fatal error(s) when merging prefixes

[danielpalazzo]

Hello,
I am trying to install py-fenics-dolfinx and paraview in a spack environment. I have very little experience with spack, And I am getting the following error:

$ spack env create pv-fenicsx
$ spack env activate pv-fenicsx
$ spack add paraview+osmesa+python3 py-fenics-dolfinx ^petsc+mumps
$ spack install
[...]
==> Installing environment pv-fenicsx
==> All of the packages are already installed
==> Updating view at /home/user/Documents/spack/var/spack/environments/pv-fenicsx/.spack-env/view
==> Error: 221 fatal error(s) when merging prefixes:
    `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-inofdcvafekiecvfqvelezueikfigugn/.spack/install_environment.json` and `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-kefzicvuq7lvchducvririsgsrzpfdrp/.spack/install_environment.json` both project to `.spack/hdf5/install_environment.json`
    `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-inofdcvafekiecvfqvelezueikfigugn/.spack/install_manifest.json` and `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-kefzicvuq7lvchducvririsgsrzpfdrp/.spack/install_manifest.json` both project to `.spack/hdf5/install_manifest.json`
    `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-inofdcvafekiecvfqvelezueikfigugn/.spack/install_times.json` and `/home/user/Documents/spack/opt/spack/linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1-kefzicvuq7lvchducvririsgsrzpfdrp/.spack/install_times.json` both project to `.spack/hdf5/install_times.json`

What does the error mean? Obviously I have two different linux-ubuntu20.04-sandybridge/gcc-9.4.0/hdf5-1.12.1 packages. But what is their difference, and how can I solve this problem?

System information:

$ spack debug report
* **Spack:** 0.18.0.dev0 (7893be7712ed709f6136ac83f49afc3d718d5ddc)
* **Python:** 3.8.10
* **Platform:** linux-ubuntu20.04-sandybridge
* **Concretizer:** clingo

Thank you for your time
Daniel

[danielpalazzo]

Ok, I found that paraview has a dependency on hdf5+hl, py-fenics-dolfinx on hdf5~hl.

Is there anything I can do about this? It should be possible to have two different hdf5-installations in one environment, for example if they are linked to different names like hdf5_with_hl and hdf5_without_hl. But how do I get this done?

$ spack find -v hdf5
==> In environment pv-fenicsx
==> Root specs
paraview +osmesa+python3  py-fenics-dolfinx

==> 2 installed packages
-- linux-ubuntu20.04-sandybridge / gcc@9.4.0 --------------------
hdf5@1.12.1~cxx~fortran~hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo patches=ee351eb
hdf5@1.12.1~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo patches=ee351eb

[haampie]

You want to use concretization: together in your environment s.t. every package appears just once and everything is consistent. After you've activated the environment, use spack config edit to open an editor for the spack.yaml file, edit it s.t. it looks like this:

spack:
  concretization: together
  ...

Then concretize your environment again: spack concretize --force, it will show you what will build. Then spack install.

If you're tired of rebuilding paraview and think concretization: together should be the default behavior, please give a 👍 on #29942.

[danielpalazzo]

Thank you, that solved my issues.