Emmy Core Modules
Warning
This software revision is a available for testing on a small number of AlmaLinux 10 test nodes. It cannot be used on the main HPC system. It should not be used for production workloads yet!
These modules are loadable by default. No other modules have to be loaded first.
Tip
The software packages loaded on each phase are optimized for the particular CPU and GPU architecture (machine kind) of that phase (e.g Intel Cascadelake or Intel Sapphirerapids).
You can print the current machine kind by using the command: /sw/rev_profile/26.07/machine-kind
If you compile your own code (e.g. by using gcc or pip) please take care to compile on the same machine kind that the code will also be executed on.
List of Modules
| Module Names | Description | Homepage |
|---|---|---|
| ant/1.10.14 | 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 | https://ant.apache.org/ |
| apptainer/1.2.5 apptainer/1.3.6 apptainer/1.4.4 | Apptainer is an open source container platform designed to be simple, fast, and secure. Many container platforms are available, but Apptainer is designed for ease-of-use on shared systems and in high performance computing (HPC) environments. | |
| autoconf/2.72 | Autoconf – system configuration part of autotools | |
| autoconf-archive/2024.10.16 | The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf. | |
| automake/1.18.1 | Automake – make file builder part of autotools | |
| bat/0.26.1 | A cat(1) clone with wings. | |
| binutils/2.46.1 | GNU binutils, which contain the linker, assembler, objdump and others | |
| bison/3.8.2 | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. | |
| cairo/1.18.4 | Cairo is a 2D graphics library with support for multiple output devices. | https://www.cairographics.org/ |
| chimera/1.18 | UCSF CHIMERA: an Extensible Molecular Modeling System | https://www.cgl.ucsf.edu/chimera/ |
| cmake/3.31.12 cmake/4.3.3 | A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | |
| diffutils/3.12 | GNU Diffutils is a package of several programs related to finding differences between files. | |
| dynamo/1.1.552 | Dynamo is a software environment for subtomogram averaging of cryo-EM data. | https://www.dynamo-em.org/w/index.php?title=Main_Page |
| elfutils/0.194 | elfutils is a collection of various binary tools such as eu-objdump, eu-readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils. | |
| fd/10.4.2 | fd is a program to find entries in your filesystem. It is a simple, fast and user-friendly alternative to the traditional ‘find’ command. While it does not aim to support all of find’s powerful functionality, it provides sensible defaults for most use cases. | |
| findutils/4.10.0 | The GNU Find Utilities are the basic directory searching utilities of the GNU operating system. | |
| fish/4.2.0 | fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family. | |
| flex/2.6.4 | Flex is a tool for generating scanners. | https://github.com/westes/flex |
| fribidi/1.0.12 | GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm. | https://github.com/fribidi/fribidi |
| fzf/0.74.1 | A general-purpose command-line fuzzy finder that provides fast, interactive filtering for files, processes, git commits, and more. It supports fuzzy search with real-time preview and various input sources. | |
| gawk/5.4.0 | If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time-consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. | |
| gcc/13.4.0 gcc/15.3.0 | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. | |
| gengetopt/2.23 | Tool to write command line option parsing code for C programs | https://www.gnu.org/software/gengetopt/gengetopt.html |
| git/2.55.0 | 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. | https://git-scm.com |
| git-lfs/3.7.1 | Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special ‘pointer files’ in the repository, while storing the actual file contents on a Git LFS server. | |
| glib/2.86.3 | GLib provides the core application building blocks for libraries and applications written in C. | https://developer.gnome.org/glib/ |
| gmake/4.4.1 | GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program’s source files. | |
| gnuplot/5.4.10 gnuplot/6.0.0 | Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don’t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986 | http://www.gnuplot.info |
| go/1.26.5 | The golang compiler and build environment | |
| gobject-introspection/1.86.0 | The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output | https://wiki.gnome.org/Projects/GObjectIntrospection |
| harfbuzz/13.1.1 | The Harfbuzz package contains an OpenType text shaping engine. | https://github.com/harfbuzz/harfbuzz |
| hisat2/2.2.1 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). | https://daehwankimlab.github.io/hisat2/ |
| imagej/1.54r | ImageJ is public domain software for processing and analyzing scientific images. It is written in Java, which allows it to run on many different platforms. For further information, see: The ImageJ website, the primary home of this project. The ImageJ wiki, a community-built knowledge base covering ImageJ and its derivatives and flavors, including ImageJ2, Fiji, and others. The ImageJ mailing list and Image.sc Forum for community support. The Contributing page of the ImageJ wiki for details on how to contribute. | https://www.imagej.net |
| intel-oneapi-compilers/2025.3.2 | Intel oneAPI Compilers. Includes: icx, icpx, ifx, and ifort. Releases before 2024.0 include icc/icpc LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at intel.ly/393CijO. | |
| intel-oneapi-compilers-classic/2021.10.0 | Relies on intel-oneapi-compilers to install the compilers, and configures modules for icc/icpc/ifort. | |
| intel-oneapi-compilers-llvm/2025.3.2 | The internal LLVM components of the Intel oneAPI Compilers. Includes: clang, clang++, llvm-ar, llvm-profgen, … | |
| jq/1.8.2 | jq is a lightweight and flexible command-line JSON processor. | |
| julia/1.12.6 | The Julia Language: A fresh approach to technical computing This package installs the x86_64-linux-gnu version provided by Julia Computing | |
| lftp/4.9.3 | LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent). | |
| libffi/3.5.2 | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time. | https://sourceware.org/libffi/ |
| libpng/1.6.47 | libpng is the official PNG reference library. | http://www.libpng.org/pub/png/libpng.html |
| libtool/2.5.4 | libtool – library building part of autotools. | |
| libxml2/2.15.3 | Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License. | https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home |
| llvm/22.1.8 llvm/22.1.8-oneapi | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name ‘LLVM’ itself is not an acronym; it is the full name of the project. | https://llvm.org/ |
| m4/1.4.21 | GNU M4 is an implementation of the traditional Unix macro processor. | |
| mercurial/7.1.2 | Mercurial is a free, distributed source control management tool. | https://www.mercurial-scm.org |
| meson/1.11.1 | Meson is a portable open source build system meant to be both extremely fast, and as user friendly as possible. | https://mesonbuild.com/ |
| miniforge3/24.3.0-0 miniforge3/25.3.0-3 miniforge3/26.3.2-3 | Miniforge3 is a minimal installer for conda and mamba specific to conda-forge. | |
| ncurses/6.6 | 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. | |
| nextflow/26.04.0-standalone | Data-driven computational pipelines. | https://www.nextflow.io |
| ninja/1.13.2 | Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible. | |
| openjdk/25.0.2_10 | The free and open-source java implementation | |
| parallel/20240822 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. | |
| patchelf/0.17.2 | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | |
| perl/5.42.2 | Perl 5 is a highly capable, feature-rich programming language with over 27 years of development. | |
| picard/3.3.0 | Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | https://broadinstitute.github.io/picard/ |
| pigz/2.8 | A parallel implementation of gzip for modern multi-processor, multi-core machines. | |
| pkgconf/2.5.1 | pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility. | |
| py-setuptools/80.9.0 | A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages. | https://github.com/pypa/setuptools |
| py-wheel/0.45.1 | A built-package format for Python. | https://github.com/pypa/wheel |
| python/3.13.13 | The Python programming language. | |
| rclone/1.74.3 | Rclone is a command line program to sync files and directories to and from various cloud storage providers | |
| rdma-core/60.1 | RDMA core userspace libraries and daemons | |
| ripgrep/15.1.0 | ripgrep is a line-oriented search tool that recursively searches your current directory for a regex pattern. ripgrep is similar to other popular search tools like The Silver Searcher, ack and grep. | https://github.com/BurntSushi/ripgrep |
| rust/1.97.1 | The Rust programming language toolchain. | |
| scala/2.13.14 | Scala is a general-purpose programming language providing support for functional programming and a strong static type system. Designed to be concise, many of Scala’s design decisions were designed to build from criticisms of Java. | |
| skopeo/0.1.40 | skopeo is a command line utility that performs various operations on container images and image repositories. | https://github.com/containers/skopeo |
| spack/1.2.2 | Spack is a multi-platform package manager that builds and installs multiple versions and configurations of software. It works on Linux, macOS, and many supercomputers. Spack is non-destructive: installing a new version of a package does not break existing installations, so many configurations of the same package can coexist. | https://spack.io/ |
| sqlite/3.53.1 | SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. | https://www.sqlite.org |
| subversion/1.14.5 | Apache Subversion - an open source version control system. | |
| tar/1.35 | GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation. | |
| tcsh/6.24.14 | Tcsh is an enhanced but completely compatible version of csh, the C shell. Tcsh is a command language interpreter which can be used both as an interactive login shell and as a shell script command processor. Tcsh includes a command line editor, programmable word completion, spelling correction, a history mechanism, job control and a C language like syntax. | https://www.tcsh.org/ |
| texinfo/7.2 | Texinfo is the official documentation format of the GNU project. | |
| tree/2.1.0 | Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty. Tree has been ported and reported to work under the following operating systems: Linux, FreeBSD, OS X, Solaris, HP/UX, Cygwin, HP Nonstop and OS/2. | http://mama.indstate.edu/users/ice/tree/ |
| vim/9.2.0000 | Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often called a ‘programmer’s editor,’ and so useful for programming that many consider it an entire IDE. It’s not just for programmers, though. Vim is perfect for all kinds of text editing, from composing email to editing configuration files. | https://www.vim.org |
| which/2.23 | GNU which - is a utility that is used to find which executable (or alias or shell function) is executed when entered on the shell prompt. | https://savannah.gnu.org/projects/which/ |
| xz/5.8.3 | XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils. | https://tukaani.org/xz/ |
| zlib-ng/2.3.3 | zlib replacement with optimizations for next generation systems. | https://github.com/zlib-ng/zlib-ng |
| zsh/5.9 | Zsh is a shell designed for interactive use, although it is also a powerful scripting language. Many of the useful features of bash, ksh, and tcsh were incorporated into zsh; many original features were added. | |
| zstd/1.5.7 | Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. | https://facebook.github.io/zstd/ |