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Software environment

A rich user software environment is available on MeluXina and can be used through environment modules. It comprises:

  • tools for HPC, HPDA and AI application development

    • compilers & programming languages
    • common use libraries for math & data
    • tools for performance engineering
  • scientific computing applications, libraries and frameworks

    • general-purpose HPC, HPDA or AI
    • or domain-specific

The MeluXina User Software Environment (MUSE)

The EasyBuild system is used on MeluXina to deploy software stacks, with applications and libraries provided in several revisions: compiled with different compilers, MPI suites, accelerated and non-accelerated versions. EasyBuild automatically generated software modules that enables the use of the different application revisions, and dependencies on particular support libraries.

The naming scheme used for the modules follows the application/version schema, e.g. NAMD/2.14-foss-2022a-ucx-CUDA-11.7.0 which shows that the NAMD application is available in version 2.14 built with the foss toolchain in the 2022a release, and with CUDA support.

For a deeper overview on versioning and toolchains see the EasyBuild documentation specific to Common toolchains and Available toolchains.

We release a new software stack at least once a year. The software stacks can be either: Production (current), Maintained (previous, not updated with new tools/versions), Retired (not maintained and should not be used any more) or Staging (preproduction envioronment for testing purposes).

MUSE release Based on EasyBuild toolchain(s) Status Path
2023.1 2023a Production and default from 2024-02-15 /apps/USE/easybuild/release/2023.1/modules/all/
2022.1 2022a Current Production and default since 2023-01-15 /apps/USE/easybuild/release/2022.1/modules/all/
2021.3 2021a Deprecated Production, not maintained from 2024-02-15 /apps/USE/easybuild/release/2021.3/modules/all
2021.5 2021a Deprecated Production, optimized version of 2021.3 stack and tracking it /apps/USE/easybuild/release/2021.5/modules/all/
2022.1 2023a Staging /apps/USE/easybuild/staging/2023.1/modules/all/
2022.1 2022a Staging, not maintained from 2024-02-15 /apps/USE/easybuild/staging/2022.1/modules/all/

Using different MUSE releases

To load modules from a software release other than the default Production stack, you can:

  • Use the dedicated software environment modules in the 'env/' branch, e.g. module load env/staging/2022.1
  • Or directly configure LMod to use the appropriate modules path, e.g.:
    module use /apps/USE/easybuild/staging/2022.1/modules/all/

The following table lists highlighted HPC applications, libraries and support tools available in the latest release of the MeluXina User Software Environment.

Software Available versions Has GPU accelerated version?
AMD-uProf 4.1.424
AOCC 4.0.0-GCCcore-12.3.0
Advisor 2023.2.0
Linaro-Forge 23.0.3-GCC-12.3.0
aws-cli 2.7.1
BLIS 0.9.0-GCC-12.3.0
Bazel 6.3.1-GCCcore-12.3.0
Blender 4.0.2-linux-x64
Boost 1.82.0-GCC-12.3.0
CGAL 5.6-GCCcore-12.3.0
CMake 3.26.3-GCCcore-12.3.0
CUDA 11.7.0, 12.2.0
Clang 16.0.6-GCCcore-12.3.0-CUDA-12.2.0, 16.0.6-GCCcore-12.3.0 Yes
cuDNN 8.9.2.26-CUDA-12.2.0 Yes
cuQuantum 23.10.0-CUDA-12.2.0
cuQuantum-Python 23.10.0-foss-2023a.CUDA-12.2.0
Doxygen 1.9.7-GCCcore-12.3.0
DualSPHysics 5.0.233-foss-2023a, 5.0.233-GCC-12.3.0 Yes
Eigen 3.4.0-GCCcore-12.3.0
FFTW 3.3.10-GCC-12.3.0
FFTW.MPI 3.3.10-gompi-2023a
FlexiBLAS 3.3.1-GCC-12.3.0
foss 2023a
GCC 12.3.0
GCCcore 12.3.0
GDAL 3.7.1-foss-2023a
GDB 13.2-GCCcore-12.3.0
GROMACS 2023.3-foss-2023a-CUDA-12.2.0, 2023.3-foss-2023a, 2022.5-foss-2023a-CUDA-12.2.0-PLUMED-2.9.0 Yes
gnuplot 5.4.8-GCCcore-12.3.0
Go 1.20.4
gompi 2023a
gperf 3.1-GCCcore-12.3.0
gperftools 2.12-GCCcore-12.3.0
h5py 3.9.0-foss-2023a-CUDA-12.2.0, 3.9.0-foss-2023a Yes
HDF5 1.14.0-gompi-2023a, 1.14.0-impi-2023a
HPCX 2.16-GCCcore-12.3.0
hwloc 2.9.1-GCCcore-12.3.0
iOR 3.3.0-gompi-2023a
ifpgasdk 20.4
iimpi 2023a
imkl 2023.1.0
imkl-FFTW 2023.1.0-iimpi-2023a
impi 2021.9.0-intel-compilers-2023.1.0
intel 2023a
intel-compilers 2023.1.0
itac 2021.10.0
Java 11.0.18, 17.0.6
Julia 1.9.3-linux-x86_64
JupyterHub 4.0.2-GCCcore-12.3.0
JupyterLab 4.0.5-GCCcore-12.3.0
Kokkos 4.1.0-GCC-12.3.0
MCR R2023a
METIS 5.1.0-GCCcore-12.3.0
mpifileutils 0.11.1-foss-2023a
NAMD 3.0b5-multicore-AVX512-bin, 3.0b5-multicore-bin, 3.0b5-multicore-CUDA-bin Yes
NCCL 2.18.3-GCCcore-12.3.0-CUDA-12.2.0 Yes
NVHPC 23.7-CUDA-12.2.0, 23.7 Yes
NVSHMEM 2.9.0-gompi-2023a-CUDA-12.2.0 Yes
netCDF 4.9.2-gompi-2023a
Ninja 1.11.1-GCCcore-12.3.0
numactl 2.0.16-GCCcore-12.3.0
nvompic 2023a
OSU-Micro-Benchmarks 7.2-gompi-2023a-CUDA-12.2.0, 7.2-gompi-2023a Yes
OpenBLAS 0.3.23-GCC-12.3.0
OpenCV 4.8.1-foss-2023a-CUDA-12.2.0-contrib Yes
OpenFOAM v2306-foss-2023a, 10-foss-2023a
OpenMPI 4.1.5-GCC-12.3.0, 5.0.0-GCC-12.3.0, 4.1.5-NVHPC-23.7-CUDA-12.2.0, 4.1.5-NVHPC-23.7 Yes
PAPI 7.0.1-GCCcore-12.3.0
PETSc 3.19.4-foss-2023a
PLUMED 2.9.0-foss-2023a
PMIx 4.2.6-GCCcore-12.3.0
ParaView 5.11.2-foss-2023a-mpi
psmpi 5.9.2-1-GCC-12.3.0-CUDA-12.2.0, 5.9.2-1-GCC-12.3.0 Yes
PyTorch 2.1.0-CUDA-12.2.0-NGC-23.10 Yes
Python 3.11.3-GCCcore-12.3.0, 3.10.8-GCCcore-12.3.0
Python-bundle-PyPI 2023.06-GCCcore-12.3.0-python-3.10.8, 2023.06-GCCcore-12.3.0
QMCPACK v3.16.0-CUDA-12.2.0-NGC-23.10
qsimcirq 0.17.0-foss-2023a
cirq-core 1.2.0-foss-2023a
QuantumESPRESSO 7.2-foss-2023a, 7.1-CUDA-12.2.0-NGC-23.10
R 4.3.2-foss-2023a-bare, 4.3.2-foss-2023a
rapidsai 23.10.0-foss-2023a-CUDA-12.2.0-python-3.10.8
ReFrame 4.4.0
Rust 1.70.0-GCCcore-12.3.0
s3cmd 2.2.0
SCOTCH 7.0.3-gompi-2023a
ScaLAPACK 2.2.0-gompi-2023a-fb
Scalasca 2.6.1-gompi-2023a-CUDA-12.2.0, 2.6.1-gompi-2023a Yes
SciPy-bundle 2023.07-gfbf-2023a, 2023.07-gfbf-2023a-python-3.10.8
Scikit-image 0.22.0-foss-2023a
Scikit-learn 1.3.1-foss-2023a
Score-P 8.1-gompi-2023a-CUDA-12.2.0, 8.1-gompi-2023a Yes
Apptainer 1.2.4-GCCcore-12.3.0
Spark 3.5.0-foss-2023a Yes
TBB 2021.10.0-GCCcore-12.3.0
TensorFlow 2.13.0-foss-2023a, 2.13.0-CUDA-12.2.0-NGC-23.10
UCX 1.14.1-GCCcore-12.3.0
UCX-CUDA 1.14.1-GCCcore-12.3.0-CUDA-12.2.0 Yes
VTune 2023.2.0
Valgrind 3.21.0-gompi-2023a
Voro++ 0.4.6-GCCcore-12.3.0
520nmx 20.4

Requesting new software and features

You may request the installation of new applications or features through the servicedesk.lxp.lu. Depending on a project's requirements, new software may be installed in the corresponding project directory or in the global software stack. All new tools are first deployed in the Staging area for testing.

Environment modules

The environment modules system simplifies the use of applications and supporting libraries that may come in different versions and revisions. The software modules provide a way to easily switch between e.g. multiple revisions of the same application, where one revision may provide a set of functionality not available in another revision.

The core command by which software modules can be listed, loaded (activated), and unloaded (deactivated) is module, followed by an appropriate command.

The modules work by setting specific environment variables needed for the respective software program when the software module corresponding to the application is loaded. Often, this is simply adding the program to the $PATH variable, but software containing libraries and headers will also set $LD_LIBRARY_PATH. Any other variable that the software may need can be set and so the contents of the modules can be fairly simple or complex.

There are several advantages to using software modules to set up your environment, especially on a supercomputer:

  • ease of use
  • ability to revert to your previous environment
  • ability to easily switch your environment to try different versions of a program
    • e.g. when single and double-precision versions of the program exist
    • e.g. when a program has been compiled with different features that cannot coexist in a single build of the program
    • e.g. when a program has been compiled with different compilers or MPI suites

Using modules

The module command is only available on compute nodes and not on the login nodes. The applications provided through the software modules system must be used only on compute nodes.

MeluXina uses the Lmod software modules system, the table below summarizes the most common module commands:

Module Command Description
module avail List/browse available modules
module list Show modules currently loaded (active)
module load module_name Load a specific module (may load additional modules as dependencies)
module unload module_name Unload a loaded module (does not unload modules activated as dependencies)
module swap module_name1 module_name2 Unload module_name1 and load module_name2
module purge Unload all loaded modules
module reset Reset loaded modules to system defaults
module show module_name Display the contents of a selected module
module spider List all modules and the short description of each
module spider package Display the description and various versions available of an application
module use path Add path to the MODULEPATH search path

Using environment modules

  • Finding applications: module avail

To lists all available (loadable) modules and module groups. With the information of these two commands:

module avail
Output
    ---------------------------------
    AOCC/3.0.0-GCCcore-10.2.0                GCC/10.2.0                                    ...
    Autoconf/2.69-GCCcore-10.2.0             GCCcore/10.2.0                                ...
    Automake/1.16.2-GCCcore-10.2.0           GDRCopy/2.1-GCCcore-10.2.0-CUDA-11.2.2        ...
    Autotools/20200321-GCCcore-10.2.0        GMP/6.2.0-GCCcore-10.2.0                      ...
    BLIS/0.8.1-GCCcore-10.2.0                Go/1.16.3                                     ...
    BLIS/3.0-GCCcore-10.2.0           (D)    HPCX/2.8.1                                    ...
    Bison/3.7.1-GCCcore-10.2.0               M4/1.4.18-GCCcore-10.2.0                      ...
    Bison/3.7.1                              M4/1.4.18                              (D)    ...
    Bison/3.7.4                       (D)    NVHPC/21.3                                    ...
    CMake/3.18.4-GCCcore-10.2.0              OSU-Micro-Benchmarks/5.7-gompic-2020b         ...
    CUDA/11.2.2-GCC-10.2.0                   OpenBLAS/0.3.12-GCC-10.2.0                    ...
    CUDAcore/11.2.2                          OpenMPI/4.0.5-GCC-10.2.0-with-orte            ...
    Check/0.15.2-GCCcore-10.2.0              OpenMPI/4.0.5-GCC-10.2.0                      ...
    DB/18.1.40-GCCcore-10.2.0                OpenMPI/4.0.5-gcccuda-2020b            (D)    ...
    FFTW/3.3.8-gompi-2020b                   PMIx/3.2.3-GCCcore-10.2.0                     ...
    FFTW/3.3.8-gompic-2020b           (D)
  • Listing loaded application profiles: module list

To get a list of all currently loaded modules:

module list
  • Loading or unloading application profiles: module load/unload

To load a specific module

module load <module_name>

Default version

In case of multiple software versions, one version will always be defined as the default version, and can be identified by its (D) mark in the module avail output. When loading a software module, if the version is not specified, the default is loaded (e.g. module load FFTW will activate FFTW/3.3.8-gompic-2020b if this is the default). Fully specifying the software module (name+version) should always be preferred to ensure that the correct version is being activated.

Unloading an environment module will undo the changes that module made to the environment, restoring any variables set to their previous values. To unload a specific module you can use the following:

module unload <module_name>
  • Unloading all profiles: module purge
module purge
  • Switching profiles: module switch

To swap a specific module for another one (especially useful to switch between different versions of the same program) use the following:

module switch <old_module_name> <new_module_name>