local_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.
gcccuda GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
gompi GNU Compiler Collection (GCC) based local_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.
iccifort Intel C, C++ & Fortran compilers
iimpi Intel C/C++ and Fortran compilers, alongside Intel MPI.
intel Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
iomkl Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
iompi Intel C/C++ and Fortran compilers, alongside Open MPI.
OAMD AMD Compiler Collection (aocc) based local_compiler toolchain, including OpenMPI for MPI support, AOCL.

Tools

Module Description
ANSYS ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
aria2 aria2 is a lightweight multi-protocol & multi-source command-line download utility.
awscli Universal Command Line Environment for AWS
binutils binutils: GNU binary utilities
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.
CppUnit CppUnit is the C++ port of the famous JUnit framework for unit testing.
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.
DB Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
deepdiff DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
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.
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.
FPM Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.
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
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.
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.
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.
gperftools gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
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
help2man help2man produces simple manual pages from the '--help' and '--version' output of other commands.
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.
Inspector Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications
itac The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
jax Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
KAROLINA Disclaimer: this post investigates how recent MKL versions behave on Zen CPUs. You should read the MKL license before using MKL. I shall not be held responsible for how you use MKL. Intel MKL has been known to use a SSE code paths on AMD CPUs that support newer SIMD instructions such as those that use the Zen microarchitecture. A (by now) well-known trick has been to set the MKL_DEBUG_CPU_TYPE environment variable to the value 5 to force the use of AVX2 kernels on AMD Zen CPUs. Unfortunately, this variable has been removed from Intel MKL 2020 Update 1 and later. This can be confirmed easily by running a program that uses MKL with ltrace -e getenv.
libarchive Multi-format archive and compression library
Meson Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
MIKE MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide.
networkx NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Ninja Ninja is a small build system with a focus on speed.
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.
parallel parallel: Build and execute shell commands in parallel
poetry Python packaging and dependency management made easy
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.
rocm-smi The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications.
ROCR-Runtime The user-mode API interfaces and libraries necessary for host applications to launch compute kernels to available HSA ROCm kernel agents
ROCT-Thunk-Interface The user-mode API interfaces used to interact with the ROCk driver
s3cmd S3cmd is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage or DreamHost DreamObjects. It is best suited for power users who are familiar with command line programs. It is also ideal for batch scripts and automated backup to S3, triggered from cron, etc.
SavvySuite Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes. This software was written by Matthew Wakeling at the University of Exeter, and was presented at the 2017 ASHG meeting in Orlando, Florida. To cite this software, please use the following references. For SavvyCNV, use: https://www.biorxiv.org/content/10.1101/617605v1 For all other parts of SavvySuite, cite the ASHG conference presentation: Wakeling, MN, De Franco E, Hattersley AT, Ellard S. Making the most of targeted sequencing: detecting CNVs and homozygous regions using offtarget reads with SavvyCNV. 67th Annual Meeting of the American Society of Human Genetics. Orlando, FL; 17–21 October 2017. and if desired, cite this web site too: Wakeling MN. SavvySuite. 2018. https://github.com/rdemolgen/SavvySuite.
Singularity Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way.
Szip Szip compression software, providing lossless compression of scientific data
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.
util-linux Set of Linux utilities
vaspkit VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code.
VirtualGL VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.
VTune Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
WRF Old module, description not available.
XZ xz: XZ utilities
Z3 Z3 is a theorem prover from Microsoft Research.
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

Vis

Module Description
at-spi2-atk AT-SPI 2 toolkit bridge
at-spi2-core Assistive Technology Service Provider Interface.
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.
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.
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
FFmpeg A complete, cross-platform solution to record, convert and stream audio and video.
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.
fontconfig Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
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.
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.
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
GLib GLib is one of the base libraries of the GTK+ project
gnuplot Portable interactive, function plotting utility
grace Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
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.
HarfBuzz HarfBuzz is an OpenType text shaping engine.
ImageMagick ImageMagick is a software suite to create, edit, compose, or convert bitmap images
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.
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.
libGLU The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
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.
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
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
OptiX OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms.
OVITO OVITO is a scientific visualization and analysis software for atomistic and particle simulation data.
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.
ParaView ParaView is a scientific parallel visualizer.
Pillow Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
pixman Pixman is a low-level software library for pixel manipulation, providing features such as image local_compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
plotly.py An open-source, interactive graphing library for Python
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.
QtiPlot QtiPlot is a cross-platform scientific application for data analysis and visualisation.
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.
VESTA VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.
VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
X11 The X Window System (X11) is a windowing system for bitmap displays
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.
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.
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.

Comments