Hi, David, yes, here it is.
On Thursday, January 30, 2020 at 6:02:56 PM UTC+2, David Wells wrote: > > Hi Ihar, > > I'm not sure what went wrong - everything looks right except that > deal.II did not find hypre. > > Could you also send > > /Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h > > to check something else? > > > On Tue, Jan 28, 2020 at 10:14 AM Ihar Suvorau <[email protected] > <javascript:>> wrote: > > > > Hi, David, > > > > okay, please, attaching these files also. > > > > On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote: > >> > >> Hi Ihar, > >> > >> It looks like nothing went wrong with PETsc. Would you please also > >> send a copy of deal.II's detailed.log and, if available, > >> CMakeCache.txt from the build directory? > >> > >> Thanks, > >> David > >> > >> On Mon, Jan 27, 2020 at 5:59 PM Ihar Suvorau <[email protected]> > wrote: > >> > > >> > Sure, attaching a file, please. > >> > > >> > On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote: > >> >> > >> >> Hi Ihar, > >> >> > >> >> This sounds like something has gone wrong inside either PETSc's or > >> >> deal.II's build process. Would you please show us a copy of PETSc's > >> >> configure.log? > >> >> > >> >> Thanks, > >> >> David > >> >> > >> >> On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau <[email protected]> > wrote: > >> >> > > >> >> > Not yet, I have a running version via docker images though. I'll > try the bundle also, thank you, before I was thinking that it shouldn't > support parallel programming, but now I see it is configured with > "DEAL_II_WITH_MPI set up with external dependencies" and > "DEAL_II_WITH_PETSC set up with external dependencies" and has all packages > installed. > >> >> > > >> >> > But I'm still interested in solving the issue with "Your PETSc > installation does not include a copy of the hypre package necessary for > this preconditioner" when I do have the hypre package installed via the > option "--download-hypre=1" while configuring PETSc. > >> >> > > >> >> > On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai > wrote: > >> >> >> > >> >> >> Did you try the pre-compiled deal.II package? > >> >> >> > >> >> >> Both > >> >> >> > >> >> >> dealii-9.1.1-clang-9.0.0.dmg > >> >> >> > >> >> >> and > >> >> >> > >> >> >> dealii-9.1.1-catalina-haswell-ro.dmg.zip > >> >> >> > >> >> >> > >> >> >> from https://github.com/dealii/dealii/releases/tag/v9.1.1 > >> >> >> > >> >> >> should work. > >> >> >> > >> >> >> Luca. > >> >> >> > >> >> >> > On 25 Jan 2020, at 21:29, Ihar Suvorau <[email protected]> > wrote: > >> >> >> > > >> >> >> > > >> >> >> > Software: > >> >> >> > • macOS Catalina 10.15.2 > >> >> >> > • deal.ii 9.1.1 > >> >> >> > • PETSc 3.12 > >> >> >> > Question: > >> >> >> > > >> >> >> > Hey, does somebody know a potential reason for this message > while running a well-compiled step-40 program: > >> >> >> > > >> >> >> > ihar@husky build3 % ./step-40 > >> >> >> > > >> >> >> > > >> >> >> > Running with PETSc on 1 MPI rank(s)... > >> >> >> > > >> >> >> > Cycle 0: > >> >> >> > > >> >> >> > Number of active cells: 1024 > >> >> >> > > >> >> >> > Number of degrees of freedom: 4225 > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > ------------------------------------------------------- > >> >> >> > > >> >> >> > > >> >> >> > An error occurred in line <543> of file > </Users/ihar/lib/dealii-9.1.1/source/lac/petsc_precondition.cc> in function > >> >> >> > > >> >> >> > void > dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const > dealii::PETScWrappers::MatrixBase &, const > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &) > >> >> >> > > >> >> >> > The violated condition was: > >> >> >> > > >> >> >> > false > >> >> >> > > >> >> >> > Additional information: > >> >> >> > > >> >> >> > Your PETSc installation does not include a copy of the hypre > package necessary for this preconditioner. > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > Stacktrace: > >> >> >> > > >> >> >> > ----------- > >> >> >> > > >> >> >> > #0 2 libdeal_II.g.9.1.1.dylib 0x000000011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > + 95: 2 libdeal_II.g.9.1.1.dylib 0x000000011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > > >> >> >> > > >> >> >> > #1 3 step-40 0x000000010643881a > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3 step-40 > 0x000000010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv > >> >> >> > > >> >> >> > #2 4 step-40 0x000000010642e633 > _ZN6Step4014LaplaceProblemILi2EE3runEv + 451: 4 step-40 > 0x000000010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv > >> >> >> > > >> >> >> > #3 5 step-40 0x000000010642e23a > main + 106: 5 step-40 0x000000010642e23a main > >> >> >> > > >> >> >> > #4 6 libdyld.dylib 0x00007fff6350f7fd > start + 1: 6 libdyld.dylib 0x00007fff6350f7fd start > >> >> >> > > >> >> >> > -------------------------------------------------------- > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > [husky:92536] *** Process received signal *** > >> >> >> > > >> >> >> > [husky:92536] Signal: Abort trap: 6 (6) > >> >> >> > > >> >> >> > [husky:92536] Signal code: (0) > >> >> >> > > >> >> >> > [husky:92536] [ 0] 0 libsystem_platform.dylib > 0x00007fff6370842d _sigtramp + 29 > >> >> >> > > >> >> >> > [husky:92536] [ 1] 0 ??? > 0x00007ffee97d8838 0x0 + 140732815738936 > >> >> >> > > >> >> >> > [husky:92536] [ 2] 0 libsystem_c.dylib > 0x00007fff635dda1c abort + 120 > >> >> >> > > >> >> >> > [husky:92536] [ 3] 0 libdeal_II.g.9.1.1.dylib > 0x00000001119ec74d > _ZN6dealii18deal_II_exceptions9internals5abortERKNS_13ExceptionBaseE + 205 > >> >> >> > > >> >> >> > [husky:92536] [ 4] 0 libdeal_II.g.9.1.1.dylib > 0x000000010de0f63f > _ZN6dealii18deal_II_exceptions9internals20issue_error_noreturnINS_18StandardExceptions10ExcMessageEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_ > > + 223 > >> >> >> > > >> >> >> > [husky:92536] [ 5] 0 libdeal_II.g.9.1.1.dylib > 0x000000011188b86f > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE > > + 95 > >> >> >> > > >> >> >> > [husky:92536] [ 6] 0 step-40 > 0x000000010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266 > >> >> >> > > >> >> >> > [husky:92536] [ 7] 0 step-40 > 0x000000010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv + 451 > >> >> >> > > >> >> >> > [husky:92536] [ 8] 0 step-40 > 0x000000010642e23a main + 106 > >> >> >> > > >> >> >> > [husky:92536] [ 9] 0 libdyld.dylib > 0x00007fff6350f7fd start + 1 > >> >> >> > > >> >> >> > [husky:92536] *** End of error message *** > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > The thing is that I've compiled PETSC with the > "--download-hypre=1" option and there is a compiled library with the name > "libHYPRE-2.18.2.dylib" alongside "libpetsc.3.12.3.dylib" and others in the > folder for my architecture "arch-darwin-c-debug". Environment variables > "PETSC_DIR" and "PETSC_ARCH" all point to the correct folder like in the > instruction at https://www.dealii.org/developer/external-libs/petsc.html. > >> >> >> > > >> >> >> > Did I miss something? > >> >> >> > > >> >> >> > I'm trying to install all the packages with "dealii/candi", but > PETSc compilation fails there also, but for a different reason though ( > https://github.com/dealii/candi/issues/133). > >> >> >> > > >> >> >> > -- > >> >> >> > 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 [email protected]. > >> >> >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/dd55f761-c2fe-458f-964f-399addab2122%40googlegroups.com. > > > >> >> >> > >> >> > -- > >> >> > 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 [email protected]. > >> >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/170d62e8-6377-4648-a49b-971b15bc8581%40googlegroups.com. > > > >> > > >> > -- > >> > 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 [email protected]. > >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/c37e134d-35cc-41c1-8dfd-d74ba41311c7%40googlegroups.com. > > > > > > -- > > 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 [email protected] <javascript:>. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/d4707b9f-89bd-4dd0-95d2-6239e508255c%40googlegroups.com. > > > -- 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. 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#if !defined(INCLUDED_PETSCCONF_H) #define INCLUDED_PETSCCONF_H #define IS_COLORING_MAX USHRT_MAX #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_ARCH "arch-darwin-c-debug" #define PETSC_ATTRIBUTEALIGNED(size) __attribute((aligned(size))) #define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated)) #define PETSC_DEPRECATED_FUNCTION(why) __attribute((deprecated)) #define PETSC_DEPRECATED_MACRO(why) #define PETSC_DEPRECATED_TYPEDEF(why) __attribute((deprecated)) #define PETSC_DIR "/Users/ihar/lib/petsc-3.12.3" #define PETSC_DIR_SEPARATOR '/' #define PETSC_FUNCTION_NAME_C __func__ #define PETSC_FUNCTION_NAME_CXX __func__ #define PETSC_HAVE_ATOLL 1 #define PETSC_HAVE_ATTRIBUTEALIGNED 1 #define PETSC_HAVE_BUILTIN_EXPECT 1 #define PETSC_HAVE_CXX 1 #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1 #define PETSC_HAVE_FBLASLAPACK 1 #define PETSC_HAVE_FORTRAN 1 #define PETSC_HAVE_HYPRE 1 #define PETSC_HAVE_METIS 1 #define PETSC_HAVE_MUMPS 1 #define PETSC_HAVE_PARMETIS 1 #define PETSC_HAVE_PTHREAD 1 #define PETSC_HAVE_SCALAPACK 1 #define PETSC_HAVE_SO_REUSEADDR 1 #define PETSC_HAVE_SUPERLU 1 #define PETSC_HAVE_SUPERLU_DIST 1 #define PETSC_HAVE_XMMINTRIN_H 1 #define PETSC_LIB_DIR "/Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/lib" #define PETSC_MPICC_SHOW "clang -I/usr/local/Cellar/open-mpi/4.0.2/include -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/4.0.2/lib -lmpi" #define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA #define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0 #define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1 #define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2 #define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c)) #define PETSC_REPLACE_DIR_SEPARATOR '\\' #define PETSC_RTLD_DEFAULT 1 #define PETSC_SLSUFFIX "dylib" #define PETSC_UINTPTR_T uintptr_t #define PETSC_UNUSED __attribute((unused)) #define PETSC_USE_ISATTY 1 #define PETSC_USE_SINGLE_LIBRARY 1 #define PETSC_USE_SOCKET_VIEWER 1 #define PETSC_CLANGUAGE_CXX 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T size_t #define PETSC_HAVE_C99 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_CXX_DIALECT_CXX14 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_MACHINE_ENDIAN_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_STRUCT_SIGACTION 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_SIGNAL_CAST #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90 1 #define PETSC_USING_F90FREEFORM 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "lldb" #define PETSC_BLASLAPACK_UNDERSCORE 1 #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE OMP #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPI_COMBINER_NAMED 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IALLREDUCE 1 #define PETSC_HAVE_MPI_IBARRIER 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_INT64_T 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_OMPI_MAJOR_VERSION 4 #define PETSC_HAVE_OMPI_MINOR_VERSION 0 #define PETSC_HAVE_OMPI_RELEASE_VERSION 2 #define PETSC_HAVE_SYS_SYSCTL_H 1 #define PETSC_Alignx(a,b) #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_DEBUG 1 #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_MEMALIGN 16 #define PETSC_LEVEL1_DCACHE_LINESIZE 32 #define PETSC_HAVE_CLOSURE 1 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_PYTHON_EXE "/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python" #endif
