Installation problem using spack

[Marco Nawijn]

Dear All,

I run into an issue when trying to install dealii using spack. The error is as follows:

  Could not find the hdf5 library!

  Insufficient hdf5 installation found!

  hdf5 has to be configured with MPI support.

  Please ensure that a suitable hdf5 library is installed on your computer.

  If the library is not at a default location, either provide some hints for
  autodetection,

A complete log and additional information is provided in the two attachments.

I am a little lost at the moment because as far as I can tell, the installation process finds the correct HDF5 folder (I checked the tags). In addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I added the output of `tree` to the attachment).

I am a little at loss now, because I don't know what dealii is exactly missing from the HDF5 installation.

The system is just a laptop, so nothing cluster like.

Just as a side note. I am pretty impressed with the easy and flexibility of spack. All other dependencies installed without a hitch (petsc, sundials, trilinios etc.).

Does anybody have an idea of what the problem is?

Any help is highly appreciated.

Marco

P.S. I am a complete novice with dealii, but otherwise comfortable in the linux eco-system.

[Daniel Arndt]

Marco,

It appears that

-- Insufficient hdf5 installation found: hdf5 has to be configured with MPI support.

is the problem. HDF5 has not been compiled with MPI support. Thus, you can either try to make sure that HDF5 is built with MPI support or, in case you are not going to use HDF5 anyway, just disable the dependency.

Best,

Daniel

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[Timo Heister]

Your issue might be related to the bug https://github.com/dealii/dealii/issues/14065 (see the discussion and the linked PR that should solve the problem for deal.II master, but not 9.4)

[Marco Nawijn]

Hi Daniel and Timo,

Thanks for the feedback. The bug indeed seems to be the problem, since the spack HDF5 package is definitely build with MPI support. I first thought it was because by default spack doesn't seem to build HDF5 with C++ support, but that did not help (of course now I know why).

Building without HDF5 would be an option for me for the short term, but I will first try to see if I can get it working.

Again, I am pretty impressed by the spack. It works like a charm and it provides a lot of flexibility.

Kind regards,

Marco

[Jean-Paul Pelteret]

Hi Marco,

I've open a PR in Spack (https://github.com/spack/spack/pull/32079) that backports the patches that we added to the development version to 9.4. Feel free to try it and provide some feedback as to whether or not it works for you.

Best,

Jean-Paul

[Marco Nawijn]

Hi Jean-Paul,

I can confirm that the patch works like a charm. Thanks!

I now run into another issue, when running step-17. It fails with the following message:

      ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size: 137438953480 bytes

I did a quick search on the internet and it seems to be related to Metis 5.1.0.

Just for information, when you run the example with MPI on 1 processor (so -np 1), the process runs fine. Any value >1 results in this error. The error itself makes sense because it requests a massive amount of memory (I am running on a laptop at the moment). A quick fix (based on what I found on the internet) is to downgrade the version of Metis. However, ideally for Deal-II newbies using straightforward laptops/workstations, it would be nice to just run `spack install dealii` and it just works.

If there is anything I can do to help, I am more than willing to.

Kind regards,

Marco

[Wolfgang Bangerth]

On 8/15/22 00:50, Marco Nawijn wrote:
>
> Just for information, when you run the example with MPI on 1 processor (so -np
> 1), the process runs fine. Any value >1 results in this error. The error
> itself makes sense because it requests a massive amount of memory (I am
> running on a laptop at the moment). A quick fix (based on what I found on the
> internet) is to downgrade the version of Metis. However, ideally for Deal-II
> newbies using straightforward laptops/workstations, it would be nice to just
> run `spack install dealii` and it just works.
>
> If there is anything I can do to help, I am more than willing to.

The question is whether METIS' excessive memory allocation is because of a bug
in METIS, or because we call it in a way it doesn't expect. Did your search
for the source of the error indicate anything to this effect?

Best
W.

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Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[Marco Nawijn]

Hi Wolfgang,

No, I didn't check. I was just running a few example programs that were compiled during the installation process.

However, I believe it is a good exercise for me to see if I can find the bug :). So, I will give it a try and report back if I find anything or get stuck.

Marco