salome,-med,-medcoupling: new versions, new/changed variants #46576

capitalaslash · 2024-09-25T12:45:14Z

Update of salome-medcoupling and related packages

capitalaslash · 2024-10-23T10:33:40Z

@bernhardkaindl thanks for the review. I should have fixed the errors that you reported, even if I was not able to reproduce all of them.

var/spack/repos/builtin/packages/salome-med/package.py

bernhardkaindl

About the errors related to not finding elsize variable:

libs/python/src/numpy/dtype.cpp: In member function 'int boost:python:numpy:dtype:get_itemsize() const':
libs/python/src/numpy/dtype.cpp:101:83: error: 'PyArray_Descr' {aka 'struct _PyArray_Descr'} has no member named 'elsize'
  101 | int dtype:get_itemsize() const { return reinterpret_cast<PyArray_Descr*>(ptr())->elsize;}
      |                                                                                   ^~~~~~

As this appears to be related to numpy and possibly boost, I tried adding ^numpy@1 to the abstract spec. I'm not sure about it because of the issue on hitting the hdf5 dependency version hole(s) (see above), but this led to an initial successful build (by experimentation):

Click to Expand:

bin/spack install -v salome-medcoupling~mpi build_type=MinSizeRel ^py-numpy@1 ^salome-med@4.1.1

bin/spack find -d -v salome-medcoupling
-- linux-ubuntu22.04-skylake / gcc@13.1.0 -----------------------
salome-medcoupling@9.13.0~int64~ipo~metis~mpi~partitioner~scotch~static build_system=cmake build_type=MinSizeRel generator=make
    boost@1.86.0~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+multithreaded~nowide+numpy~pic~program_options+python~random~regex~serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout~test~thread~timer~type_erasure~url~versionedlayout~wave build_system=generic cxxstd=11 patches=a440f96,b8569d7 visibility=hidden
    cmake@3.30.5~doc+ncurses+ownlibs~qtgui build_system=generic build_type=Release patches=dbc3892
        curl@8.10.1~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl
            nghttp2@1.63.0 build_system=autotools
        ncurses@6.5~symlinks+termlib abi=none build_system=autotools patches=7a351bc
        zlib-ng@2.2.1+compat~new_strategies+opt+pic+shared build_system=autotools
    cppunit@1.15.1 build_system=autotools cxxstd=default libs=shared,static
    gcc-runtime@13.1.0 build_system=generic
    glibc@2.35 build_system=autotools
    gmake@4.4.1~guile build_system=generic
    libtirpc@1.3.3 build_system=autotools
        krb5@1.21.3+shared build_system=autotools
            bison@3.8.2~color build_system=autotools
                m4@1.4.19+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7
                    libsigsegv@2.14 build_system=autotools
            diffutils@3.10 build_system=autotools
            findutils@4.9.0 build_system=autotools patches=440b954
            perl@5.40.0+cpanm+opcode+open+shared+threads build_system=generic
                berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc
    libxml2@2.10.3+pic~python+shared build_system=autotools
        pkgconf@2.2.0 build_system=autotools
        xz@5.4.6~pic build_system=autotools libs=shared,static
    py-numpy@1.26.4 build_system=python_pip patches=873745d
        openblas@0.3.28~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile patches=d0b9276 symbol_suffix=none threads=none
        py-cython@3.0.11 build_system=python_pip
            py-setuptools@69.2.0 build_system=generic
        py-meson-python@0.16.0 build_system=python_pip
            meson@1.5.1 build_system=python_pip patches=0f0b1bd
            py-packaging@24.1 build_system=python_pip
                py-flit-core@3.9.0 build_system=python_pip
            py-pyproject-metadata@0.7.1 build_system=python_pip
        py-pip@23.1.2 build_system=generic
        py-wheel@0.41.2 build_system=generic
        python-venv@1.0 build_system=generic
    py-scipy@1.14.1 build_system=python_pip
        py-pybind11@2.13.5+ipo build_system=cmake build_type=Release generator=ninja
            ninja@1.12.1+re2c build_system=generic
                re2c@3.1 build_system=autotools
        py-pythran@0.16.1 build_system=python_pip
            py-beniget@0.4.1 build_system=python_pip
            py-gast@0.5.4 build_system=python_pip
            py-ply@3.11 build_system=python_pip
    python@3.11.9+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060
        bzip2@1.0.8~debug~pic+shared build_system=generic
        expat@2.6.3+libbsd build_system=autotools
            libbsd@0.12.2 build_system=autotools
                libmd@1.0.4 build_system=autotools
        gdbm@1.23 build_system=autotools
        gettext@0.22.5+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools
            tar@1.34 build_system=autotools zip=pigz
                pigz@2.8 build_system=makefile
                zstd@1.5.6+programs build_system=makefile compression=none libs=shared,static
        libffi@3.4.6 build_system=autotools
        libxcrypt@4.4.35~obsolete_api build_system=autotools patches=4885da3
        openssl@3.3.1~docs+shared build_system=generic certs=mozilla
            ca-certificates-mozilla@2023-05-30 build_system=generic
        readline@8.2 build_system=autotools patches=bbf97f1
        sqlite@3.46.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools
        util-linux-uuid@2.40.2 build_system=autotools
    salome-configuration@9.13.0 build_system=generic patches=bb7c401
    salome-med@4.1.1~fortran~int64~ipo~mpi~static build_system=cmake build_type=Release generator=make
        hdf5@1.10.3~cxx~fortran~hl~ipo~java~mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make patches=f42732a
    swig@4.1.1 build_system=autotools
        pcre2@10.44~jit+multibyte build_system=autotools

==> 1 installed package

That is a big initial joy! ;-)

So, it should be possible to test which combination of versions triggered the error, or maybe a changelog or Google could have reports about the change.

PS: The draft status is mostly useful to prevent the GitLab CI pipeline from getting started on each git push, because it consumes quite a lot of compute time, energy and some cost/budget too:

As the changes in this PR are not part of the configured list of specs that are tested in it, it does not make sense to let GitLab CI pipeline run until the specs in PR are able to build in a fresh checkout of spack with having the version ranges for patches and dependencies sorted.

When this batch of failing conditions is fixed (those are just using the fresh versions that a fresh spack installation selects), you can re-request another review in the top-right corner from me, and of course you can mention me (and in case my review queue is very long) of course other reviewers too.

When a fresh build works, it would be also possible to copy the branch and create new PR (but mentioning reviewers should definitely help, it is just a very busy time)

Update:

I or Google struck Gold:

https://www.google.com/search?client=firefox-b-d&q=boost+numpy+version+2
- Support NumPy 2.0 rdkit/rdkit#7477
  - Support numpy 2.0.0b1 boostorg/python#432
    - https://github.com/boostorg/python/pull/432/files - Gotcha!

Backports (do not show for which versions, maybe identical):
dennisklein/FairSoft@f7eb6ab
dennisklein/FairSoft@6fc47d5

pybind11 is/was also affected, and this issue has a long list of references at the end and maybe there are more fixes:
pybind/pybind11#5009

The PR about it has a wealth of information: pybind/pybind11#5050

Table of Numpy Ecosystem packages that may need updates/patces: numpy/numpy#26191

Unfortunately there is no newer boost release with the fix, so to try py-numpy@2, this patch would be needed.

If this patch is not sufficient, either salome-medcoupling or boost+python+numpy itself should likely add some conflict (or dependency) to the effect of (this would be for boost+python+numpy itself):

conflicts("numpy@2:", when="@:1.86", msg="boost.Python @:1.86 does not support Numpy-2.x yet")`

API change discussion with a link to the migration guide entry at the end: numpy/numpy#25943

…ndencies

capitalaslash · 2024-10-25T12:27:04Z

@bernhardkaindl thank you for the help!
I can confirm that the current failures are only related to boost.python.
The bug is already acknowledged in the package recipe, I just changed the upper bound for the version.
I do not understand why [email protected] does not include the patch that you linked.

x64-Linux-Builder

Hello @franciskloss and @hainest, I generated some build results:

ℹ️ spack install on the changed recipes of this PR was successful¹ on Ubuntu 22.04.4 LTS!

Click here for a summary of the successful builds.

These changed specs were found using gh pr diff:

Click here to show/hide the report on spack find for linux-ubuntu22.04-skylake / [email protected].