petsc: update to use hdf5-mpi

[abhinavsns]

Please see discussion on previous PR: #165097

[chenrui333]

@abhinavsns thanks for breaking down, any docs links for this?

Petsc in general relies on openMPI, any other library is likely to use petsc and hdf5-mpi together.

[abhinavsns]

Yes. Please checkout the following issues where it is suggested to use hdf5-mpi:
https://groups.google.com/g/dealii/c/haqbBqbnZeg
https://lists.mcs.anl.gov/pipermail/petsc-users/2018-February/034382.html
https://fenicsproject.org/qa/9552/hdf5-error-when-building-dolfin/

We also maintain an open-source library (openFPM) and the issue is the same. (http://openfpm.mpi-cbg.de/building/)

Only reason I can think of to not go for this change would mean the user probably does not care about parallel read/write and possibly does not care about MPI as well. In that case, maybe one can add additional formula where petsc is compiled without MPI and then serial hdf5 could be used with netcdf. Or going for the other way round, like introducing petsc-mpi, petsc-complex-mpi.

[chenrui333]

@abhinavsns make sense, thanks for the references!!

[chenrui333]

@abhinavsns thanks for your first contribution to homebrew-core! 🎉

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[BrushXue]

@chenrui333 Now the upgrade fails because of a conflict. I can't have netcdf and petsc at the same time!

~ brew upgrade
==> Upgrading 1 outdated package:
petsc 3.20.5 -> 3.20.5_1
==> Downloading https://ghcr.io/v2/homebrew/core/petsc/manifests/3.20.5_1
==> Fetching dependencies for petsc: hdf5-mpi
==> Downloading https://ghcr.io/v2/homebrew/core/hdf5-mpi/manifests/1.14.3
==> Fetching hdf5-mpi
==> Downloading https://ghcr.io/v2/homebrew/core/hdf5-mpi/blobs/sha256:edaecb37c
==> Fetching petsc
==> Downloading https://ghcr.io/v2/homebrew/core/petsc/blobs/sha256:b1faad1c3141
==> Upgrading petsc
  3.20.5 -> 3.20.5_1
==> Installing dependencies for petsc: hdf5-mpi
==> Installing petsc dependency: hdf5-mpi
Error: Cannot install hdf5-mpi because conflicting formulae are installed.
  hdf5: because hdf5-mpi is a variant of hdf5, one can only use one or the other

Please `brew unlink hdf5` before continuing.

Unlinking removes a formula's symlinks from /opt/homebrew. You can
link the formula again after the install finishes. You can `--force` this
install, but the build may fail or cause obscure side effects in the
resulting software.

[BrushXue]

I think this change should be reverted. A lot of packages are using hdf5. You have to change everything, or please find a way to make hdf5 and hdf5-mpi coexist.

[abhinavsns]

I agree with @BrushXue. The following packages have hdf5 as dependency and now will conflict with petsc.
Another idea could be to update hdf5 to use open-mpi and remove hdf5-mpi? This will install the parallel version as default and should not have a problem for single core applications. Currently hdf5-mpi is not used in any package and hence can be removed?
I will create another PR for hdf5 just in case we decide to go this route.

brew uses hdf5 --eval-all

1. alembic
2. caffe
3. cgns
4. field3d
5. itk
6. netcdf
7. octave
8. sratoolkit
9. alpscore
10. cdi
11. csound
12. flann
13. kallisto
14. netcdf-cxx
15. openmodelica
16. vtk
17. armadillo
18. cdo
19. dynare
20. gdal
21. libmatio
22. netcdf-fortran
23. pdal