Bug#851726: liggghts: FTBFS on single-CPU machines (not enough slots available)
Santiago Vila
sanvila at debian.org
Wed Jan 18 00:08:12 UTC 2017
Package: src:liggghts
Version: 3.5.0+repack1-8
Severity: serious
Dear maintainer:
I tried to build this package in stretch with "dpkg-buildpackage -A"
but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --buildsystem=cmake --builddirectory=/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build --parallel
dh_testdir -i -O--buildsystem=cmake -O--builddirectory=/<<BUILDDIR>>/liggghts-3.5.0\+repack1/debian/build -O--parallel
dh_update_autotools_config -i -O--buildsystem=cmake -O--builddirectory=/<<BUILDDIR>>/liggghts-3.5.0\+repack1/debian/build -O--parallel
dh_auto_configure -i -O--buildsystem=cmake -O--builddirectory=/<<BUILDDIR>>/liggghts-3.5.0\+repack1/debian/build -O--parallel
cmake ../.. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-- The C compiler identification is GNU 6.2.1
-- The CXX compiler identification is GNU 6.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
[... snipped ...]
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/mpicxx -Dlibliggghts_EXPORTS -DvtkRenderingCore_AUTOINIT="3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL)" -I/usr/include/vtk-6.3 -I/usr/include/freetype2 -I/usr/include/x86_64-linux-gnu -I/usr/include/eigen3 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/liggghts-3.5.0+repack1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMMPS_VTK6 -DLAMMPS_VTK -std=c++0x -DLAMMPS_JPEG -fPIC -o CMakeFiles/libliggghts.dir/write_dump.cpp.o -c /<<BUILDDIR>>/liggghts-3.5.0+repack1/src/write_dump.cpp
[ 98%] Building CXX object src/CMakeFiles/libliggghts.dir/write_restart.cpp.o
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/mpicxx -Dlibliggghts_EXPORTS -DvtkRenderingCore_AUTOINIT="3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL)" -I/usr/include/vtk-6.3 -I/usr/include/freetype2 -I/usr/include/x86_64-linux-gnu -I/usr/include/eigen3 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/liggghts-3.5.0+repack1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMMPS_VTK6 -DLAMMPS_VTK -std=c++0x -DLAMMPS_JPEG -fPIC -o CMakeFiles/libliggghts.dir/write_restart.cpp.o -c /<<BUILDDIR>>/liggghts-3.5.0+repack1/src/write_restart.cpp
[ 99%] Linking CXX shared library libliggghts.so
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/libliggghts.dir/link.txt --verbose=1
/usr/bin/mpicxx -fPIC -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/liggghts-3.5.0+repack1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMMPS_VTK6 -DLAMMPS_VTK -std=c++0x -DLAMMPS_JPEG -Wl,-z,relro -Wl,--as-needed -shared -Wl,-soname,libliggghts.so.3 -o libliggghts.so.3.3.1 CMakeFiles/libliggghts.dir/angle.cpp.o CMakeFiles/libliggghts.dir/angle_hybrid.cpp.o CMakeFiles/libliggghts.dir/atom.cpp.o CMakeFiles/libliggghts.dir/atom_map.cpp.o CMakeFiles/libliggghts.dir/atom_vec.cpp.o CMakeFiles/libliggghts.dir/atom_vec_atomic.cpp.o CMakeFiles/libliggghts.dir/atom_vec_charge.cpp.o CMakeFiles/libliggghts.dir/atom_vec_ellipsoid.cpp.o CMakeFiles/libliggghts.dir/atom_vec_hybrid.cpp.o CMakeFiles/libliggghts.dir/atom_vec_line.cpp.o CMakeFiles/libliggghts.dir/atom_vec_sph.cpp.o CMakeFiles/libliggghts.dir/atom_vec_sph_var.cpp.o CMakeFiles/libliggghts.dir/atom_vec_sphere.cpp.o CMakeFiles/libliggghts.dir/atom_vec_sphere_w.cpp.o 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CMakeFiles/libliggghts.dir/timer.cpp.o CMakeFiles/libliggghts.dir/tri_mesh.cpp.o CMakeFiles/libliggghts.dir/tri_mesh_planar.cpp.o CMakeFiles/libliggghts.dir/universe.cpp.o CMakeFiles/libliggghts.dir/update.cpp.o CMakeFiles/libliggghts.dir/variable.cpp.o CMakeFiles/libliggghts.dir/velocity.cpp.o CMakeFiles/libliggghts.dir/verlet.cpp.o CMakeFiles/libliggghts.dir/write_data.cpp.o CMakeFiles/libliggghts.dir/write_dump.cpp.o CMakeFiles/libliggghts.dir/write_restart.cpp.o -lboost_mpi -lboost_serialization -ljpeg /usr/lib/x86_64-linux-gnu/libvtkChartsCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkInfovisCore-6.3.so.6.3.0 -lfreetype -lz /usr/lib/x86_64-linux-gnu/libvtkViewsContext2D-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkViewsCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkInteractionWidgets-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersHybrid-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersModeling-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingGeneral-6.3.so.6.3.0 -ljpeg -lpng -ltiff /usr/lib/x86_64-linux-gnu/libvtkInteractionStyle-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingAnnotation-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingColor-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingVolume-6.3.so.6.3.0 -lexpat /usr/lib/x86_64-linux-gnu/libvtkRenderingOpenGL-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOParallelXML-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkParallelCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingContext2D-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingSources-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingFreeType-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkftgl-6.3.so.6.3.0 -lfreetype /usr/lib/x86_64-linux-gnu/libvtkRenderingCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonColor-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersExtraction-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersStatistics-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingFourier-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkalglib-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersSources-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersGeneral-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonComputationalGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingHybrid-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOImage-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkDICOMParser-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkmetaio-6.3.so.6.3.0 -lz -lGLU -lGL -lSM -lICE -lX11 -lXext -lXt /usr/lib/x86_64-linux-gnu/libvtkIOXML-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOXMLParser-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOLegacy-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonDataModel-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonMisc-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonSystem-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtksys-6.3.so.6.3.0 -ldl /usr/lib/x86_64-linux-gnu/libvtkCommonTransforms-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonMath-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonCore-6.3.so.6.3.0
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/cmake -E cmake_symlink_library libliggghts.so.3.3.1 libliggghts.so.3 libliggghts.so
make[3]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
[ 99%] Built target libliggghts
make -f src/CMakeFiles/liggghts.dir/build.make src/CMakeFiles/liggghts.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/liggghts-3.5.0+repack1 /<<BUILDDIR>>/liggghts-3.5.0+repack1/src /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src/CMakeFiles/liggghts.dir/DependInfo.cmake --color=
Scanning dependencies of target liggghts
make[3]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
make -f src/CMakeFiles/liggghts.dir/build.make src/CMakeFiles/liggghts.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
[ 99%] Building CXX object src/CMakeFiles/liggghts.dir/main.cpp.o
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/mpicxx -DvtkRenderingCore_AUTOINIT="3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL)" -I/usr/include/vtk-6.3 -I/usr/include/freetype2 -I/usr/include/x86_64-linux-gnu -I/usr/include/eigen3 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1 -I/<<BUILDDIR>>/liggghts-3.5.0+repack1/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/liggghts-3.5.0+repack1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMMPS_VTK6 -DLAMMPS_VTK -std=c++0x -DLAMMPS_JPEG -o CMakeFiles/liggghts.dir/main.cpp.o -c /<<BUILDDIR>>/liggghts-3.5.0+repack1/src/main.cpp
[100%] Linking CXX executable liggghts
cd /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/liggghts.dir/link.txt --verbose=1
/usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/liggghts-3.5.0+repack1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMMPS_VTK6 -DLAMMPS_VTK -std=c++0x -DLAMMPS_JPEG -Wl,-z,relro -Wl,--as-needed CMakeFiles/liggghts.dir/main.cpp.o -o liggghts -Wl,-rpath,/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src: -rdynamic libliggghts.so.3.3.1 -lboost_mpi -lboost_serialization -ljpeg /usr/lib/x86_64-linux-gnu/libvtkChartsCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkInfovisCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkViewsContext2D-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingContext2D-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkViewsCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkInteractionWidgets-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersHybrid-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersModeling-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingGeneral-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingSources-6.3.so.6.3.0 -lpng -ltiff /usr/lib/x86_64-linux-gnu/libvtkInteractionStyle-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingAnnotation-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingFreeType-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkftgl-6.3.so.6.3.0 -lfreetype /usr/lib/x86_64-linux-gnu/libvtkImagingColor-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingVolume-6.3.so.6.3.0 -lexpat /usr/lib/x86_64-linux-gnu/libvtkRenderingOpenGL-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkRenderingCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonColor-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersExtraction-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersStatistics-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingFourier-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkalglib-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersSources-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersGeneral-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkFiltersCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonComputationalGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingHybrid-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkImagingCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOImage-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkDICOMParser-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkmetaio-6.3.so.6.3.0 -lz -lGLU -lGL -lSM -lICE -lX11 -lXext -lXt /usr/lib/x86_64-linux-gnu/libvtkIOParallelXML-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOXML-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOGeometry-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOXMLParser-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkParallelCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOLegacy-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkIOCore-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonDataModel-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonMisc-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonSystem-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtksys-6.3.so.6.3.0 -ldl /usr/lib/x86_64-linux-gnu/libvtkCommonTransforms-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonMath-6.3.so.6.3.0 /usr/lib/x86_64-linux-gnu/libvtkCommonCore-6.3.so.6.3.0
make[3]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
[100%] Built target liggghts
make[2]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/CMakeFiles 0
make[1]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1'
mkdir test
cp -r examples/LIGGGHTS/Tutorials_public/heatTransfer_1/* test/
cd test; mpirun -np 2 /<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src/liggghts < in.heatGran
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 2 slots
that were requested by the application:
/<<BUILDDIR>>/liggghts-3.5.0+repack1/debian/build/src/liggghts
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
debian/rules:15: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/liggghts-3.5.0+repack1'
debian/rules:5: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------
I think this is a known problem in many applications using mpi, so I trust that
you will know what to do. If you need a full build log, just say so.
The bug should be reproducible with sbuild on a single CPU virtual machine.
Thanks.
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