Bug 2377370

Summary: petsc: Stop using deprecated %py3_build/%py3_install macros
Product: [Fedora] Fedora Reporter: Miro Hrončok <mhroncok>
Component: petscAssignee: Antonio T. sagitter <sagitterghostproton.me>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: rawhideKeywords: Reopened
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: petsc-3.24.3-4.fc44 Doc Type: ---
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2026-01-13 22:08:27 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Bug Depends On:    
Bug Blocks: 2376118, 2387582    

Description Miro Hrončok 2025-07-08 14:12:50 UTC 
Dear package maintainer,

this bugzilla is automated becasue the number of impacted packages it too high to go trough manually.


It appears that your package uses the deprecated %py3_build and/or %py3_install macro.

See https://fedoraproject.org/wiki/Changes/DeprecateSetuppyMacros for why the macros are deprecated.

%py3_install expands to python setup.py install. This has been a deprecated command for 5 years and will likely stop working in Fedora 45.



Please migrate to %pyproject_buildrequires + %pyproject_wheel + %pyproject_install macros instead.

See https://fedoraproject.org/wiki/Changes/DeprecateSetuppyMacros#Migrating_to_%pyproject_macros for migration guide.

See https://github.com/hroncok/pyprojectize/ for a tool that can help you automate the migration.


Thank you. Let me know if you need help.
Comment 1 Antonio T. sagitter 2025-08-09 20:19:11 UTC 
Looks like %pyproject_install is changing PETSc.cpython-313-x86_64-linux-gnu.so that is correctly compiled

$ ldd ./PETSc.cpython-313-x86_64-linux-gnu.so
	linux-vdso.so.1 (0x00007f57a3d32000)
	libpetsc.so.3.23 => /home/sagitter/rpmbuild/BUILD/petsc-3.23.5-build/petsc-3.23.5/buildopenmpi_dir/x86_64/lib/libpetsc.so.3.23 (0x00007f57a1a00000)
	libmpi.so.40 => /usr/lib64/openmpi/lib/libmpi.so.40 (0x00007f57a1600000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f57a140f000)
	libHYPRE.so.2.1 => /usr/lib64/openmpi/lib/libHYPRE.so.2.1 (0x00007f57a0e00000)
	libsuperlu_dist.so.8 => /usr/lib64/openmpi/lib/libsuperlu_dist.so.8 (0x00007f57a0ca2000)
	libdmumps-5.7.so => /usr/lib64/openmpi/lib/libdmumps-5.7.so (0x00007f57a0a00000)
	libscalapack.so.2 => /usr/lib64/openmpi/lib/libscalapack.so.2 (0x00007f57a0400000)
	libflexiblas.so.3 => /lib64/libflexiblas.so.3 (0x00007f57a0000000)
	libptscotch.so.7.0 => /usr/lib64/openmpi/lib/libptscotch.so.7.0 (0x00007f57a3584000)
	libscotch.so.7.0 => /usr/lib64/openmpi/lib/libscotch.so.7.0 (0x00007f57a34f0000)
	libmetis.so.0 => /lib64/libmetis.so.0 (0x00007f57a1992000)
	libhdf5.so.310 => /usr/lib64/openmpi/lib/libhdf5.so.310 (0x00007f579fa00000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f579ff12000)
	libX11.so.6 => /lib64/libX11.so.6 (0x00007f579f8bb000)
	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f579f600000)
	libmpi_mpifh.so.40 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.40 (0x00007f57a13a2000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f57a34c4000)
	libpvfs2.so.2.9.7 => /lib64/libpvfs2.so.2.9.7 (0x00007f579f501000)
	libpsm2.so.2 => /lib64/libpsm2.so.2 (0x00007f57a0396000)
	libopen-pal.so.80 => /usr/lib64/openmpi/lib/libopen-pal.so.80 (0x00007f579f405000)
	libfabric.so.1 => /lib64/libfabric.so.1 (0x00007f579ee00000)
	libucp.so.0 => /lib64/libucp.so.0 (0x00007f579fe43000)
	libucs.so.0 => /lib64/libucs.so.0 (0x00007f579f3a2000)
	libucm.so.0 => /lib64/libucm.so.0 (0x00007f57a1385000)
	libuct.so.0 => /lib64/libuct.so.0 (0x00007f57a0c67000)
	libevent_core-2.1.so.7 => /lib64/libevent_core-2.1.so.7 (0x00007f57a09c7000)
	libevent_pthreads-2.1.so.7 => /lib64/libevent_pthreads-2.1.so.7 (0x00007f57a3d1d000)
	libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007f579f33e000)
	libpmix.so.2 => /lib64/libpmix.so.2 (0x00007f579ec17000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f57a3d34000)
	libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f579ebbf000)
	libptscotcherr.so.7.0 => /usr/lib64/openmpi/lib/libptscotcherr.so.7.0 (0x00007f57a3d17000)
	libptscotcherrexit.so.7.0 => /usr/lib64/openmpi/lib/libptscotcherrexit.so.7.0 (0x00007f57a3d13000)
	libcolamd.so.3 => /lib64/libcolamd.so.3 (0x00007f57a34bb000)
	libblas.so => /usr/lib64/openmpi/lib/libblas.so (0x00007f57a136b000)
	libmumps_common-5.7.so => /usr/lib64/openmpi/lib/libmumps_common-5.7.so (0x00007f579eb52000)
	libptscotchparmetisv3.so.7.0 => /usr/lib64/openmpi/lib/libptscotchparmetisv3.so.7.0 (0x00007f57a34b5000)
	libpord-5.7.so => /usr/lib64/openmpi/lib/libpord-5.7.so (0x00007f57a09ad000)
	libesmumps.so.7.0 => /usr/lib64/openmpi/lib/libesmumps.so.7.0 (0x00007f57a1989000)
	libscotcherr.so.7.0 => /usr/lib64/openmpi/lib/libscotcherr.so.7.0 (0x00007f57a34af000)
	libptesmumps.so.7.0 => /usr/lib64/openmpi/lib/libptesmumps.so.7.0 (0x00007f57a1980000)
	libmpi_usempif08.so.40 => /usr/lib64/openmpi/lib/libmpi_usempif08.so.40 (0x00007f579f87c000)
	libmpi_usempi_ignore_tkr.so.40 => /usr/lib64/openmpi/lib/libmpi_usempi_ignore_tkr.so.40 (0x00007f57a0c58000)
	libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f579e800000)
	libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f579e7b9000)
	libz.so.1 => /lib64/libz.so.1 (0x00007f579e796000)
	libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f579fe2e000)
	liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f579e761000)
	libpcre2-posix.so.3 => /lib64/libpcre2-posix.so.3 (0x00007f57a1367000)
	libsz.so.2 => /lib64/libsz.so.2 (0x00007f57a0c4e000)
	libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f579e737000)
	libcrypto.so.3 => /lib64/libcrypto.so.3 (0x00007f579e200000)
	libibverbs.so.1 => /lib64/libibverbs.so.1 (0x00007f579e717000)
	libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f57a0388000)
	librdmacm.so.1 => /lib64/librdmacm.so.1 (0x00007f579e6fb000)
	libefa.so.1 => /lib64/libefa.so.1 (0x00007f579e6ef000)
	libnl-3.so.200 => /lib64/libnl-3.so.200 (0x00007f579e6cd000)
	libnl-route-3.so.200 => /lib64/libnl-route-3.so.200 (0x00007f579e16b000)
	libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f579fe25000)
	libudev.so.1 => /lib64/libudev.so.1 (0x00007f579e124000)
	libmunge.so.2 => /lib64/libmunge.so.2 (0x00007f579e6c5000)
	libsuitesparseconfig.so.7 => /lib64/libsuitesparseconfig.so.7 (0x00007f579f877000)
	libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f579e079000)
	libXau.so.6 => /lib64/libXau.so.6 (0x00007f579e6bf000)
	libcap.so.2 => /lib64/libcap.so.2 (0x00007f579e6b3000)

But it is installed in buildroot as

$ ldd ./PETSc.cpython-313-x86_64-linux-gnu.so
	linux-vdso.so.1 (0x00007faf07940000)
	libpetsc.so.3.23 => not found
	libmpi.so.12 => not found
	libc.so.6 => /lib64/libc.so.6 (0x00007faf06fe0000)
	/lib64/ld-linux-x86-64.so.2 (0x00007faf07942000)

!?

You can see this behavior in latest petsc-3.23.5 build (https://koji.fedoraproject.org/koji/taskinfo?taskID=135875152); tests are disabled because ./PETSc.cpython-313-x86_64-linux-gnu.so is not working.

Since some days i'm trying to find a solution but without success.
Comment 2 Fedora Update System 2025-08-09 20:29:59 UTC 
FEDORA-2025-8c03357409 (petsc-3.23.5-2.fc43) has been submitted as an update to Fedora 43.
https://bodhi.fedoraproject.org/updates/FEDORA-2025-8c03357409
Comment 3 Fedora Update System 2025-08-09 20:34:14 UTC 
FEDORA-2025-8c03357409 (petsc-3.23.5-2.fc43) has been pushed to the Fedora 43 stable repository.
If problem still persists, please make note of it in this bug report.
Comment 4 Miro Hrončok 2025-08-11 10:27:52 UTC 
(In reply to Antonio T. sagitter from comment #1)
> Looks like %pyproject_install is changing
> PETSc.cpython-313-x86_64-linux-gnu.so that is correctly compiled
> 
> $ ldd ./PETSc.cpython-313-x86_64-linux-gnu.so
> 	linux-vdso.so.1 (0x00007f57a3d32000)
> 	libpetsc.so.3.23 =>
> /home/sagitter/rpmbuild/BUILD/petsc-3.23.5-build/petsc-3.23.5/
> buildopenmpi_dir/x86_64/lib/libpetsc.so.3.23 (0x00007f57a1a00000)
> 	libmpi.so.40 => /usr/lib64/openmpi/lib/libmpi.so.40 (0x00007f57a1600000)
> 	libc.so.6 => /lib64/libc.so.6 (0x00007f57a140f000)
> 	libHYPRE.so.2.1 => /usr/lib64/openmpi/lib/libHYPRE.so.2.1
> (0x00007f57a0e00000)
> 	libsuperlu_dist.so.8 => /usr/lib64/openmpi/lib/libsuperlu_dist.so.8
> (0x00007f57a0ca2000)
> 	libdmumps-5.7.so => /usr/lib64/openmpi/lib/libdmumps-5.7.so
> (0x00007f57a0a00000)
> 	libscalapack.so.2 => /usr/lib64/openmpi/lib/libscalapack.so.2
> (0x00007f57a0400000)
> 	libflexiblas.so.3 => /lib64/libflexiblas.so.3 (0x00007f57a0000000)
> 	libptscotch.so.7.0 => /usr/lib64/openmpi/lib/libptscotch.so.7.0
> (0x00007f57a3584000)
> 	libscotch.so.7.0 => /usr/lib64/openmpi/lib/libscotch.so.7.0
> (0x00007f57a34f0000)
> 	libmetis.so.0 => /lib64/libmetis.so.0 (0x00007f57a1992000)
> 	libhdf5.so.310 => /usr/lib64/openmpi/lib/libhdf5.so.310 (0x00007f579fa00000)
> 	libm.so.6 => /lib64/libm.so.6 (0x00007f579ff12000)
> 	libX11.so.6 => /lib64/libX11.so.6 (0x00007f579f8bb000)
> 	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f579f600000)
> 	libmpi_mpifh.so.40 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.40
> (0x00007f57a13a2000)
> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f57a34c4000)
> 	libpvfs2.so.2.9.7 => /lib64/libpvfs2.so.2.9.7 (0x00007f579f501000)
> 	libpsm2.so.2 => /lib64/libpsm2.so.2 (0x00007f57a0396000)
> 	libopen-pal.so.80 => /usr/lib64/openmpi/lib/libopen-pal.so.80
> (0x00007f579f405000)
> 	libfabric.so.1 => /lib64/libfabric.so.1 (0x00007f579ee00000)
> 	libucp.so.0 => /lib64/libucp.so.0 (0x00007f579fe43000)
> 	libucs.so.0 => /lib64/libucs.so.0 (0x00007f579f3a2000)
> 	libucm.so.0 => /lib64/libucm.so.0 (0x00007f57a1385000)
> 	libuct.so.0 => /lib64/libuct.so.0 (0x00007f57a0c67000)
> 	libevent_core-2.1.so.7 => /lib64/libevent_core-2.1.so.7 (0x00007f57a09c7000)
> 	libevent_pthreads-2.1.so.7 => /lib64/libevent_pthreads-2.1.so.7
> (0x00007f57a3d1d000)
> 	libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007f579f33e000)
> 	libpmix.so.2 => /lib64/libpmix.so.2 (0x00007f579ec17000)
> 	/lib64/ld-linux-x86-64.so.2 (0x00007f57a3d34000)
> 	libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f579ebbf000)
> 	libptscotcherr.so.7.0 => /usr/lib64/openmpi/lib/libptscotcherr.so.7.0
> (0x00007f57a3d17000)
> 	libptscotcherrexit.so.7.0 =>
> /usr/lib64/openmpi/lib/libptscotcherrexit.so.7.0 (0x00007f57a3d13000)
> 	libcolamd.so.3 => /lib64/libcolamd.so.3 (0x00007f57a34bb000)
> 	libblas.so => /usr/lib64/openmpi/lib/libblas.so (0x00007f57a136b000)
> 	libmumps_common-5.7.so => /usr/lib64/openmpi/lib/libmumps_common-5.7.so
> (0x00007f579eb52000)
> 	libptscotchparmetisv3.so.7.0 =>
> /usr/lib64/openmpi/lib/libptscotchparmetisv3.so.7.0 (0x00007f57a34b5000)
> 	libpord-5.7.so => /usr/lib64/openmpi/lib/libpord-5.7.so (0x00007f57a09ad000)
> 	libesmumps.so.7.0 => /usr/lib64/openmpi/lib/libesmumps.so.7.0
> (0x00007f57a1989000)
> 	libscotcherr.so.7.0 => /usr/lib64/openmpi/lib/libscotcherr.so.7.0
> (0x00007f57a34af000)
> 	libptesmumps.so.7.0 => /usr/lib64/openmpi/lib/libptesmumps.so.7.0
> (0x00007f57a1980000)
> 	libmpi_usempif08.so.40 => /usr/lib64/openmpi/lib/libmpi_usempif08.so.40
> (0x00007f579f87c000)
> 	libmpi_usempi_ignore_tkr.so.40 =>
> /usr/lib64/openmpi/lib/libmpi_usempi_ignore_tkr.so.40 (0x00007f57a0c58000)
> 	libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f579e800000)
> 	libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f579e7b9000)
> 	libz.so.1 => /lib64/libz.so.1 (0x00007f579e796000)
> 	libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f579fe2e000)
> 	liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f579e761000)
> 	libpcre2-posix.so.3 => /lib64/libpcre2-posix.so.3 (0x00007f57a1367000)
> 	libsz.so.2 => /lib64/libsz.so.2 (0x00007f57a0c4e000)
> 	libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f579e737000)
> 	libcrypto.so.3 => /lib64/libcrypto.so.3 (0x00007f579e200000)
> 	libibverbs.so.1 => /lib64/libibverbs.so.1 (0x00007f579e717000)
> 	libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f57a0388000)
> 	librdmacm.so.1 => /lib64/librdmacm.so.1 (0x00007f579e6fb000)
> 	libefa.so.1 => /lib64/libefa.so.1 (0x00007f579e6ef000)
> 	libnl-3.so.200 => /lib64/libnl-3.so.200 (0x00007f579e6cd000)
> 	libnl-route-3.so.200 => /lib64/libnl-route-3.so.200 (0x00007f579e16b000)
> 	libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f579fe25000)
> 	libudev.so.1 => /lib64/libudev.so.1 (0x00007f579e124000)
> 	libmunge.so.2 => /lib64/libmunge.so.2 (0x00007f579e6c5000)
> 	libsuitesparseconfig.so.7 => /lib64/libsuitesparseconfig.so.7
> (0x00007f579f877000)
> 	libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f579e079000)
> 	libXau.so.6 => /lib64/libXau.so.6 (0x00007f579e6bf000)
> 	libcap.so.2 => /lib64/libcap.so.2 (0x00007f579e6b3000)
> 
> But it is installed in buildroot as
> 
> $ ldd ./PETSc.cpython-313-x86_64-linux-gnu.so
> 	linux-vdso.so.1 (0x00007faf07940000)
> 	libpetsc.so.3.23 => not found
> 	libmpi.so.12 => not found
> 	libc.so.6 => /lib64/libc.so.6 (0x00007faf06fe0000)
> 	/lib64/ld-linux-x86-64.so.2 (0x00007faf07942000)
> 
> !?
> 
> You can see this behavior in latest petsc-3.23.5 build
> (https://koji.fedoraproject.org/koji/taskinfo?taskID=135875152); tests are
> disabled because ./PETSc.cpython-313-x86_64-linux-gnu.so is not working.
> 
> Since some days i'm trying to find a solution but without success.

I am not entirely sure I understand the problem. Could you please describe this better, preferably at python-devel mailing list or in another (not closed) bugzilla?
Comment 5 Antonio T. sagitter 2025-08-11 12:23:39 UTC 
Ticket reopened.

> I am not entirely sure I understand the problem. Could you please describe this better, preferably at python-devel mailing list or in another (not closed) bugzilla?

Sorry.

I have modified PETSc SPEC file to use %pyproject_wheel and %pyproject_install; starting build release 3.23.5-2, the rpms are successfully built but the `PETSc.cpython-313-x86_64-linux-gnu.so` library is broke somewhere during RPM builds.

If you try to locally rebuild this srpm https://koji.fedoraproject.org/koji/buildinfo?buildID=2787896, you'll see that the cpython library compiled in the buildsrc/buildopenmpi_dir/src/binding/petsc4py/build/lib.linux-x86_64-cpython-313/petsc4py/lib/x86_64/ (correctly compiled and linked to libmpi.so.40 in Fedora 42) is different by the same cpython library installed in the BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/petsc4py/lib/x86_64/ (linked to libmpi.so.12 !!).

This not happen if i switch back to the old %py3_install
Comment 6 Antonio T. sagitter 2025-08-11 12:26:55 UTC 
In fact, https://bugzilla.redhat.com/show_bug.cgi?id=2387582
Comment 7 Miro Hrončok 2025-08-11 17:13:24 UTC 
Could this have something to do with the fixPythonWheel added in https://gitlab.com/petsc/petsc/-/commit/5ee53db2299ec483123346965f05fffc8e6cbc9f ?
Later amended by https://gitlab.com/petsc/petsc/-/commit/6e8294f68f5aed480a30b64681aaabebca5c529b


Try adding this into %prep:

  sed -i 's/self.fixPythonWheel()/pass/' %{name}-%{version}/config/install.py

And see if it helps.

-------------


As a side note I realized you run %pyproject_buildrequires in %prep, not in %generate_buildrequires section. That does nothing.
Comment 8 Antonio T. sagitter 2025-08-11 21:12:37 UTC 
I have added the sed command, it did not work unfortunately.

(In reply to Miro Hrončok from comment #7)
> Could this have something to do with the fixPythonWheel added in
> https://gitlab.com/petsc/petsc/-/commit/
> 5ee53db2299ec483123346965f05fffc8e6cbc9f ?
> Later amended by
> https://gitlab.com/petsc/petsc/-/commit/
> 6e8294f68f5aed480a30b64681aaabebca5c529b
> 
> 
> Try adding this into %prep:
> 
>   sed -i 's/self.fixPythonWheel()/pass/' %{name}-%{version}/config/install.py
> 
> And see if it helps.
> 
> -------------
> 
> 
> As a side note I realized you run %pyproject_buildrequires in %prep, not in
> %generate_buildrequires section. That does nothing.
Comment 9 Miro Hrončok 2025-08-11 21:17:59 UTC 
Let's revert the changes for now, then?
Comment 10 Antonio T. sagitter 2025-08-12 13:23:46 UTC 
(In reply to Miro Hrončok from comment #9)
> Let's revert the changes for now, then?

Yes. I will contact the upstream maintainer about this issue.
Comment 11 Antonio T. sagitter 2025-08-14 12:24:28 UTC 
Regard to my comment in upstream issue (https://gitlab.com/petsc/petsc/-/issues/1800#note_2686551393), can %pyproject_wheel be used two times in a SPEC file?
Comment 12 Miro Hrončok 2025-08-14 12:33:33 UTC 
Yes it can, but it was not designed with mpich/openmpi/etc. in mind. Likely one wheel overrides the other here.

See also https://bugzilla.redhat.com/show_bug.cgi?id=2377285#c3
Comment 13 Fedora Admin user for bugzilla script actions 2026-01-05 04:10:42 UTC 
This package has changed maintainer in Fedora. Reassigning to the new maintainer of this component.
Comment 14 Fedora Update System 2026-01-13 21:18:39 UTC 
FEDORA-2026-152ccac3c1 (petsc-3.24.3-4.fc44) has been submitted as an update to Fedora 44.
https://bodhi.fedoraproject.org/updates/FEDORA-2026-152ccac3c1
Comment 15 Fedora Update System 2026-01-13 22:08:27 UTC 
FEDORA-2026-152ccac3c1 (petsc-3.24.3-4.fc44) has been pushed to the Fedora 44 stable repository.
If problem still persists, please make note of it in this bug report.