Arch Linux User Repository

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

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)

Hi @zhushazang, I guess is an issue from pkg_search_module() function when parse metadata from /opt/slepc/linux-c-opt/lib/pkgconfig/slepc.pc. For example if we consider the CMakeLists.txt below.

cmake_minimum_required(VERSION 3.19)
project(FOO VERSION "0.1.0")

find_package(PkgConfig REQUIRED)

pkg_search_module(PETSC REQUIRED IMPORTED_TARGET PETSc>=3.15 petsc>=3.15)
pkg_search_module(SLEPC REQUIRED IMPORTED_TARGET SLEPc>=3.15 slepc>=3.15)

message("Found PETSc version ${PETSC_VERSION}, prefix: ${PETSC_PREFIX}")
message("Found SLEPc version ${SLEPC_VERSION}, prefix: ${SLEPC_PREFIX}")

And run cmake -S . -B build, then we will look a wrong path, let me investigate (debug) more in order to formulate an issue from SLEPc side.

Make sure with env that the variables are set.

Nice, that means that cmake configuration could be improved for avoid error, but post installation is fine.

Installing slepc after dolfinx and running the script:

EPS Object: 1 MPI process type: krylovschur 50% of basis vectors kept after restart using the locking variant problem type: generalized symmetric eigenvalue problem selected portion of the spectrum: closest to target: 5. (in magnitude) postprocessing eigenvectors with purification number of eigenvalues (nev): 12 number of column vectors (ncv): 27 maximum dimension of projected problem (mpd): 27 maximum number of iterations: 131 tolerance: 1e-08 convergence test: relative to the eigenvalue BV Object: 1 MPI process type: mat 28 columns of global length 1776 vector orthogonalization method: classical Gram-Schmidt orthogonalization refinement: if needed (eta: 0.7071) block orthogonalization method: GS non-standard inner product tolerance for definite inner product: 2.22045e-15 inner product matrix: Mat Object: (st_) 1 MPI process type: seqaij rows=1776, cols=1776 total: nonzeros=8688, allocated nonzeros=8688 total number of mallocs used during MatSetValues calls=0 not using I-node routines doing matmult as a single matrix-matrix product DS Object: 1 MPI process type: hep solving the problem with: Implicit QR method (steqr) ST Object: 1 MPI process type: shift shift: 0. number of matrices: 2 nonzero pattern of the matrices: UNKNOWN KSP Object: (st) 1 MPI process type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-08, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (st_) 1 MPI process type: lu out-of-place factorization tolerance for zero pivot 2.22045e-14 matrix ordering: nd factor fill ratio given 5., needed 5.42703 Factored matrix follows: Mat Object: (st_) 1 MPI process type: seqaij rows=1776, cols=1776 package used to perform factorization: petsc total: nonzeros=47150, allocated nonzeros=47150 not using I-node routines linear system matrix = precond matrix: Mat Object: (st_) 1 MPI process type: seqaij rows=1776, cols=1776 total: nonzeros=8688, allocated nonzeros=8688 total number of mallocs used during MatSetValues calls=0 not using I-node routines

No worries @zhushazang, did you see this message error

-- Found PkgConfig: /usr/sbin/pkg-config (found version "2.1.0") 
-- Checking for one of the modules 'PETSc;petsc'
-- Checking for one of the modules 'SLEPc;slepc'
-- Configuring done (4.3s)
CMake Error in CMakeLists.txt:
  Imported target "dolfinx" includes non-existent path

    "/tmp/makepkg/slepc/pkg/slepc/opt/slepc/linux-c-opt/include"

  in its INTERFACE_INCLUDE_DIRECTORIES.  Possible reasons include:

  * The path was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and references files it does not
  provide.



CMake Error in CMakeLists.txt:
  Imported target "dolfinx" includes non-existent path

    "/tmp/makepkg/slepc/pkg/slepc/opt/slepc/linux-c-opt/include"

  in its INTERFACE_INCLUDE_DIRECTORIES.  Possible reasons include:

  * The path was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and references files it does not
  provide.



-- Generating done (0.0s)
CMake Generate step failed.  Build files cannot be regenerated correctly.

What happens if you install SLEPc after python-fenics-dolfinx and run this script?