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 <kraft.pas...@gmail.com> 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): >> /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 > > -- > The deal.II project is located at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=_uMHDofFQY2qbLcLayon0hPc4p9fn5H4fs9ZbHPEBZw&s=R4sHFVoHRElg61ed83K2Eol210M34BBWWgUopjB73rA&e= > For mailing list/forum options, see > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=_uMHDofFQY2qbLcLayon0hPc4p9fn5H4fs9ZbHPEBZw&s=9fDnmOSCxS5yFCw120CTH9AshVulxZQWCoOKMTVli6o&e= > --- > 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://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=_uMHDofFQY2qbLcLayon0hPc4p9fn5H4fs9ZbHPEBZw&s=0mTJwVVGzgJs97oHTI1Uz9noyVoTtVIydbR047NYQTk&e=. -- Timo Heister http://www.math.clemson.edu/~heister/ -- 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. 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