Package: libopenmpi-dev
Version: 4.0.2-2
Severity: important
Dear Maintainer,
The upgrade of Open MPI components from 3.1.3 to 4.0.2-2 did not
complete successfully. During upgrade I got these warnings:
Setting up libopenmpi-dev:amd64 (4.0.2-2) ...
update-alternatives: warning: forcing reinstallation of alternative
/usr/lib/x86_64-linux-gnu/openmpi/include because link group
mpi-x86_64-linux-gnu is broken
update-alternatives: warning: skip creation of
/usr/lib/x86_64-linux-gnu/libmpi++.so because associated file
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (of link group
mpi-x86_64-linux-gnu) doesn't exist
update-alternatives: warning: skip creation of
/usr/lib/x86_64-linux-gnu/libmpi.so because associated file
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (of link group
mpi-x86_64-linux-gnu) doesn't exist
As installed the libraries were not usable:
$ make
mpicc -O2 -march=native -fpie -std=c11 -D_Linux -D_XOPEN_SOURCE=700 -o
mpi_mm.o -c mpi_mm.c
mpicc mpi_mm.o -pie -Wl,-z,now -Wl,-z,relro -o mpi_mm_c.linux-gnu.x86_64
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -levent
/usr/bin/ld: cannot find -levent_pthreads
collect2: error: ld returned 1 exit status
make: *** [makefile:31: mpi_mm_c.linux-gnu.x86_64] Error 1
I found that the failure to locate -levent and -levent_pthreads was
because libevent-dev needs to be installed.
The -lmpi load failure is because the symlink
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -> libmpi.so.40.20.2
was missing when setup tried to create the symlinks
/etc/alternatives/libmpi.so-x86_64-linux-gnu ->
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
and
/usr/lib/x86_64-linux-gnu/libmpi.so ->
/etc/alternatives/libmpi.so-x86_64-linux-gnu
Running dpkg-query -L libopenmpi-dev shows that
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
should have been created, but it wasn't.
On the off chance that a reinstallation might help, I reinstalled
all the 4.0.2-2 packages. That time there were no issues reported,
the symlinks appear to be good, and Open MPI 4.0.2 works on my
test programs.
$ showlinks /usr/lib/x86_64-linux-gnu/libmpi.so
lrwxrwxrwx 1 root root 44 Nov 19 18:11 /usr/lib/x86_64-linux-gnu/libmpi.so ->
/etc/alternatives/libmpi.so-x86_64-linux-gnu
lrwxrwxrwx 1 root root 47 Nov 19 18:11
/etc/alternatives/libmpi.so-x86_64-linux-gnu ->
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
lrwxrwxrwx 1 root root 17 Nov 19 05:55
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -> libmpi.so.40.20.2
-rw-r--r-- 1 root root 1126552 Nov 19 05:55
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.2
That's similar to the 3.1.3 scheme that I still have on my Buster host.
Is it possible that the installation script has a sequencing problem
such that it tries to target
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
with a symlink from /etc/alternatives before it's been created?
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 5.3.0-2-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
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] 4:9.2.1-3.1
ii gfortran-9 [gfortran-mod-15] 9.2.1-19
ii libhwloc-dev 1.11.13-1
ii libibverbs-dev 26.0-2
ii libopenmpi3 4.0.2-2
ii openmpi-bin 4.0.2-2
ii openmpi-common 4.0.2-2
Versions of packages libopenmpi-dev recommends:
ii libcoarrays-openmpi-dev 2.8.0-1
Versions of packages libopenmpi-dev suggests:
pn openmpi-doc <none>
-- no debconf information
