salome,-med,-medcoupling: new versions, new/changed variants by capitalaslash · Pull Request #46576 · spack/spack

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.

bernhardkaindl

About the errors related to not finding elsize variable:

libs/python/src/numpy/dtype.cpp: Inmemberfunction'int boost:python:numpy:dtype:get_itemsize() const':
libs/python/src/numpy/dtype.cpp:101:83: error: 'PyArray_Descr' {aka'struct _PyArray_Descr'} hasnomembernamed'elsize'101|intdtype:get_itemsize() const { returnreinterpret_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/spackinstall-vsalome-medcoupling~mpibuild_type=MinSizeRel^py-numpy@1^salome-med@4.1.1

bin/spackfind-d-vsalome-medcoupling--linux-ubuntu22.04-skylake/gcc@13.1.0-----------------------salome-medcoupling@9.13.0~int64~ipo~metis~mpi~partitioner~scotch~staticbuild_system=cmakebuild_type=MinSizeRelgenerator=makeboost@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~wavebuild_system=genericcxxstd=11patches=a440f96,b8569d7visibility=hiddencmake@3.30.5~doc+ncurses+ownlibs~qtguibuild_system=genericbuild_type=Releasepatches=dbc3892curl@8.10.1~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2build_system=autotoolslibs=shared,statictls=opensslnghttp2@1.63.0build_system=autotoolsncurses@6.5~symlinks+termlibabi=nonebuild_system=autotoolspatches=7a351bczlib-ng@2.2.1+compat~new_strategies+opt+pic+sharedbuild_system=autotoolscppunit@1.15.1build_system=autotoolscxxstd=defaultlibs=shared,staticgcc-runtime@13.1.0build_system=genericglibc@2.35build_system=autotoolsgmake@4.4.1~guilebuild_system=genericlibtirpc@1.3.3build_system=autotoolskrb5@1.21.3+sharedbuild_system=autotoolsbison@3.8.2~colorbuild_system=autotoolsm4@1.4.19+sigsegvbuild_system=autotoolspatches=9dc5fbd,bfdffa7libsigsegv@2.14build_system=autotoolsdiffutils@3.10build_system=autotoolsfindutils@4.9.0build_system=autotoolspatches=440b954perl@5.40.0+cpanm+opcode+open+shared+threadsbuild_system=genericberkeley-db@18.1.40+cxx~docs+stlbuild_system=autotoolspatches=26090f4,b231fcclibxml2@2.10.3+pic~python+sharedbuild_system=autotoolspkgconf@2.2.0build_system=autotoolsxz@5.4.6~picbuild_system=autotoolslibs=shared,staticpy-numpy@1.26.4build_system=python_pippatches=873745dopenblas@0.3.28~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+sharedbuild_system=makefilepatches=d0b9276symbol_suffix=nonethreads=nonepy-cython@3.0.11build_system=python_pippy-setuptools@69.2.0build_system=genericpy-meson-python@0.16.0build_system=python_pipmeson@1.5.1build_system=python_pippatches=0f0b1bdpy-packaging@24.1build_system=python_pippy-flit-core@3.9.0build_system=python_pippy-pyproject-metadata@0.7.1build_system=python_pippy-pip@23.1.2build_system=genericpy-wheel@0.41.2build_system=genericpython-venv@1.0build_system=genericpy-scipy@1.14.1build_system=python_pippy-pybind11@2.13.5+ipobuild_system=cmakebuild_type=Releasegenerator=ninjaninja@1.12.1+re2cbuild_system=genericre2c@3.1build_system=autotoolspy-pythran@0.16.1build_system=python_pippy-beniget@0.4.1build_system=python_pippy-gast@0.5.4build_system=python_pippy-ply@3.11build_system=python_pippython@3.11.9+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlibbuild_system=genericpatches=13fa8bf,b0615b2,ebdca64,f2fd060bzip2@1.0.8~debug~pic+sharedbuild_system=genericexpat@2.6.3+libbsdbuild_system=autotoolslibbsd@0.12.2build_system=autotoolslibmd@1.0.4build_system=autotoolsgdbm@1.23build_system=autotoolsgettext@0.22.5+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xzbuild_system=autotoolstar@1.34build_system=autotoolszip=pigzpigz@2.8build_system=makefilezstd@1.5.6+programsbuild_system=makefilecompression=nonelibs=shared,staticlibffi@3.4.6build_system=autotoolslibxcrypt@4.4.35~obsolete_apibuild_system=autotoolspatches=4885da3openssl@3.3.1~docs+sharedbuild_system=genericcerts=mozillaca-certificates-mozilla@2023-05-30build_system=genericreadline@8.2build_system=autotoolspatches=bbf97f1sqlite@3.46.0+column_metadata+dynamic_extensions+fts~functions+rtreebuild_system=autotoolsutil-linux-uuid@2.40.2build_system=autotoolssalome-configuration@9.13.0build_system=genericpatches=bb7c401salome-med@4.1.1~fortran~int64~ipo~mpi~staticbuild_system=cmakebuild_type=Releasegenerator=makehdf5@1.10.3~cxx~fortran~hl~ipo~java~mpi+shared~szip~threadsafe+toolsapi=defaultbuild_system=cmakebuild_type=Releasegenerator=makepatches=f42732aswig@4.1.1build_system=autotoolspcre2@10.44~jit+multibytebuild_system=autotools==>1installedpackage

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
- rdkit/rdkit#7477
  - 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 boost@1.86 does not include the patch that you linked.

bendamasio

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:

boost
salome-configuration@9.13.0
salome-configuration@9.12.0
salome-configuration@9.11.0
salome-configuration@9.10.0
salome-configuration@9.9.0
salome-configuration@9.8.0
salome-med+int64@5.0.0
salome-med+int64@4.1.1
salome-medcoupling+int64@9.13.0
salome-medcoupling+int64@9.12.0
salome-medcoupling+int64@9.11.0
salome-medcoupling+int64@9.10.0
salome-medcoupling+int64@9.9.0
salome-medcoupling+int64@9.8.0

Click here to show/hide the report on spack find for linux-ubuntu22.04-skylake / gcc@13.1.0.