Bug#1086007: FTBFS: undefined reference to `ompi_mpi_cxx_op_intercept' etc.

[Stefano Rivera]

Source: lammps
Version: 20240207+dfsg-1.1
Severity: serious
Tags: ftbfs
Justification: FTBFS

Dear maintainer,

During a test rebuild, lammps failed to rebuild.

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[...]
[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

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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