Compilation error - small_vector - no matching function for call to small_vector(std::size

JGM

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Jun 20, 2018, 5:50:47 AM6/20/18

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Dear colleagues

I am trying to compile deal.ii.

My objective is to follow tutorials Step-12 and Step-33.

I have configured the build as:

$ cmake -DCMAKE_INSTALL_PREFIX=/home/jgaricano/bin/DEAL.II /home/jgaricano/Downloads/dealii-9.0.0 \

-DTRILINOS_DIR=/home/jgaricano/bin/TRILINOS \

-DDEAL_II_WITH_MPI=ON \

-DDEAL_II_ALLOW_AUTODETECTION=ON

The configuration reports

BOOST_VERSION: 1.59.0

When issuing the command make, compilation stops when dealing with manifold_lib.

The error message is (see an excerpt below) is related to small_vector from boost.

Could you please help with this compilation error?

Thanks

Here the erro message:

[ 45%] Building CXX object source/grid/CMakeFiles/obj_grid_release.dir/manifold_lib.cc.o

/home/jgaricano/Downloads/dealii-9.0.0/source/grid/manifold_lib.cc: In instantiation of ‘void dealii::SphericalManifold<dim, spacedim>::get_new_points(const dealii::ArrayView<const dealii::Point<spacedim> >&, const dealii::ArrayView<const double>&, dealii::ArrayView<dealii::Point<spacedim> >) const [with int dim = 1; int spacedim = 1]’:

/home/jgaricano/bin/dealii-9.0.0/build/source/grid/manifold_lib.inst:12:17: required from here

/home/jgaricano/Downloads/dealii-9.0.0/source/grid/manifold_lib.cc:559:114: error: no matching function for call to ‘boost::container::small_vector<dealii::Tensor<1, 1>, 100ul, boost::container::new_allocator<dealii::Tensor<1, 1> > >::small_vector(std::size_t, dealii::Point<1, double>)’

boost::container::small_vector<Tensor<1, spacedim>, 100> directions(surrounding_points.size(),Point<spacedim>());

^

/home/jgaricano/Downloads/dealii-9.0.0/source/grid/manifold_lib.cc:559:114: note: candidates are:

In file included from /home/jgaricano/Downloads/dealii-9.0.0/include/deal.II/grid/manifold_lib.h:25:0,

from /home/jgaricano/Downloads/dealii-9.0.0/source/grid/manifold_lib.cc:22:

/usr/local/include/boost/container/small_vector.hpp:515:4: note: boost::container::small_vector<T, N, Allocator>::small_vector(std::initializer_list<typename boost::container::small_vector_base<T, Allocator>::value_type>, const allocator_type&) [with T = dealii::Tensor<1, 1>; long unsigned int N = 100ul; Allocator = boost::container::new_allocator<dealii::Tensor<1, 1> >; typename boost::container::small_vector_base<T, Allocator>::value_type = dealii::Tensor<1, 1>; boost::container::small_vector<T, N, Allocator>::allocator_type = boost::container::small_vector_allocator<boost::container::new_allocator<dealii::Tensor<1, 1> > >]

small_vector(std::initializer_list<value_type> il, const allocator_type& a = allocator_type())

^

/usr/local/include/boost/container/small_vector.hpp:515:4: note: no known conversion for argument 1 from ‘std::size_t {aka long unsigned int}’ to ‘std::initializer_list<dealii::Tensor<1, 1> >’

/usr/local/include/boost/container/small_vector.hpp:510:4: note: boost::container::small_vector<T, N, Allocator>::small_vector(boost::container::small_vector<T, N, Allocator>&&, const allocator_type&) [with T = dealii::Tensor<1, 1>; long unsigned int N = 100ul; Allocator = boost::container::new_allocator<dealii::Tensor<1, 1> >; boost::container::small_vector<T, N, Allocator>::allocator_type = boost::container::small_vector_allocator<boost::container::new_allocator<dealii::Tensor<1, 1> > >]

small_vector(BOOST_RV_REF(small_vector) other, const allocator_type &a)

^

/usr/local/include/boost/container/small_vector.hpp:510:4: note: no known conversion for argument 1 from ‘std::size_t {aka long unsigned int}’ to ‘boost::container::small_vector<dealii::Tensor<1, 1>, 100ul, boost::container::new_allocator<dealii::Tensor<1, 1> > >&&’

/usr/local/include/boost/container/small_vector.hpp:506:4: note: boost::container::small_vector<T, N, Allocator>::small_vector(boost::container::small_vector<T, N, Allocator>&&) [with T = dealii::Tensor<1, 1>; long unsigned int N = 100ul; Allocator = boost::container::new_allocator<dealii::Tensor<1, 1> >]

small_vector(BOOST_RV_REF(small_vector) other)

^

/usr/local/include/boost/container/small_vector.hpp:506:4: note: candidate expects 1 argument, 2 provided

/usr/local/include/boost/container/small_vector.hpp:502:4: note: boost::container::small_vector<T, N, Allocator>::small_vector(const boost::container::small_vector<T, N, Allocator>&, const allocator_type&) [with T = dealii::Tensor<1, 1>; long unsigned int N = 100ul; Allocator = boost::container::new_allocator<dealii::Tensor<1, 1> >; boost::container::small_vector<T, N, Allocator>::allocator_type = boost::container::small_vector_allocator<boost::container::new_allocator<dealii::Tensor<1, 1> > >]

small_vector(const small_vector &other, const allocator_type &a)

(not all shown)

...

Bruno Turcksin

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Jun 20, 2018, 7:59:43 AM6/20/18

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Hi,

Can you post the detailed.log file.

Best,

Bruno

JGM

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Jun 20, 2018, 8:33:37 AM6/20/18

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Dear Bruno,

These are the contents of file detailed.log:

###

#

# deal.II configuration:

# CMAKE_BUILD_TYPE: DebugRelease

# BUILD_SHARED_LIBS: ON

# CMAKE_INSTALL_PREFIX: /home/jgaricano/bin/DEAL.II

# CMAKE_SOURCE_DIR: /home/jgaricano/Downloads/dealii-9.0.0

# (version 9.0.0)

# CMAKE_BINARY_DIR: /home/jgaricano/bin/dealii-9.0.0/build

# CMAKE_CXX_COMPILER: GNU 4.9.2 on platform Linux x86_64

# /usr/bin/c++

# CMAKE_C_COMPILER: /usr/bin/cc

# CMAKE_Fortran_COMPILER: /usr/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-deprecated-declarations -Wno-literal-suffix -fopenmp-simd -std=c++11

# DEAL_II_CXX_FLAGS_RELEASE: -O2 -funroll-loops -funroll-all-loops -fstrict-aliasing -Wno-unused-local-typedefs

# DEAL_II_CXX_FLAGS_DEBUG: -Og -ggdb -Wa,--compress-debug-sections

# DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic -fuse-ld=gold

# DEAL_II_LINKER_FLAGS_RELEASE:

# DEAL_II_LINKER_FLAGS_DEBUG: -ggdb

# DEAL_II_DEFINITIONS:

# DEAL_II_DEFINITIONS_RELEASE:

# DEAL_II_DEFINITIONS_DEBUG: DEBUG

# DEAL_II_USER_DEFINITIONS:

# DEAL_II_USER_DEFINITIONS_REL:

# 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_RELEASE:

# DEAL_II_LIBRARIES_DEBUG:

# DEAL_II_COMPILER_VECTORIZATION_LEVEL: 1

#

# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = OFF):

# ( 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 external dependencies

# BOOST_VERSION = 1.59.0

# BOOST_CXX_FLAGS = -Wno-unused-local-typedefs

# BOOST_INCLUDE_DIRS = /usr/local/include

# BOOST_USER_INCLUDE_DIRS = /usr/local/include

# BOOST_LIBRARIES = /usr/local/lib/libboost_serialization.so;/usr/local/lib/libboost_system.so;/usr/local/lib/libboost_thread.so;pthread

# ( DEAL_II_WITH_CUDA = OFF )

# ( DEAL_II_WITH_CXX14 = OFF )

# ( DEAL_II_WITH_CXX17 = OFF )

# ( DEAL_II_WITH_GMSH = OFF )

# ( DEAL_II_WITH_GSL = OFF )

# ( DEAL_II_WITH_HDF5 = OFF )

# ( DEAL_II_WITH_LAPACK = OFF )

# ( DEAL_II_WITH_METIS = OFF )

# DEAL_II_WITH_MPI set up with external dependencies

# MPI_VERSION = 3.0

# MPI_C_COMPILER = /usr/local/bin/mpicc

# MPI_CXX_COMPILER = /usr/local/bin/mpicxx

# MPI_Fortran_COMPILER = /usr/local/bin/mpif90

# MPI_CXX_FLAGS =

# MPI_LINKER_FLAGS = -Wl,-rpath -Wl,/usr/local/lib -Wl,--enable-new-dtags

# MPI_INCLUDE_DIRS = /usr/local/include

# MPI_USER_INCLUDE_DIRS = /usr/local/include

# MPI_LIBRARIES = /usr/local/lib/libmpi_cxx.so;/usr/local/lib/libmpi_usempif08.so;/usr/local/lib/libmpi_usempi_ignore_tkr.so;/usr/local/lib/libmpi_mpifh.so;/usr/local/lib/libmpi.so

# ( DEAL_II_WITH_MUPARSER = OFF )

# ( DEAL_II_WITH_NANOFLANN = OFF )

# ( DEAL_II_WITH_NETCDF = OFF )

# ( DEAL_II_WITH_OPENCASCADE = OFF )

# ( DEAL_II_WITH_P4EST = OFF )

# ( DEAL_II_WITH_PETSC = OFF )

# ( DEAL_II_WITH_SCALAPACK = OFF )

# ( DEAL_II_WITH_SLEPC = OFF )

# ( DEAL_II_WITH_SUNDIALS = OFF )

# ( DEAL_II_WITH_THREADS = OFF )

# ( DEAL_II_WITH_TRILINOS = OFF )

# ( DEAL_II_WITH_UMFPACK = OFF )

# ( DEAL_II_WITH_ZLIB = OFF )

#

# Component configuration:

# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )

# DEAL_II_COMPONENT_EXAMPLES

# ( DEAL_II_COMPONENT_PACKAGE = OFF )

# ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )

#

###

Cheers,

J.

Bruno Turcksin

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Jun 20, 2018, 4:42:09 PM6/20/18

to dea...@googlegroups.com

Can you to reconfigure (and recompile) deal.II with the following option -D DEAL_II_FORCE_BUNDLED_BOOST=ON

Best

Bruno

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JGM

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Jun 25, 2018, 6:02:40 AM6/25/18

to deal.II User Group

Hi,

I did as suggested, but then I got the error message reported below.

Additionally, I found something odd: I had to execute twice the command:

$cmake -DCMAKE_INSTALL_PREFIX=/home/jgaricano/bin/DEAL.II /home/jgaricano/Downloads/dealii-9.0.0 -DTRILINOS_DIR=/home/jgaricano/bin/TRILINOS -DDEAL_II_WITH_MPI=ON -DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON

to have the configuration to acknowledge trilinos, i.e. to get the message:

...

DEAL_II_WITH_TRILINOS set up with external dependencies

...

Error message:

...

[ 33%] Building CXX object source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o

[ 33%] Building CXX object source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In member function ‘void dealii::ScaLAPACKMatrix<NumberType>::save_parallel(const char*, const std::pair<unsigned int, unsigned int>&) const’:
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1830:60: error: there are no arguments to ‘H5Pset_dxpl_mpio’ that depend on a template parameter, so a declaration of ‘H5Pset_dxpl_mpio’ must be available [-fpermissive]
   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
                                                            ^
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1830:60: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In instantiation of ‘void dealii::ScaLAPACKMatrix<NumberType>::save_parallel(const char*, const std::pair<unsigned int, unsigned int>&) const [with NumberType = double]’:
/home/jgaricano/bin/dealii-9.0.0/build/source/lac/scalapack.inst:10:16:   required from here
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1765:71: error: ‘H5Pset_fapl_mpio’ was not declared in this scope
   status = H5Pset_fapl_mpio(plist_id, tmp.grid->mpi_communicator, info);
                                                                       ^
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1830:60: error: ‘H5Pset_dxpl_mpio’ was not declared in this scope
   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);

/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In instantiation of ‘void dealii::ScaLAPACKMatrix<NumberType>::load_parallel(const char*) [with NumberType = double]’:
/home/jgaricano/bin/dealii-9.0.0/build/source/lac/scalapack.inst:10:16:   required from here
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:2088:61: warning: unused parameter ‘filename’ [-Wunused-parameter]
void ScaLAPACKMatrix<NumberType>::load_parallel(const char *filename)
                                                             ^
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In instantiation of ‘void dealii::ScaLAPACKMatrix<NumberType>::save_parallel(const char*, const std::pair<unsigned int, unsigned int>&) const [with NumberType = float]’:
/home/jgaricano/bin/dealii-9.0.0/build/source/lac/scalapack.inst:20:16:   required from here
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1765:71: error: ‘H5Pset_fapl_mpio’ was not declared in this scope
   status = H5Pset_fapl_mpio(plist_id, tmp.grid->mpi_communicator, info);
                                                                       ^
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1830:60: error: ‘H5Pset_dxpl_mpio’ was not declared in this scope
   status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
                                                            ^
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In instantiation of ‘void dealii::ScaLAPACKMatrix<NumberType>::load_parallel(const char*) [with NumberType = float]’:
/home/jgaricano/bin/dealii-9.0.0/build/source/lac/scalapack.inst:20:16:   required from here
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:2088:61: warning: unused parameter ‘filename’ [-Wunused-parameter]
void ScaLAPACKMatrix<NumberType>::load_parallel(const char *filename)
                                                             ^
source/lac/CMakeFiles/obj_lac_release.dir/build.make:330: recipe for target 'source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o' failed
make[2]: *** [source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o] Error 1
CMakeFiles/Makefile2:1575: recipe for target 'source/lac/CMakeFiles/obj_lac_release.dir/all' failed
make[1]: *** [source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
Makefile:117: recipe for target 'all' failed
make: *** [all] Error 2

Best,

To unsubscribe from this group and all its topics, send an email to dealii+un...@googlegroups.com.

Bruno Turcksin

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Jun 25, 2018, 8:20:10 AM6/25/18

to dea...@googlegroups.com

Hi,

2018-06-25 6:02 GMT-04:00 JGM <jgar...@gmail.com>:

I did as suggested, but then I got the error message reported below.
Additionally, I found something odd: I had to execute twice the command:
$cmake -DCMAKE_INSTALL_PREFIX=/home/jgaricano/bin/DEAL.II /home/jgaricano/Downloads/dealii-9.0.0 -DTRILINOS_DIR=/home/jgaricano/bin/TRILINOS -DDEAL_II_WITH_MPI=ON -DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON

You usually want to reconfigure in a new directory because cmake keeps a cache that is not always updated.

[ 33%] Building CXX object source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o
[ 33%] Building CXX object source/lac/CMakeFiles/obj_lac_release.dir/scalapack.cc.o
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc: In member function ‘void dealii::ScaLAPACKMatrix<NumberType>::save_parallel(const char*, const std::pair<unsigned int, unsigned int>&) const’:
/home/jgaricano/Downloads/dealii-9.0.0/source/lac/scalapack.cc:1830:60: error: there are no arguments to ‘H5Pset_dxpl_mpio’ that depend on a template parameter, so a declaration of ‘H5Pset_dxpl_mpio’ must be available [-fpermissive]

This is a problem with scalapack that was not compiled with a parallel version of HDF5. If you don't need scalapack just turn it off -DDEAL_II_WITH_SCALAPACK=OFF otherwise, you need to recompile it and link it with parallel HDF5.

Best,

Bruno

Denis Davydov

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Jun 26, 2018, 12:33:22 AM6/26/18

to deal.II User Group

Nope, Scalapack does not know anything about HDF5. It's our wrappers that have extra functionality to load/save parallel dense matrices with HDF5.

This chunk of the code is being wrapped in

# ifndef DEAL_II_WITH_HDF5

and given that HDF5 is disabled (according to the post above), i guess it's a remainder of un-clean build directory.

Compilation error - small_vector - no matching function for call to small_vector(std::size_t, dealii::Point<1, double>)

JGM

Bruno Turcksin

JGM

Bruno Turcksin

JGM

Bruno Turcksin

Denis Davydov