Your message dated Fri, 27 Aug 2021 12:48:54 +0000 with message-id <[email protected]> and subject line Bug#945120: fixed in openmpi 4.1.1-3 has caused the Debian Bug report #945120, regarding libopenmpi-dev: Sid upgrade to libopenmpi-dev 4.0.2-2 has issues in setup step 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 [email protected] immediately.) -- 945120: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=945120 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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
--- End Message ---
--- Begin Message ---Source: openmpi Source-Version: 4.1.1-3 Done: Alastair McKinstry <[email protected]> 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alastair McKinstry <[email protected]> (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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 27 Aug 2021 12:04:06 +0100 Source: openmpi Architecture: source Version: 4.1.1-3 Distribution: unstable Urgency: medium Maintainer: Alastair McKinstry <[email protected]> Changed-By: Alastair McKinstry <[email protected]> Closes: 945120 975995 979877 990254 993038 993041 Changes: openmpi (4.1.1-3) unstable; urgency=medium . * Don't embed username, hostname in binaries. Closes: #990254. Thanks, Vagrant Cascadian * Ship libopen-orted-mpir.so in -dev pkg only. Closes: #993041, #993038 * Close bug fixed in previous release. Closes: #945120 * Fix FTBFS with missing javadocs in stage1/no java builds. Closes: #979877, #975995 Checksums-Sha1: e85223155c6f50aadcf627ac84d00e5bc62e5302 2670 openmpi_4.1.1-3.dsc ed5a024f43e8da6375915fa14cd69bf8827c9744 67892 openmpi_4.1.1-3.debian.tar.xz Checksums-Sha256: 16f256bbc0f110e77832ec80ed40b320e508618b528b601899ea5ca621fdd7ce 2670 openmpi_4.1.1-3.dsc 9fd21d22c4c5c6954f9a169440e8b0c086f28e84c33038406854d5cf2a0d73a4 67892 openmpi_4.1.1-3.debian.tar.xz Files: c4a0101377f56ae461f498b1aefb13f1 2670 net optional openmpi_4.1.1-3.dsc c1d8b8bdf9c36bc44821d172850fb729 67892 net optional openmpi_4.1.1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEgjg86RZbNHx4cIGiy+a7Tl2a06UFAmEo3L0ACgkQy+a7Tl2a 06V+Hg/+MmupV2cHje1rpVXWrDcV5b1BU9X+6Q++p6NGhgIEeZAztk+uT3fuIitC EvrYjRqNx2GH21yFd7UGKeHfp3/lfRzxGPkKcqZLgUIP3NICiNHsUhwd3bQAp/ZZ L7JUWzH9o6L6+scD6+mnO66ZNd6Ko0AvM+KXorbKq67EOOTBoqTaiMdHThzHl3Ip 0KpYXslyEmG1GRPKaF3uvERyHvDVSI8uFtwL9sKBIhokMpB72UzO944VTnqfDpAd twOYg4TIkoCtrix3BqR3tRiVYDJ2C6cmPX1/UDqjn36c4jEhreKZ78d39s+xYENC YxDzrXvneC08T56Swg1o+WOi0ayZ2wmvIdSNbS+ERdwBsMJMe9HcnMiKm5o2X5H/ +DmujaHoruUDSh4NOiK6bGNmbxtpTRyURTfWeABoYOyPWzkfLQWMcDotJiYr/T0Q JtfS0SxqV9blZcXzcfA7P2HhM0B6f1/wRd5qRtUSZTt0lEMBqomuL4staa/lThQm gNRFNe6F6wBpLRA4KbQG2PSoaIST3OYchutuPkQfCUdKzaF/7m93lHRMrJ/bi9Rh jVwWEhJEAT4e5NmutG0M6HTcdUsArhNWwm+4E52TkHVwM6WMLRll8ElQW7X9Xq4g vxmHTVHoxaZwExPqmWfC0u2K+GULyTbw3LFcczQlwVbAiiXIkw4= =HcZI -----END PGP SIGNATURE-----
--- End Message ---
