Installation issue

[hoangn...@gmail.com]

Hi all,

I'm installing MoFEM on a Mac machine and having an issue.

Right after this command line is executed

spack install --only dependencies mofem-cephas ^petsc+X

It complains about the Bzip2 package

==> Error: Package Bzip2 has no version with a URL.

This message appears for any packages when I try spack install. I also tried with both installation from source and mirror.

It would be great if you can help to resolve the issue.

The current platform and setup I have as follows

- macOS Monterey 12.1

- Xcode: 13.2

- cl...@13.0.0

- spack in develop branch

Thank you.

Hoang

[Andrei G. Shvarts]

Hi Hoang,

I had exactly the same issue while installing MoFEM on macOS Big Sur. From what I understood, the problem occurs when bzip2 is installed using homebrew, and then for some reason it cannot be used by spack. The solution for me was to have it installed by spack itself. The problem can occur with other packages, so I uninstalled all packages installed with homebrew. Then I did not install anything using homebrew (previously our instructions were saying to install a few packages, including bzip2, but now I deleted that from http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html#autotoc_md11
The only package you might need to install with homebrew is gcc 9 (at the time I was doing this - August 2021 - MUMPS could not be compiled using gcc 10 or gcc 11).        

Let me know if this works,
Regards,
Andrei

[Karol Lewandowski]

Are you trying to install mofem on Apple Silicon? (M1 Mac) 

[hoangn...@gmail.com]

Hi Andrei. Thank you for the details. I didn't install Bzip2 by homebrew and when I tried to install using spack, it gave a similar message. I will try again tomorrow.

Hi Karol. It's Intel.

Hoang

[hoangn...@gmail.com]

I managed to install by uninstalling all the packages installed in home brew and start the installation from the beginning as suggested by Andrei.

Thank you.

Hoang

[Lukasz Kaczmraczyk]

Hello All,

I made an update of spack to version v0.17.1. Is in branch lukasz/spack_v0.17.1.

Hoang, Karol, see if that works for you if you still have problems. If not, please report problems here.

Kind regards,

Lukasz

[Felipe Pires]

Hello all,

I have faced a similar issue while installing mofem (install_mofem_developer.sh) on my linux machine (Ubuntu 20.04.6 LTS).

The installation runs well until the command "spack install --only dependencies mofem-cephas ^petsc+X" is typed.

I have tried running the original ".sh" file and creating a mirror for spack (commented lines in the install_mofem_developer.sh file: lines 149-161).

Moreover, I do not have "homebrew" installed in this machine.

Would you know how to help?

The error message is shown below.

Best,

Felipe

pack install --only dependencies mofem-cephas ^petsc+X

==> Bootstrapping clingo from pre-built binaries
==> Bootstrapping clingo from sources
[+] /usr (external bison-3.5.1-nggfxvv33iyzgy2emkdqyqrx4khu4ffs)
[+] /usr/local (external cmake-3.21.3-nwsoow6t2654olt3ant5n6wqaf3meqqo)
[+] /opt/intel/oneapi/intelpython/latest (external python-3.7-wa6pgyy74qfunfivtuhn4acoa7kwe5c3)
==> Installing re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm
==> No binary for re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0f/0fc45e4130a8a555d68e230d1795de0216dfe99096b61b28e67c86dfd7d86bda.tar.xz
==> Error: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/EMSE2000\\f.sempertegui/spack-stage/spack-stage-re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm/re2c-2.2.tar.xz'

/home/f.sempertegui/mofem_dev/mofem_install/spack/lib/spack/spack/package.py:1406, in do_fetch:
       1403
       1404        self.stage.create()
       1405        err_msg = None if not self.manual_download else self.download_instr
  >>   1406        start_time = time.time()
       1407        self.stage.fetch(mirror_only, err_msg=err_msg)
       1408        self._fetch_time = time.time() - start_time
       1409

See build log for details:
  /tmp/EMSE2000\f.sempertegui/spack-stage/spack-stage-re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm/spack-build-out.txt

==> Warning: Skipping build of clingo-bootstrap-spack-ejilmbb2vkspy7o6oacm4ra5hpphchlt since re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm failed
==> Error: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %gcc target=x86_64" due to the following failures:
    'spack-install' raised InstallError: Terminating after first install failure: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/EMSE2000\\f.sempertegui/spack-stage/spack-stage-re2c-2.2-wfvnq777f4g2lmmgtc3lv2cf7k6ywvjm/re2c-2.2.tar.xz'
    Please run `spack -d spec zlib` for more verbose error messages