subject:"\[deal.II\] Re\: After \"make install\", there are some Errors when install Deal.II\-9.0.1"

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-30 Thread Wolfgang Bangerth



> $ make -j2
> and it shows:
> In file included from 
> /vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src/source/base/flow_function.cc:18:0:
> /vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src/include/deal.II/base/flow_function.h:59:13:
>  
> internal compiler error: in use_thunk, at cp/method.c:338
>       virtual ~FlowFunction() = default;
>               ^

I bet you are running out of memory at this point and that this is the 
cause of the internal compiler error. Try again with 'make -j1'.


> and  I download a new dealii-9.0.1.tar.gz and build a new file 
> folder: /vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1
> source directory:/vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src
> and the command line :(in the directory: 
> /vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src/build)
> $ cmake /vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src 
> -DCMAKE_INSTALL_PREFIX=/vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/deal.II
>  
> -DDEAL_II_WITH_MPI=ON -DMPI_DIR=/usr/local/mpi3 
> -DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx 
> -DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
> -DDEAL_II_FORCE_BUNDLED_BOOST=ON -DDEAL_II_ALLOW_AUTODETECTION=ON
> $make -j2 deal_II
> $make install
> 
> and it shows:
> 
> [ 81%] Built target obj_multigrid_release
> [ 82%] Built target obj_distributed_release
> [ 82%] Built target obj_algorithms_release
> [ 82%] Built target obj_matrix_free_release
> [ 83%] Built target obj_meshworker_release
> [ 84%] Built target obj_opencascade_release
> [ 84%] Built target obj_differentiation_ad_release
> [ 84%] Built target obj_particle_release
> [ 84%] Built target obj_physics_release
> [ 84%] Built target obj_physics_elasticity_release
> [ 84%] Built target deal_II.g
> [ 85%] Built target obj_non_matching_release
> [ 85%] Built target obj_rol_release
> [ 85%] Built target obj_rol_debug
> Scanning dependencies of target step-7.debug
> Scanning dependencies of target step-6.debug
> [ 85%] Building CXX object 
> examples/CMakeFiles/step-7.debug.dir/step-7/step-7.cc.o
> [ 85%] Building CXX object 
> examples/CMakeFiles/step-6.debug.dir/step-6/step-6.cc.o
> [ 85%] Linking CXX executable ../bin/step-7.debug
> [ 85%] Linking CXX executable ../bin/step-6.debug
> ../lib/libdeal_II.g.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'

Hm, good question. What happens if you say
   /usr/local/mpi3/bin/mpicxx -v
and
   gcc -v
? Are they the same compiler version?


> And I don't know why this happens. I use dealii-8.5.1 before, and I 
> finished my test code using block sparse matrix and block vector like 
> step-20 with fewer dofs. Now I need to try these codes with larger dofs 
> more than 200K dofs in each loop, and the time steps are more than 
> 5. So I want to rewrite the codes and use method for parallel like 
> step-40, step-55, step-32. So I need to reinstall my dealii. And I start 
> again. But it seems not so easy.

My best guess is that there is a disconnect between two compilers 
installed on your system.

An alternative would be for you to use the current development version 
(which is actually quite stable). If you want to try that out, just 
clone the github repository onto your hard drive and go through the same 
configuration steps you do above.

Best
  W.


-- 

Wolfgang Bangerth  email: bange...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-27 Thread chucui1016

Dear Wolfgang,

Thanks for your advice, and Matthias's. Thank you very much!

>
>
> I don't think any of us has seen this error before. Can you try what 
> happens if you delete the build directory, re-create it, and then just 
> use the minimal command line 
>cmake /vol7/... 
> ? Make things as simple as possible if you don't know what causes a 
> particular problem. If the problem goes away, then repeat by adding one 
> flag at a time until the problem re-appears -- at which time you know 
> what change must have caused it. 
>
 I download a new dealii-9.0.1.tar.gz and build a new file folder:
/vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/ 
source directory:/vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src
and the command line :(in the directory: 
/vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src/build)
$ cmake /vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src
$ make -j2
and it shows:
In file included from 
/vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src/source/base/flow_function.cc:18:0:
/vol7/home/zhaoyucan1016/reinstall2-dealii-9.0.1/src/include/deal.II/base/flow_function.h:59:13:
 
internal compiler error: in use_thunk, at cp/method.c:338
 virtual ~FlowFunction() = default;
 ^
0x595884 use_thunk(tree_node*, bool)
../.././gcc/cp/method.c:338
0x5a078c emit_associated_thunks(tree_node*)
../.././gcc/cp/semantics.c:3763
0x5a0a47 expand_or_defer_fn(tree_node*)
../.././gcc/cp/semantics.c:3890
0x5b83a5 maybe_clone_body(tree_node*)
../.././gcc/cp/optimize.c:428
0x5a083d expand_or_defer_fn_1(tree_node*)
../.././gcc/cp/semantics.c:3814
0x5a0a18 expand_or_defer_fn(tree_node*)
../.././gcc/cp/semantics.c:3884
0x5969ef synthesize_method(tree_node*)
../.././gcc/cp/method.c:809
0x5434aa mark_used(tree_node*)
../.././gcc/cp/decl2.c:4677
0x4f01cc build_over_call
../.././gcc/cp/call.c:7055
0x4ed678 build_new_method_call_1
../.././gcc/cp/call.c:7715
0x4ed678 build_new_method_call(tree_node*, tree_node*, vec**, tree_node*, int, tree_node**, int)
../.././gcc/cp/call.c:7785
0x4edf1e build_special_member_call(tree_node*, tree_node*, vec**, tree_node*, int, int)
../.././gcc/cp/call.c:7352
0x58e0ff expand_cleanup_for_base
../.././gcc/cp/init.c:1217
0x5925f1 expand_cleanup_for_base
../.././gcc/cp/init.c:1112
0x5925f1 emit_mem_initializers(tree_node*)
../.././gcc/cp/init.c:1097
0x56a47c cp_parser_mem_initializer_list
../.././gcc/cp/parser.c:11731
0x56a47c cp_parser_ctor_initializer_opt
../.././gcc/cp/parser.c:11642
0x56a47c cp_parser_ctor_initializer_opt_and_function_body
../.././gcc/cp/parser.c:17848
0x56aacf cp_parser_function_definition_after_declarator
../.././gcc/cp/parser.c:21843
0x56b6e3 cp_parser_function_definition_from_specifiers_and_declarator
../.././gcc/cp/parser.c:21764
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See  for instructions.
make[2]: *** [source/base/CMakeFiles/obj_base_debug.dir/flow_function.cc.o] 
Error 1
make[1]: *** [source/base/CMakeFiles/obj_base_debug.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_ilu.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_matrix_ez.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_mic.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_vanka.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparsity_pattern.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparsity_tools.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/swappable_vector.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/tridiagonal_matrix.cc.o
[ 42%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/vector.cc.o
[ 43%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/vector_memory.cc.o
[ 43%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/vector_view.cc.o
[ 43%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_matrix.cc.o
[ 43%] Building CXX object 
source/lac/CMakeFiles/obj_lac_debug.dir/sparse_matrix_inst2.cc.o
[ 43%] Built target obj_lac_debug
make: *** [all] Error 2

and  I download a new dealii-9.0.1.tar.gz and build a new file 
folder: /vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1
source directory:/vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src
and the command line :(in the directory: 
/vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src/build)
$ cmake /vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/src 
-DCMAKE_INSTALL_PREFIX=/vol7/home/zhaoyucan1016/reinstall-dealii-9.0.1/deal.II 
-DDEAL_II_WITH_MPI=ON -DMPI_DIR=/usr/local/mpi3 
-DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx 
-DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
-DDEAL_II_FORCE_BUNDLED_BOOST=ON -DDEAL_II_ALLOW_AUTODETECTION=ON
$make -j2 deal_II
$make

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-24 Thread Matthias Maier



On Wed, Oct 24, 2018, at 18:18 CDT, Wolfgang Bangerth  
wrote:

> Chucui,
>
>> My command lines are
>>
>> $cmake /vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1  
>> [...]
>> -DCMAKE_INSTALL_PREFIX=/vol7/home/zhaoyucan1016/dealii-9.0.1/build 

This looks odd. You are configuring in-source and installing into the
build directory.

Would you mind to (in addition to Wolfgang's suggestions)

 * download dealii-9.0.1.tar.gz again (verify that the archive is
   complete and not corrupted).

 * unpack the sources to a *new* source directory, say
   /vol7/home/zhaoyucan1016/dealii-9.0.1/sources

 * delete the build directory and simply configure with

   $ mkdir -p /vol7/home/zhaoyucan1016/dealii-9.0.1/build
   $ cd /vol7/home/zhaoyucan1016/dealii-9.0.1/build
   $ cmake ../sources
   $ make ...
   $ make test

 * if above step succeeds, reconfigure by enabling all external packages
   you want.

Best,
Matthias

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[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-20 Thread chucui1016

Dear Matthias,

The newest result are still the same. After "make install" it shows:

[ 82%] Built target obj_rol_debug
Scanning dependencies of target step-3.release
[ 82%] Building CXX object 
examples/CMakeFiles/step-3.release.dir/step-3/step-3.cc.o
[ 82%] Linking CXX executable ../bin/step-3.release
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 1>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<3, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<3, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 1>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 2>::StraightBoundary()'
make[2]: *** [bin/step-3.release] Error 1
make[1]: *** [examples/CMakeFiles/step-3.release.dir/all] Error 2
make: *** [all] Error 2

And  I am on the 
directory: /vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1

My command lines are
$cmake /vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1  
-DDEAL_II_WITH_MPI=ON  -DCMAKE_C_COMPILER=/usr/local/mpi3/bin/mpicc  
-DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx  
-DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
-DCMAKE_INSTALL_PREFIX=/vol7/home/zhaoyucan1016/dealii-9.0.1/build 
-DMPI_DIR=/usr/local/mpi3 
-DP4EST_DIR=/vol7/home/zhaoyucan1016/p4est/p4est-2.0 
-DPETSC_DIR=/vol7/home/zhaoyucan1016/petsc-3.7.7/petsc-3.7.7 
-DHDF5_DIR=/usr/lib64/ 
-DMETIS_DIR=/vol7/home/zhaoyucan1016/metis-5.1.0/metis-5.1.0 
-DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_PETSC=ON 
-DDEAL_II_WITH_P4EST=OFF -DDEAL_II_WITH_MPI=ON 
-DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON 
$make -j2 deal.II
$make install

And under the directory: /vol7/home/zhaoyucan1016/dealii-9.0.1/build
There are only : CMakeCache.txt  CMakeFiles (Folder)

Hope these informations can help.

Best,
Chucui


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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /vol7/home/zhaoyucan1016/dealii-9.0.1/build
#CMAKE_SOURCE_DIR:   
/vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1
#(version 9.0.1)
#CMAKE_BINARY_DIR:   
/vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1
#CMAKE_CXX_COMPILER: Intel 15.0.1.20141023 on platform Linux x86_64
#/usr/local/mpi3/bin/mpicxx
#CMAKE_C_COMPILER:   /usr/local/mpi3/bin/mpicc
#CMAKE_Fortran_COMPILER: /usr/local/mpi3/bin/mpifort
#CMAKE_GENERATOR:Unix Makefiles
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-fpic -ansi -w2 -diag-disable=remark 
-wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 
-wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd3415 -wd15531 -wd111 -wd128 -wd185 
-wd186 -wd280 -qopenmp-simd -std=c++11
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -no-ansi-alias -ip -funroll-loops 
-no-vec
#DEAL_II_CXX_FLAGS_DEBUG:  -O0 -g -gdwarf-2 -grecord-gcc-switches
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -qopenmp 
-rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE: 
#DEAL_II_LINKER_FLAGS_DEBUG:   
#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

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-19 Thread chucui1016

Dear Matthias,

I am sorry to delete the originial file and configure it again, but 
everything seems not change. And attached is the newest detailed.log. Thank 
you very much!

Best,
Chucui

在 2018年10月19日星期五 UTC+8上午11:53:35，Matthias Maier写道：
>
>
> On Thu, Oct 18, 2018, at 17:48 CDT, David Wells  > wrote: 
>
> > Hi Chucui, 
> > 
> > StraightBoundary was removed in deal.II 9.0; it should not show up in 
> any 
> > object files so these errors don't make any sense. Did you use a clean 
> > build directory? 
>
> Not quite. It got completely removed in the current development version. 
>
> In version 9.0.1 it is present in the library. What is surprising though 
> is the fact that we completely instantiate the class: 
>
> grid/tria_boundary.inst.in (on branch dealii-9.0 
>  18 for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : 
>  SPACE_DIMENSIONS) 
>  19 { 
> 
>  20 #if deal_II_dimension <= deal_II_space_dimension   
>   
>  21 template class Boundary deal_II_space_dimension>; 
>  22 template class StraightBoundary deal_II_space_dimension>; 
>  23 #endif 
>   
>  24 } 
>
> yet, Chucui observes an undefined reference to the constructor. Which is 
> a bit puzzling. 
>
> Chucui, can you please post your full `detailed.log` please? Further, 
> can you please try to recompile again by (a) unpacking dealii-9.0.1 to a 
> new directory, and configure and compile in a new build directory? 
>
> Best, 
> Matthias 
>

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /vol7/home/zhaoyucan1016/dealii-9.0.1/build
#CMAKE_SOURCE_DIR:   
/vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1
#(version 9.0.1)
#CMAKE_BINARY_DIR:   
/vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1
#CMAKE_CXX_COMPILER: Intel 15.0.1.20141023 on platform Linux x86_64
#/usr/local/mpi3/bin/mpicxx
#CMAKE_C_COMPILER:   /usr/local/mpi3/bin/mpicc
#CMAKE_Fortran_COMPILER: /usr/local/mpi3/bin/mpifort
#CMAKE_GENERATOR:Unix Makefiles
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-fpic -ansi -w2 -diag-disable=remark 
-wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 
-wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd3415 -wd15531 -wd111 -wd128 -wd185 
-wd186 -wd280 -qopenmp-simd -std=c++11
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -no-ansi-alias -ip -funroll-loops 
-no-vec
#DEAL_II_CXX_FLAGS_DEBUG:  -O0 -g -gdwarf-2 -grecord-gcc-switches
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -qopenmp 
-rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE: 
#DEAL_II_LINKER_FLAGS_DEBUG:   
#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 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#DEAL_II_WITH_ARPACK set up with external dependencies
#ARPACK_LINKER_FLAGS = 
#ARPACK_LIBRARIES = 
/usr/lib64/libarpack.so;/usr/lib64/libopenblas.so;mpifort;mpi;rt;glex;ifcore;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl;c
#  ( DEAL_II_WITH_ASSIMP = OFF )
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_BUNDLED_INCLUDE_DIRS = 
/vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1/bundled/boost-1.62.0/include
#BOOST_LIBRARIES = rt
#  ( DEAL_II_WITH_CUDA = OFF )
#  ( DEAL_II_WITH_CXX14 = OFF )
#  ( DEAL_II_WITH_CXX17 = OFF )
#  ( DEAL_II_WITH_GMSH = OFF )
#DEAL_II_WITH_GSL set up with external dependencies
#GSL_VERSION = 1.13
#GSL_INCLUDE_DIRS = /usr/include
#GSL_USER_INCLUDE_DIRS = /usr/include
#

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-18 Thread Matthias Maier

On Thu, Oct 18, 2018, at 17:48 CDT, David Wells  wrote:

> Hi Chucui,
>
> StraightBoundary was removed in deal.II 9.0; it should not show up in any 
> object files so these errors don't make any sense. Did you use a clean 
> build directory?

Not quite. It got completely removed in the current development version.

In version 9.0.1 it is present in the library. What is surprising though
is the fact that we completely instantiate the class:

grid/tria_boundary.inst.in (on branch dealii-9.0
 18 for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension :  
SPACE_DIMENSIONS)
 19 {   

 20 #if deal_II_dimension <= deal_II_space_dimension

 21 template class Boundary;

 22 template class StraightBoundary; 
 23 #endif  

 24 } 

yet, Chucui observes an undefined reference to the constructor. Which is
a bit puzzling.

Chucui, can you please post your full `detailed.log` please? Further,
can you please try to recompile again by (a) unpacking dealii-9.0.1 to a
new directory, and configure and compile in a new build directory?

Best,
Matthias

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[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

2018-10-18 Thread David Wells

Hi Chucui,

StraightBoundary was removed in deal.II 9.0; it should not show up in any 
object files so these errors don't make any sense. Did you use a clean 
build directory?

Thanks,
David Wells

On Thursday, October 18, 2018 at 8:27:40 AM UTC-4, chucu...@gmail.com wrote:
>
> Dear all, 
>
> I want to reinstall my deal.ii because I need to run some codes in 
> parallel just like Step-40, step-55 and Step-32, and I choose deal.ii-9.0.1 
> The command lines I use are: 
>
> $cmake ../dealii-9.0.1/dealii-9.0.1  -DDEAL_II_WITH_MPI=ON  
> -DCMAKE_C_COMPILER=/usr/local/mpi3/bin/mpicc  
> -DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx  
> -DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
> -DCMAKE_INSTALL_PREFIX=../dealii-9.0.1/build -DMPI_DIR=/usr/local/mpi3 
> -DP4EST_DIR=../p4est/p4est-2.0 -DPETSC_DIR=../new-petsc-3.7.7/petsc-3.7.7 
> -DHDF5_DIR=/usr/lib64/ -DMETIS_DIR=../metis-5.1.0/metis-5.1.0 
> -DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_PETSC=ON 
> -DDEAL_II_WITH_P4EST=OFF -DDEAL_II_WITH_MPI=ON 
> -DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON
>
> $make
>
> $make install
>
> But after "make install", the installation was interupped, and the errors 
> are showed as:
>
> Scanning dependencies of target obj_rol_debug
> [ 82%] Built target obj_rol_debug
> Scanning dependencies of target step-3.release
> [ 82%] Building CXX object 
> examples/CMakeFiles/step-3.release.dir/step-3/step-3.cc.o
> [ 82%] Linking CXX executable ../bin/step-3.release
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> make[2]: *** [bin/step-3.release] Error 1
> make[1]: *** [examples/CMakeFiles/step-3.release.dir/all] Error 2
> make: *** [all] Error 2
>
> So, I don't what happened and know how to do. Hope some suggestions! 
> Thanks in advance!
>
> Best,
> Chucui
>
>
>
>
>

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Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

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