Compiling with MacOS arm64

[sblondel]

The code is currently not compiling with this architecture, it brakes when PETSc builds Kokkos or Kokkos-kernel.

[PhilipFackler]

@sblondel gh actions on macos pass. Can we test this again with latest develop?

[sanjoymazumder13]

Hi, I am facing issues making Xolotl (stable) with macOS. I have tried macOS systems with both arm64 and x86_64 architecture, but get the same error. I have used the following cmake command to configure.

cmake -DCMAKE_BUILD_TYPE=Release -DKokkos_DIR=$KOKKOS_DIR/install -DPETSC_DIR=$PETSC_DIR
-DPETSC_ARCH=$PETSC_ARCH -DCMAKE_CXX_COMPILER=mpicxx
-DBUILD_SHARED_LIBS=yes -DCMAKE_CXX_FLAGS_RELEASE="-O3 -fPIC" -DBUILD_TESTING=OFF
-DCMAKE_INSTALL_PREFIX=$XOLOTL_DIR/install ..

The error that I get is:

[ 91%] Linking CXX shared library libxolotlSolver.dylib
Undefined symbols for architecture arm64:
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const**, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver0DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver0DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::updateConcentration(_p_TS*&, _p_Vec*&, _p_Vec*&, double) in PetscSolver1DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver1DHandler.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeAlloy(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeAlphaZr(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
...
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const***, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver2DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver2DHandler.cpp.o
xolotl::solver::handler::PetscSolver2DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver2DHandler.cpp.o
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const****, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver3DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver3DHandler.cpp.o
xolotl::solver::handler::PetscSolver3DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver3DHandler.cpp.o
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const**, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver0DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver0DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::updateConcentration(_p_TS*&, _p_Vec*&, _p_Vec*&, double) in PetscSolver1DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver1DHandler.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeAlloy(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
xolotl::solver::monitor::PetscMonitor0D::computeAlphaZr(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
...
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const***, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver2DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver2DHandler.cpp.o
xolotl::solver::handler::PetscSolver2DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver2DHandler.cpp.o
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double const****, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver3DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver3DHandler.cpp.o
xolotl::solver::handler::PetscSolver3DHandler::computeJacobian(_p_TS*&, _p_Vec*&, _p_Mat*&, double) in PetscSolver3DHandler.cpp.o
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double****, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver3DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver3DHandler.cpp.o
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double***, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver2DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver2DHandler.cpp.o
"PetscErrorCode DMDAVecGetKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double**, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver0DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::updateConcentration(_p_TS*&, _p_Vec*&, _p_Vec*&, double) in PetscSolver1DHandler.cpp.o
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double****, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver3DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver3DHandler.cpp.o
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double***, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver2DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver2DHandler.cpp.o
"PetscErrorCode DMDAVecRestoreKokkosOffsetViewDOFWriteKokkos::HostSpace(_p_DM*, _p_Vec*, Kokkos::Experimental::OffsetView<double**, Kokkos::LayoutRight, Kokkos::HostSpace>)", referenced from:
xolotl::solver::handler::PetscSolver0DHandler::updateConcentration(_p_TS&, _p_Vec*&, _p_Vec*&, double) in PetscSolver0DHandler.cpp.o
xolotl::solver::handler::PetscSolver1DHandler::updateConcentration(_p_TS*&, _p_Vec*&, _p_Vec*&, double) in PetscSolver1DHandler.cpp.o
"xolotl::core::network::ReactionNetworkxolotl::core::network::NEReactionNetwork::getTotalVolumeRatio(Kokkos::View<double const*, Kokkos::MemoryTraits<1u>>, xolotl::core::network::NESpecies, unsigned int)", referenced from:
xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
"xolotl::core::network::ReactionNetworkxolotl::core::network::NEReactionNetwork::getTotalRatioVariance(Kokkos::View<double const*, Kokkos::MemoryTraits<1u>>, xolotl::core::network::NESpecies, double, unsigned int)", referenced from:
xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o
ld: symbol(s) not found for architecture arm64
arm64-apple-darwin20.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [xolotl/solver/CMakeFiles/xolotlSolver.dir/build.make:318: xolotl/solver/libxolotlSolver.dylib] Error 1
make[1]: *** [CMakeFiles/Makefile2:683: xolotl/solver/CMakeFiles/xolotlSolver.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

I felt it would be relevant regarding this open issue. Just wanted to know if it is adifferent problem or related to the same issue. Thanks in advance.

[sblondel]

@sanjoymazumder13 Thank you for your post. stable doesn't include the commits related to this issue yet. Can you try switching to the latest version of develop ? The README is not up-to-date, Xolotl cmake can now build all the dependencies directly (no need to clone PETSc forehand):
cmake -DCMAKE_BUILD_TYPE=Release -DXolotl_BUILD_PETSC=1 ../xolotl-source/

[sanjoymazumder13]

Thanks @sblondel for the information. This was helpful. I am working with the develop branch using Xolotl cmake to build the dependencies. I am getting an error while building the target xolotlSolver. The error is shown below. I get the same error with both x86_64 and arm64 architectures. Is there any specific library that needs to be defined. Thanks in advance.

#---------#

Linking CXX shared library libxolotlSolver.dylib Undefined symbols for architecture x86_64: "xolotl::core::network::ReactionNetwork<xolotl::core::network::NEReactionNetwork>::getTotalVolumeRatio(Kokkos::View<double const*, Kokkos::MemoryTraits<1u>>, xolotl::core::network::NESpecies, unsigned int)", referenced from: xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o "xolotl::core::network::ReactionNetwork<xolotl::core::network::NEReactionNetwork>::getTotalRatioVariance(Kokkos::View<double const*, Kokkos::MemoryTraits<1u>>, xolotl::core::network::NESpecies, double, unsigned int)", referenced from: xolotl::solver::monitor::PetscMonitor0D::computeXenonRetention(_p_TS*, long long, double, _p_Vec*) in PetscMonitor0D.cpp.o ld: symbol(s) not found for architecture x86_64 x86_64-apple-darwin13.4: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [xolotl/solver/CMakeFiles/xolotlSolver.dir/build.make:318: xolotl/solver/libxolotlSolver.dylib] Error 1 make[1]: *** [CMakeFiles/Makefile2:1899: xolotl/solver/CMakeFiles/xolotlSolver.dir/all] Error 2

[PhilipFackler]

Try using -DXolotl_INCLUDE_RN_TPP_FILES=ON in your cmake command.

[sanjoymazumder13]

Thanks @PhilipFackler. It worked with both the architectures.