Your message dated Thu, 21 Dec 2023 14:50:15 +0000 with message-id <[email protected]> and subject line Bug#1058876: fixed in openmpi 4.1.6-3 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: 4.1.6-3 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: Thu, 21 Dec 2023 14:06:07 +0000 Source: openmpi Architecture: source Version: 4.1.6-3 Distribution: unstable Urgency: medium Maintainer: Alastair McKinstry <[email protected]> Changed-By: Alastair McKinstry <[email protected]> Closes: 1058876 Changes: openmpi (4.1.6-3) unstable; urgency=medium . * Pass FMODDIR into pkg-config. Closes: #1058876 * Update mpi wrappers data for fmoddir * Now ship pkg-config ompi-f77.pc, opal.pc links in d/libopenmpi-dev * Expand debian/tests to cover mpi wrapper, pkg-config compiles Checksums-Sha1: 609b5382f4b4f752de19b040f93d53ccb2685dbe 2743 openmpi_4.1.6-3.dsc 046425b8d3991ed9a4db9a4f5e4c6242ed075c8d 69304 openmpi_4.1.6-3.debian.tar.xz Checksums-Sha256: a3feac9f66c4be38e59557ba30e65533d5a0d5c9af6fd5c2cf5fad9659fbcbb3 2743 openmpi_4.1.6-3.dsc be61ce1ccafc19871bbfff9efdf096589988941e257b70901eb508b19658f46e 69304 openmpi_4.1.6-3.debian.tar.xz Files: 7b3e8d86543ed02e637772e23c897c85 2743 net optional openmpi_4.1.6-3.dsc 85447f2867545ea1532c0e50c6bdea48 69304 net optional openmpi_4.1.6-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEgjg86RZbNHx4cIGiy+a7Tl2a06UFAmWETNgACgkQy+a7Tl2a 06W86Q//S0l0TPqRoermEwiy07EwajQt99/bsNca1NsEjhGgvMA+aGYW09nvwzdL ++PnwV2omQgLCAqhy4HSPEopfgn45akZc+dz5UGepoVKuOVp9ruplYU4wxwZ8m+G xkbt+VF6SZzjiskJlisdJMQThfiCCDN31pwX8KB39eQGzlIZKaWvsPSE3nt0FejQ IITiAoDukBRgpPrrhqHkzU24qGMmGkf864Lh1xF4NPy+3FKYsgoMQZR68Y3x/W7Z 9e3igc9GIMrvuiuZP5vHofmBgLCXao6aWqQ/41iOhV1FmB3A/Bu7aaL09/rEtE/z B17bpLF79U+B7RqNH9ahw1poXofMyORX4+QUREnO2aG7PfXc4DUoLKvJ9v6aH5+y r8ituO2UlUYttHE0weabKJHL2SO9d26j31aJvVgckFsiOFwolc+59nCEeJVh1c1u +0CLGnQIBeSmQ7kMehAsrbyhxngAJaF2leEYRIh92uw7R6N2O3KLjHuMNU6g/UMm O7D7IDPgzcu0YlaxO5NLR8sw+LBkxl3QUeCHWcEesxcvjkpRW7DCLw9LRryn8V/X uxx6qKOS9ahK7bMkOJXwzcw3OTfRByKQRCWQTNYrGx1ffmfbT7z9lzioZhewwGf5 s0AernUZFq0LZJvNeHuHvv+92bQ/GHIrxqc7c6FqzM4/6ZltQQ4= =3KKM -----END PGP SIGNATURE-----
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