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ATHENA software

Uwaga

Some software in the list below may require an additional licence and may not be generally available to all PLGrid users.

AlphaFold

AlphaFold2

Versions:

Module Default
module load AlphaFold/2.3.2
module load AlphaFold/2.3.1

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.

Versions:

Module Default
module load Autoconf/2.71

Automake

Automake: GNU Standards-compliant Makefile generator

Versions:

Module Default
module load Automake/1.16.5

Autotools

This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

Versions:

Module Default
module load Autotools/20220317

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.

Versions:

Module Default
module load Bison/3.8.2

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.

Versions:

Module Default
module load Blender/3.5.0-linux-x86_64-CUDA-11.7.0
module load Blender/3.3.2-linux-x86_64-CUDA-11.7.0

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.

Versions:

Module Default
module load Brotli/1.0.9

CMake

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

Versions:

Module Default
module load CMake/3.23.1

CUDA

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

Versions:

Module Default
module load CUDA/12.0.0
module load CUDA/11.8.0
module load CUDA/11.7.0
module load CUDA/11.6.0
module load CUDA/11.4.1
module load CUDA/11.3.1
module load CUDA/10.0.130

DB

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

Versions:

Module Default
module load DB/18.1.40

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,...).

Versions:

Module Default
module load GCC/12.3.0
module load GCC/12.2.0
module load GCC/11.3.0
module load GCC/11.2.0
module load GCC/10.3.0

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,...).

Versions:

Module Default
module load GCCcore/12.3.0
module load GCCcore/12.2.0
module load GCCcore/11.3.0
module load GCCcore/11.2.0
module load GCCcore/10.3.0

GMP

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

Versions:

Module Default
module load GMP/6.2.1

Go

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

Versions:

Module Default
module load Go/1.17.3

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).

Versions:

Module Default
module load HH-suite/3.3.0

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

Versions:

Module Default
module load Java/13.0.2
module load Java/11.0.2

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")

Versions:

Module Default
module load LLVM/14.0.3

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.

Versions:

Module Default
module load M4/1.4.19
module load M4/1.4.18

Mako

A super-fast templating language that borrows the best ideas from the existing templating languages

Versions:

Module Default
module load Mako/1.2.0

Mesa

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

Versions:

Module Default
module load Mesa/22.0.3

Meson

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

Versions:

Module Default
module load Meson/0.62.1

Miniconda3

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.

Versions:

Module Default
module load Miniconda3/4.9.2
module load Miniconda3/23.3.1-0

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Versions:

Module Default
module load NAMD/3.0b3-Linux-x86_64-multicore-CUDA

NASM

NASM: General-purpose x86 assembler

Versions:

Module Default
module load NASM/2.15.05

NVHPC

C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

Versions:

Module Default
module load NVHPC/22.7
module load NVHPC/22.11-CUDA-11.7.0

Ninja

Ninja is a small build system with a focus on speed.

Versions:

Module Default
module load Ninja/1.10.2

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.

Versions:

Module Default
module load OpenSSL/1.1

Perl

Larry Wall's Practical Extraction and Report Language

Versions:

Module Default
module load Perl/5.34.1

Python

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

Versions:

Module Default
module load Python/3.10.4

Rust

Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.

Versions:

Module Default
module load Rust/1.60.0

SQLite

SQLite: SQL Database Engine in a C Library

Versions:

Module Default
module load SQLite/3.38.3

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.

Versions:

Module Default
module load Tcl/8.6.12

TeraChem

TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.

Versions:

Module Default
module load TeraChem/1.95

TurboVNC

TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.

Versions:

Module Default
module load TurboVNC/3.0.1

UnZip

UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles

Versions:

Module Default
module load UnZip/6.0

X11

The X Window System (X11) is a windowing system for bitmap displays

Versions:

Module Default
module load X11/20220504

XZ

xz: XZ utilities

Versions:

Module Default
module load XZ/5.2.5

Z3

Z3 is a theorem prover from Microsoft Research.

Versions:

Module Default
module load Z3/4.10.2

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.

Versions:

Module Default
module load ant/1.10.9-Java-11

binutils

binutils: GNU binary utilities

Versions:

Module Default
module load binutils/2.40
module load binutils/2.39
module load binutils/2.38
module load binutils/2.37
module load binutils/2.36.1

bio-embeddings

Versions:

Module Default
module load bio-embeddings/0.2.2

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.

Versions:

Module Default
module load bzip2/1.0.8

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.

Versions:

Module Default
module load cURL/7.83.0

cryoSPARC

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.

Versions:

Module Default
module load cryoSPARC/4.3.0
module load cryoSPARC/4.2.1-230621
module load cryoSPARC/4.2.1-230403
module load cryoSPARC/4.2.0-230302

cuDNN

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

Versions:

Module Default
module load cuDNN/8.6.0.163-CUDA-11.8.0
module load cuDNN/8.4.1.50-CUDA-11.7.0
module load cuDNN/8.4.1.50-CUDA-11.6.0
module load cuDNN/8.2.2.26-CUDA-11.4.1
module load cuDNN/8.2.1.32-CUDA-11.3.1

elfutils

The elfutils project provides libraries and tools for ELF files and DWARF data.

Versions:

Module Default
module load elfutils/0.187

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)

Versions:

Module Default
module load expat/2.4.8

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.

Versions:

Module Default
module load flex/2.6.4

fontconfig

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

Versions:

Module Default
module load fontconfig/2.14.0

foss

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

Versions:

Module Default
module load foss/2023a
module load foss/2022b
module load foss/2022a
module load foss/2021b
module load foss/2021a

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.

Versions:

Module Default
module load freetype/2.12.1

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

Versions:

Module Default
module load gettext/0.21.1
module load gettext/0.21

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.

Versions:

Module Default
module load git/2.36.0-nodocs

gompi

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

Versions:

Module Default
module load gompi/2023a
module load gompi/2022b
module load gompi/2022a-mpi-thread-multiple
module load gompi/2022a
module load gompi/2021b
module load gompi/2021a

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.

Versions:

Module Default
module load gperf/3.1

groff

Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.

Versions:

Module Default
module load groff/1.22.4

gzip

gzip (GNU zip) is a popular data compression program as a replacement for compress

Versions:

Module Default
module load gzip/1.12

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.

Versions:

Module Default
module load hwloc/2.7.1

iimpi

Intel C/C++ and Fortran compilers, alongside Intel MPI.

Versions:

Module Default
module load iimpi/2022a

imkl

Intel oneAPI Math Kernel Library

Versions:

Module Default
module load imkl/2022.1.0
module load imkl/2022.0.1
module load imkl/2021.4.0

intel-compilers

Intel C, C++ & Fortran compilers (classic and oneAPI)

Versions:

Module Default
module load intel-compilers/2023.0.0
module load intel-compilers/2022.1.0
module load intel-compilers/2021.4.0

intel

Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).

Versions:

Module Default
module load intel/2022a

intltool

intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

Versions:

Module Default
module load intltool/0.51.0

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.

Versions:

Module Default
module load itac/2021.6.0

libGLU

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

Versions:

Module Default
module load libGLU/9.0.2

libarchive

Multi-format archive and compression library

Versions:

Module Default
module load libarchive/3.6.1

libdrm

Direct Rendering Manager runtime library.

Versions:

Module Default
module load libdrm/2.4.110

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.

Versions:

Module Default
module load libffi/3.4.2

libglvnd

libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.

Versions:

Module Default
module load libglvnd/1.4.0

libjpeg-turbo

libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

Versions:

Module Default
module load libjpeg-turbo/2.1.3

libpciaccess

Generic PCI access library.

Versions:

Module Default
module load libpciaccess/0.16

libpng

libpng is the official PNG reference library

Versions:

Module Default
module load libpng/1.6.37
module load libpng/1.2.58

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.

Versions:

Module Default
module load libreadline/8.2
module load libreadline/8.1.2

libtool

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

Versions:

Module Default
module load libtool/2.4.7

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

Versions:

Module Default
module load libunwind/1.6.2

libxml2

Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

Versions:

Module Default
module load libxml2/2.9.13

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.

Versions:

Module Default
module load lz4/1.9.3

monai

Medical Open Network for AI

Versions:

Module Default
module load monai/1.2.0
module load monai/1.0.1

nano

GNU nano text editor.

Versions:

Module Default
module load nano/6.2

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.

Versions:

Module Default
module load ncurses/6.3
module load ncurses/6.2

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.

Versions:

Module Default
module load numactl/2.0.14

nvompic

NVHPC based compiler toolchain, including OpenMPI for MPI support.

Versions:

Module Default
module load nvompic/2022a
module load nvompic/2021b

pixman

Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

Versions:

Module Default
module load pixman/0.40.0

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.

Versions:

Module Default
module load pkgconf/1.8.0

rclone

Rclone is a command line program to sync files and directories to and from a variety of online storage services

Versions:

Module Default
module load rclone/1.60.1

s3cmd

Amazon S3 Tools: Command Line S3 Client Software and S3 Backup.

Versions:

Module Default
module load s3cmd/2.3.0

util-linux

Set of Linux utilities

Versions:

Module Default
module load util-linux/2.38

xorg-macros

X.org macros utilities.

Versions:

Module Default
module load xorg-macros/1.19.3

zlib

zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.

Versions:

Module Default
module load zlib/1.2.13
module load zlib/1.2.12
module load zlib/1.2.11

zsh

Zsh is a shell designed for interactive use, although it is also a powerful scripting language.

Versions:

Module Default
module load zsh/5.9

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.

Versions:

Module Default
module load zstd/1.5.2

Last update: January 29, 2024