Re: [deal.II] Re: Can't configure with cmake
Ran into the same problem. The bundled folder is not installed, since no bundled libraries are used, but the cmake targets still reference them. As a workaround, you can just create the bundled folder. I haven't had the time to dig through the cmake files to fix it, but for the moment opened an issue here https://github.com/dealii/dealii/issues/16605 bruno.t...@gmail.com schrieb am Mittwoch, 7. Februar 2024 um 14:47:22 UTC+1: > Sean, > > If the configuration steps errors out, there is no point in trying to > compile the code. You probably want to remove the deal.II files that have > been installed and reinstall the library. > > Best, > > Bruno > > Le mar. 6 févr. 2024 à 18:26, Sean Johnson a écrit : > >> Bruno, >> >> I apparently spoke to soon. It passed "make test" with 0 failed test. >> However, when I run "cmake ." in the directory of step-1 I get this output: >> >> >> -- Using the deal.II-9.5.2 installation found at /usr/local >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_add_test.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_query_git_information.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_deal_ii_setup_target.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_shell_escape_option_groups.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_target_compile_flags.cmake >> -- Include macro >> /usr/local/share/deal.II/macros/macro_target_link_flags.cmake >> -- Autopilot invoked >> -- Run $ make info to print a detailed help message >> -- Configuring done >> CMake Error in CMakeLists.txt: >> Imported target "dealii::dealii_debug" includes non-existent path >> >> "/usr/local/include/deal.II/bundled" >> >> 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 >> CMake Generate step failed. Build files cannot be regenerated correctly. >> >> >> >> Then when I try "make" I get this: >> >> >> >> [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o >> In file included from /usr/local/include/deal.II/grid/tria.h:20, >> from >> /home/sean/dealii-9.5.2/examples/step-1/step-1.cc:22: >> /usr/local/include/deal.II/base/config.h:588:12: fatal error: mpi.h: No >> such file or directory >> 588 | # include >> |^~~ >> compilation terminated. >> make[3]: *** [CMakeFiles/step-1.dir/build.make:76: >> CMakeFiles/step-1.dir/step-1.cc.o] Error 1 >> make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/step-1.dir/all] Error 2 >> make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 >> make: *** [Makefile:137: run] Error 2 >> >> I am currently recompiling with fewer jobs to see if any errors pop up or >> if recompiling might help. >> >> Thanks, >> Sean >> >> On Tuesday, February 6, 2024 at 3:17:42 PM UTC-7 bruno.t...@gmail.com >> wrote: >> >>> Sean, >>> >>> That's great to hear. We don't mark problems as solved. So there is >>> nothing to do. >>> >>> Best, >>> >>> Bruno >>> >>> Le mar. 6 févr. 2024 à 16:41, Sean Johnson a >>> écrit : >>> Thanks again! The using a newer version of Boost helped me get further and realize I made another bone headed mistake of compiling kokkos as a static library. I am all compiled and passed all tests now. Thanks for your help and let me know if I have to do anything for this to be marked as solved. Best, Sean On Tuesday, February 6, 2024 at 8:30:19 AM UTC-7 bruno.t...@gmail.com wrote: > Sean, > > I am not sure what's the issue. It's probably not the issue but make > sure that mpi is using nvcc_wrapper as the underlying compiler. If you > use > OpenMPI, you can use export `OMPI_CXX=nvcc_wrapper`. You could also try > to > use a newer version of Boost. The bundled version is pretty old. Since > you > are using Ubuntu 22.04, you can just use your package manager to install > a > newer version of boost. > > Best, > > Bruno > > Le mar. 6 févr. 2024 à 09:37, Sean Johnson a > écrit : > >> Thanks, >> >> I tried lowering it down to 2 and it looks like two of them were >> caught a lot earlier. Now I don't make it past 6%. I erased everything >> from >> before and recompiled the cmake files and ran with just 2 jobs and again >> it >> stuck in the
Re: [deal.II] Re: Can't configure with cmake
Sean, If the configuration steps errors out, there is no point in trying to compile the code. You probably want to remove the deal.II files that have been installed and reinstall the library. Best, Bruno Le mar. 6 févr. 2024 à 18:26, Sean Johnson a écrit : > Bruno, > > I apparently spoke to soon. It passed "make test" with 0 failed test. > However, when I run "cmake ." in the directory of step-1 I get this output: > > > -- Using the deal.II-9.5.2 installation found at /usr/local > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_add_test.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_query_git_information.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_setup_target.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_shell_escape_option_groups.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_target_compile_flags.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_target_link_flags.cmake > -- Autopilot invoked > -- Run $ make info to print a detailed help message > -- Configuring done > CMake Error in CMakeLists.txt: > Imported target "dealii::dealii_debug" includes non-existent path > > "/usr/local/include/deal.II/bundled" > > 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 > CMake Generate step failed. Build files cannot be regenerated correctly. > > > > Then when I try "make" I get this: > > > > [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o > In file included from /usr/local/include/deal.II/grid/tria.h:20, > from /home/sean/dealii-9.5.2/examples/step-1/step-1.cc:22: > /usr/local/include/deal.II/base/config.h:588:12: fatal error: mpi.h: No > such file or directory > 588 | # include > |^~~ > compilation terminated. > make[3]: *** [CMakeFiles/step-1.dir/build.make:76: > CMakeFiles/step-1.dir/step-1.cc.o] Error 1 > make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/step-1.dir/all] Error 2 > make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 > make: *** [Makefile:137: run] Error 2 > > I am currently recompiling with fewer jobs to see if any errors pop up or > if recompiling might help. > > Thanks, > Sean > > On Tuesday, February 6, 2024 at 3:17:42 PM UTC-7 bruno.t...@gmail.com > wrote: > >> Sean, >> >> That's great to hear. We don't mark problems as solved. So there is >> nothing to do. >> >> Best, >> >> Bruno >> >> Le mar. 6 févr. 2024 à 16:41, Sean Johnson a écrit : >> >>> Thanks again! >>> >>> The using a newer version of Boost helped me get further and realize I >>> made another bone headed mistake of compiling kokkos as a static library. >>> >>> I am all compiled and passed all tests now. >>> >>> Thanks for your help and let me know if I have to do anything for this >>> to be marked as solved. >>> >>> Best, >>> Sean >>> >>> On Tuesday, February 6, 2024 at 8:30:19 AM UTC-7 bruno.t...@gmail.com >>> wrote: >>> Sean, I am not sure what's the issue. It's probably not the issue but make sure that mpi is using nvcc_wrapper as the underlying compiler. If you use OpenMPI, you can use export `OMPI_CXX=nvcc_wrapper`. You could also try to use a newer version of Boost. The bundled version is pretty old. Since you are using Ubuntu 22.04, you can just use your package manager to install a newer version of boost. Best, Bruno Le mar. 6 févr. 2024 à 09:37, Sean Johnson a écrit : > Thanks, > > I tried lowering it down to 2 and it looks like two of them were > caught a lot earlier. Now I don't make it past 6%. I erased everything > from > before and recompiled the cmake files and ran with just 2 jobs and again > it > stuck in the same spot. > > Here are the last few lines and logs. > > [ 6%] Building CXX object > bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/gzip.cpp.o > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:193:42: > warning: unnecessary parentheses in declaration of ‘assert_arg’ > [-Wparentheses] > 193 | template< typename Pred > > | ^ > > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:193:42: > note: remove
Re: [deal.II] Re: Can't configure with cmake
Sean, that problem doesn't sound specific to compiling with Kokkos+Cuda. Can you make sure to start from a clean work directory and again select `nvcc_wrapper` as compiler? Best, Daniel On Tue, Feb 6, 2024 at 6:26 PM Sean Johnson wrote: > Bruno, > > I apparently spoke to soon. It passed "make test" with 0 failed test. > However, when I run "cmake ." in the directory of step-1 I get this output: > > > -- Using the deal.II-9.5.2 installation found at /usr/local > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_add_test.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_query_git_information.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_deal_ii_setup_target.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_shell_escape_option_groups.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_target_compile_flags.cmake > -- Include macro > /usr/local/share/deal.II/macros/macro_target_link_flags.cmake > -- Autopilot invoked > -- Run $ make info to print a detailed help message > -- Configuring done > CMake Error in CMakeLists.txt: > Imported target "dealii::dealii_debug" includes non-existent path > > "/usr/local/include/deal.II/bundled" > > 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 > CMake Generate step failed. Build files cannot be regenerated correctly. > > > > Then when I try "make" I get this: > > > > [ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o > In file included from /usr/local/include/deal.II/grid/tria.h:20, > from /home/sean/dealii-9.5.2/examples/step-1/step-1.cc:22: > /usr/local/include/deal.II/base/config.h:588:12: fatal error: mpi.h: No > such file or directory > 588 | # include > |^~~ > compilation terminated. > make[3]: *** [CMakeFiles/step-1.dir/build.make:76: > CMakeFiles/step-1.dir/step-1.cc.o] Error 1 > make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/step-1.dir/all] Error 2 > make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 > make: *** [Makefile:137: run] Error 2 > > I am currently recompiling with fewer jobs to see if any errors pop up or > if recompiling might help. > > Thanks, > Sean > > On Tuesday, February 6, 2024 at 3:17:42 PM UTC-7 bruno.t...@gmail.com > wrote: > >> Sean, >> >> That's great to hear. We don't mark problems as solved. So there is >> nothing to do. >> >> Best, >> >> Bruno >> >> Le mar. 6 févr. 2024 à 16:41, Sean Johnson a écrit : >> >>> Thanks again! >>> >>> The using a newer version of Boost helped me get further and realize I >>> made another bone headed mistake of compiling kokkos as a static library. >>> >>> I am all compiled and passed all tests now. >>> >>> Thanks for your help and let me know if I have to do anything for this >>> to be marked as solved. >>> >>> Best, >>> Sean >>> >>> On Tuesday, February 6, 2024 at 8:30:19 AM UTC-7 bruno.t...@gmail.com >>> wrote: >>> Sean, I am not sure what's the issue. It's probably not the issue but make sure that mpi is using nvcc_wrapper as the underlying compiler. If you use OpenMPI, you can use export `OMPI_CXX=nvcc_wrapper`. You could also try to use a newer version of Boost. The bundled version is pretty old. Since you are using Ubuntu 22.04, you can just use your package manager to install a newer version of boost. Best, Bruno Le mar. 6 févr. 2024 à 09:37, Sean Johnson a écrit : > Thanks, > > I tried lowering it down to 2 and it looks like two of them were > caught a lot earlier. Now I don't make it past 6%. I erased everything > from > before and recompiled the cmake files and ran with just 2 jobs and again > it > stuck in the same spot. > > Here are the last few lines and logs. > > [ 6%] Building CXX object > bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/gzip.cpp.o > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:193:42: > warning: unnecessary parentheses in declaration of ‘assert_arg’ > [-Wparentheses] > 193 | template< typename Pred > > | ^ > > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:193:42: > note: remove parentheses >
