Bug#912437: openmpi-bin: Fails to upgrade: update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc
Package: openmpi-bin Version: 3.1.3-1 Severity: serious openmpi-bin fails to upgrade from 3.1.2-6 to 3.1.3-1 as follows for me: Setting up openmpi-bin (3.1.3-1) ... update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc dpkg: error processing package openmpi-bin (--configure): installed openmpi-bin package post-installation script subprocess returned error exit status 2 Errors were encountered while processing: openmpi-bin -- System Information: Debian Release: buster/sid APT prefers unstable APT policy: (990, 'unstable'), (600, 'testing'), (500, 'unstable-debug'), (500, 'buildd-unstable'), (110, 'experimental'), (1, 'experimental-debug'), (1, 'buildd-experimental') Architecture: amd64 (x86_64) Kernel: Linux 4.18.0-2-amd64 (SMP w/8 CPU cores) Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: sysvinit (via /sbin/init) LSM: AppArmor: enabled Versions of packages openmpi-bin depends on: ii libc62.27-8 ii libevent-2.1-6 2.1.8-stable-4 ii libevent-pthreads-2.1-6 2.1.8-stable-4 ii libhwloc51.11.11-2 ii libopenmpi3 3.1.3-1 ii openmpi-common 3.1.3-1 ii openssh-client [ssh-client] 1:7.9p1-1 ii zlib1g 1:1.2.11.dfsg-1 Versions of packages openmpi-bin recommends: pn libopenmpi-dev Versions of packages openmpi-bin suggests: ii gfortran 4:8.2.0-2 -- no debconf information
Bug#912437: openmpi-bin: Fails to upgrade: update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc
Thanks for this report. I'm unable to reproduce this, and have no failures testing 3.1.2-6 -> 3.1.3-1 upgrade. The change made in the openmpi-bin.postinst script was to enable "set -e" properly (avoiding a conditional in the script that relied on testing non-zero return code). I suspect that /var/lib/dpkg/alternatives/mpi was corrupt from a previous upgrade (quite likely; major changes happened in the 2->3 transition due to multiarch handling). So, I think: (1) the current package is actually technically ok. (2) Some more handling needs to be added to cope with 'inheriting' a corrupt mpi alternatives. regards Alastair On 31/10/2018 14:28, Axel Beckert wrote: Package: openmpi-bin Version: 3.1.3-1 Severity: serious openmpi-bin fails to upgrade from 3.1.2-6 to 3.1.3-1 as follows for me: Setting up openmpi-bin (3.1.3-1) ... update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc dpkg: error processing package openmpi-bin (--configure): installed openmpi-bin package post-installation script subprocess returned error exit status 2 Errors were encountered while processing: openmpi-bin -- System Information: Debian Release: buster/sid APT prefers unstable APT policy: (990, 'unstable'), (600, 'testing'), (500, 'unstable-debug'), (500, 'buildd-unstable'), (110, 'experimental'), (1, 'experimental-debug'), (1, 'buildd-experimental') Architecture: amd64 (x86_64) Kernel: Linux 4.18.0-2-amd64 (SMP w/8 CPU cores) Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: sysvinit (via /sbin/init) LSM: AppArmor: enabled Versions of packages openmpi-bin depends on: ii libc62.27-8 ii libevent-2.1-6 2.1.8-stable-4 ii libevent-pthreads-2.1-6 2.1.8-stable-4 ii libhwloc51.11.11-2 ii libopenmpi3 3.1.3-1 ii openmpi-common 3.1.3-1 ii openssh-client [ssh-client] 1:7.9p1-1 ii zlib1g 1:1.2.11.dfsg-1 Versions of packages openmpi-bin recommends: pn libopenmpi-dev Versions of packages openmpi-bin suggests: ii gfortran 4:8.2.0-2 -- no debconf information -- Alastair McKinstry, , , https://diaspora.sceal.ie/u/amckinstry Commander Vimes didn’t like the phrase “The innocent have nothing to fear,” believing the innocent had everything to fear, mostly from the guilty but in the longer term even more from those who say things like “The innocent have nothing to fear.” - T. Pratchett, Snuff
Bug#912437: openmpi-bin: Fails to upgrade: update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc
Hi Alastair, Alastair McKinstry wrote: > The change made in the openmpi-bin.postinst script was to enable > "set -e" properly (avoiding a conditional in the script that relied > on testing non-zero return code). I suspect that > /var/lib/dpkg/alternatives/mpi was corrupt from a previous upgrade > (quite likely; major changes happened in the 2->3 transition due to > multiarch handling). Indeed, this system has about 2.5 years of Debian Unstable history, yes. :-) Attached the contents of /var/lib/dpkg/alternatives/mpi. Since I can still reproduce the issue by calling e.g. "dpkg --configure -a", this doesn't seem to be a one-time issue. I hope the attached file enables you to find the root cause. Regards, Axel -- ,''`. | Axel Beckert , https://people.debian.org/~abe/ : :' : | Debian Developer, ftp.ch.debian.org Admin `. `' | 4096R: 2517 B724 C5F6 CA99 5329 6E61 2FF9 CD59 6126 16B5 `-| 1024D: F067 EA27 26B9 C3FC 1486 202E C09E 1D89 9593 0EDE auto /usr/bin/mpicc libmpi++.so /usr/lib/libmpi++.so libmpi.so /usr/lib/libmpi.so libmpicxx.so /usr/lib/libmpicxx.so libmpif77.so /usr/lib/libmpif77.so libmpif90.so /usr/lib/libmpif90.so libmpifort.so /usr/lib/libmpifort.so mpi.pc /usr/lib/x86_64-linux-gnu/pkgconfig/mpi.pc mpiCC /usr/bin/mpiCC mpiCC.1.gz /usr/share/man/man1/mpiCC.1.gz mpic++ /usr/bin/mpic++ mpic++.1.gz /usr/share/man/man1/mpic++.1.gz mpicc /usr/bin/mpicc mpicc.1.gz /usr/share/man/man1/mpicc.1.gz mpicxx /usr/bin/mpicxx mpicxx.1.gz /usr/share/man/man1/mpicxx.1.gz mpif77 /usr/bin/mpif77 mpif77.1.gz /usr/share/man/man1/mpif77.1.gz mpif90 /usr/bin/mpif90 mpif90.1.gz /usr/share/man/man1/mpif90.1.gz mpifort /usr/bin/mpifort mpifort.1.gz /usr/share/man/man1/mpifort.1.gz /usr/bin/mpicc.openmpi 50 /usr/bin/mpic++.openmpi /usr/share/man/man1/mpiCC.openmpi.1.gz /usr/bin/mpic++.openmpi /usr/share/man/man1/mpic++.openmpi.1.gz /usr/share/man/man1/mpicc.openmpi.1.gz /usr/bin/mpic++.openmpi /usr/share/man/man1/mpicxx.openmpi.1.gz /usr/bin/mpif77.openmpi /usr/share/man/man1/mpif77.openmpi.1.gz /usr/bin/mpif90.openmpi /usr/share/man/man1/mpif90.openmpi.1.gz /usr/bin/mpifort.openmpi /usr/share/man/man1/mpifort.openmpi.1.gz /usr/include/mpich 40 /usr/lib/x86_64-linux-gnu/libmpichcxx.so /usr/lib/x86_64-linux-gnu/libmpich.so /usr/lib/x86_64-linux-gnu/libmpichcxx.so /usr/lib/x86_64-linux-gnu/libmpichfort.so /usr/lib/x86_64-linux-gnu/libmpichfort.so /usr/lib/x86_64-linux-gnu/libmpichfort.so /usr/lib/x86_64-linux-gnu/pkgconfig/mpich.pc /usr/bin/mpicxx.mpich /usr/share/man/man1/mpicxx.mpich.1.gz /usr/bin/mpicxx.mpich /usr/share/man/man1/mpicxx.mpich.1.gz /usr/bin/mpicc.mpich /usr/share/man/man1/mpicc.mpich.1.gz /usr/bin/mpicxx.mpich /usr/share/man/man1/mpicxx.mpich.1.gz /usr/bin/mpifort.mpich /usr/share/man/man1/mpif77.mpich.1.gz /usr/bin/mpifort.mpich /usr/share/man/man1/mpif90.mpich.1.gz /usr/bin/mpifort.mpich /usr/share/man/man1/mpifort.mpich.1.gz
Bug#912437: openmpi-bin: Fails to upgrade: update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc
Control: clone -1 -2 Control: reassign -2 mpich 3.3~b3-3 Control: retitle -2 mpich: Fails to upgrade: update-alternatives: error: /var/lib/dpkg/alternatives/mpi corrupt: slave link same as main link /usr/bin/mpicc Hi Alastair, Alastair McKinstry wrote: > I'm unable to reproduce this, and have no failures testing 3.1.2-6 > -> 3.1.3-1 upgrade. Same for the mpich 3.3~b3-2 to 3.3~b3-3 upgrade (on the same machine). Cloning the bug, as I assume that this needs to be applied to both packages: > (2) Some more handling needs to be added to cope with 'inheriting' a > corrupt mpi alternatives. Regards, Axel -- ,''`. | Axel Beckert , https://people.debian.org/~abe/ : :' : | Debian Developer, ftp.ch.debian.org Admin `. `' | 4096R: 2517 B724 C5F6 CA99 5329 6E61 2FF9 CD59 6126 16B5 `-| 1024D: F067 EA27 26B9 C3FC 1486 202E C09E 1D89 9593 0EDE
