Bug#980709: dolfin: FTBFS: tests failed
Lucas Nussbaum
lucas at debian.org
Wed Jan 20 21:12:15 GMT 2021
Source: dolfin
Version: 2019.2.0~git20200629.946dbd3+lfs-4
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):
> make[8]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Building CXX object demo/undocumented/waveguide/cpp/CMakeFiles/demo_waveguide.dir/main.cpp.o
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo/undocumented/waveguide/cpp" && /usr/bin/c++ -DDOLFIN_VERSION=\"2019.2.0.dev0\" -DHAS_CHOLMOD -DHAS_HDF5 -DHAS_MPI -DHAS_PETSC -DHAS_SCOTCH -DHAS_UMFPACK -DHAS_ZLIB -DNDEBUG -I"/<<PKGBUILDDIR>>" -I"/<<PKGBUILDDIR>>/dolfin" -I"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu" -isystem /usr/lib/python3/dist-packages/ffc/backends/ufc -isystem /usr/include/eigen3 -isystem /usr/include/hdf5/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/petscdir/petsc3.14/x86_64-linux-gnu-real/include -Wno-comment -fpermissive -O2 -g -DNDEBUG -std=c++11 -o CMakeFiles/demo_waveguide.dir/main.cpp.o -c "/<<PKGBUILDDIR>>/demo/undocumented/waveguide/cpp/main.cpp"
> [ 98%] Linking CXX executable demo_spatial-coordinates
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo/undocumented/spatial-coordinates/cpp" && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_spatial-coordinates.dir/link.txt --verbose=1
> /usr/bin/c++ -Wno-comment -fpermissive -O2 -g -DNDEBUG -Wl,-z,relro CMakeFiles/demo_spatial-coordinates.dir/main.cpp.o -o demo_spatial-coordinates ../../../../dolfin/libdolfin.so.2019.2.0.dev0 /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/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
> make[8]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Built target demo_spatial-coordinates
> [ 98%] Linking CXX executable demo_waveguide
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo/undocumented/waveguide/cpp" && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_waveguide.dir/link.txt --verbose=1
> /usr/bin/c++ -Wno-comment -fpermissive -O2 -g -DNDEBUG -Wl,-z,relro CMakeFiles/demo_waveguide.dir/main.cpp.o -o demo_waveguide ../../../../dolfin/libdolfin.so.2019.2.0.dev0 /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/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
> make[8]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Built target demo_waveguide
> [100%] Linking CXX executable demo_sym-dirichlet-bc
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo/undocumented/sym-dirichlet-bc/cpp" && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_sym-dirichlet-bc.dir/link.txt --verbose=1
> /usr/bin/c++ -Wno-comment -fpermissive -O2 -g -DNDEBUG -Wl,-z,relro CMakeFiles/demo_sym-dirichlet-bc.dir/main.cpp.o -o demo_sym-dirichlet-bc ../../../../dolfin/libdolfin.so.2019.2.0.dev0 /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/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
> make[8]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [100%] Built target demo_sym-dirichlet-bc
> [100%] Linking CXX executable demo_time-series
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo/undocumented/time-series/cpp" && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_time-series.dir/link.txt --verbose=1
> /usr/bin/c++ -Wno-comment -fpermissive -O2 -g -DNDEBUG -Wl,-z,relro CMakeFiles/demo_time-series.dir/main.cpp.o -o demo_time-series ../../../../dolfin/libdolfin.so.2019.2.0.dev0 /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/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
> make[8]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [100%] Built target demo_time-series
> make[7]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> /usr/bin/cmake -E cmake_progress_start "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles" 0
> make[6]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/demo'
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> Built target demos
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> /usr/bin/cmake -E cmake_progress_start "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles" 0
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> Run C++ unit tests (serial)
> Test project /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> Start 1: unittests
> 1/1 Test #1: unittests ........................ Passed 4.99 sec
>
> 100% tests passed, 0 tests failed out of 1
>
> Total Test time (real) = 5.00 sec
> Run C++ regressions tests (serial)
> Test project /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> Start 3: demo_auto-adaptive-poisson_serial
> Start 5: demo_bcs_serial
> Start 7: demo_biharmonic_serial
> Start 9: demo_built-in-meshes_serial
> 1/49 Test #9: demo_built-in-meshes_serial ............... Passed 1.33 sec
> Start 12: demo_eigenvalue_serial
> 2/49 Test #12: demo_eigenvalue_serial ....................***Failed 0.02 sec
> *** The MPI_Comm_rank() function was called before MPI_INIT was invoked.
> *** This is disallowed by the MPI standard.
> *** Your MPI job will now abort.
> [ip-172-31-13-75:28976] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
>
> Start 14: demo_mixed-poisson_serial
> 3/49 Test #7: demo_biharmonic_serial .................... Passed 2.56 sec
> Start 16: demo_navier-stokes_serial
> 4/49 Test #5: demo_bcs_serial ........................... Passed 3.63 sec
> Start 18: demo_neumann-poisson_serial
> 5/49 Test #18: demo_neumann-poisson_serial ............... Passed 2.00 sec
> Start 20: demo_nonlinear-poisson_serial
> 6/49 Test #16: demo_navier-stokes_serial ................. Passed 3.35 sec
> Start 22: demo_nonmatching-interpolation_serial
> 7/49 Test #14: demo_mixed-poisson_serial ................. Passed 4.70 sec
> Start 24: demo_periodic_serial
> 8/49 Test #20: demo_nonlinear-poisson_serial ............. Passed 1.36 sec
> Start 26: demo_poisson_serial
> 9/49 Test #22: demo_nonmatching-interpolation_serial ..... Passed 1.35 sec
> Start 28: demo_singular-poisson_serial
> 10/49 Test #24: demo_periodic_serial ...................... Passed 1.32 sec
> Start 30: demo_stokes-iterative_serial
> 11/49 Test #26: demo_poisson_serial ....................... Passed 1.34 sec
> Start 32: demo_stokes-taylor-hood_serial
> 12/49 Test #28: demo_singular-poisson_serial .............. Passed 1.55 sec
> Start 34: demo_subdomains_serial
> 13/49 Test #3: demo_auto-adaptive-poisson_serial ......... Passed 9.13 sec
> Start 36: demo_advection-diffusion_serial
> 14/49 Test #34: demo_subdomains_serial .................... Passed 1.44 sec
> Start 38: demo_ale_serial
> 15/49 Test #36: demo_advection-diffusion_serial ........... Passed 2.37 sec
> Start 40: demo_auto-adaptive-navier-stokes_serial
> 16/49 Test #38: demo_ale_serial ........................... Passed 1.41 sec
> Start 42: demo_block-matrix_serial
> 17/49 Test #42: demo_block-matrix_serial .................. Passed 1.35 sec
> Start 44: demo_conditional_serial
> 18/49 Test #44: demo_conditional_serial ................... Passed 7.74 sec
> Start 46: demo_contact-vi-snes_serial
> 19/49 Test #46: demo_contact-vi-snes_serial ............... Passed 1.81 sec
> Start 48: demo_contact-vi-tao_serial
> 20/49 Test #48: demo_contact-vi-tao_serial ................ Passed 1.58 sec
> Start 50: demo_curl-curl_serial
> 21/49 Test #50: demo_curl-curl_serial ..................... Passed 5.83 sec
> Start 52: demo_dg-advection-diffusion_serial
> 22/49 Test #30: demo_stokes-iterative_serial .............. Passed 30.75 sec
> Start 54: demo_dg-poisson_serial
> 23/49 Test #32: demo_stokes-taylor-hood_serial ............ Passed 30.61 sec
> Start 56: demo_elasticity_serial
> 24/49 Test #54: demo_dg-poisson_serial .................... Passed 1.89 sec
> Start 57: demo_elastodynamics_serial
> 25/49 Test #56: demo_elasticity_serial .................... Passed 6.50 sec
> Start 59: demo_eval_serial
> 26/49 Test #59: demo_eval_serial .......................... Passed 6.82 sec
> Start 61: demo_extrapolation_serial
> 27/49 Test #61: demo_extrapolation_serial ................. Passed 1.40 sec
> Start 63: demo_functional_serial
> 28/49 Test #63: demo_functional_serial .................... Passed 1.38 sec
> Start 65: demo_gmg-poisson_serial
> 29/49 Test #65: demo_gmg-poisson_serial ................... Passed 1.46 sec
> Start 67: demo_lift-drag_serial
> 30/49 Test #67: demo_lift-drag_serial ..................... Passed 1.41 sec
> Start 69: demo_mesh-quality_serial
> 31/49 Test #69: demo_mesh-quality_serial .................. Passed 1.40 sec
> Start 71: demo_meshfunction-refinement_serial
> 32/49 Test #71: demo_meshfunction-refinement_serial ....... Passed 1.39 sec
> Start 73: demo_multimesh-poisson_serial
> 33/49 Test #73: demo_multimesh-poisson_serial ............. Passed 2.93 sec
> Start 75: demo_multimesh-stokes_serial
> 34/49 Test #75: demo_multimesh-stokes_serial .............. Passed 3.36 sec
> Start 77: demo_nonmatching-projection_serial
> 35/49 Test #77: demo_nonmatching-projection_serial ........ Passed 1.99 sec
> Start 79: demo_parallel-refinement_serial
> 36/49 Test #79: demo_parallel-refinement_serial ........... Passed 1.41 sec
> Start 81: demo_parameters_serial
> 37/49 Test #81: demo_parameters_serial .................... Passed 1.39 sec
> Start 83: demo_poisson1D_serial
> 38/49 Test #52: demo_dg-advection-diffusion_serial ........ Passed 42.69 sec
> Start 85: demo_poisson1D-in-2D_serial
> 39/49 Test #83: demo_poisson1D_serial ..................... Passed 1.38 sec
> Start 87: demo_poisson-disc_serial
> 40/49 Test #85: demo_poisson1D-in-2D_serial ............... Passed 1.35 sec
> Start 89: demo_refinement_serial
> 41/49 Test #89: demo_refinement_serial .................... Passed 1.41 sec
> Start 91: demo_spatial-coordinates_serial
> 42/49 Test #91: demo_spatial-coordinates_serial ........... Passed 1.44 sec
> Start 93: demo_submesh_serial
> 43/49 Test #93: demo_submesh_serial ....................... Passed 1.42 sec
> Start 95: demo_sym-dirichlet-bc_serial
> 44/49 Test #40: demo_auto-adaptive-navier-stokes_serial ... Passed 67.46 sec
> Start 97: demo_time-series_serial
> 45/49 Test #97: demo_time-series_serial ................... Passed 1.41 sec
> Start 99: demo_waveguide_serial
> 46/49 Test #99: demo_waveguide_serial .....................***Failed 0.02 sec
> *** The MPI_Comm_rank() function was called before MPI_INIT was invoked.
> *** This is disallowed by the MPI standard.
> *** Your MPI job will now abort.
> [ip-172-31-13-75:29364] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
>
> 47/49 Test #87: demo_poisson-disc_serial .................. Passed 7.31 sec
> 48/49 Test #57: demo_elastodynamics_serial ................ Passed 114.98 sec
> 49/49 Test #95: demo_sym-dirichlet-bc_serial .............. Passed 180.77 sec
>
> 96% tests passed, 2 tests failed out of 49
>
> Total Test time (real) = 259.06 sec
>
> The following tests FAILED:
> 12 - demo_eigenvalue_serial (Failed)
> 99 - demo_waveguide_serial (Failed)
> Errors while running CTest
> make[1]: *** [debian/rules:248: override_dh_auto_test-arch] Error 8
The full build log is available from:
http://qa-logs.debian.net/2021/01/20/dolfin_2019.2.0~git20200629.946dbd3+lfs-4_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.
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