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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
2022.1 2022a Next Production and default(!) from 2023-01-15 /apps/USE/easybuild/release/2022.1/modules/all/
2021.3 2021a Current Production and default until 2023-01-14, maintained afterwards /apps/USE/easybuild/release/2021.3/modules/all
2021.5 2021a Production, optimized version of 2021.3 stack and tracking it /apps/USE/easybuild/release/2021.5/modules/all/
2022.1 2022a Staging /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 3.6.449
AOCC 3.2.0-GCCcore-11.3.0
Advisor 2022.1.0
Arm-Forge 22.0.4-GCC-11.3.0
Autoconf 2.69-GCCcore-11.3.0, 2.71-GCCcore-11.3.0
aws-cli 2.7.1
BLIS 0.9.0-GCC-11.3.0
Bazel 5.1.1-GCCcore-11.3.0
Blender 3.2.2-linux-x64
Boost 1.79.0-GCC-11.3.0
CGAL 4.14.3-gompi-2022a, 5.2-gompi-2022a
CMake 3.23.1-GCCcore-11.3.0
CUDA 11.7.0
Clang 13.0.1-GCCcore-11.3.0-CUDA-11.7.0, 13.0.1-GCCcore-11.3.0 Yes
cuDNN Yes
Dakota 6.16.0-foss-2022a
Doxygen 1.9.4-GCCcore-11.3.0
DualSPHysics 5.0.175-foss-2022a, 5.0.175-GCC-11.3.0-CUDA-11.7.0, 5.0.175-GCC-11.3.0 Yes
[Eigen]Eigen 3.4.0-GCCcore-11.3.0
FFTW 3.3.10-GCC-11.3.0
FFTW.MPI 3.3.10-gompi-2022a
FlexiBLAS 3.2.0-GCC-11.3.0
foss 2022a
GCC 11.3.0
GCCcore 11.3.0
GDAL 3.5.1-foss-2022a
GDB 11.1-GCCcore-11.3.0
GROMACS 2022.3-foss-2022a-CUDA-11.7.0, 2022.3-foss-2022a Yes
gnuplot 5.4.2-GCCcore-11.3.0, 5.4.4-GCCcore-11.3.0
Go 1.19.1
gompi 2022a-prte, 2022a
gperf 3.1-GCCcore-11.3.0
gperftools 2.10-GCCcore-11.3.0
h5py 3.7.0-foss-2022a-CUDA-11.7.0, 3.7.0-foss-2022a Yes
HDF5 1.12.2-gompi-2022a-serial, 1.12.2-gompi-2022a
HPCX 2.12-GCCcore-11.3.0
Horovod 0.26.0-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0 Yes
hwloc 2.7.1-GCCcore-11.3.0
iOR 3.3.0-gompi-2022a
ifpgasdk 20.4
iimpi 2022a
imkl 2022.1.0
imkl-FFTW 2022.1.0-iimpi-2022a
impi 2021.6.0-intel-compilers-2022.1.0
intel 2022a
intel-compilers 2022.1.0
itac 2021.6.0
Java 11.0.16
Julia 1.8.2-linux-x86_64
JupyterHub 2.3.1-GCCcore-11.3.0
JupyterLab 3.2.8-GCCcore-11.3.0
Keras 2.9.0-foss-2022a
Kokkos 3.6.01-GCC-11.3.0
LAMMPS 23Jun2022-foss-2022a-kokkos-CUDA-11.7.0, 23Jun2022-foss-2022a-kokkos Yes
MCR R2022a
METIS 5.1.0-GCCcore-11.3.0
mpifileutils 0.11.1-foss-2022a
NAMD 2.14-foss-2022a-mpi, 2.14-foss-2022a-ucx-CUDA-11.7.0 Yes
NCCL 2.12.12-GCCcore-11.3.0-CUDA-11.7.0 Yes
NVHPC 22.7-CUDA-11.7.0, 22.7 Yes
NVSHMEM 2.6.0-gompi-2022a-CUDA-11.7.0 Yes
netCDF 4.9.0-gompi-2022a
Ninja 1.10.2-GCCcore-11.3.0
numactl 2.0.14-GCCcore-11.3.0
nvompic 2022a
OSU-Micro-Benchmarks 6.0-gompi-2022a-CUDA-11.7.0, 6.0-gompi-2022a-prte, 6.0-gompi-2022a, 6.0-iimpi-2022a Yes
OpenBLAS 0.3.20-GCC-11.3.0
OpenCV 4.6.0-foss-2022a-contrib, 4.6.0-foss-2022a-CUDA-11.7.0-contrib Yes
OpenFOAM v2206-foss-2022a, 9-foss-2022a
OpenMPI 4.1.4-GCC-11.3.0-prte, 4.1.4-GCC-11.3.0, 4.1.4-NVHPC-22.7-CUDA-11.7.0, 4.1.4-NVHPC-22.7 Yes
PETSc 3.17.4-foss-2022a
PLUMED 2.8.0-foss-2022a
PMIx 4.2.2-GCCcore-11.3.0
ParaView 5.10.1-foss-2022a-mpi
psmpi 5.6.0-1-GCC-11.3.0-CUDA-11.7.0, 5.6.0-1-GCC-11.3.0 Yes
PyTorch 1.12.0-foss-2022a-CUDA-11.7.0, 1.12.0-foss-2022a Yes
Python 2.7.18-GCCcore-11.3.0-bare, 3.10.4-GCCcore-11.3.0-bare, 3.10.4-GCCcore-11.3.0
QMCPACK 3.14.0-foss-2022a
QUDA 1.1.0-foss-2022a-CUDA-11.7.0 Yes
Qsimcirq 0.14.0-foss-2022a
QuantumESPRESSO 7.1-foss-2022a, 7.1-nvompic-2022a-NVHPC-22.7
R 4.2.1-foss-2022a-bare, 4.2.1-foss-2022a
ReFrame 3.12.0
Rust 1.60.0-GCCcore-11.3.0
s3cmd 2.2.0
SCOTCH 7.0.1-gompi-2022a
ScaLAPACK 2.2.0-gompi-2022a-fb
Scalasca 2.6-gompi-2022a-CUDA-11.7.0, 2.6-gompi-2022a Yes
SciPy-bundle 2022.05-foss-2022a
Scikit-image 0.19.3-foss-2022a
Scikit-learn 1.1.2-foss-2022a
Score-P 7.1-gompi-2022a-CUDA-11.7.0, 7.1-gompi-2022a Yes
Singularity-CE 3.10.2-GCCcore-11.3.0
Spark 3.3.0-foss-2022a-CUDA-11.7.0, 3.3.0-foss-2022a Yes
TBB 2021.5.0-GCCcore-11.3.0
TensorFlow 2.9.1-foss-2022a
Torchtext 0.12.0-foss-2022a
Torchvision 0.13.1-foss-2022a-CUDA-11.7.0, 0.13.1-foss-2022a Yes
UCX 1.13.1-GCCcore-11.3.0
UCX-CUDA 1.13.1-GCCcore-11.3.0-CUDA-11.7.0 Yes
VTune 2022.3.0
Valgrind 3.19.0-gompi-2022a
Voro++ 0.4.6-GCCcore-11.3.0
520nmx 20.4

Requesting new software and features

You may request the installation of new applications or features through the 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
    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>