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_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;quadmath;m;c;gcc_s;gcc;/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;/home/kraft/p4est/DEBUG/lib/libp4est.so;/home/kraft/p4est/DEBUG/lib/libsc.so
>>
>> Call Stack (most recent call first):
>> cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>> CMakeLists.txt:132 (VERBOSE_INCLUDE)
>>
>>
>> -- Configuring incomplete, errors occurred!
>>
> in the error log i find several errors - it is appended - and I will also
> append the log.
>
> I continued to try to compile the source code mentioned in the error log
> manually. I saved the source-code in a file and called /usr/bin/c++
> -mavx512f -o a.o -c a.cpp. Compilation ran without errors but after that I
> could not execute the binary from the bash with an error saying "cannot
> execute binary file: Exec format error" but I'm not sure if this should
> work anyway without further parameters for calling the binary. I have not
> tried the other code-segments.
> On the exact same setup with the same library dependencies, 8.5.1
> configures and runs fine.
> Is there anything I missed?
>
> With kind regards and thank you for your time in advance,
> Pascal Kraft
>
--
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