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-ubuntu18.04-skylake_avx512 this architecture is preloaded by default.)

  • Use module add Arch/linux-ubuntu18.04-skylake_avx512 for queues express3, astro, core36 - nodes r3X and r4X
  • Use module add Arch/linux-ubuntu18.04-ivybridge for queues express/short/long nodes r2X
  • Use module add Arch/linux-ubuntu18.04-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-ubuntu18.04-skylake_avx512/Nonfree -------------------------------
   comsol/35a    comsol/42        (D)    mathematica/12.1 (D)    matlab/R2018b (D)    tecplot/2016        tecplotchorus/2016
   comsol/41     mathematica/10.3        matlab/R2016a           orca/4.2.1           tecplot/2018 (D)    tecplotchorus/2018 (D)

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu18.04-skylake_avx512/Tools --------------------------------
   hwloc/2.2.0        (T)    mesa/18.3.6           (T)    paraview/5.8.0 (T,D)    vmtk/master (E)
   image-magick/7.0.8 (T)    paraview/5.8.0-server (T)    triangle/1.6   (T)

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu18.04-skylake_avx512/Math ---------------------------------
   atlas/3.10.3-gcc7.4.0          hdf5/1.10.5-ompi3.1.4-gcc7.4.0                pandas/1.1.2
   cp2k/6.1                       hdf5/1.10.5-serial-gcc7.4.0                   petsc/3.11.3
   cp2k/7.1              (D)      hdf5/1.10.6-ompi3.1.4-gcc7.4.0                petsc/3.11.4                    (D)
   ga4py/5.7                      hdf5/1.10.6-serial-gcc7.4.0            (D)    petsc4py/3.11.0
   globalarrays/5.7               matplotlib/3.2.2                              scipy/1.1.0
   glpk/4.65-gcc7.4.0             mpi4py/3.0.3                                  scipy/1.5.0                     (D)
   gmsh/4.5.4            (T)      numpy/1.15.2                                  suite-sparse/5.7.2-gcc7.4.0
   gmsh/4.6.0            (T,D)    numpy/1.19.0                           (D)    suite-sparse/5.7.2-omp-gcc7.4.0 (D)
   gromacs/2019.4                 openblas/0.3.10-gcc7.4.0                      sympy/1.1.1
   gsl/2.6-gcc7.4.0               openblas/0.3.10-single-thread-gcc7.4.0 (D)    sympy/1.4                       (D)

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu18.04-skylake_avx512/Sets ---------------------------------
   fenics/2019.1.0 (E)    python-env/sci+num+sym+ga+petsc    python-env/sci+num+sym+pandas (D)

-------------------------------- /usr/local/pkg/Modules/User/linux-ubuntu18.04-skylake_avx512/Core ---------------------------------
   R/3.6.1 (E)      dmd/2.084.1        julia/1.0.5        julia/1.5.1            (T,D)    python/3.7.7-gcc7.4.0
   R/4.0.2 (E,D)    gcc/7.4.0   (S)    julia/1.3.1 (T)    openmpi/3.1.4-gcc7.4.0          slurm/20.02           (S)