Your message dated Sun, 31 Dec 2023 17:04:42 +0000 with message-id <[email protected]> and subject line Bug#1058876: fixed in openmpi 4.1.6-4 has caused the Debian Bug report #1058876, regarding libopenmpi-dev: paths missing /usr/include...(for fortran mpi.mod) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 1058876: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058876 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: libopenmpi-dev Version: 4.1.6-2 Severity: serious Justification: ftbfs (other) openmpi 4.1.6-2 moved the fortran mod files from /usr/lib to /usr/include. This is probably correct, but has some consequences we need to sort out. Applications using cmake for configuration are still looking for the mod files in /usr/lib, so their builds now fail. An example is adios2, with error message: [384/1029] /usr/bin/gfortran -I/build/adios2-2.9.2+dfsg1/examples/hello/bpWriter -I/build/adios2-2.9.2+dfsg1/build-mpi/bindings/Fortran -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_ 64-linux-gnu/openmpi/lib -g -O2 -ffile-prefix-map=/build/adios2-2.9.2+dfsg1=. -fstack-protector-strong -fstack-clash-protection -fcf-protection -Jexamples/hello/bpWriter -fpreprocessed -c examples/hello/bpWriter /CMakeFiles/hello_bpWriter_f_mpi.dir/helloBPWriter.F90-pp.f90 -o examples/hello/bpWriter/CMakeFiles/hello_bpWriter_f_mpi.dir/helloBPWriter.F90.o FAILED: examples/hello/bpWriter/CMakeFiles/hello_bpWriter_f_mpi.dir/helloBPWriter.F90.o /usr/bin/gfortran -I/build/adios2-2.9.2+dfsg1/examples/hello/bpWriter -I/build/adios2-2.9.2+dfsg1/build-mpi/bindings/Fortran -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gn u/openmpi/lib -g -O2 -ffile-prefix-map=/build/adios2-2.9.2+dfsg1=. -fstack-protector-strong -fstack-clash-protection -fcf-protection -Jexamples/hello/bpWriter -fpreprocessed -c examples/hello/bpWriter/CMakeFiles /hello_bpWriter_f_mpi.dir/helloBPWriter.F90-pp.f90 -o examples/hello/bpWriter/CMakeFiles/hello_bpWriter_f_mpi.dir/helloBPWriter.F90.o /build/adios2-2.9.2+dfsg1/examples/hello/bpWriter/helloBPWriter.F90:3:9: 3 | use mpi | 1 Fatal Error: Cannot open module file ‘mpi.mod’ for reading at (1): No such file or directory compilation terminated. We can see that the compilation got configured to use -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi which would be why it can't find mpi.mod in /usr/include As far as I can tell, adios2 is not making assumptions itself about the location of the mod files. I suspect the configuration is coming from cmake's FindMPI.cmake I guess we don't want openmpi 4.1.6-2 to migrate to testing until this issue is resolved, which is why I've marked Severity: serious. There are openmpi's pkgconfig files. $ pkg-config --cflags mpi-fort -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/lib The fortrandir variable set in ompi-fort.pc is also located in /usr/lib (perhaps it should be so) So /usr/include is not used in the include path flags. But /usr/lib is. This must be the origin of the problem. cmake's FindMPI.cmake does indeed use pkgconfig to extract the paths: "if(_MPI_PKG AND PKG_CONFIG_FOUND)" -- System Information: Debian Release: trixie/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.5.0-5-amd64 (SMP w/8 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages libopenmpi-dev depends on: ii gfortran [gfortran-mod-15] 4:13.2.0-2 ii gfortran-11 [gfortran-mod-15] 11.4.0-7 ii gfortran-12 [gfortran-mod-15] 12.3.0-13 ii gfortran-13 [gfortran-mod-15] 13.2.0-9 ii libevent-dev 2.1.12-stable-8 ii libhwloc-dev 2.10.0-1 ii libibverbs-dev 48.0-1 ii libjs-jquery 3.6.1+dfsg+~3.5.14-1 ii libjs-jquery-ui 1.13.2+dfsg-1 ii libopenmpi3 4.1.6-2 ii libpmix-dev 5.0.1-4 ii openmpi-bin 4.1.6-2 ii openmpi-common 4.1.6-2 ii zlib1g-dev 1:1.3.dfsg-3 Versions of packages libopenmpi-dev recommends: ii libcoarrays-openmpi-dev 2.10.1-1+b1 Versions of packages libopenmpi-dev suggests: pn openmpi-doc <none> -- no debconf information
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--- Begin Message ---Source: openmpi Source-Version: 4.1.6-4 Done: Alastair McKinstry <[email protected]> We believe that the bug you reported is fixed in the latest version of openmpi, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alastair McKinstry <[email protected]> (supplier of updated openmpi package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 31 Dec 2023 15:56:25 +0000 Source: openmpi Architecture: source Version: 4.1.6-4 Distribution: unstable Urgency: medium Maintainer: Alastair McKinstry <[email protected]> Changed-By: Alastair McKinstry <[email protected]> Closes: 1058876 Changes: openmpi (4.1.6-4) unstable; urgency=medium . * Revert FMODDIR to libdir via dh-fortran-mod >= 0.31. Closes: #1058876 * Add fortran-suppport.mk * Add fortran:Depends, fortran:Recommends to libopenmpi-dev * Depend on dh-fortran-mod (>= 0.31) Checksums-Sha1: e88029ad14836a64ce99d2d69d63a61301c5d4aa 2734 openmpi_4.1.6-4.dsc 376e1b8d7cc47ef764a7bc23c871b681035b61a2 69240 openmpi_4.1.6-4.debian.tar.xz Checksums-Sha256: 134ff525104bfa6ab4eb04464ced548997e048d83910cee90f8b25e8629fa6da 2734 openmpi_4.1.6-4.dsc 93a2e5b9a74b31100907a5a4ca86dd1db639feb300c1dfb29b15c17d13981b83 69240 openmpi_4.1.6-4.debian.tar.xz Files: 92bd5bcf4e35f5b11215d420dbe6c128 2734 net optional openmpi_4.1.6-4.dsc e02e44f678a4d216f3222809f3870e9b 69240 net optional openmpi_4.1.6-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEgjg86RZbNHx4cIGiy+a7Tl2a06UFAmWRmiAACgkQy+a7Tl2a 06WAyQ/9FCdiLVgFahWYfsRKFywzLsyU6Fpa/5MzjqI8t/Tqj5MvOhxURaKcqroV k7NoKVBrUnLhiKtbhDPT3rFr5CEKjbIm506vb03ORGlmpRDK9PReOwSsQsjkF58L jJ24XQ46juUNSIxMW7W7glvZ4lAgZNjP72RPa+NtwriCxCp2L9PyfoFqrET/z/iL AYr5lIAwuDO02Y5sH7hsV/L8MUghwONWyPB/CKM/w/2ijkhuIy9spdQMwCaiZrHR c4szlkP3rJN4kqMqHsxoLDsBnmot9XHdZE0RC+pNZS26EoCvV52Rrk9PU/04X+yJ ufWzMLm7cHbnTDbbMUeIBDKrg+107GHpAGX9OCzb2Pebm0mfieJoBo3eaMIF0DAn ZRm0ZksdQ/CJ3Io+oRMpl3j79sDrj78op+e/X9KdnXj6yDOlMvGr4HRqXBdpu/tg ry7l3056SKGS31o541klLAM4Em5ocKP2UzGr8w0VrrxlHodtjOZiZtnAR0544eNY B6a21FY0ThdvMWr66DQghKBZXB3H74nPJ0KPDk9ECfZtDrD4Em12m488EoUljtOB r0E0tYoT91/yZ2F3elCb39U4ySSH1F/VEpyJX5zA3zCHgIRKeIQnqYcJ0nv2yYE4 S9jKLke5mK1hEd8wa+OfMGjAJZY4lP0jWaRlx6dTXmzG3UsjUGs= =MX0P -----END PGP SIGNATURE-----
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