Re: [deal.II] Error during configuration since 9.0.0

2018-05-15 Thread Pascal Kraft 
Dear Timo,

I can check that tomorrow when I'm on that machine again. However: To make 
certain that it wasnt a mistake with my setup I downloaded dealii 8.5.1 
after the problem occured and configured and built it without errors and 
the exact same cmake command. 
In the past (I will also be able to check this tomorrow) I also ran 
mpi-enabled codes of mine on that machine. Could there still be a problem 
with my openmpi-install?

With kind regards,
Pascal Kraft

Am Dienstag, 15. Mai 2018 21:30:12 UTC+2 schrieb Timo Heister:
>
> You need to look at the last error in CMakeError.log: 
>
> > Linking CXX executable cmTC_7254e 
> > /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7254e.dir/link.txt 
> --verbose=1 
> > /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 
> CMakeFiles/cmTC_7254e.dir/src.cxx.o  -o cmTC_7254e 
> -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 
> > /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' 
>
> It looks like a problem with the MPI-installation/detection. Can you 
> link a simple hello-mpi example? 
>
>
>
>
>
> On Tue, May 15, 2018 at 7:38 PM, Pascal Kraft  > wrote: 
> > 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): 
> >> 
>

Re: [deal.II] Error during configuration since 9.0.0

2018-05-15 Thread Timo Heister 
You need to look at the last error in CMakeError.log:

> Linking CXX executable cmTC_7254e
> /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7254e.dir/link.txt 
> --verbose=1
> /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 
> CMakeFiles/cmTC_7254e.dir/src.cxx.o  -o cmTC_7254e 
> -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
> /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'

It looks like a problem with the MPI-installation/detection. Can you
link a simple hello-mpi example?





On Tue, May 15, 2018 at 7:38 PM, Pascal Kraft  wrote:
> 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):
>>