Installing Asimov-Contact

General
1

Dear community.

I would like to try some Hertzian contact problems between two bodies using dolfinx. One of the approach is to use the Asimov-contact repo from Wells-group. However, I don’t know how to install the repo, or if is usable without installing. I’m getting the exact same error as in Problem with installing asimov-contact library bug in RayTracing.h.

Consolidate compiler generated dependencies of target dolfinx_contact
[  5%] Building CXX object CMakeFiles/dolfinx_contact.dir/utils.cpp.o
[ 11%] Building CXX object CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o
[ 17%] Building CXX object CMakeFiles/dolfinx_contact.dir/SubMesh.cpp.o
[ 23%] Building CXX object CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o
In file included from /home/pietro/asimov-contact/cpp/utils.h:10,
                 from /home/pietro/asimov-contact/cpp/KernelData.h:11,
                 from /home/pietro/asimov-contact/cpp/meshtie_kernels.h:9,
                 from /home/pietro/asimov-contact/cpp/meshtie_kernels.cpp:7:
/home/pietro/asimov-contact/cpp/RayTracing.h:14:10: fatal error: spglog/spdlog.h: No such file or directory
   14 | #include <spglog/spdlog.h>
      |          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/build.make:146: CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /home/pietro/asimov-contact/cpp/utils.h:10,
                 from /home/pietro/asimov-contact/cpp/utils.cpp:7:
/home/pietro/asimov-contact/cpp/RayTracing.h:14:10: fatal error: spglog/spdlog.h: No such file or directory
   14 | #include <spglog/spdlog.h>
      |          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/build.make:76: CMakeFiles/dolfinx_contact.dir/utils.cpp.o] Error 1
In file included from /home/pietro/asimov-contact/cpp/utils.h:10,
                 from /home/pietro/asimov-contact/cpp/KernelData.h:11,
                 from /home/pietro/asimov-contact/cpp/contact_kernels.h:9,
                 from /home/pietro/asimov-contact/cpp/contact_kernels.cpp:7:
/home/pietro/asimov-contact/cpp/RayTracing.h:14:10: fatal error: spglog/spdlog.h: No such file or directory
   14 | #include <spglog/spdlog.h>
      |          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/build.make:104: CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o] Error 1
In file included from /home/pietro/asimov-contact/cpp/utils.h:10,
                 from /home/pietro/asimov-contact/cpp/SubMesh.cpp:8:
/home/pietro/asimov-contact/cpp/RayTracing.h:14:10: fatal error: spglog/spdlog.h: No such file or directory
   14 | #include <spglog/spdlog.h>
      |          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/build.make:160: CMakeFiles/dolfinx_contact.dir/SubMesh.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/dolfinx_contact.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

Maybe this is not the right place to ask, but I would like to know how to use this repo on a MacOS with anaconda environment (for example, what version of dolfinx to use?).

Sorry there is no MWE.

2

Well, the obvious question would be if you have spdlog installed. If so, and if it is not in a default location, maybe try to add that location to CPATH or a similar environment variable until the issue is fixed upstream.

It would have been helpful to post your own error message, rather than Pietro’s one.

1 Like
3

Thanks for the response, @francesco-ballarin. To be more precise, I have followed the steps provided in Errors while running asimov-contact demos · Issue #168 · Wells-Group/asimov-contact · GitHub. I have installed spdlog and all the conda dependencies mentioned there using conda install -c conda-forge ..... According to the repo dates, I have installed fenics-dolfinx=0.8.0.

Running cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX .. gives

-- The C compiler identification is Clang 17.0.6
-- The CXX compiler identification is Clang 17.0.6
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/anaconda3/envs/asimov-contact/bin/arm64-apple-darwin20.0.0-clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/anaconda3/envs/asimov-contact/bin/arm64-apple-darwin20.0.0-clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Found MPI_C: /opt/anaconda3/envs/asimov-contact/lib/libmpi.dylib (found version "4.1")
-- Found MPI_CXX: /opt/anaconda3/envs/asimov-contact/lib/libmpicxx.dylib (found version "4.1")
-- Found MPI: TRUE (found version "4.1")
CMake Warning (dev) at /opt/anaconda3/envs/asimov-contact/share/cmake-3.31/Modules/CMakeFindDependencyMacro.cmake:76 (find_package):
  Policy CMP0167 is not set: The FindBoost module is removed.  Run "cmake
  --help-policy CMP0167" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

Call Stack (most recent call first):
  /opt/anaconda3/envs/asimov-contact/lib/cmake/dolfinx/DOLFINXConfig.cmake:44 (find_dependency)
  CMakeLists.txt:63 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Boost 1.86.0 at /opt/anaconda3/envs/asimov-contact/lib/cmake/Boost-1.86.0
--   Requested configuration: QUIET REQUIRED COMPONENTS timer;filesystem
-- Found boost_headers 1.86.0 at /opt/anaconda3/envs/asimov-contact/lib/cmake/boost_headers-1.86.0
-- Found boost_timer 1.86.0 at /opt/anaconda3/envs/asimov-contact/lib/cmake/boost_timer-1.86.0
--   [x] libboost_timer.dylib
-- Adding boost_timer dependencies: headers
-- Found boost_filesystem 1.86.0 at /opt/anaconda3/envs/asimov-contact/lib/cmake/boost_filesystem-1.86.0
--   [x] libboost_filesystem.dylib
-- Adding boost_filesystem dependencies: atomic;headers
-- Found boost_atomic 1.86.0 at /opt/anaconda3/envs/asimov-contact/lib/cmake/boost_atomic-1.86.0
--   [x] libboost_atomic.dylib
-- Adding boost_atomic dependencies: headers
-- Found Boost: /opt/anaconda3/envs/asimov-contact/lib/cmake/Boost-1.86.0/BoostConfig.cmake (found suitable version "1.86.0", minimum required is "1.70") found components: timer filesystem
-- Found Python3: /opt/anaconda3/envs/asimov-contact/bin/python3.13 (found version "3.13.0") found components: Interpreter
-- Adding /opt/anaconda3/envs/asimov-contact/lib/python3.13/site-packages/basix to Basix search hints
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /opt/anaconda3/envs/asimov-contact/lib/libhdf5.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcrypto.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcurl.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libpthread.tbd;/opt/anaconda3/envs/asimov-contact/lib/libsz.dylib;/opt/anaconda3/envs/asimov-contact/lib/libz.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd (found version "1.14.3") found components: C
-- HDF5_DIR: HDF5_DIR-NOTFOUND
-- HDF5_DEFINITIONS: -D_FORTIFY_SOURCE=2
-- HDF5_INCLUDE_DIRS: /opt/anaconda3/envs/asimov-contact/include
-- HDF5_LIBRARIES: /opt/anaconda3/envs/asimov-contact/lib/libhdf5.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcrypto.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcurl.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libpthread.tbd;/opt/anaconda3/envs/asimov-contact/lib/libsz.dylib;/opt/anaconda3/envs/asimov-contact/lib/libz.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd
-- HDF5_HL_LIBRARIES: 
-- HDF5_C_DEFINITIONS: -D_FORTIFY_SOURCE=2
-- HDF5_C_INCLUDE_DIR: 
-- HDF5_C_INCLUDE_DIRS: /opt/anaconda3/envs/asimov-contact/include
-- HDF5_C_LIBRARY: 
-- HDF5_C_LIBRARIES: /opt/anaconda3/envs/asimov-contact/lib/libhdf5.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcrypto.dylib;/opt/anaconda3/envs/asimov-contact/lib/libcurl.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libpthread.tbd;/opt/anaconda3/envs/asimov-contact/lib/libsz.dylib;/opt/anaconda3/envs/asimov-contact/lib/libz.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd
-- HDF5_C_HL_LIBRARY: 
-- HDF5_C_HL_LIBRARIES: 
-- Defined targets (if any):
-- ... hdf5::hdf5
-- Found PkgConfig: /opt/anaconda3/envs/asimov-contact/bin/pkg-config (found version "0.29.2")
-- Checking for one of the modules 'PETSc;petsc'
-- Checking for one of the modules 'SLEPc;slepc'
-- Found ADIOS2: /opt/anaconda3/envs/asimov-contact/lib/cmake/adios2/adios2-config.cmake (found suitable version "2.10.1", minimum required is "2.8.1") found components: C CXX MPI
-- The following features have been enabled:

 * BUILD_SHARED_LIBS, Build DOLFINX_CONTACT with shared libraries.
 * CMAKE_INSTALL_RPATH_USE_LINK_PATH, Add paths to linker search and installed rpath.

-- The following OPTIONAL packages have been found:

 * Python3

-- The following REQUIRED packages have been found:

 * boost_timer (required version == 1.86.0)
 * boost_atomic (required version == 1.86.0)
 * boost_headers (required version == 1.86.0)
 * boost_filesystem (required version == 1.86.0)
 * PkgConfig
 * DOLFINX (required version >= 0.8.0.0)
 * Basix (required version >= 0.8.0.0)

-- Configuring done (15.8s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/jesus/asimov-contact/cpp/build

Then, running make -j4 gives the following error output

[ 11%] Building CXX object CMakeFiles/dolfinx_contact.dir/utils.cpp.o
[ 11%] Building CXX object CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o
[ 17%] Building CXX object CMakeFiles/dolfinx_contact.dir/elasticity.cpp.o
[ 23%] Building CXX object CMakeFiles/dolfinx_contact.dir/coefficients.cpp.o
[ 29%] Building CXX object CMakeFiles/dolfinx_contact.dir/geometric_quantities.cpp.o
In file included from /Users/jesus/asimov-contact/cpp/contact_kernels.cpp:7:
In file included from /Users/jesus/asimov-contact/cpp/contact_kernels.h:9:
In file included from /Users/jesus/asimov-contact/cpp/KernelData.h:11:
In file included from /Users/jesus/asimov-contact/cpp/utils.h:10:
/Users/jesus/asimov-contact/cpp/RayTracing.h:532:5: error: use of undeclared identifier 'spdlog'
  532 |     spdlog::warn("No ray through the facets have been found");
      |     ^
In file included from /Users/jesus/asimov-contact/cpp/utils.cpp:7:
In file included from /Users/jesus/asimov-contact/cpp/utils.h:10:
/Users/jesus/asimov-contact/cpp/RayTracing.h:532:5: error: use of undeclared identifier 'spdlog'
  532 |     spdlog::warn("No ray through the facets have been found");
      |     ^
[ 35%] Building CXX object CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o
1 error generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
1 error generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/utils.cpp.o] Error 1
In file included from /Users/jesus/asimov-contact/cpp/meshtie_kernels.cpp:7:
In file included from /Users/jesus/asimov-contact/cpp/meshtie_kernels.h:9:
In file included from /Users/jesus/asimov-contact/cpp/KernelData.h:11:
In file included from /Users/jesus/asimov-contact/cpp/utils.h:10:
/Users/jesus/asimov-contact/cpp/RayTracing.h:532:5: error: use of undeclared identifier 'spdlog'
  532 |     spdlog::warn("No ray through the facets have been found");
      |     ^
1 error generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o] Error 1
make[1]: *** [CMakeFiles/dolfinx_contact.dir/all] Error 2
make: *** [all] Error 2

Could you please guide me on how to perform this step?

4

Try to add a #include <spdlog/spdlog.h> in /Users/jesus/asimov-contact/cpp/RayTracing.h

1 Like
5

And, as was said in the other post, you definitely need to upgrade to 0.9.0.

6

Asimov contact is in a weird state between 0.8 and 0.9 of DOLFINx. I might have bandwidth to push it towards 0.9 of DOLFINx at some point.

1 Like
7

Thank you @francesco-ballarin. I have made that modification to /Users/jesus/asimov-contact/cpp/RayTracing.h and /Users/jesus/asimov-contact/cpp/parallel_mesh_ghosting.h

Indeed @dokken, both versions produces very different error outputs.

Running make -j4 with fenicsx-dolfin=0.8.0 results in the error output

[  5%] Building CXX object CMakeFiles/dolfinx_contact.dir/utils.cpp.o
[ 17%] Building CXX object CMakeFiles/dolfinx_contact.dir/elasticity.cpp.o
[ 17%] Building CXX object CMakeFiles/dolfinx_contact.dir/coefficients.cpp.o
[ 23%] Building CXX object CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o
[ 29%] Building CXX object CMakeFiles/dolfinx_contact.dir/geometric_quantities.cpp.o
[ 35%] Building CXX object CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o
[ 41%] Building CXX object CMakeFiles/dolfinx_contact.dir/SubMesh.cpp.o
[ 47%] Building CXX object CMakeFiles/dolfinx_contact.dir/QuadratureRule.cpp.o
[ 52%] Building CXX object CMakeFiles/dolfinx_contact.dir/Contact.cpp.o
[ 58%] Building CXX object CMakeFiles/dolfinx_contact.dir/MeshTie.cpp.o
[ 64%] Building CXX object CMakeFiles/dolfinx_contact.dir/RayTracing.cpp.o
[ 70%] Building CXX object CMakeFiles/dolfinx_contact.dir/KernelData.cpp.o
[ 76%] Building CXX object CMakeFiles/dolfinx_contact.dir/error_handling.cpp.o
[ 82%] Building CXX object CMakeFiles/dolfinx_contact.dir/rigid_surface_kernels.cpp.o
[ 88%] Building CXX object CMakeFiles/dolfinx_contact.dir/point_cloud.cpp.o
[ 94%] Building CXX object CMakeFiles/dolfinx_contact.dir/parallel_mesh_ghosting.cpp.o
/Users/jesus/asimov-contact/cpp/parallel_mesh_ghosting.cpp:197:19: error: no matching function for call to 'create_mesh'
  197 |   auto new_mesh = dolfinx::mesh::create_mesh(
      |                   ^~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/anaconda3/envs/asimov-contact/include/dolfinx/mesh/utils.h:785:64: note: candidate function template not viable: no known conversion from '(lambda at /Users/jesus/asimov-contact/cpp/parallel_mesh_ghosting.cpp:174:9)' to 'const CellPartitionFunction' (aka 'const function<AdjacencyList<int> (int, int, dolfinx::mesh::CellType, const AdjacencyList<long long> &)>') for 8th argument
  785 | Mesh<typename std::remove_reference_t<typename U::value_type>> create_mesh(
      |                                                                ^
  786 |     MPI_Comm comm, MPI_Comm commt, std::span<const std::int64_t> cells,
  787 |     const fem::CoordinateElement<
  788 |         typename std::remove_reference_t<typename U::value_type>>& element,
  789 |     MPI_Comm commg, const U& x, std::array<std::size_t, 2> xshape,
  790 |     const CellPartitionFunction& partitioner)
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/anaconda3/envs/asimov-contact/include/dolfinx/mesh/utils.h:934:1: note: candidate function template not viable: requires 6 arguments, but 8 were provided
  934 | create_mesh(MPI_Comm comm, std::span<const std::int64_t> cells,
      | ^           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  935 |             const fem::CoordinateElement<
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  936 |                 std::remove_reference_t<typename U::value_type>>& elements,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  937 |             const U& x, std::array<std::size_t, 2> xshape, GhostMode ghost_mode)
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/parallel_mesh_ghosting.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/dolfinx_contact.dir/all] Error 2
make: *** [all] Error 2

while running the same but with fenicsx-dolfin=0.9.0 produces the error

[ 11%] Building CXX object CMakeFiles/dolfinx_contact.dir/utils.cpp.o
[ 11%] Building CXX object CMakeFiles/dolfinx_contact.dir/elasticity.cpp.o
[ 17%] Building CXX object CMakeFiles/dolfinx_contact.dir/coefficients.cpp.o
[ 23%] Building CXX object CMakeFiles/dolfinx_contact.dir/contact_kernels.cpp.o
[ 29%] Building CXX object CMakeFiles/dolfinx_contact.dir/geometric_quantities.cpp.o
/Users/jesus/asimov-contact/cpp/utils.cpp:197:12: error: no member named 'argsort_radix' in namespace 'dolfinx'
  197 |   dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |   ~~~~~~~~~^
/Users/jesus/asimov-contact/cpp/utils.cpp:197:38: error: expected '(' for function-style cast or type construction
  197 |   dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |                          ~~~~~~~~~~~~^
/Users/jesus/asimov-contact/cpp/utils.cpp:197:40: warning: left operand of comma operator has no effect [-Wunused-value]
  197 |   dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |                                        ^~~~~
[ 35%] Building CXX object CMakeFiles/dolfinx_contact.dir/meshtie_kernels.cpp.o
/Users/jesus/asimov-contact/cpp/utils.cpp:697:14: error: no member named 'argsort_radix' in namespace 'dolfinx'
  697 |     dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |     ~~~~~~~~~^
/Users/jesus/asimov-contact/cpp/utils.cpp:697:40: error: expected '(' for function-style cast or type construction
  697 |     dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |                            ~~~~~~~~~~~~^
/Users/jesus/asimov-contact/cpp/utils.cpp:697:42: warning: left operand of comma operator has no effect [-Wunused-value]
  697 |     dolfinx::argsort_radix<std::int32_t>(cells, perm);
      |                                          ^~~~~
[ 41%] Building CXX object CMakeFiles/dolfinx_contact.dir/SubMesh.cpp.o
[ 47%] Building CXX object CMakeFiles/dolfinx_contact.dir/QuadratureRule.cpp.o
2 warnings and 4 errors generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/utils.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/Users/jesus/asimov-contact/cpp/SubMesh.cpp:24:12: error: 'radix_sort' does not name a template but is followed by template arguments
   24 |   dolfinx::radix_sort<std::int32_t>(std::span(cells.data(), cells.size()));
      |            ^         ~~~~~~~~~~~~~~
/opt/anaconda3/envs/asimov-contact090/include/dolfinx/common/sort.h:124:31: note: non-template declaration found by name lookup
  124 | inline constexpr __radix_sort radix_sort{};
      |                               ^
1 error generated.
make[2]: *** [CMakeFiles/dolfinx_contact.dir/SubMesh.cpp.o] Error 1
make[1]: *** [CMakeFiles/dolfinx_contact.dir/all] Error 2
make: *** [all] Error 2