Hi all
I found that DoFRenumbering with distributed dof_handler does not work on
my mac (Mac OS X 10.13.2). My dealii is built with PETSc and Step-40 runs
fine. But once I added DoFRenumbering::Cuthill_McKee(dof_handler)
after dof_handler.distribute_dofs (fe), it gave me runtime error:
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 65482 RUNNING AT zhangl-macpro12
= EXIT CODE: 6
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Abort trap: 6 (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
Of course I included the necessary header file. I tried both Debug and
Release modes, same issue. My cmake command was
cmake /usr/local/dealii -GNinja -DBUILD_SHARED_LIBS=ON
-DCMAKE_BUILD_TYPE=Debug -DDEAL_II_WITH_CXX14=ON -DDEAL_II_WITH_LAPACK=ON
-DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON
-DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DPETSC_ARCH=arch-darwin-c-debug
-DPETSC_DIR=/usr/local/petsc -DDEAL_II_WITH_P4EST=ON
-DP4EST_DIR=/usr/local/p4est-1.1/localI
and I have attached the detailed.log from my Debug build.
Thanks in advance.
Jie
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###
#
# deal.II configuration:
# CMAKE_BUILD_TYPE: Debug
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /usr/local
# CMAKE_SOURCE_DIR: /usr/local/dealii
# (version 9.0.0-pre, shortrev 41d792cf11)
# CMAKE_BINARY_DIR: /Users/jiecheng/tmp-build
# CMAKE_CXX_COMPILER: AppleClang 9.0.0.9000039 on platform Darwin
x86_64
# /Library/Developer/CommandLineTools/usr/bin/c++
# CMAKE_C_COMPILER: /Library/Developer/CommandLineTools/usr/bin/cc
# CMAKE_GENERATOR: Ninja
#
# 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-deprecated-declarations -Qunused-arguments
-Wno-unsupported-friend -Wno-unused-parameter -Wno-undefined-var-template
-openmp-simd -std=c++1z -std=c++1z -ftemplate-depth=1024
# DEAL_II_CXX_FLAGS_DEBUG: -Og -ggdb -Wa,--compress-debug-sections
# DEAL_II_LINKER_FLAGS:
# DEAL_II_LINKER_FLAGS_DEBUG: -ggdb
# DEAL_II_DEFINITIONS:
# DEAL_II_DEFINITIONS_DEBUG: DEBUG
# DEAL_II_USER_DEFINITIONS:
# DEAL_II_USER_DEFINITIONS_DEB: DEBUG
# DEAL_II_INCLUDE_DIRS
# DEAL_II_USER_INCLUDE_DIRS:
# DEAL_II_BUNDLED_INCLUDE_DIRS:
# DEAL_II_LIBRARIES: m
# DEAL_II_LIBRARIES_DEBUG:
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION
= ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ADOLC = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# ( DEAL_II_WITH_ASSIMP = OFF )
# DEAL_II_WITH_BOOST set up with bundled packages
# BOOST_CXX_FLAGS = -Wno-unused-local-typedefs
# BOOST_BUNDLED_INCLUDE_DIRS =
/usr/local/dealii/bundled/boost-1.62.0/include
# ( DEAL_II_WITH_CUDA = OFF )
# DEAL_II_WITH_CXX14 = ON
# DEAL_II_WITH_CXX17 = ON
# ( DEAL_II_WITH_GMSH = OFF )
# ( DEAL_II_WITH_GSL = OFF )
# ( DEAL_II_WITH_HDF5 = OFF )
# DEAL_II_WITH_LAPACK set up with external dependencies
# LAPACK_WITH_64BIT_BLAS_INDICES = OFF
# LAPACK_LINKER_FLAGS =
# LAPACK_LIBRARIES =
/System/Library/Frameworks/Accelerate.framework;m;c
# DEAL_II_WITH_METIS set up with external dependencies
# METIS_VERSION = 5.1.0
# METIS_INCLUDE_DIRS = /usr/local/include
# METIS_USER_INCLUDE_DIRS = /usr/local/include
# METIS_LIBRARIES =
/usr/local/lib/libmetis.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libmpi.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libpmpi.dylib
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 3.1
# MPI_C_COMPILER = /usr/local/bin/mpicc
# MPI_CXX_COMPILER = /usr/local/bin/mpicxx
# MPI_CXX_FLAGS =
# MPI_LINKER_FLAGS = -Wl,-flat_namespace -Wl,-commons,use_dylibs
# MPI_INCLUDE_DIRS = /usr/local/Cellar/mpich/3.2.1/include
# MPI_USER_INCLUDE_DIRS = /usr/local/Cellar/mpich/3.2.1/include
# MPI_LIBRARIES =
/usr/local/Cellar/mpich/3.2.1/lib/libmpicxx.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libmpi.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libpmpi.dylib
# DEAL_II_WITH_MUPARSER set up with bundled packages
# MUPARSER_BUNDLED_INCLUDE_DIRS =
/usr/local/dealii/bundled/muparser_v2_2_4//include
# ( DEAL_II_WITH_NANOFLANN = OFF )
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# DEAL_II_WITH_P4EST set up with external dependencies
# P4EST_VERSION = 1.1
# P4EST_DIR = /usr/local/p4est-1.1/local
# P4EST_INCLUDE_DIRS = /usr/local/p4est-1.1/local/include
# P4EST_USER_INCLUDE_DIRS = /usr/local/p4est-1.1/local/include
# P4EST_LIBRARIES =
/usr/local/p4est-1.1/local/lib/libp4est.dylib;/usr/local/p4est-1.1/local/lib/libsc.dylib;/System/Library/Frameworks/Accelerate.framework;m;c;/usr/local/Cellar/mpich/3.2.1/lib/libmpi.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libpmpi.dylib
# DEAL_II_WITH_PETSC set up with external dependencies
# PETSC_VERSION = 3.8.3.0
# PETSC_DIR = /usr/local/petsc
# PETSC_INCLUDE_DIRS =
/usr/local/petsc/include;/usr/local/petsc/arch-darwin-c-debug/include
# PETSC_USER_INCLUDE_DIRS =
/usr/local/petsc/include;/usr/local/petsc/arch-darwin-c-debug/include
# PETSC_LIBRARIES =
/usr/local/petsc/arch-darwin-c-debug/lib/libpetsc.dylib;/usr/local/petsc/arch-darwin-c-debug/lib/libHYPRE.a;/usr/local/petsc/arch-darwin-c-debug/lib/libcmumps.a;/usr/local/petsc/arch-darwin-c-debug/lib/libdmumps.a;/usr/local/petsc/arch-darwin-c-debug/lib/libsmumps.a;/usr/local/petsc/arch-darwin-c-debug/lib/libzmumps.a;/usr/local/petsc/arch-darwin-c-debug/lib/libmumps_common.a;/usr/local/petsc/arch-darwin-c-debug/lib/libpord.a;/usr/local/petsc/arch-darwin-c-debug/lib/libscalapack.a;/usr/lib/liblapack.dylib;/usr/lib/libblas.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libmpifort.dylib;/usr/local/Cellar/gcc/7.2.0/lib/gcc/7/libgcc_ext.10.5.dylib;m;/usr/local/Cellar/mpich/3.2.1/lib/libmpicxx.dylib;/usr/lib/libc++.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libmpi.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libpmpi.dylib;/System/Library/Frameworks/System.framework;dl
# ( DEAL_II_WITH_SCALAPACK = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# ( DEAL_II_WITH_SUNDIALS = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# THREADS_CXX_FLAGS = -Wno-parentheses
# THREADS_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1
# THREADS_USER_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1
# THREADS_BUNDLED_INCLUDE_DIRS =
/usr/local/dealii/bundled/tbb41_20130401oss/include
# ( DEAL_II_WITH_TRILINOS = OFF )
# DEAL_II_WITH_UMFPACK set up with bundled packages
# UMFPACK_BUNDLED_INCLUDE_DIRS =
/usr/local/dealii/bundled/umfpack/UMFPACK/Include;/usr/local/dealii/bundled/umfpack/AMD/Include
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.11
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib/libz.dylib
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
###
