Re: [deal.II] Building issue: undefined reference to SolutionTransfer
Hi Timo Thanks for your help! I disabled DEAL_II_WITH_THREADS and now it runs fine! Just out of curiosity, what do I lose with it disabled? What additional library do I need to build if I want to have it? (Internet is banned on the cluster I use, everything has to be built from source.) Best Jie On Tue, Apr 24, 2018 at 12:01 PM Timo Heister wrote: > can you post your detailed.log? > > If a tutorial like step-1 crashes, please > 1. check the dynamic libraries by doing "ldd step-1" and post the > output. Maybe you have conflicting libraries you are linking. > 2. run under gdb: "gdb step-1" then "run" then "backtrace" to see > where you crash. > > > On Mon, Apr 23, 2018 at 8:49 PM, Jie Cheng wrote: > > Hi Wolfgang > > > > Sorry for not updating this issue for so long. I've been developing on my > > local machine until recently I started to test my code on cluster again. > > This issue has not been resolved, linking to SolutionTransfer will fail > if I > > build static library (solution_transfer is compiled). But now I tried to > > build shared libraries instead. I did a minimum build of dealii (using > all > > of the default building options), configuration, compiling and linking > went > > smoothly without any error. But I could not run any tutorial, all of them > > gave me segmentation fault immediately (no useful info, only segment > fault). > > I was not even able to run a "hello world" problem if I link it with > dealii. > > Building in debug mode did not help. I completely have no clue how this > > could happen. Can you please point me a direction to understand the > problem? > > > > The source code I used is up-to-date (SHA: 3d0c7ab699dace76); > > System is Scientific Linux 6.9 (Carbon) > > gcc version is 7.3.0 > > > > I've attached my CMakeCache and summary.log. > > > > Thank you! > > Jie > > > > > > -- > > The deal.II project is located at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=POnss3ormS1XXiqg54YqF_mukzlGpflHaAItgpvWE3Y&e= > > For mailing list/forum options, see > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=GYouR_JzJGhPjFcghkqeOFIAY5ZDJ9D4zi4F_JqIRlo&e= > > --- > > You received this message because you are subscribed to the Google Groups > > "deal.II User Group" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to dealii+unsubscr...@googlegroups.com. > > For more options, visit > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=rxGsQICkV6INJ7F-q3Zq9rk0AX9DimjYhTfWbSoLGIg&e= > . > > > > -- > Timo Heister > http://www.math.clemson.edu/~heister/ > > -- > The deal.II project is located at http://www.dealii.org/ > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > --- > You received this message because you are subscribed to a topic in the > Google Groups "deal.II User Group" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/dealii/Ea-kSSnwLYg/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > dealii+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Building issue: undefined reference to SolutionTransfer
can you post your detailed.log? If a tutorial like step-1 crashes, please 1. check the dynamic libraries by doing "ldd step-1" and post the output. Maybe you have conflicting libraries you are linking. 2. run under gdb: "gdb step-1" then "run" then "backtrace" to see where you crash. On Mon, Apr 23, 2018 at 8:49 PM, Jie Cheng wrote: > Hi Wolfgang > > Sorry for not updating this issue for so long. I've been developing on my > local machine until recently I started to test my code on cluster again. > This issue has not been resolved, linking to SolutionTransfer will fail if I > build static library (solution_transfer is compiled). But now I tried to > build shared libraries instead. I did a minimum build of dealii (using all > of the default building options), configuration, compiling and linking went > smoothly without any error. But I could not run any tutorial, all of them > gave me segmentation fault immediately (no useful info, only segment fault). > I was not even able to run a "hello world" problem if I link it with dealii. > Building in debug mode did not help. I completely have no clue how this > could happen. Can you please point me a direction to understand the problem? > > The source code I used is up-to-date (SHA: 3d0c7ab699dace76); > System is Scientific Linux 6.9 (Carbon) > gcc version is 7.3.0 > > I've attached my CMakeCache and summary.log. > > Thank you! > Jie > > > -- > The deal.II project is located at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=POnss3ormS1XXiqg54YqF_mukzlGpflHaAItgpvWE3Y&e= > For mailing list/forum options, see > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=GYouR_JzJGhPjFcghkqeOFIAY5ZDJ9D4zi4F_JqIRlo&e= > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > For more options, visit > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=TjzN-LMQUtQJoM1bxgcw94aP7tCtQ2r10bl2qQSpDPw&s=rxGsQICkV6INJ7F-q3Zq9rk0AX9DimjYhTfWbSoLGIg&e=. -- Timo Heister http://www.math.clemson.edu/~heister/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Building issue: undefined reference to SolutionTransfer
Hi Wolfgang Sorry for not updating this issue for so long. I've been developing on my local machine until recently I started to test my code on cluster again. This issue has not been resolved, linking to SolutionTransfer will fail if I build static library (solution_transfer is compiled). But now I tried to build shared libraries instead. I did a minimum build of dealii (using all of the default building options), configuration, compiling and linking went smoothly without any error. But I could not run any tutorial, all of them gave me segmentation fault immediately (no useful info, only segment fault). I was not even able to run a "hello world" problem if I link it with dealii. Building in debug mode did not help. I completely have no clue how this could happen. Can you please point me a direction to understand the problem? The source code I used is up-to-date (SHA: 3d0c7ab699dace76); System is Scientific Linux 6.9 (Carbon) gcc version is 7.3.0 I've attached my CMakeCache and summary.log. Thank you! Jie -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. # This is the CMakeCache file. # For build in directory: /gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii-minimum # It was generated by CMake: /usr/bin/cmake # You can edit this file to change values found and used by cmake. # If you do not want to change any of the values, simply exit the editor. # If you do want to change a value, simply edit, save, and exit the editor. # The syntax for the file is as follows: # KEY:TYPE=VALUE # KEY is the name of a variable in the cache. # TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. # VALUE is the current value for the KEY. # EXTERNAL cache entries //An optional hint to an ADOL-C installation ADOLC_DIR:PATH= //An optional hint to a Assimp installation ASSIMP_DIR:PATH= //Path to a library. BLAS_Accelerate_LIBRARY:FILEPATH=BLAS_Accelerate_LIBRARY-NOTFOUND //An optional hint to a BLAS installation BLAS_DIR:PATH= //Path to a library. BLAS_acml_LIBRARY:FILEPATH=BLAS_acml_LIBRARY-NOTFOUND //Path to a library. BLAS_acml_mp_LIBRARY:FILEPATH=BLAS_acml_mp_LIBRARY-NOTFOUND //Path to a library. BLAS_blas_LIBRARY:FILEPATH=BLAS_blas_LIBRARY-NOTFOUND //Path to a library. BLAS_complib.sgimath_LIBRARY:FILEPATH=BLAS_complib.sgimath_LIBRARY-NOTFOUND //Path to a library. BLAS_cxml_LIBRARY:FILEPATH=BLAS_cxml_LIBRARY-NOTFOUND //Path to a library. BLAS_dxml_LIBRARY:FILEPATH=BLAS_dxml_LIBRARY-NOTFOUND //Path to a library. BLAS_essl_LIBRARY:FILEPATH=BLAS_essl_LIBRARY-NOTFOUND //Path to a library. BLAS_f77blas_LIBRARY:FILEPATH=BLAS_f77blas_LIBRARY-NOTFOUND //Path to a library. BLAS_goto2_LIBRARY:FILEPATH=BLAS_goto2_LIBRARY-NOTFOUND //Path to a library. BLAS_mkl_LIBRARY:FILEPATH=BLAS_mkl_LIBRARY-NOTFOUND //Path to a library. BLAS_mkl_em64t_LIBRARY:FILEPATH=BLAS_mkl_em64t_LIBRARY-NOTFOUND //Path to a library. BLAS_mkl_ia32_LIBRARY:FILEPATH=BLAS_mkl_ia32_LIBRARY-NOTFOUND //Path to a library. BLAS_mkl_intel_LIBRARY:FILEPATH=BLAS_mkl_intel_LIBRARY-NOTFOUND //Path to a library. BLAS_mkl_intel_lp64_LIBRARY:FILEPATH=BLAS_mkl_intel_lp64_LIBRARY-NOTFOUND //Path to a library. BLAS_scsl_LIBRARY:FILEPATH=BLAS_scsl_LIBRARY-NOTFOUND //Path to a library. BLAS_sgemm_LIBRARY:FILEPATH=BLAS_sgemm_LIBRARY-NOTFOUND //Path to a library. BLAS_sunperf_LIBRARY:FILEPATH=BLAS_sunperf_LIBRARY-NOTFOUND //Path to a library. BLAS_vecLib_LIBRARY:FILEPATH=BLAS_vecLib_LIBRARY-NOTFOUND //An optional hint to a BOOST installation BOOST_DIR:PATH= //Build a shared library BUILD_SHARED_LIBS:BOOL=1 //Path to a file. Boost_INCLUDE_DIR:PATH=/usr/include //Choose the type of build, options are: Debug, Release and DebugRelease. CMAKE_BUILD_TYPE:STRING=DebugRelease //Enable/Disable color output during build. CMAKE_COLOR_MAKEFILE:BOOL=ON //CXX compiler. CMAKE_CXX_COMPILER:FILEPATH=/gpfs/u/software/amd64-rhel6/compilers/gcc/7.3.0_1/bin/c++ //C compiler. CMAKE_C_COMPILER:FILEPATH=/gpfs/u/software/amd64-rhel6/compilers/gcc/7.3.0_1/bin/gcc //Flags used by the linker. CMAKE_EXE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Enable/Disable output of compile commands during generation. CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF //Fortran compiler. CM
Re: [deal.II] Building issue: undefined reference to SolutionTransfer
I am trying to build deal.II on a cluster with x86_64 architecture, Scientific Linux 6.9 (Carbon), gcc 7.2.0 and openmpi 3.0.0. (Yes, I am building dealii everywhere, as our entire research group just began to use dealii.) This time, I got linking error related to SolutionTransfer as follows: Linking CXX executable ../bin/step-15.release CMakeFiles/step-15.release.dir/step-15/step-15.cc.o: In function `Step15::MinimalSurfaceProblem<2>::refine_mesh()': step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x1c0): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, This is strange. SolutionTransfer is used in a number of tutorial programs, for example step-26. Can you link that file? The source code is the latest up to Jan 27. Everything else seems to be fine: I am able to run step-18, but not step-15 because the latter uses SolutionTransfer. The error message does not provide any information, I don't know where to start debugging. I've attached my building logs. Any advice is appreciated! The function should have been produced from the file source/numeric/solution_transfer.cc. What happens if you do touch /path/to/sources-of-dealii/source/numerics/solution_transfer.cc cd /path/to/your/build/directory make -j1 install I can only imagine that the build of this file failed for some reason (out of memory?) and the commands above just force a re-build. P.S. dealii was built with: cmake ../dealii -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Release -DDEAL_II_WITH_CXX14=ON -DDEAL_II_WITH_LAPACK=ON -DLAPACK_DIR=../lapack-build -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=../p4est-1.1/local -DDEAL_II_WITH_PETSC=ON -DPETSC_ARCH=arch-linux2-c-opt -DPETSC_DIR=../petsc-3.8.2 You are building with static (i.e., without shared) libraries. This is uncommon these days? What are you reasons for doing so? It will take forever for you to link any application. It will also take enormous amounts of disk space if you build multiple applications. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Building issue: undefined reference to SolutionTransfer
Hi everyone I am trying to build deal.II on a cluster with x86_64 architecture, Scientific Linux 6.9 (Carbon), gcc 7.2.0 and openmpi 3.0.0. (Yes, I am building dealii everywhere, as our entire research group just began to use dealii.) This time, I got linking error related to SolutionTransfer as follows: Linking CXX executable ../bin/step-15.release CMakeFiles/step-15.release.dir/step-15/step-15.cc.o: In function `Step15::MinimalSurfaceProblem<2>::refine_mesh()': step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x1c0): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, dealii::DoFHandler<2, 2> >::SolutionTransfer(dealii::DoFHandler<2, 2> const&)' step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x1cf): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, dealii::DoFHandler<2, 2> >::prepare_for_coarsening_and_refinement(dealii::Vector const&)' step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x206): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, dealii::DoFHandler<2, 2> >::interpolate(dealii::Vector const&, dealii::Vector&) const' step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x273): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()' step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x2d7): undefined reference to `dealii::SolutionTransfer<2, dealii::Vector, dealii::DoFHandler<2, 2> >::~SolutionTransfer()' collect2: error: ld returned 1 exit status make[2]: *** [bin/step-15.release] Error 1 make[1]: *** [examples/CMakeFiles/step-15.release.dir/all] Error 2 make: *** [all] Error 2 The source code is the latest up to Jan 27. Everything else seems to be fine: I am able to run step-18, but not step-15 because the latter uses SolutionTransfer. The error message does not provide any information, I don't know where to start debugging. I've attached my building logs. Any advice is appreciated! P.S. dealii was built with: cmake ../dealii -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Release -DDEAL_II_WITH_CXX14=ON -DDEAL_II_WITH_LAPACK=ON -DLAPACK_DIR=../lapack-build -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=../p4est-1.1/local -DDEAL_II_WITH_PETSC=ON -DPETSC_ARCH=arch-linux2-c-opt -DPETSC_DIR=../petsc-3.8.2 P.P.S. lapack, p4est, PETSc (including MUMPS and scalapack) are all built from source. Thank you Jie -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. ### # # deal.II configuration: #CMAKE_BUILD_TYPE: Release #BUILD_SHARED_LIBS: OFF #CMAKE_INSTALL_PREFIX: /usr/local #CMAKE_SOURCE_DIR: /gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii #(version 9.0.0-pre, shortrev fdc9fe0) #CMAKE_BINARY_DIR: /gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii-build #CMAKE_CXX_COMPILER: GNU 7.2.0 on platform Linux x86_64 # /gpfs/u/software/amd64-rhel6/compilers/gcc/7.2.0_1/bin/c++ #CMAKE_C_COMPILER: /gpfs/u/software/amd64-rhel6/compilers/gcc/7.2.0_1/bin/gcc #CMAKE_Fortran_COMPILER: /gpfs/u/software/amd64-rhel6/compilers/gcc/7.2.0_1/bin/gfortran #CMAKE_GENERATOR:Unix Makefiles # # Base configuration (prior to feature configuration): #DEAL_II_CXX_FLAGS:-pedantic -fPIC -Wall -Wextra -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -fopenmp-simd -std=c++17 #DEAL_II_CXX_FLAGS_RELEASE:-O2 -funroll-loops -funroll-all-loops -fstrict-aliasing -Wno-unused-local-typedefs #DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic #DEAL_II_LINKER_FLAGS_RELEASE: #DEAL_II_DEFINITIONS: #DEAL_II_DEFINITIONS_RELEASE: #DEAL_II_USER_DEFINITIONS: #DEAL_II_USER_DEFINITIONS_REL: #DEAL_II_INCLUDE_DIRS #DEAL_II_USER_INCLUDE_DIRS: #DEAL_II_BUNDLED_INCLUDE_DIRS: #DEAL_II_LIBRARIES:m #DEAL_II_LIBRARIES_RELEASE: # # Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW
