[deal.II] Constrain specific dofs to given value
Hi all, I want to solve a 2D linear elastic problem with a Dirichlet boundary condition that keeps only one node fixed. And I encountered convergence problem by modifying codes in step-8 as following: In the setup_system() function, I used the "add_line" functions to contrain dof 0 and dof 1 to zero: -- hanging_node_constraints.clear(); DoFTools::make_hanging_node_constraints(dof_handler, hanging_node_constraints); hanging_node_constraints.add_line(0); hanging_node_constraints.add_line(1); hanging_node_constraints.close(); -- In my case there is actually no hanging nodes (I used a 4*4 mesh without refinement in this test). And I commented the codes in assemble_system() that applies Dirichlet b.c. (I just want to fix one node) as: -- // std::map boundary_values; // VectorTools::interpolate_boundary_values(dof_handler, 0, ZeroFunction(dim), boundary_values); // MatrixTools::apply_boundary_values(boundary_values, system_matrix, solution, system_rhs); -- By modifying with above codes, the cg solver does not converge. I guess this may be caused by the way the constraints are applied. *Actually I just want to apply the Dirichlet b.c. on one node with the same commend as "VectorTools::interpolate_boundary_values(dof_handler, 0, ZeroFunction(dim), boundary_values);", but this **function only supports interpolation on basis of boundary id instead of specific dofs or nodes.* *So is there a way to apply Dirichlet b.c. on one node (I mean in form of natural boundary condition instead of constrains)?* Many thanks in advance! Best, Pai -- 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 dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Problem about modifying CMakeList.txt to add library
Dear David Wells,
Thank you for your reply! Your explanation helps me to understand this
process better. Yestoday I tried to use "FIND_PACKAGE" as following and it
works:
_
FIND_PACKAGE(Armadillo)
INCLUDE_DIRECTORIES(${ARMADILLO_INCLUDE_DIRS})
ADD_EXECUTABLE(${TARGET} ${TARGET_SRC})
DEAL_II_SETUP_TARGET(${TARGET})
TARGET_LINK_LIBRARIES(${TARGET} ${ARMADILLO_LIBRARIES})
_
I will try the commends you recommended later! Thank you very much!
Best,
Pai
On Thursday, May 17, 2018 at 1:53:36 AM UTC+8, David Wells wrote:
>
> Hi Pai,
>
> I think that there is an easier way to do this. More exactly: armadillo
> should not be a target since we don't have to compile anything: we should
> just be able to specify the library we need to link against and (possibly)
> a path to the headers and be done.
>
> Have you installed armadillo in a standard location? If so then you should
> be able to just append
>
> TARGET_LINK_LIBRARIES(${TARGET} armadillo)
>
> to the end of CMakeLists.txt (after the call to PROJECT and
> DEAL_II_INVOKE_AUTOPILOT)
>
> and things should work correctly.
>
> Thanks,
> David Wells
>
> P.S. the CMake module for setting up armadillo looks for a lot of things
> that don't exist on my computer; I recommend avoiding using FIND_PACKAGE.
>
> On Wednesday, May 16, 2018 at 2:54:39 AM UTC-4, Pai Liu wrote:
>>
>> Hi all,
>>
>> I am learning Step-8 in the tutorial. I want to use the library
>> "Armadillo" (which is a library for scientific computing and linear
>> algebra) together with dealii in step-8.cc.
>> To compile a cpp file that only depends on the Armadillo library, one
>> needs to excute the following commends at the commend line : "g++
>> example.cpp -o example -O2 -larmadillo"
>> So I replace "mylib" in dealii documentation about modifying
>> cmakelist.txt with "armadillo", and modify the CMakeList.txt file as the
>> following
>>
>> _
>> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
>>
>> FIND_PACKAGE(deal.II 8.5.0 REQUIRED
>> HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
>> )
>> DEAL_II_INITIALIZE_CACHED_VARIABLES()
>>
>> PROJECT(myproject)
>>
>> ADD_LIBRARY(armadillo)
>> DEAL_II_SETUP_TARGET(armadillo)
>>
>> ADD_EXECUTABLE(mycode step-8.cc)
>> DEAL_II_SETUP_TARGET(mycode)
>>
>> TARGET_LINK_LIBRARIES(mycode armadillo)
>> _
>>
>> And I got the the following error:
>>
>> -- Using the deal.II-8.5.1 installation found at
>> /home/liu/deal.ii-candi/deal.II-v8.5.1
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_setup_target.cmake
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_add_test.cmake
>> -- Include macro
>> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
>> You have called ADD_LIBRARY for library armadillo without any source
>> files. This typically indicates a problem with your CMakeLists.txt file
>> -- Configuring done
>> CMake Error: Cannot determine link language for target "armadillo".
>> CMake Error: CMake can not determine linker language for target: armadillo
>> -- Generating done
>> -- Build files have been written to: /home/liu/P/homogenization
>>
>>
>>
>>
>>
>> Can anyone help me about this issue about add library?
>> Many thanks in advance!
>>
>>
>
--
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
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[deal.II] Re: Problem about modifying CMakeList.txt to add library
Dear Daniel Arndt, Thank you for your reply! The link is very helpful! Now my CMakeList.txt works! Best, Pai On Thursday, May 17, 2018 at 5:47:11 AM UTC+8, Daniel Arndt wrote: > > Pal, > > We also just updated the CMakeLists.txt file for an example in our > code-gallery that uses armadillo. > You might want to look at > https://github.com/dealii/code-gallery/blob/master/CeresFE/CMakeLists.txt. > > Best, > Daniel > -- 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 dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Problem about modifying CMakeList.txt to add library
Pal, We also just updated the CMakeLists.txt file for an example in our code-gallery that uses armadillo. You might want to look at https://github.com/dealii/code-gallery/blob/master/CeresFE/CMakeLists.txt. Best, Daniel -- 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 dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Problem about modifying CMakeList.txt to add library
Hi Pai,
I think that there is an easier way to do this. More exactly: armadillo
should not be a target since we don't have to compile anything: we should
just be able to specify the library we need to link against and (possibly)
a path to the headers and be done.
Have you installed armadillo in a standard location? If so then you should
be able to just append
TARGET_LINK_LIBRARIES(${TARGET} armadillo)
to the end of CMakeLists.txt (after the call to PROJECT and
DEAL_II_INVOKE_AUTOPILOT)
and things should work correctly.
Thanks,
David Wells
P.S. the CMake module for setting up armadillo looks for a lot of things
that don't exist on my computer; I recommend avoiding using FIND_PACKAGE.
On Wednesday, May 16, 2018 at 2:54:39 AM UTC-4, Pai Liu wrote:
>
> Hi all,
>
> I am learning Step-8 in the tutorial. I want to use the library
> "Armadillo" (which is a library for scientific computing and linear
> algebra) together with dealii in step-8.cc.
> To compile a cpp file that only depends on the Armadillo library, one
> needs to excute the following commends at the commend line : "g++
> example.cpp -o example -O2 -larmadillo"
> So I replace "mylib" in dealii documentation about modifying
> cmakelist.txt with "armadillo", and modify the CMakeList.txt file as the
> following
>
> _
> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
>
> FIND_PACKAGE(deal.II 8.5.0 REQUIRED
> HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
> )
> DEAL_II_INITIALIZE_CACHED_VARIABLES()
>
> PROJECT(myproject)
>
> ADD_LIBRARY(armadillo)
> DEAL_II_SETUP_TARGET(armadillo)
>
> ADD_EXECUTABLE(mycode step-8.cc)
> DEAL_II_SETUP_TARGET(mycode)
>
> TARGET_LINK_LIBRARIES(mycode armadillo)
> _
>
> And I got the the following error:
>
> -- Using the deal.II-8.5.1 installation found at
> /home/liu/deal.ii-candi/deal.II-v8.5.1
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_setup_target.cmake
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_add_test.cmake
> -- Include macro
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
> You have called ADD_LIBRARY for library armadillo without any source
> files. This typically indicates a problem with your CMakeLists.txt file
> -- Configuring done
> CMake Error: Cannot determine link language for target "armadillo".
> CMake Error: CMake can not determine linker language for target: armadillo
> -- Generating done
> -- Build files have been written to: /home/liu/P/homogenization
>
>
>
>
>
> Can anyone help me about this issue about add library?
> Many thanks in advance!
>
>
--
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
---
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[deal.II] Re: Error during configuration since 9.0.0
I think the problem is the following: In the Ubuntu Package Sources for 18.04 the standard openmpi version of libscalapack is 2.0 while my system has 2.1.1 installed. I guess that causes the problems. I also checked and the problems only occur if MPI=ON and scalapack=ON. Otherwise everything is fine. So I guess this problem will appear for everyone who uses the packages "openmpi-bin" and "libscalapack-openmpi2.0". Thank you all for your time :) Am Dienstag, 15. Mai 2018 19:38:03 UTC+2 schrieb Pascal Kraft: > > Dear Deal.ii devs, > > first off: Thanks for your great work and the many new features in 9.0.0! > I have compiled 9.0.0 successfully on a cluster however there seems to be > some kind of bug on my desktop (Ubuntu 18.04) where the configuration of > 8.5.1 works completely fine. > I run my cmake command and all dependencies are found. Then the test suite > for compilerflags crashes stating: > > ... > >> -- Include /home/kraft/Downloads/dealii-9.0.0/cmake/setup_finalize.cmake >> CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE): >> >> Configuration error: Cannot compile a test program with the final set >> of >> compiler and linker flags: >> CXX flags (DEBUG): -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 -pthread -Wno-unused-local-typedefs -Og -ggdb >> -Wa,--compress-debug-sections >> LD flags (DEBUG): -Wl,--as-needed -rdynamic -pthread -pthread -ggdb >> LIBRARIES (DEBUG): >> /usr/lib/x86_64-linux-gnu/libtbb.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_serialization.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_thread.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_date_time.so;/usr/lib/x86_64-linux-gnu/libboost_atomic.so;pthread;/home/kraft/trilinos/lib/libmuelu-adapters.so;/home/kraft/trilinos/lib/libmuelu-interface.so;/home/kraft/trilinos/lib/libmuelu.so;/home/kraft/trilinos/lib/libteko.so;/home/kraft/trilinos/lib/libstratimikos.so;/home/kraft/trilinos/lib/libstratimikosbelos.so;/home/kraft/trilinos/lib/libstratimikosaztecoo.so;/home/kraft/trilinos/lib/libstratimikosamesos.so;/home/kraft/trilinos/lib/libstratimikosml.so;/home/kraft/trilinos/lib/libstratimikosifpack.so;/home/kraft/trilinos/lib/libifpack2-adapters.so;/home/kraft/trilinos/lib/libifpack2.so;/home/kraft/trilinos/lib/libzoltan2.so;/home/kraft/trilinos/lib/libanasazitpetra.so;/home/kraft/trilinos/lib/libModeLaplace.so;/home/kraft/trilinos/lib/libanasaziepetra.so;/home/kraft/trilinos/lib/libanasazi.so;/home/kraft/trilinos/lib/libbelostpetra.so;/home/kraft/trilinos/lib/libbelosepetra.so;/home/kraft/trilinos/lib/libbelos.so;/home/kraft/trilinos/lib/libml.so;/home/kraft/trilinos/lib/libifpack.so;/home/kraft/trilinos/lib/libpamgen_extras.so;/home/kraft/trilinos/lib/libpamgen.so;/home/kraft/trilinos/lib/libamesos2.so;/home/kraft/trilinos/lib/libamesos.so;/home/kraft/trilinos/lib/libgaleri-xpetra.so;/home/kraft/trilinos/lib/libgaleri.so;/home/kraft/trilinos/lib/libaztecoo.so;/home/kraft/trilinos/lib/libisorropia.so;/home/kraft/trilinos/lib/libxpetra-sup.so;/home/kraft/trilinos/lib/libxpetra.so;/home/kraft/trilinos/lib/libthyratpetra.so;/home/kraft/trilinos/lib/libthyraepetraext.so;/home/kraft/trilinos/lib/libthyraepetra.so;/home/kraft/trilinos/lib/libthyracore.so;/home/kraft/trilinos/lib/libepetraext.so;/home/kraft/trilinos/lib/libtpetraext.so;/home/kraft/trilinos/lib/libtpetrainout.so;/home/kraft/trilinos/lib/libtpetra.so;/home/kraft/trilinos/lib/libkokkostsqr.so;/home/kraft/trilinos/lib/libtpetrakernels.so;/home/kraft/trilinos/lib/libtpetraclassiclinalg.so;/home/kraft/trilinos/lib/libtpetraclassicnodeapi.so;/home/kraft/trilinos/lib/libtpetraclassic.so;/home/kraft/trilinos/lib/libtriutils.so;/home/kraft/trilinos/lib/libzoltan.so;/home/kraft/trilinos/lib/libepetra.so;/home/kraft/trilinos/lib/libsacado.so;/home/kraft/trilinos/lib/librtop.so;/home/kraft/trilinos/lib/libteuchoskokkoscomm.so;/home/kraft/trilinos/lib/libteuchoskokkoscompat.so;/home/kraft/trilinos/lib/libteuchosremainder.so;/home/kraft/trilinos/lib/libteuchosnumerics.so;/home/kraft/trilinos/lib/libteuchoscomm.so;/home/kraft/trilinos/lib/libteuchosparameterlist.so;/home/kraft/trilinos/lib/libteuchoscore.so;/home/kraft/trilinos/lib/libkokkosalgorithms.so;/home/kraft/trilinos/lib/libkokkoscontainers.so;/home/kraft/trilinos/lib/libkokkoscore.so;/home/kraft/trilinos/lib/libgtest.so;/usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux
Re: [deal.II] Re: Error during configuration since 9.0.0
On Wed, May 16, 2018, at 06:11 CDT, Pascal Kraft wrote: > Configuration now works if I explicitely switch scalapack off > (-DDEAL_II_WITH_SCALAPACK=OFF)... I will try to find out why. My guess is that scalapack was compiled against a different MPI version. Best, Matthias -- 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 dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Error during configuration since 9.0.0
Configuration now works if I explicitely switch scalapack off (-DDEAL_II_WITH_SCALAPACK=OFF)... I will try to find out why. Am Dienstag, 15. Mai 2018 19:38:03 UTC+2 schrieb Pascal Kraft: > > Dear Deal.ii devs, > > first off: Thanks for your great work and the many new features in 9.0.0! > I have compiled 9.0.0 successfully on a cluster however there seems to be > some kind of bug on my desktop (Ubuntu 18.04) where the configuration of > 8.5.1 works completely fine. > I run my cmake command and all dependencies are found. Then the test suite > for compilerflags crashes stating: > > ... > >> -- Include /home/kraft/Downloads/dealii-9.0.0/cmake/setup_finalize.cmake >> CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE): >> >> Configuration error: Cannot compile a test program with the final set >> of >> compiler and linker flags: >> CXX flags (DEBUG): -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 -pthread -Wno-unused-local-typedefs -Og -ggdb >> -Wa,--compress-debug-sections >> LD flags (DEBUG): -Wl,--as-needed -rdynamic -pthread -pthread -ggdb >> LIBRARIES (DEBUG): >> /usr/lib/x86_64-linux-gnu/libtbb.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_serialization.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_thread.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_date_time.so;/usr/lib/x86_64-linux-gnu/libboost_atomic.so;pthread;/home/kraft/trilinos/lib/libmuelu-adapters.so;/home/kraft/trilinos/lib/libmuelu-interface.so;/home/kraft/trilinos/lib/libmuelu.so;/home/kraft/trilinos/lib/libteko.so;/home/kraft/trilinos/lib/libstratimikos.so;/home/kraft/trilinos/lib/libstratimikosbelos.so;/home/kraft/trilinos/lib/libstratimikosaztecoo.so;/home/kraft/trilinos/lib/libstratimikosamesos.so;/home/kraft/trilinos/lib/libstratimikosml.so;/home/kraft/trilinos/lib/libstratimikosifpack.so;/home/kraft/trilinos/lib/libifpack2-adapters.so;/home/kraft/trilinos/lib/libifpack2.so;/home/kraft/trilinos/lib/libzoltan2.so;/home/kraft/trilinos/lib/libanasazitpetra.so;/home/kraft/trilinos/lib/libModeLaplace.so;/home/kraft/trilinos/lib/libanasaziepetra.so;/home/kraft/trilinos/lib/libanasazi.so;/home/kraft/trilinos/lib/libbelostpetra.so;/home/kraft/trilinos/lib/libbelosepetra.so;/home/kraft/trilinos/lib/libbelos.so;/home/kraft/trilinos/lib/libml.so;/home/kraft/trilinos/lib/libifpack.so;/home/kraft/trilinos/lib/libpamgen_extras.so;/home/kraft/trilinos/lib/libpamgen.so;/home/kraft/trilinos/lib/libamesos2.so;/home/kraft/trilinos/lib/libamesos.so;/home/kraft/trilinos/lib/libgaleri-xpetra.so;/home/kraft/trilinos/lib/libgaleri.so;/home/kraft/trilinos/lib/libaztecoo.so;/home/kraft/trilinos/lib/libisorropia.so;/home/kraft/trilinos/lib/libxpetra-sup.so;/home/kraft/trilinos/lib/libxpetra.so;/home/kraft/trilinos/lib/libthyratpetra.so;/home/kraft/trilinos/lib/libthyraepetraext.so;/home/kraft/trilinos/lib/libthyraepetra.so;/home/kraft/trilinos/lib/libthyracore.so;/home/kraft/trilinos/lib/libepetraext.so;/home/kraft/trilinos/lib/libtpetraext.so;/home/kraft/trilinos/lib/libtpetrainout.so;/home/kraft/trilinos/lib/libtpetra.so;/home/kraft/trilinos/lib/libkokkostsqr.so;/home/kraft/trilinos/lib/libtpetrakernels.so;/home/kraft/trilinos/lib/libtpetraclassiclinalg.so;/home/kraft/trilinos/lib/libtpetraclassicnodeapi.so;/home/kraft/trilinos/lib/libtpetraclassic.so;/home/kraft/trilinos/lib/libtriutils.so;/home/kraft/trilinos/lib/libzoltan.so;/home/kraft/trilinos/lib/libepetra.so;/home/kraft/trilinos/lib/libsacado.so;/home/kraft/trilinos/lib/librtop.so;/home/kraft/trilinos/lib/libteuchoskokkoscomm.so;/home/kraft/trilinos/lib/libteuchoskokkoscompat.so;/home/kraft/trilinos/lib/libteuchosremainder.so;/home/kraft/trilinos/lib/libteuchosnumerics.so;/home/kraft/trilinos/lib/libteuchoscomm.so;/home/kraft/trilinos/lib/libteuchosparameterlist.so;/home/kraft/trilinos/lib/libteuchoscore.so;/home/kraft/trilinos/lib/libkokkosalgorithms.so;/home/kraft/trilinos/lib/libkokkoscontainers.so;/home/kraft/trilinos/lib/libkokkoscore.so;/home/kraft/trilinos/lib/libgtest.so;/usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libmetis.so;rt;/usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/libhdf5_hl.so;/usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/libhdf5.so;/usr/lib/libscalapack.so;/usr/lib/x86_64-linux-gnu/libopenblas.so;gfortran;q
[deal.II] Re: Error during configuration since 9.0.0
I have now tried compiling the code from the last error. First i simply
used mpicc which worked fine. The command
/usr/bin/c++-DMPI_WORKING_COMPILER -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 -pthread -o ./b.o -c ./b.cpp
also worked but
/usr/bin/c++ -DMPI_WORKING_COMPILER -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 -pthread-rdynamic ./b.o
-o b -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -rdynamic
-fuse-ld=gold -pthread -lm
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempi_ignore_tkr.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
failed with the same error messages as in the error log, aka
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined
reference to 'opal_list_item_t_class'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined
reference to 'opal_class_initialize'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined
reference to 'opal_uses_threads'
I found this dealii issue referencing the problem:
https://github.com/dealii/dealii/issues/2820 but there seems to be no
proposed solution and I find that weird since, as mentioned before, dealii
8.5.1 runs completely fine.
I have then removed the gold linker. I did this by commenting out the line
"ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")" in
cmake/checks/check_01_compiler_features.cmake
The error seems to be resolved now. However all the others remain from what
I can see. The last error ist now this:
Performing C++ SOURCE FILE Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG failed with
the following output:
Change Dir: /home/kraft/Downloads/dealbuild/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/make" "cmTC_1c675/fast"
/usr/bin/make -f CMakeFiles/cmTC_1c675.dir/build.make
CMakeFiles/cmTC_1c675.dir/build
make[1]: Entering directory
'/home/kraft/Downloads/dealbuild/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_1c675.dir/src.cxx.o
/usr/bin/c++-DDEAL_II_HAVE_USABLE_FLAGS_DEBUG -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 -pthread
-Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections -o
CMakeFiles/cmTC_1c675.dir/src.cxx.o -c
/home/kraft/Downloads/dealbuild/CMakeFiles/CMakeTmp/src.cxx
make[1]: *** No rule to make target '/usr/lib/libscalapack.so', needed by
'cmTC_1c675'. Stop.
make[1]: Leaving directory
'/home/kraft/Downloads/dealbuild/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_1c675/fast' failed
make: *** [cmTC_1c675/fast] Error 2
Source file was:
int main(){ return 0; }
However a simple call of
/usr/bin/c++ -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
-pthread -Wno-unused-local-typedefs -Og -ggdb
-Wa,--compress-debug-sections -o /home/kraft/temp/test/b_b.o -c
/home/kraft/temp/test/b.cpp
yields no errors (code in b.cpp is int main(){ return 0; }).
So am I right in suggesting that there might be an error in
-DDEAL_II_HAVE_USABLE_FLAGS_DEBUG ?
Do you have any suggestions on what I could try next?
Am Dienstag, 15. Mai 2018 19:38:03 UTC+2 schrieb Pascal Kraft:
>
> Dear Deal.ii devs,
>
> first off: Thanks for your great work and the many new features in 9.0.0!
> I have compiled 9.0.0 successfully on a cluster however there seems to be
> some kind of bug on my desktop (Ubuntu 18.04) where the configuration of
> 8.5.1 works completely fine.
> I run my cmake command and all dependencies are found. Then the test suite
> for compilerflags crashes stating:
>
> ...
>
>> -- Include /home/kraft/Downloads/dealii-9.0.0/cmake/setup_finalize.cmake
>> CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
>>
>> Configuration error: Cannot compile a test program with the final set
>> of
>> compiler and linker flags:
>> CXX flags (DEBUG): -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 -pthread -Wno-unused-local-typedefs -Og -ggdb
>> -Wa,--compress-debug-sections
>> LD flags (DEBUG): -Wl,--as-needed -rdynamic -pthread -pthread -ggdb
>> LIBRARIES (DEBUG):
>> /usr/lib/x86_64-linux-gnu/libtbb.so;/usr/lib/x86_6
