Re: [deal.II] Re: Can't configure with cmake
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 193 | template< typename Pred > | ^ | -
Re: [deal.II] Re: Can't configure with cmake
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 >>> 193 | template< typename Pred > >>> | ^ >>> >>> | - >>> - >>> /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: >>> warning: unnecessary parentheses in declaration of ‘assert_not_arg’ >>> [-Wparentheses] >>> 198 | template< typename Pred > >>> | ^ >>> >>> >>> /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: >>> note: remove parentheses >>> 198 | template< typename Pred > >>> | ^ >>> >>> >>> | - >>> >>> - >>> [ 6%] Building CXX object >>> bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/mapped_file.cpp.o >>> >>> Thanks again for your patience and help, >>> Sean >>> >>> On Monday, February 5, 2024 at 7:07:01 PM UTC-7 bruno.t...@gmail.com >>> wrote: >>> Sean, It's possible that you don't have enough RAM and that you are swapping memory which is extremely slow. Try to reinstall using fewer processors. Best, Bruno Le lun. 5 févr. 2024 à 19:01, Sean Johnson a écrit : > Thanks Bruno, > > This was definitely it. > > So I have now gotten to running make --jobs=4 install but it has > frozen at 82% > I have been sitting on it for about 6 to 7 hours with no change at > all. The last line is: > [ 82%] Built target object_non_matching_debug > > and attached are the summary.log and detailed.log > > I will keep it running still just incase but from previous > installations of dealii this has never happened. > > Thanks, > Sean > > On Monday, February 5, 2024 at 8:32:28 AM UTC-7 bruno.t...@gmail.com > wrote: > >> Sean, >> >> It looks like you are using the wrong compiler. If you want to use >> CUDA, you should use nvcc_wrapper as your C++ compiler. You want >> something >> like `-DCMAKE_CXX_COMPILER=/path/nvcc_wrapper`. You should already have >> used `nvcc_wrapper` to compiler Kokkos. >> >> Best, >> >> Bruno >> >> On Monday, February 5, 2024 at 2:40:37 AM UTC-5 sljoh...@gmail.com >> wrote: >> >>> Hey, >>> >>> I am trying to get deal.ii to compile with p4est and cuda. Due to >>> cuda it also needs MPI and Kokkos from me. I can't even make the make >>> file >>> yet. I tried to find any similar problems in the mailing list and was >>> unable to. >>> >>> I am running Ubuntu 22.04 >>> >>> The Error at the end reads: >>> [ 50%] Building CXX object >>> CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o >>> /usr/bin/c++ -fopenmp-simd -O0 -ggdb >>>
Re: [deal.II] Re: Can't configure with cmake
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 >> 193 | template< typename Pred > >> | ^ >> >> | - >> - >> /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: >> >> warning: unnecessary parentheses in declaration of ‘assert_not_arg’ >> [-Wparentheses] >> 198 | template< typename Pred > >> | ^ >> >> >> /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: >> >> note: remove parentheses >> 198 | template< typename Pred > >> | ^ >> >> >> | - >> >> - >> [ 6%] Building CXX object >> bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/mapped_file.cpp.o >> >> Thanks again for your patience and help, >> Sean >> >> On Monday, February 5, 2024 at 7:07:01 PM UTC-7 bruno.t...@gmail.com >> wrote: >> >>> Sean, >>> >>> It's possible that you don't have enough RAM and that you are swapping >>> memory which is extremely slow. Try to reinstall using fewer processors. >>> >>> Best, >>> >>> Bruno >>> >>> Le lun. 5 févr. 2024 à 19:01, Sean Johnson a >>> écrit : >>> Thanks Bruno, This was definitely it. So I have now gotten to running make --jobs=4 install but it has frozen at 82% I have been sitting on it for about 6 to 7 hours with no change at all. The last line is: [ 82%] Built target object_non_matching_debug and attached are the summary.log and detailed.log I will keep it running still just incase but from previous installations of dealii this has never happened. Thanks, Sean On Monday, February 5, 2024 at 8:32:28 AM UTC-7 bruno.t...@gmail.com wrote: > Sean, > > It looks like you are using the wrong compiler. If you want to use > CUDA, you should use nvcc_wrapper as your C++ compiler. You want > something > like `-DCMAKE_CXX_COMPILER=/path/nvcc_wrapper`. You should already have > used `nvcc_wrapper` to compiler Kokkos. > > Best, > > Bruno > > On Monday, February 5, 2024 at 2:40:37 AM UTC-5 sljoh...@gmail.com > wrote: > >> Hey, >> >> I am trying to get deal.ii to compile with p4est and cuda. Due to >> cuda it also needs MPI and Kokkos from me. I can't even make the make >> file >> yet. I tried to find any similar problems in the mailing
Re: [deal.II] Re: Can't configure with cmake
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 > 193 | template< typename Pred > > | ^ > > | - >- > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: > warning: unnecessary parentheses in declaration of ‘assert_not_arg’ > [-Wparentheses] > 198 | template< typename Pred > > | ^ > > > /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: > note: remove parentheses > 198 | template< typename Pred > > | ^ > > > | - > >- > [ 6%] Building CXX object > bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/mapped_file.cpp.o > > Thanks again for your patience and help, > Sean > > On Monday, February 5, 2024 at 7:07:01 PM UTC-7 bruno.t...@gmail.com > wrote: > >> Sean, >> >> It's possible that you don't have enough RAM and that you are swapping >> memory which is extremely slow. Try to reinstall using fewer processors. >> >> Best, >> >> Bruno >> >> Le lun. 5 févr. 2024 à 19:01, Sean Johnson a écrit : >> >>> Thanks Bruno, >>> >>> This was definitely it. >>> >>> So I have now gotten to running make --jobs=4 install but it has frozen >>> at 82% >>> I have been sitting on it for about 6 to 7 hours with no change at all. >>> The last line is: >>> [ 82%] Built target object_non_matching_debug >>> >>> and attached are the summary.log and detailed.log >>> >>> I will keep it running still just incase but from previous installations >>> of dealii this has never happened. >>> >>> Thanks, >>> Sean >>> >>> On Monday, February 5, 2024 at 8:32:28 AM UTC-7 bruno.t...@gmail.com >>> wrote: >>> Sean, It looks like you are using the wrong compiler. If you want to use CUDA, you should use nvcc_wrapper as your C++ compiler. You want something like `-DCMAKE_CXX_COMPILER=/path/nvcc_wrapper`. You should already have used `nvcc_wrapper` to compiler Kokkos. Best, Bruno On Monday, February 5, 2024 at 2:40:37 AM UTC-5 sljoh...@gmail.com wrote: > Hey, > > I am trying to get deal.ii to compile with p4est and cuda. Due to cuda > it also needs MPI and Kokkos from me. I can't even make the make file yet. > I tried to find any similar problems in the mailing list and was unable > to. > > I am running Ubuntu 22.04 > > The Error at the end reads: > [ 50%] Building CXX object > CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o > /usr/bin/c++ -fopenmp-simd -O0 -ggdb -Wa,--compress-debug-sections > -extended-lambda > -Wext-lambda-captures-this -arch=sm_89 -DKOKKOS_DEPENDENCE > -Wno-non-template-friend -o > CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o -c > /home/sean/dealii-9.5.2/cmake/macros/check_compiler_setup/dummy.cpp > c++: error: unrecognized command-line option > -Wext-lambda-captures-this > c++: error: unrecognized command-line option -arch=sm_89 > gmake[2]: *** [CMakeFiles/CheckCompilerSetupExec.dir/build.make:78: > CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o] Error 1 > gmake[2]: Leaving directory > > > '/home/sean/dealii-9.5.2/build/check_compiler_setup/DEAL_II_HAVE_USABLE_FLAGS_DEBUG' > gmake[1]: *** [CMakeFiles/Makefile2:86: > CMakeFiles/CheckCompilerSetupExec.dir/all] Error 2 > gmake[1]: Leaving directory > >
Re: [deal.II] Re: Can't configure with cmake
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 193 | template< typename Pred > | ^ | - - /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 198 | template< typename Pred > | ^ /home/sean/dealii-9.5.2/bundled/boost-1.70.0/libs/iostreams/src/../../../include/boost/mpl/assert.hpp:198:42: note: remove parentheses 198 | template< typename Pred > | ^ | - - [ 6%] Building CXX object bundled/boost-1.70.0/libs/iostreams/src/CMakeFiles/bundled_boost_iostreams_debug.dir/mapped_file.cpp.o Thanks again for your patience and help, Sean On Monday, February 5, 2024 at 7:07:01 PM UTC-7 bruno.t...@gmail.com wrote: > Sean, > > It's possible that you don't have enough RAM and that you are swapping > memory which is extremely slow. Try to reinstall using fewer processors. > > Best, > > Bruno > > Le lun. 5 févr. 2024 à 19:01, Sean Johnson a écrit : > >> Thanks Bruno, >> >> This was definitely it. >> >> So I have now gotten to running make --jobs=4 install but it has frozen >> at 82% >> I have been sitting on it for about 6 to 7 hours with no change at all. >> The last line is: >> [ 82%] Built target object_non_matching_debug >> >> and attached are the summary.log and detailed.log >> >> I will keep it running still just incase but from previous installations >> of dealii this has never happened. >> >> Thanks, >> Sean >> >> On Monday, February 5, 2024 at 8:32:28 AM UTC-7 bruno.t...@gmail.com >> wrote: >> >>> Sean, >>> >>> It looks like you are using the wrong compiler. If you want to use CUDA, >>> you should use nvcc_wrapper as your C++ compiler. You want something like >>> `-DCMAKE_CXX_COMPILER=/path/nvcc_wrapper`. You should already have used >>> `nvcc_wrapper` to compiler Kokkos. >>> >>> Best, >>> >>> Bruno >>> >>> On Monday, February 5, 2024 at 2:40:37 AM UTC-5 sljoh...@gmail.com >>> wrote: >>> Hey, I am trying to get deal.ii to compile with p4est and cuda. Due to cuda it also needs MPI and Kokkos from me. I can't even make the make file yet. I tried to find any similar problems in the mailing list and was unable to. I am running Ubuntu 22.04 The Error at the end reads: [ 50%] Building CXX object CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o /usr/bin/c++ -fopenmp-simd -O0 -ggdb -Wa,--compress-debug-sections -extended-lambda -Wext-lambda-captures-this -arch=sm_89 -DKOKKOS_DEPENDENCE -Wno-non-template-friend -o CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o -c /home/sean/dealii-9.5.2/cmake/macros/check_compiler_setup/dummy.cpp c++: error: unrecognized command-line option -Wext-lambda-captures-this c++: error: unrecognized command-line option -arch=sm_89 gmake[2]: *** [CMakeFiles/CheckCompilerSetupExec.dir/build.make:78: CMakeFiles/CheckCompilerSetupExec.dir/dummy.cpp.o] Error 1 gmake[2]: Leaving directory '/home/sean/dealii-9.5.2/build/check_compiler_setup/DEAL_II_HAVE_USABLE_FLAGS_DEBUG' gmake[1]: *** [CMakeFiles/Makefile2:86: CMakeFiles/CheckCompilerSetupExec.dir/all] Error 2 gmake[1]: Leaving directory '/home/sean/dealii-9.5.2/build/check_compiler_setup/DEAL_II_HAVE_USABLE_FLAGS_DEBUG'
