Your message dated Thu, 12 Dec 2024 08:36:52 +0000
with message-id <[email protected]>
and subject line Bug#1086007: fixed in lammps 20240207+dfsg-1.2
has caused the Debian Bug report #1086007,
regarding FTBFS: undefined reference to `ompi_mpi_cxx_op_intercept' etc.
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.
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--
1086007: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086007
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: lammps
Version: 20240207+dfsg-1.1
Severity: serious
Tags: ftbfs
Justification: FTBFS
Dear maintainer,
During a test rebuild, lammps failed to rebuild.
-------------------------------------------------------------------------------
[...]
[100%] Linking CXX shared library liblammps.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/lammps.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -mbranch-protection=standard -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib
-Wl,-z,relro -shared -Wl,-soname,liblammps.so.0 -o liblammps.so.0
@CMakeFiles/lammps.dir/objects1.rsp
-Wl,-rpath,/usr/lib/aarch64-linux-gnu/openmpi/lib:/usr/lib/aarch64-linux-gnu/hdf5/serial:
/usr/lib/aarch64-linux-gnu/libjpeg.so /usr/lib/aarch64-linux-gnu/libpng.so
/usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libfftw3.so
/usr/lib/aarch64-linux-gnu/libfftw3_omp.so
/usr/lib/aarch64-linux-gnu/libpython3.12.so
/usr/lib/aarch64-linux-gnu/libvoro++.so /usr/lib/aarch64-linux-gnu/libnetcdf.so
/usr/lib/aarch64-linux-gnu/libpnetcdf.so
/usr/lib/aarch64-linux-gnu/libvtkIOParallelXML-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libcurl.so
/usr/lib/aarch64-linux-gnu/libkim-api.so.2.3.0
/usr/lib/aarch64-linux-gnu/libz.so -lm liblammps_poems.a liblammps_atc.a
liblammps_awpmd.a liblammps_h5md.a /usr/lib/aarch64-linux-gnu/liblapack.so
/usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libblas.so
-ldl /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so
/usr/lib/aarch64-linux-gnu/libnetcdf.so
/usr/lib/aarch64-linux-gnu/libvtkIOXML-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkIOXMLParser-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkIOLegacy-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkIOCore-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkCommonExecutionModel-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkCommonDataModel-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkCommonTransforms-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkCommonMath-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkkissfft-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libvtkCommonCore-9.3.so.9.3
/usr/lib/aarch64-linux-gnu/libtbb.so.12.12
/usr/lib/aarch64-linux-gnu/libvtksys-9.3.so.9.3 -ldl
/usr/lib/aarch64-linux-gnu/libzstd.so
/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so
/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so
/usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libsz.so
/usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libdl.a -lm
/usr/bin/cmake -E cmake_symlink_library liblammps.so.0 liblammps.so.0
liblammps.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Built target lammps
make -f CMakeFiles/lmp.dir/build.make CMakeFiles/lmp.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/debian/build'
cd /<<PKGBUILDDIR>>/debian/build && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>>/cmake /<<PKGBUILDDIR>>/cmake
/<<PKGBUILDDIR>>/debian/build /<<PKGBUILDDIR>>/debian/build
/<<PKGBUILDDIR>>/debian/build/CMakeFiles/lmp.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make -f CMakeFiles/lmp.dir/build.make CMakeFiles/lmp.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/debian/build'
[100%] Building CXX object CMakeFiles/lmp.dir/<<PKGBUILDDIR>>/src/main.cpp.o
/usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX
-D_MPICC_H -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/debian/build/includes
-isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem
/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security
-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE
-fopenmp -MD -MT CMakeFiles/lmp.dir/<<PKGBUILDDIR>>/src/main.cpp.o -MF
CMakeFiles/lmp.dir/<<PKGBUILDDIR>>/src/main.cpp.o.d -o
CMakeFiles/lmp.dir/<<PKGBUILDDIR>>/src/main.cpp.o -c
/<<PKGBUILDDIR>>/src/main.cpp
[100%] Linking CXX executable lmp
/usr/bin/cmake -E cmake_link_script CMakeFiles/lmp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -mbranch-protection=standard -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-rpath
-Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib
"CMakeFiles/lmp.dir/<<PKGBUILDDIR>>/src/main.cpp.o" -o lmp
-Wl,-rpath,/<<PKGBUILDDIR>>/debian/build:/usr/lib/aarch64-linux-gnu/openmpi/lib:
liblammps.so.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so
/usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so
/usr/lib/aarch64-linux-gnu/libpthread.a
/usr/bin/ld: warning: libmpi_cxx.so.40, needed by
/lib/aarch64-linux-gnu/libpnetcdf.so.0d, not found (try using -rpath or
-rpath-link)
/usr/bin/ld: /lib/aarch64-linux-gnu/libpnetcdf.so.0d: undefined reference to
`ompi_mpi_cxx_op_intercept'
/usr/bin/ld: /lib/aarch64-linux-gnu/libpnetcdf.so.0d: undefined reference to
`MPI::Win::Free()'
/usr/bin/ld: /lib/aarch64-linux-gnu/libpnetcdf.so.0d: undefined reference to
`MPI::Datatype::Free()'
/usr/bin/ld: /lib/aarch64-linux-gnu/libpnetcdf.so.0d: undefined reference to
`ompi_op_set_cxx_callback'
/usr/bin/ld: /lib/aarch64-linux-gnu/libpnetcdf.so.0d: undefined reference to
`MPI::Comm::Comm()'
collect2: error: ld returned 1 exit status
make[3]: *** [CMakeFiles/lmp.dir/build.make:104: lmp] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[2]: *** [CMakeFiles/Makefile2:212: CMakeFiles/lmp.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
dh_auto_build: error: cd debian/build && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:13: build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit
status 2
--------------------------------------------------------------------------------
Build finished at 2024-10-24T17:33:43Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/888643/
About the archive rebuild: The build was made on debusine.debian.net,
on arm64 using sbuild.
You can find the build task here:
https://debusine.debian.net/work-request/41949/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks,
Stefano
--- End Message ---
--- Begin Message ---
Source: lammps
Source-Version: 20240207+dfsg-1.2
Done: Alastair McKinstry <[email protected]>
We believe that the bug you reported is fixed in the latest version of
lammps, 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 lammps 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: Thu, 12 Dec 2024 07:04:46 +0000
Source: lammps
Architecture: source
Version: 20240207+dfsg-1.2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Alastair McKinstry <[email protected]>
Closes: 1076465 1080623 1086007
Changes:
lammps (20240207+dfsg-1.2) unstable; urgency=medium
.
* Non-maintainer upload.
* Add build-depend on python3-setuptools. Closes: #1080623
* Rebuild for pnetcdf6 , openmpi5 transitions. Closes: #1086007
* Set oversubscribe as an OpenMPI env variable in d/rules rather
than parameter to mpirun so mpich works. Closes: #1076465
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Files:
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lammps_20240207+dfsg-1.2.dsc
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lammps_20240207+dfsg-1.2.debian.tar.xz
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