Your message dated Sat, 23 Jan 2021 20:12:15 +0100
with message-id <ab978f5d37d3bd65082bc92bcf1b5...@emerall.com>
and subject line Re: Bug#980611 mshr: FTBFS: ld:
/usr/lib/slepcdir/slepc3.14/x86_64-linux-gnu-real/lib/libslepc_real.so:
undefined reference to `MPIU_SUM'
has caused the Debian Bug report #980611,
regarding mshr: FTBFS: ld:
/usr/lib/slepcdir/slepc3.14/x86_64-linux-gnu-real/lib/libslepc_real.so:
undefined reference to `MPIU_SUM'
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
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--
980611: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980611
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: mshr
Version: 2019.2.0~git20200924.c27eb18+dfsg1-5
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20210120 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> /usr/bin/c++ -fpermissive -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG
> -Wl,-z,relro CMakeFiles/mshrable.dir/app/mshrable.cpp.o -o mshrable
> libmshr.so.2019.2.0.dev0 /usr/lib/x86_64-linux-gnu/libdolfin.so.2019.2.0.dev0
> /usr/lib/x86_64-linux-gnu/libboost_system.so
> /usr/lib/x86_64-linux-gnu/libboost_filesystem.so
> /usr/lib/x86_64-linux-gnu/libboost_program_options.so
> /usr/lib/x86_64-linux-gnu/libboost_timer.so
> /usr/lib/x86_64-linux-gnu/libboost_chrono.so
> /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
> /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so
> /usr/lib/x86_64-linux-gnu/libdl.so -lm
> /usr/lib/slepcdir/slepc3.14/x86_64-linux-gnu-real/lib/libslepc_real.so
> /usr/lib/petscdir/petsc3.14/x86_64-linux-gnu-real/lib/libpetsc_real.so
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
> /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libmpfr.so
> -ltet /usr/lib/x86_64-linux-gnu/libboost_system.so
> /usr/lib/x86_64-linux-gnu/libboost_filesystem.so
> /usr/lib/x86_64-linux-gnu/libboost_program_options.so
> /usr/bin/ld:
> /usr/lib/slepcdir/slepc3.14/x86_64-linux-gnu-real/lib/libslepc_real.so:
> undefined reference to `MPIU_SUM'
> collect2: error: ld returned 1 exit status
The full build log is available from:
http://qa-logs.debian.net/2021/01/20/mshr_2019.2.0~git20200924.c27eb18+dfsg1-5_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
As the error message indicates, this bug is inside libslepc. There was
some mismatch between slepc and openmpi, not clear why (there have have
been a volley of openmpi updates in the past month, also petsc was
updated to 3.14.3). The problem was fixed by binNMU of slepc (#980749),
hence closing this bug.
Bug#980751 is open for further discussion of why the mismatch was not
caught algorithmically by the system (was a tighter dependency on petsc
or openmpi version needed?).
Drew
--- End Message ---
