Your message dated Sun, 13 Sep 2026 15:01:45 +0200
with message-id <[email protected]>
and subject line Re: libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes
goes missing
has caused the Debian Bug report #968559,
regarding libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing
to be marked as done.
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--
968559: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=968559
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: libhdf5-openmpi-dev
Version: 1.10.6+repack-2
Severity: normal
We've set up libhdf5-openmpi-dev (and libhdf5-mpich-dev) to use the
alternatives mechanism to configure a symlink from a generic pkgconfig
file hdf5-mpi.pc to the specific hdf5-openmpi.pc (or hdf5-mpich.pc).
This allows client programs to get libs with 'pkg-config --libs hdf5-mpi'
without needing to know which specific MPI implementation is being
used.
It's a good and useful service, I think we should keep it.
But we should document (or fix if possible) that this alternatives
mechanism is a little fragile, and sometimes the link needs to be
refresh with
sudo dpkg-reconfigure libhdf5-openmpi-dev
What I mean is that sometimes the link seem to just disappear, so we get
$ pkg-config --libs hdf5-mpi
Package hdf5-mpi was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5-mpi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'hdf5-mpi' found
It gets restored by 'dpkg-reconfigure libhdf5-openmpi-dev'
(update-alternative --config hdf5-mpi would also enable it to be reset).
I'm not sure why exactly the link is being lost or if it's feasible to
make the mechanism for it more robust. I presume it happens when
openmpi gets updated (e.g. recently updated to openmpi 4.0.4).
libhdf5-openmpi-dev.postinst of course is setting the alternatives
link, though I don't understand why the link would be lost just
because openmpi got upgraded.
Filing this bug so we can document and keep watch on the problem.
Again, the workaround is to run
sudo dpkg-reconfigure libhdf5-openmpi-dev
(or dpkg-reconfigure libhdf5-mpich-dev)
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.7.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_WARN
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 libhdf5-openmpi-dev depends on:
ii libaec-dev 1.0.4-1
ii libhdf5-openmpi-103-1 1.10.6+repack-2
ii libhdf5-openmpi-cpp-103-1 1.10.6+repack-2
ii libhdf5-openmpi-fortran-102 1.10.6+repack-2
ii libhdf5-openmpi-hl-100 1.10.6+repack-2
ii libhdf5-openmpi-hl-cpp-100 1.10.6+repack-2
ii libhdf5-openmpi-hl-fortran-100 1.10.6+repack-2
ii libjpeg-dev 1:2.0.5-1.1
ii libjpeg62-turbo-dev [libjpeg-dev] 1:2.0.5-1.1
ii libopenmpi-dev 4.0.4-2
ii zlib1g-dev 1:1.2.11.dfsg-2
libhdf5-openmpi-dev recommends no packages.
Versions of packages libhdf5-openmpi-dev suggests:
pn libhdf5-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Version: 2.1.0+repack-1
Hi,
On Thu, 23 Dec 2021 21:31:00 +0100 Jerome BENOIT <[email protected]>
wrote:
Hello, I have just migrated from Buster to Bullseye.
The package libhdf5-mpi-dev was and is not installed on my box.
However `update-alternatives --display hdf5.pc` outputs
hdf5.pc - auto mode
link best version is /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc
link currently points to /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc
link hdf5.pc is /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc
/usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc - priority 35
/usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpich.pc - priority 10
/usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc - priority 20
The disturbing thing is that /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc
points to /dev/null
I guess that this issue is related to this bug.
This isn't relevant anymore starting with release 2.1.0+repack-1.
Please use hdf5_mpi.pc (hdf5-mpi.pc will be deprecated at some point in
the future).
And I'm preparing an upload with hdf5_mpi_*.pc files for components cpp,
fortran, hl, hl_cpp, and hl_fortran.
Best,
_g.
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--- End Message ---
