Spack: compiling py-scifem fails on first try

[dajuno]

Hi,

I'm trying to install scifem using spack. The installation of scifem in a fresh environment always fails on the first attempt, although fenics-dolfinx and all dependencies compile successfully. Running spack install a second time will successfully install sci-fem.

• Spack version: v1.0.2

• minimal environment spack.yaml:

  spack:
    specs:
    - py-scifem ^openmpi
    view: true
    concretizer:
      unify: true

• to reproduce:

  spack env create test-scifem spack.yaml
  spack concretize --fresh
  spack install

spack-build-out.txt:

==> py-scifem: Executing phase: 'install'
==> [2025-10-09-17:25:53.026479] '/home/david/work/dev/spack/opt/spack/linux-skylake/python-venv-1.0-ew4k26zoq5lmtyhk35aol7cshoozp43q/bin/python3' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/home/david/work/dev/spack/opt/spack/linux-skylake/py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu' '.'
Using pip 25.1.1 from /home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip (python 3.12)
Non-user install due to --prefix or --target option
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-build-tracker-ve25kr4y
Initialized build tracking at /tmp/pip-build-tracker-ve25kr4y
Created build tracker: /tmp/pip-build-tracker-ve25kr4y
Entered build tracker: /tmp/pip-build-tracker-ve25kr4y
Created temporary directory: /tmp/pip-install-d0nhzrxj
Created temporary directory: /tmp/pip-ephem-wheel-cache-s3hapshl
Processing /tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src
  Added file:///tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src to build tracker '/tmp/pip-build-tracker-ve25kr4y'
  Created temporary directory: /tmp/pip-modern-metadata-d2xm23qa
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  *** scikit-build-core 0.11.5 using CMake 3.31.8 (metadata_wheel)
  Preparing metadata (pyproject.toml): finished with status 'done'
  Source in /tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src has version 0.6.0, which satisfies requirement scifem==0.6.0 from file:///tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src
  Removed scifem==0.6.0 from file:///tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src from build tracker '/tmp/pip-build-tracker-ve25kr4y'
Created temporary directory: /tmp/pip-unpack-2dapp3r_
Building wheels for collected packages: scifem
  Created temporary directory: /tmp/pip-wheel-vxb1dkyo
  Destination directory: /tmp/pip-wheel-vxb1dkyo
  Building wheel for scifem (pyproject.toml): started
  Running command Building wheel for scifem (pyproject.toml)
  *** scikit-build-core 0.11.5 using CMake 3.31.8 (wheel)
  *** Configuring CMake...
  loading initial cache file /tmp/tmpxhx8g5l1/build/CMakeInit.txt
  -- The C compiler identification is GNU 15.2.1
  -- The CXX compiler identification is GNU 15.2.1
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working C compiler: /usr/bin/gcc - skipped
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /home/david/work/dev/spack/opt/spack/linux-skylake/compiler-wrapper-1.0-ncfreugxt37tqdl4lwzni7mnevu5ccue/libexec/spack/gcc/g++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  CMake Error at CMakeLists.txt:29 (find_package):
    Could not find a package configuration file provided by "Basix" with any of
    the following names:

      BasixConfig.cmake
      basix-config.cmake

    Add the installation prefix of "Basix" to CMAKE_PREFIX_PATH or set
    "Basix_DIR" to a directory containing one of the above files.  If "Basix"
    provides a separate development package or SDK, be sure it has been
    installed.


  -- Configuring incomplete, errors occurred!

  *** CMake configuration failed
  error: subprocess-exited-with-error
  
  × Building wheel for scifem (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /home/david/work/dev/spack/opt/spack/linux-skylake/python-venv-1.0-ew4k26zoq5lmtyhk35aol7cshoozp43q/bin/python3 /home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpx73msjqh
  cwd: /tmp/david/spack-stage/spack-stage-py-scifem-0.7.0-qhqjr5sidw63ldazqxoys456karz4jgu/spack-src
  Building wheel for scifem (pyproject.toml): finished with status 'error'
  ERROR: Failed building wheel for scifem
Failed to build scifem
ERROR: Failed to build installable wheels for some pyproject.toml based projects (scifem)
Exception information:
Traceback (most recent call last):
  File "/home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
    status = _inner_run()
             ^^^^^^^^^^^^
  File "/home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
    return self.run(options, args)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 68, in wrapper
    return func(self, options, args)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/david/work/dev/spack/opt/spack/linux-skylake/py-pip-25.1.1-4kxv4gobwlmzxrd5mqqliyoqee5chfij/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 436, in run
    raise InstallationError(
pip._internal.exceptions.InstallationError: Failed to build installable wheels for some pyproject.toml based projects (scifem)
Removed build tracker: '/tmp/pip-build-tracker-ve25kr4y'

Output of spack spec -I:

 -   py-scifem@0.7.0~adios2~biomed~hdf5~petsc build_system=python_pip platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]      ^cmake@3.31.8~doc+ncurses+ownlibs~qtgui build_system=generic build_type=Release platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^curl@8.15.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs:=shared,static tls:=openssl platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^nghttp2@1.65.0 build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^perl@5.42.0+cpanm+opcode+open+shared+threads build_system=generic platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches:=26090f4,b231fcc platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^gmake@4.4.1~guile build_system=generic platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^ncurses@6.5-20250705~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^zlib-ng@2.2.4+compat+new_strategies+opt+pic+shared build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]      ^compiler-wrapper@1.0 build_system=generic platform=linux os=arch target=skylake 
[e]      ^gcc@15.2.1~binutils+bootstrap~graphite~mold~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages:='c,c++,fortran' platform=linux os=arch target=skylake 
[+]      ^gcc-runtime@15.2.1 build_system=generic platform=linux os=arch target=skylake 
[e]      ^glibc@2.42 build_system=autotools platform=linux os=arch target=skylake 
[+]      ^py-fenics-dolfinx@0.9.0~petsc4py~slepc4py build_system=python_pip platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]          ^fenics-basix@0.9.0~ipo build_system=cmake build_type=Release generator=make platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]          ^fenics-dolfinx@0.9.0~adios2~ipo~petsc~slepc build_system=cmake build_type=Release generator=make partitioners:=parmetis platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^boost@1.88.0~atomic~charconv~chrono~clanglibcpp~cobalt~container~context~contract~coroutine~date_time~debug~exception~fiber~filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi~mqtt5+multithreaded~nowide~numpy~pic~program_options~python~random~regex~serialization+shared~signals2~singlethreaded~stacktrace~system~taggedlayout~test~thread+timer~type_erasure~url~versionedlayout~wave build_system=generic cxxstd=11 patches:=a440f96 visibility=hidden platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^fenics-ufcx@0.9.0~ipo build_system=cmake build_type=Release generator=make platform=linux os=arch target=skylake 
[+]              ^openmpi@5.0.8+atomics~cuda~debug+fortran~gpfs~internal-hwloc~internal-libevent~internal-pmix~ipv6~java~lustre~memchecker~openshmem~rocm~romio+rsh~static~two_level_namespace+vt+wrapper-rpath build_system=autotools fabrics:=none romio-filesystem:=none schedulers:=none platform=linux os=arch target=skylake %c,cxx,fortran=gcc@15.2.1
[+]                  ^autoconf@2.72 build_system=autotools platform=linux os=arch target=skylake 
[+]                      ^m4@1.4.20+sigsegv build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                          ^libsigsegv@2.14 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^automake@1.16.5 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^hwloc@2.11.1~cairo~cuda~gl~level_zero~libudev+libxml2~nvml~opencl+pci~rocm build_system=autotools libs:=shared,static platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                      ^libpciaccess@0.17 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                          ^util-macros@1.20.1 build_system=autotools platform=linux os=arch target=skylake 
[+]                  ^libevent@2.1.12+openssl build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^libtool@2.4.7 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                      ^findutils@4.10.0 build_system=autotools patches:=440b954 platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^numactl@2.0.18 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^openssh@9.9p1+gssapi build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                      ^krb5@1.21.3+shared build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                          ^bison@3.8.2~color build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                      ^libedit@3.1-20240808 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^pmix@6.0.0~munge~python build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^prrte@4.0.0 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                      ^flex@2.6.3+lex~nls build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^parmetis@4.0.3~gdb~int64~ipo+shared build_system=cmake build_type=Release generator=make patches:=4f89253,50ed208,704b84f platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                  ^metis@5.1.0~gdb~int64~ipo~no_warning~real64+shared build_system=cmake build_type=Release generator=make patches:=4991da9,93a7903,b1225da platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^pugixml@1.14~ipo+pic+shared build_system=cmake build_type=Release generator=make platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]              ^spdlog@1.15.2~ipo+shared build_system=cmake build_type=Release generator=make patches:=fdc325d platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]                  ^fmt@11.2.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^hdf5@1.14.6~cxx~fortran~hl~ipo~java~map+mpi+shared~subfiling~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^pkgconf@2.5.1 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^py-cffi@1.16.0 build_system=python_pip platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]              ^py-pycparser@2.21 build_system=python_pip platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^py-fenics-basix@0.9.0 build_system=python_pip platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]          ^py-fenics-ffcx@0.9.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]          ^py-fenics-ufl@2024.2.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]          ^py-mpi4py@4.0.1 build_system=python_pip platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]      ^py-nanobind@2.8.0 build_system=python_pip commit=0e7aa61a75052034453cd2b906a79fe222792697 platform=linux os=arch target=skylake %cxx=gcc@15.2.1
[+]      ^py-numpy@2.3.2 build_system=python_pip patches:=873745d platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^openblas@0.3.30~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=none platform=linux os=arch target=skylake %c,cxx,fortran=gcc@15.2.1
[+]          ^py-cython@3.1.3 build_system=python_pip platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^py-meson-python@0.18.0 build_system=python_pip platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]              ^meson@1.8.2 build_system=python_pip patches:=0f0b1bd platform=linux os=arch target=skylake 
[+]              ^ninja@1.13.0+re2c build_system=generic platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]                  ^re2c@3.1 build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^py-pyproject-metadata@0.9.1 build_system=python_pip platform=linux os=arch target=skylake 
[+]      ^py-packaging@25.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]          ^py-flit-core@3.12.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]      ^py-pip@25.1.1 build_system=generic platform=linux os=arch target=skylake 
[+]      ^py-scikit-build-core@0.11.5+pyproject build_system=python_pip platform=linux os=arch target=skylake %c,cxx,fortran=gcc@15.2.1
[+]          ^py-hatch-vcs@0.4.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]              ^py-setuptools-scm@8.2.1+toml build_system=python_pip platform=linux os=arch target=skylake 
[+]                  ^git@2.48.1+man+nls+perl+subtree~svn~tcltk build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                      ^libidn2@2.3.7 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                          ^libunistring@1.2 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                      ^pcre2@10.44~jit+multibyte+pic build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^py-hatchling@1.27.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]              ^py-pluggy@1.5.0 build_system=python_pip platform=linux os=arch target=skylake 
[+]              ^py-trove-classifiers@2025.5.9.12 build_system=python_pip platform=linux os=arch target=skylake 
[+]                  ^py-calver@2025.4.17 build_system=python_pip platform=linux os=arch target=skylake 
[+]          ^py-pathspec@0.12.1 build_system=python_pip platform=linux os=arch target=skylake 
[+]      ^py-setuptools@80.9.0 build_system=generic platform=linux os=arch target=skylake 
[+]      ^py-wheel@0.45.1 build_system=generic platform=linux os=arch target=skylake 
[+]      ^python@3.12.9+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^bzip2@1.0.8~debug~pic+shared build_system=generic platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]              ^diffutils@3.12 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^expat@2.7.1+libbsd build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^libbsd@0.12.2 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^libmd@1.1.0 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^gdbm@1.23 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^gettext@0.23.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^libiconv@1.18 build_system=autotools libs:=shared,static platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]              ^libxml2@2.13.5~http+pic~python+shared build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]              ^tar@1.35 build_system=autotools zip=pigz platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^pigz@2.8 build_system=makefile platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]                  ^zstd@1.5.7+programs build_system=makefile compression:=none libs:=shared,static platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^libffi@3.4.8 build_system=autotools platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]          ^libxcrypt@4.4.38~obsolete_api build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^openssl@3.4.1~docs+shared build_system=generic certs=mozilla platform=linux os=arch target=skylake %c,cxx=gcc@15.2.1
[+]              ^ca-certificates-mozilla@2025-05-20 build_system=generic platform=linux os=arch target=skylake 
[+]          ^readline@8.3 build_system=autotools patches:=21f0a03 platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^sqlite@3.46.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^util-linux-uuid@2.41 build_system=autotools platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]          ^xz@5.6.3~pic build_system=autotools libs:=shared,static platform=linux os=arch target=skylake %c=gcc@15.2.1
[+]      ^python-venv@1.0 build_system=generic platform=linux os=arch target=skylake 

It would be nice to be able to install the environment in one go. Thanks!

[finsberg]

Hi @dajuno. Thanks for notifying us about this.

Looking at the spack configuration file (https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/py_scifem/package.py) we might need to specifically add basix as a dependency since this is actually needed to build the package, or what do you think @jorgensd ?

BTW: I can also reproduce the error locally.

[jorgensd]

We should probably add:

    depends_on("fenics-dolfinx@0.9:", when="@0.4:", type="build")
    depends_on("fenics-dolfinx@main", when="@main", type="build")
    depends_on("fenics-basix@0.9:", when="@0.4:", type="build")
    depends_on("fenics-basix@main", when="@main", type="build")

As we require both basix and fenics-dolfinx in the cmakefile.

[finsberg]

Hi @dajuno. This should be OK in the next release on spack after this fix: spack/spack-packages@9558652

[dajuno]

Hi @dajuno. This should be OK in the next release on spack after this fix: spack/spack-packages@9558652

Great, thanks