Your message dated Sun, 31 Dec 2023 17:04:42 +0000
with message-id <e1rjzew-004mvc...@fasolo.debian.org>
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 ow...@bugs.debian.org
immediately.)
--
1058876: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058876
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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
--- End Message ---
--- Begin Message ---
Source: openmpi
Source-Version: 4.1.6-4
Done: Alastair McKinstry <mckins...@debian.org>
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 1058...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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 <mckins...@debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
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-----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=MX0P
-----END PGP SIGNATURE-----
--- End Message ---
