Software

For the software installation we are using the spack package manager.
The packages are available trough the enviromental modules Lmod.
Available modules cover mainly these areas:

numerical linear algebra tools: openblas, matlab, lapack/scalapack
scientific computation tools: suite-sparse, petsc, trilinos, hypre, fenics
programming tools: R, comsol, matlab, julia, Mathematica
parallel HPC tools: OpenMPI, globalarrays, PETSc
vizualization tools: Paraview, Tecplot

Architecture selection

Since there are currently 3 different processor generations on the cluster nodes, the user has to select the deisred target architecture. (since the login node r3d3 is in the class Arch/linux-ubuntu20.04-skylake_avx512 this architecture is preloaded by default.)

Use module add Arch/linux-ubuntu20.04-skylake_avx512 for queues express3, long3, astro, core36 - nodes r3X and r4X
Use module add Arch/linux-ubuntu20.04-ivybridge for queues express/short/long for nodes r2X
Use module add Arch/linux-ubuntu20.04-sandybridge for queue edu (nodes rX)

Full list of currently available modules:

> module available
Modules currently installed on cluster snehurka:
------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu20.04-skylake_avx512/Nonfree -------------------------------
   mathematica/10.3        matlab/R2019b        orca/4.2.1      tecplot/2018       (D)    tecplotchorus/2018 (D)
   mathematica/12.1 (D)    matlab/R2024a (D)    tecplot/2016    tecplotchorus/2016

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu20.04-skylake_avx512/Tools --------------------------------
   cleaver/2.4     (T)    hwloc/2.9.1        (T)    meshio/5.3.4           paraview/5.11.2-server-osmesa (T)
   cmake/3.26.3    (T)    image-magick/7.0.8 (T)    netgen/5.3.1    (T)    paraview/5.11.2               (T,D)
   ftetwild/master (T)    jupyter/1.0.0             paraview/5.10.1 (T)    saws/0.1.1                    (T)
   graphviz/8.0.1  (T)    mesa/20.2.1        (T)    paraview/5.11.0 (T)    triangle/1.6                  (T)

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu20.04-skylake_avx512/Math ---------------------------------
   cp2k/7.1                  gromacs/2023.1     (D)    mpi4py/3.1.4                         petsc4py/3.19.1
   cp2k/2023.1        (D)    gsl/2.6                   mumps/5.5.1                          scalapack/2.2.0
   ga4py/main                h5py/3.8.0                nlopt/2.7.1                          scipy/1.10.1
   globalarrays/5.8.2        hdf5/1.10.9-serial        numpy/1.24.3                         suite-sparse/5.13.0-openmp
   glpk/5.0                  hdf5/1.10.9        (D)    openblas/0.3.23-single-thread        suite-sparse/5.13.0        (D)
   gmsh/4.11.1        (T)    intel-mkl/2023.1.0        openblas/0.3.23               (D)    sympy/1.11.1
   gromacs/2020.3            ipopt/main                pandas/2.0.1                         vmtk/master                (E)
   gromacs/2020.4            matplotlib/3.7.1          petsc/3.19.1

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu20.04-skylake_avx512/Sets ---------------------------------
   fenics-x/0.6.0 (E)    fenics/2019.1.0-petsc3.12 (E)    fenics/2019.1.0  (E,D)    firedrake/2023.0 (E,D)
   fenics/master  (E)    fenics/2019.1.0-petsc3.15 (E)    firedrake/master (E)      python-env/scipy

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu20.04-skylake_avx512/Core ---------------------------------
   R/4.2.2     (E)    gcc/9.4.0         (S,D)    julia/1.9.1            (T)    openmpi/4.1.6-gcc9.4.0 (D)
   dmd/2.081.1        intelmpi/2021.9.0          openmpi/4.0.6-gcc9.4.0        python/3.9.16
   gcc/sys     (S)    ipython/8.11.0             openmpi/4.1.5-gcc9.4.0        slurm/22.05            (S)

---------------------------------------------------- /usr/local/pkg/modulefiles ----------------------------------------------------
   Arch/linux-ubuntu20.04-sandybridge             Arch/linux-ubuntu20.04-x86_64_v3
   Arch/linux-ubuntu20.04-skylake_avx512 (L,D)    Arch/StdEnv

  Where:
   L:  Module is loaded
   T:  Testing
   E:  Experimental
   S:  System (Ubuntu)
   D:  Default Module