Gilles Filippini a écrit le 07/11/2020 à 19:36 : > Drew Parsons a écrit le 06/11/2020 à 04:02 : >> On 2020-11-06 02:09, Gilles Filippini wrote: >>>> >>>> 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. >> ... >>> >>> Do you have a scenario leading to this alternative disparition? >>> >> >> >> It's not completely clear to me. But my suspicion is that it happens >> when there is an upgrade to openmpi. Evidently then hdf5 needs to update >> its alternatives against the updated openmpi. >> >> It's a little strange though, since a simple openmpi update is not an >> ABI update. The alternatives links would be the same after running >> dpkg-reconfigure libhdf5-openmpi-dev. Not obvious why an openmpi update >> would cause them to disappear. > > After a test into a clean chroot I can now confirm this hypothesis.
The loss of the alternative is easily triggered by the reinstallation of openmpi-bin: # pkg-config --libs hdf5-mpi -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lhdf5 -lmpi # apt-get install --reinstall ipenmpi-bin Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package ipenmpi-bin (unstable-amd64-sbuild)root@pinibrem15:/tmp# pkg-config --libs hdf5-mpi -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lhdf5 -lmpi (unstable-amd64-sbuild)root@pinibrem15:/tmp# apt-get install --reinstall openmpi-bin Reading package lists... Done Building dependency tree Reading state information... Done 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 3 not upgraded. Need to get 0 B/127 kB of archives. After this operation, 0 B of additional disk space will be used. debconf: delaying package configuration, since apt-utils is not installed (Reading database ... 18500 files and directories currently installed.) Preparing to unpack .../openmpi-bin_4.0.5-7_amd64.deb ... Unpacking openmpi-bin (4.0.5-7) over (4.0.5-7) ... Setting up openmpi-bin (4.0.5-7) ... update-alternatives: warning: forcing reinstallation of alternative /usr/bin/mpicc.openmpi because link group mpi is broken # 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 happens when reinstalling mpich as well, if the mpi alternative was previously set to mpich. I have no idea how to fix it, other than asking openmpi and mpich maintainers to take care of the hdf5-mpi.pc slave alternative when it exists. What do you think? Thanks, Note the warning notice above. Honestly I have no idea how this could be fixed.
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