.. _software:

Software on JADE
================

The software initially installed on the machine is listed in the following table:

.. csv-table::
   :header: Application,Version,Note
   :widths: 20, 20, 10

    GNU compiler suite,	13.3.0,	
    GNU compiler suite,	12.3.0,
    OpenMPI,   5.0.3, Inlcudes multi-thread support
    Gromacs,	2024.3,	
    

This software has been built from source and installed as modules. To list the source built applications do:

.. code-block:: console

   [user@jade-login ~]$ module avail

   ------------------------------------------ /apps/system/modules -------------------------------------------
      AMD-LLVM/6.2.1-foss-2024a                        AdaptiveCpp/24.06.0-foss-2024a (D)
      AMD-LLVM/6.2.2-foss-2024a                 (D)    GROMACS/2024.3-foss-2024a-mpi
      AdaptiveCpp/24.06.0-foss-2024a-ROCm-6.2.1        GROMACS/2024.3-foss-2024a-tmpi (D)
      AdaptiveCpp/24.06.0-foss-2024a-ROCm-6.2.2

   ----------------------------------- /apps/system/easybuild/modules/all ------------------------------------
      Anaconda3/2024.02-1                      XZ/5.4.5-GCCcore-13.3.0
      Autoconf/2.71-GCCcore-12.3.0             Z3/4.13.0-GCCcore-13.3.0
      Autoconf/2.72-GCCcore-13.3.0      (D)    binutils/2.40-GCCcore-12.3.0
      Automake/1.16.5-GCCcore-12.3.0           binutils/2.40
      Automake/1.16.5-GCCcore-13.3.0    (D)    binutils/2.42-GCCcore-13.3.0
      Autotools/20220317-GCCcore-12.3.0        binutils/2.42                      (D)
      Autotools/20231222-GCCcore-13.3.0 (D)    bzip2/1.0.8-GCCcore-12.3.0
      BLIS/1.0-GCC-13.3.0                      bzip2/1.0.8-GCCcore-13.3.0         (D)
      Bison/3.8.2-GCCcore-12.3.0               cURL/8.0.1-GCCcore-12.3.0
      Bison/3.8.2-GCCcore-13.3.0               cURL/8.7.1-GCCcore-13.3.0          (D)
      Bison/3.8.2                       (D)    fio/3.36-GCCcore-12.3.0
      Boost/1.85.0-GCC-13.3.0                  flex/2.6.4-GCCcore-12.3.0
      CMake/3.29.3-GCCcore-13.3.0              flex/2.6.4-GCCcore-13.3.0
      Clang/18.1.8-GCCcore-13.3.0              flex/2.6.4                         (D)
      EasyBuild/4.9.4                          foss/2024a
      FFTW.MPI/3.3.10-gompi-2024a              gettext/0.22.5
      FFTW/3.3.10-GCC-12.3.0                   gompi/2024a
      FFTW/3.3.10-GCC-13.3.0            (D)    gzip/1.13-GCCcore-13.3.0
      FlexiBLAS/3.4.4-GCC-13.3.0               help2man/1.49.3-GCCcore-12.3.0
      GCC/12.3.0                               help2man/1.49.3-GCCcore-13.3.0     (D)
      GCC/13.3.0                        (D)    hwloc/2.10.0-GCCcore-13.3.0
      GCCcore/12.3.0                           libarchive/3.7.4-GCCcore-13.3.0
      GCCcore/13.3.0                    (D)    libevent/2.1.12-GCCcore-12.3.0
      GMP/6.3.0-GCCcore-13.3.0                 libevent/2.1.12-GCCcore-13.3.0     (D)
      ICU/75.1-GCCcore-13.3.0                  libfabric/1.18.0-GCCcore-12.3.0
      LAPACK/3.12.0-GCC-13.3.0                 libfabric/1.21.0-GCCcore-13.3.0    (D)
      LLVM/18.1.8-GCCcore-13.3.0               libffi/3.4.4-GCCcore-12.3.0
      M4/1.4.19-GCCcore-12.3.0                 libffi/3.4.5-GCCcore-13.3.0        (D)
      M4/1.4.19-GCCcore-13.3.0                 libpciaccess/0.17-GCCcore-12.3.0
      M4/1.4.19                         (D)    libpciaccess/0.18.1-GCCcore-13.3.0 (D)
      Meson/1.4.0-GCCcore-13.3.0               libreadline/8.2-GCCcore-12.3.0
      Miniconda3/23.10.0-1                     libreadline/8.2-GCCcore-13.3.0     (D)
      Ninja/1.12.1-GCCcore-13.3.0              libtool/2.4.7-GCCcore-12.3.0
      OpenBLAS/0.3.27-GCC-13.3.0               libtool/2.4.7-GCCcore-13.3.0       (D)
      OpenMPI/5.0.3-GCC-13.3.0                 libxml2/2.12.7-GCCcore-13.3.0
      OpenSSL/1.1                              lz4/1.9.4-GCCcore-13.3.0
      OpenSSL/1.1.1w-GCCcore-12.3.0            make/4.4.1-GCCcore-12.3.0
      OpenSSL/3                         (D)    make/4.4.1-GCCcore-13.3.0          (D)
      PMIx/5.0.2-GCCcore-13.3.0                ncurses/6.4-GCCcore-12.3.0
      PRRTE/3.0.5-GCCcore-13.3.0               ncurses/6.5-GCCcore-13.3.0
      Perl/5.36.1-GCCcore-12.3.0               ncurses/6.5                        (D)
      Perl/5.38.0                              numactl/2.0.16-GCCcore-12.3.0
      Perl/5.38.2-GCCcore-13.3.0        (D)    numactl/2.0.18-GCCcore-13.3.0      (D)
      Python/3.12.3-GCCcore-13.3.0             pkgconf/1.8.0
      SQLite/3.42.0-GCCcore-12.3.0             pkgconf/1.9.5-GCCcore-12.3.0
      SQLite/3.45.3-GCCcore-13.3.0      (D)    pkgconf/2.2.0-GCCcore-13.3.0       (D)
      ScaLAPACK/2.2.0-gompi-2024a-fb           xorg-macros/1.20.0-GCCcore-12.3.0
      Tcl/8.6.13-GCCcore-12.3.0                xorg-macros/1.20.1-GCCcore-13.3.0  (D)
      Tcl/8.6.14-GCCcore-13.3.0         (D)    zlib/1.2.13-GCCcore-12.3.0
      UCC/1.3.0-GCCcore-13.3.0                 zlib/1.2.13
      UCX/1.14.1-GCCcore-12.3.0                zlib/1.3.1-GCCcore-13.3.0
      UCX/1.16.0-GCCcore-13.3.0         (D)    zlib/1.3.1                         (D)
      UnZip/6.0-GCCcore-12.3.0                 zstd/1.5.6-GCCcore-13.3.0
      UnZip/6.0-GCCcore-13.3.0          (D)

     Where:
      D:  Default Module


The following are the available applications, libraries and development tools on the JADE cluster:

.. toctree::
    :maxdepth: 2
    :glob:

    machine-learning/index
    molecular-dynamics/index
    python
    git