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<double>,
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<double>,
dealii::DoFHandler<2, 2>
>::prepare_for_coarsening_and_refinement(dealii::Vector<double> const&)'
step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x206):
undefined reference to `dealii::SolutionTransfer<2, dealii::Vector<double>,
dealii::DoFHandler<2, 2> >::interpolate(dealii::Vector<double> const&,
dealii::Vector<double>&) const'
step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x273):
undefined reference to `dealii::SolutionTransfer<2, dealii::Vector<double>,
dealii::DoFHandler<2, 2> >::~SolutionTransfer()'
step-15.cc:(.text._ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv[_ZN6Step1521MinimalSurfaceProblemILi2EE11refine_meshEv]+0x2d7):
undefined reference to `dealii::SolutionTransfer<2, dealii::Vector<double>,
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
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###
#
# 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_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 =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii/bundled/boost-1.62.0/include
# BOOST_LIBRARIES = rt
# ( 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_DIR = /gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build
# LAPACK_WITH_64BIT_BLAS_INDICES = OFF
# LAPACK_LINKER_FLAGS =
# LAPACK_LIBRARIES =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/liblapack.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/libblas.a;gfortran;quadmath;m;c
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 3.1
# OMPI_VERSION = 3.0.0
# MPI_C_COMPILER =
/gpfs/u/software/amd64-rhel6/mpi/openmpi/3.0.0_1/gcc-7.2.0_1/bin/mpicc
# MPI_CXX_COMPILER =
/gpfs/u/software/amd64-rhel6/mpi/openmpi/3.0.0_1/gcc-7.2.0_1/bin/mpicxx
# MPI_Fortran_COMPILER =
/gpfs/u/software/amd64-rhel6/mpi/openmpi/3.0.0_1/gcc-7.2.0_1/bin/mpif90
# MPI_CXX_FLAGS =
# MPI_LINKER_FLAGS = -Wl,-rpath
-Wl,/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib
-Wl,--enable-new-dtags
# MPI_INCLUDE_DIRS =
/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/include
# MPI_USER_INCLUDE_DIRS =
/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/include
# MPI_LIBRARIES =
/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_usempif08.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_usempi_ignore_tkr.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_mpifh.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi.so
# DEAL_II_WITH_MUPARSER set up with bundled packages
# MUPARSER_BUNDLED_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii/bundled/muparser_v2_2_4//include
# ( DEAL_II_WITH_NANOFLANN = OFF )
# DEAL_II_WITH_NETCDF set up with external dependencies
# NETCDF_INCLUDE_DIRS = /usr/include
# NETCDF_LIBRARIES =
/usr/lib64/libnetcdf_c++.so;/usr/lib64/libnetcdf.so
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# DEAL_II_WITH_P4EST set up with external dependencies
# P4EST_VERSION = 1.1
# P4EST_DIR = /gpfs/u/home/CFSI/CFSIhngj/barn-shared/p4est-1.1/local
# P4EST_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/p4est-1.1/local/include
# P4EST_USER_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/p4est-1.1/local/include
# P4EST_LIBRARIES =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/p4est-1.1/local/lib/libp4est.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/p4est-1.1/local/lib/libsc.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/liblapack.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/libblas.a;gfortran;quadmath;m;c;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi.so
# DEAL_II_WITH_PETSC set up with external dependencies
# PETSC_VERSION = 3.8.2.0
# PETSC_DIR = /gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2
# PETSC_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2/include;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2/arch-linux2-c-opt/include;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/include
# PETSC_USER_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2/include;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2/arch-linux2-c-opt/include;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/include
# PETSC_LIBRARIES =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/petsc-3.8.2/arch-linux2-c-opt/lib/libpetsc.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libcmumps.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libdmumps.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libsmumps.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libzmumps.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libmumps_common.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/MUMPS_5.1.2/lib/libpord.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/scalapack-2.0.2/libscalapack.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/liblapack.a;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/lapack-build/lib/libblas.a;/usr/lib64/libX11.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_usempif08.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_usempi_ignore_tkr.so;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi_mpifh.so;gfortran;quadmath;m;/gpfs/u/software/amd64-rhel6/mpi/openmpi-3.0.0-gcc-7.2.0/1/lib/libmpi.so;pthread;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_LINKER_FLAGS = -pthread
# THREADS_BUNDLED_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii/bundled/tbb41_20130401oss/include
# THREADS_LIBRARIES = dl
# ( DEAL_II_WITH_TRILINOS = OFF )
# DEAL_II_WITH_UMFPACK set up with bundled packages
# UMFPACK_BUNDLED_INCLUDE_DIRS =
/gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii/bundled/umfpack/UMFPACK/Include;/gpfs/u/home/CFSI/CFSIhngj/barn-shared/dealii/bundled/umfpack/AMD/Include
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.3
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib64/libz.so
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
###
###
#
# 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++
#
# 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
# ( 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
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# DEAL_II_WITH_MUPARSER set up with bundled packages
# ( DEAL_II_WITH_NANOFLANN = OFF )
# DEAL_II_WITH_NETCDF set up with external dependencies
# ( DEAL_II_WITH_OPENCASCADE = OFF )
# DEAL_II_WITH_P4EST set up with external dependencies
# DEAL_II_WITH_PETSC set up with external dependencies
# ( DEAL_II_WITH_SCALAPACK = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# ( DEAL_II_WITH_SUNDIALS = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# ( DEAL_II_WITH_TRILINOS = OFF )
# DEAL_II_WITH_UMFPACK set up with bundled packages
# DEAL_II_WITH_ZLIB set up with external dependencies
#
# Component configuration:
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# ( DEAL_II_COMPONENT_PACKAGE = OFF )
# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
# Detailed information (compiler flags, feature configuration) can be found in
detailed.log
#
# Run $ make info to print a help message with a list of top level targets
#
###
