AgR eRI compute cluster - applications as modules

Release Update - 04 December 2023

New and Improved

Applications compiled as modules are available to all users
(See the current list of modules using the command module spider like the example below.)
Fixes

N/A
Example

$ module spider

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The following is a list of the modules and extensions currently available:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  BCL-Convert: BCL-Convert/4.2.4
    Converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files

  BLIS: BLIS/0.9.0-GCC-12.3.0, BLIS/4.1-GCC-12.3.0-amd
    BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

  CMake: CMake/3.27.7
    CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

  EasyBuild: EasyBuild/4.8.1
    EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.

  FFTW: FFTW/3.3.10-GCC-12.3.0
    FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

  FFTW.MPI: FFTW.MPI/3.3.10-gompi-2023a
    FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

  FlexiBLAS: FlexiBLAS/3.3.1-GCC-12.3.0
    FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.

  FriBidi: FriBidi/1.0.12-GCC-12.3.0
    Free Implementation of the Unicode Bidirectional Algorithm.

  GCC: GCC/12.3.0
    The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

  GCCcore: GCCcore/12.3.0
    The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

  GMP: GMP/6.2.1-GCCcore-12.3.0
    GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. 

  HDF5: HDF5/1.14.3-gompi-2023a
    HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high
    volume and complex data.

  HarfBuzz: HarfBuzz/4.4.1-GCC-12.3.0
    HarfBuzz is an OpenType text shaping engine.

  Java: Java/20.0.2
    Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. 

  LLVM: LLVM/14.0.6-GCC-12.3.0-static
    The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These
    libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is
    particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.

  LibTIFF: LibTIFF/4.4.0-GCCcore-12.3.0
    tiff: Library and tools for reading and writing TIFF data files

  Meson: Meson/0.62.1
    Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

  Miniconda3: Miniconda3/23.10.0-1
    A platform for Python-based data analytics

  NASM: NASM/2.15.05
    NASM: General-purpose x86 assembler

  NLopt: NLopt/2.7.1-GCC-12.3.0
    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

  Ninja: Ninja/1.11.1
    Ninja is a small build system with a focus on speed.

  OpenBLAS: OpenBLAS/0.3.23-GCC-12.3.0
    OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

  OpenMPI: OpenMPI/4.1.5-GCC-12.3.0
    The Open MPI Project is an open source MPI-3 implementation.

  OpenSSL: OpenSSL/1.1
    The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and
    Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. 

  PCRE2: PCRE2/10.42-GCCcore-12.3.0
    The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. 

  Python: Python/3.11.6-foss-2023a
    Python is a programming language that lets you work more quickly and integrate your systems more effectively.

  R: R/4.3.2-foss-2023a
    R is a free software environment for statistical computing and graphics.

  Rust: Rust/1.73.0-GCC-12.3.0
    Systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.

  SQLite: SQLite/3.42.0-GCCcore-12.3.0
    SQLite: SQL Database Engine in a C Library

  SWIG: SWIG/3.0.8
    SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

  ScaLAPACK: ScaLAPACK/2.2.0-gompi-2023a-fb
    The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

  Szip: Szip/2.1.1-GCCcore-12.3.0
    Szip compression software, providing lossless compression of scientific data 

  Tcl: Tcl/8.6.10-GCCcore-12.3.0
    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.

  Tk: Tk/8.6.10-GCCcore-12.3.0
    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.

  UCC: UCC/1.2.0-GCCcore-12.3.0
    UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models
    and runtimes. 

  UCX: UCX/1.14.1-GCCcore-12.3.0
    Unified Communication X An open-source production grade communication framework for data centric and high-performance applications 

  XZ: XZ/5.4.2-GCCcore-12.3.0
    xz: XZ utilities

  ZeroMQ: ZeroMQ/4.3.5-GCCcore-12.3.0
    ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process,
    inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply.

  binutils: binutils/2.40-GCCcore-12.3.0, binutils/2.40
    binutils: GNU binary utilities

  bzip2: bzip2/1.0.8-GCCcore-12.3.0
    bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of
    statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. 

  cURL: cURL/8.3.0-GCCcore-12.3.0
    libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP,
    SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic,
    Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. 

  foss: foss/2023a
    GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

  freetype: freetype/2.13.2-GCCcore-12.3.0
    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. 

  gompi: gompi/2023a
    GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

  libgit2: libgit2/1.6.4-GCC-12.3.0
    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.

  libjpeg-turbo: libjpeg-turbo/2.1.5.1-GCCcore-12.3.0
    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. 

  libpng: libpng/1.6.40-GCCcore-12.3.0
    EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
    libpng is the official PNG reference library
  libreadline: libreadline/8.2-GCCcore-12.3.0
    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. 
  libxml2: libxml2/2.11.4-GCCcore-12.3.0
    Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). 
  libxslt: libxslt/1.1.38-GCCcore-12.3.0
    Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
  ncurses: ncurses/6.4-GCCcore-12.3.0
    The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and
    forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. 
  netCDF: netCDF/4.9.2-gompi-2023a
    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.
  nodejs: nodejs/18.18.2-GCCcore-12.3.0
    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.
  numactl: numactl/2.0.16-GCCcore-12.3.0
    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. 
  snakemake: snakemake/7.32.3-foss-2023a-Python-3.11.6
    The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
  zlib: zlib/1.2.13-GCCcore-12.3.0, zlib/1.2.13
    zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer
    hardware and operating system.
  zstd: zstd/1.5.5-GCCcore-12.3.0
    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.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
To learn more about a package execute:
   $ module spider Foo
where "Foo" is the name of a module.
To find detailed information about a particular package you
must specify the version if there is more than one version:
   $ module spider Foo/11.1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------