Arch Linux User Repository

Pre-built binaries of this package and its dependencies can be found in the arch4edu repository.

Thank you @AutoUpdateBot

Hello, I'm the auto update bot from arch4edu.

I've updated dolfinx to 0.10.0.post5. The build succeeded but the check phase failed:

Error: unittests test aborted - 1/1 Test #1: unittests ........................Subprocess aborted - 0% tests passed, 1 tests failed out of 1 - Errors while running CTest

Build and package phases completed successfully. Only the unit test crashed.

Full logs: https://github.com/arch4edu/aur-auto-update/actions/runs/22281196765

Looks like upstream issue.

It looks like the FindHDF5 cmake component is not working properly here anymore:

Found HDF5 at /usr/lib/cmake/hdf5 via NO_MODULE. Now trying to extract locations etc.
-- Trying to get properties of target hdf5-shared
-- Found imported configurations: NONE
-- Start search through imported configurations in the following order: RELWITHDEBINFO;RELEASE;DEBUG;NONE
-- Selected imported configuration: NONE
-- Found HDF5: hdf5-shared (found version "2.0.0") found components: C
-- HDF5_DIR: /usr/lib/cmake/hdf5
-- HDF5_DEFINITIONS:
-- HDF5_INCLUDE_DIRS: /usr/include
-- HDF5_LIBRARIES: hdf5-shared
-- HDF5_HL_LIBRARIES:
-- HDF5_C_DEFINITIONS:
-- HDF5_C_INCLUDE_DIR:
-- HDF5_C_INCLUDE_DIRS: /usr/include
-- HDF5_C_LIBRARY: /usr/lib/libhdf5.so.320.0.0
-- HDF5_C_LIBRARIES: hdf5-shared
-- HDF5_C_HL_LIBRARY:
-- HDF5_C_HL_LIBRARIES:
-- Defined targets (if any):
-- ... hdf5::hdf5
-- ... hdf5-shared
-- ... hdf5_hl-shared
-- ... hdf5_cpp-shared
-- ... hdf5_hl_cpp-shared
-- ... hdf5_fortran-shared
-- ... hdf5_hl_fortran-shared
CMake Error at /home/user/.cache/paru/clone/dolfinx/src/tmp_install/usr/lib/cmake/dolfinx/DOLFINXConfig.cmake:105 (message):
  Found serial HDF5 build, MPI HDF5 build required

pacman -Qs hdf5
local/hdf5-openmpi 2.0.0-3
local/python-h5py-openmpi 3.15.1-2

@carlosal1015 I think you should comment this test :

  CMAKE_PREFIX_PATH="${srcdir}/tmp_install/usr/lib/cmake/${pkgname}" cmake \
    -S ${pkgname}-${pkgver}/cpp/test \
    -B build_test
  cmake --build build_test
  ctest --test-dir build_test

I have tested everything. Even I've contacted the developer and he assume that the problem is from default cmake flags not from the source code.

Maybe it will be solved in next release

Maybe we must restore export LDFLAGS=$LDFLAGS before run test.

@carlosal1015 this is the output of the log that I found in the LastTest.log file:

/usr/src/debug/dolfinx/dolfinx-0.9.0.post1/cpp/test/mesh/distributed_mesh.cpp:193: FAILED:
  CHECK_NOTHROW( test_distributed_mesh(mesh::create_cell_partitioner( mesh::GhostMode::none, graph::kahip::partitioner(1, 1, 0.03, false))) )
due to unexpected exception with message:
  std::bad_alloc

===============================================================================
test cases:    39 |    36 passed | 1 failed | 2 skipped
assertions: 27116 | 27115 passed | 1 failed

Caught signal 11 (Segmentation fault: address not mapped to object at address 0xdcf065fa)
==== backtrace (tid: 431263) ====
 0 0x000000000004c822 ucs_event_set_fd_get()  ???:0
 1 0x000000000004c9ed ucs_event_set_fd_get()  ???:0
 2 0x000000000003d1d0 __sigaction()  ???:0
 3 0x000000000014f0b9 std::basic_streambuf<char, std::char_traits<char> >::pubsync()  /usr/src/debug/gcc/gcc-build/x86_64-pc-linux-gnu/libstdc++-v3/include/streambuf:278
 4 0x000000000014f0b9 std::ostream::flush()  /usr/src/debug/gcc/gcc-build/x86_64-pc-linux-gnu/libstdc++-v3/include/bits/ostream.tcc:237
 5 0x00000000000c2c77 std::ios_base::Init::~Init()  /usr/src/debug/gcc/gcc/libstdc++-v3/src/c++98/ios_init.cc:134
 6 0x000000000003f340 __cxa_finalize()  ???:0
 7 0x00000000000aa788 __do_global_dtors_aux()  crtstuff.c:0
=================================
<end of output>

@carlosal1015 I found a solution for the build process but get error in the check process The solution is adding export LDFLAGS="-lkahip $LDFLAGS" in the build process before the cmake command. Now I'm trying to found solution for check.

I had the same issue too, for example when I installed kahip compiled from GitHub runners and go it for dolfinx, I guess is something dependency with glibc, but when I compiled in my machine and after install dolfinx, no issues anymore, try it please.

@carlosal1015 I get this error from build process:

CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
  KaHIP could not be found/configured.  (missing: KAHIP_TEST_RUNS)
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
  cmake/modules/FindKaHIP.cmake:98 (find_package_handle_standard_args)
  CMakeLists.txt:495 (find_package)