Dolfinx in spack

androd · March 17, 2023, 4:05pm

Dear FEniCS community,
I’m trying to install dolfinx on a HPC resource via spack using the GitHub instructions.
I’m facing two problems:

some packages like gmsh and matplotlib were not installed and I added them manually through pip, not sure it is the right way to add packages on spack, but I couldn’t find a better solution.
through spack find I can see that py-petsc4py@3.18.3 is installed but seems that mumps (and umfpack) is not working and I obtain this error:

[0] Could not locate solver type mumps for factorization type LU and matrix type seqaij. Perhaps you must ./configure with --download-mumps

If someone could point some tips out, it would be very helpful.
Thank you very much.

dokken · March 17, 2023, 4:29pm

As PETSc has mumps as a variant, you need to use the variants command in spack:

github.com

spack/spack/blob/develop/var/spack/repos/builtin/packages/petsc/package.py#L92


      
              "ptscotch", default=False, description="Activates support for PTScotch (only parallel)"
          )
          variant("hdf5", default=True, description="Activates support for HDF5 (only parallel)")
          variant("hypre", default=True, description="Activates support for Hypre (only parallel)")
          variant("hpddm", default=False, description="Activates support for HPDDM (only parallel)")
          variant("mmg", default=False, description="Activates support for MMG")
          variant("parmmg", default=False, description="Activates support for ParMMG (only parallel)")
          variant("tetgen", default=False, description="Activates support for Tetgen")
          # Mumps is disabled by default, because it depends on Scalapack
          # which is not portable to all HPC systems
          variant("mumps", default=False, description="Activates support for MUMPS (only parallel)")
          variant(
              "superlu-dist",
              default=True,
              when="+fortran",
              description="Activates support for superlu-dist (only parallel)",
          )
          variant("strumpack", default=False, description="Activates support for Strumpack")
          variant(
              "scalapack", default=False, when="+fortran", description="Activates support for Scalapack"
          )

https://spack.readthedocs.io/en/latest/packaging_guide.html#variants
For instance, you can see: dolfinx/spack.yml at main · FEniCS/dolfinx · GitHub
adds adios2 which is a variant in: spack/package.py at develop · spack/spack · GitHub

You can also see: Basic Usage — Spack 0.20.0.dev0 documentation

You can also add gmsh through spack: Package List — Spack 0.20.0.dev0 documentation

androd · March 21, 2023, 9:26am

(post deleted by author)

androd · March 21, 2023, 9:50am

I solved it in the following way, not sure it is the best one though:

Installed dolfinx via spack as in GitHub - FEniCS/dolfinx: Next generation FEniCS problem solving environment
Added packages by modifying the file spack/var/spack/environments/fenicsx-env/spack.yaml
2a. specs:[py-fenics-dolfinx, other-packages]
2b. unify: when_possible
the list of packages is available here: Package List — Spack 0.20.0.dev0 documentation

I added gmsh to the specs but still I couldn’t manage to import dolfinx.io.gmshio so I installed py-gmsh through pip: Installation - pip documentation v23.0.1
To switch on the variant mumps in PETSc I modified the file spack/var/spack/repos/builtin/packages/fenics-dolfinx/package.py at the line:
depends_on("petsc+mpi+shared+mumps")

It is actually working now, but I imagine there is a simpler way to get it done.
Thank you again!
ar