> In your log file, the error comes from using -lpthreads (not the 's' at the
> end).
And by “not” you mean “note”?
> You don't say what the exact error message is,
Is the last error in the CMakeError.log the relevant one?
Configuration error: Cannot compile a test program with the final set of
compiler and linker flags:
CXX flags (DEBUG): -fpic -ansi -w2 -diag-disable=remark -wd21 -wd68
-wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 -wd1418 -wd1478
-wd1572 -wd2259 -wd2536 -wd2651
-wd3415 -wd15531 -wd111 -wd128 -wd185 -wd186 -wd280 -qopenmp-simd -std=c++14
-Wno-parentheses -O0 -g -gdwarf-2 -grecord-gcc-switches -g -march=native
-I/opt/intel/compilers_and_librarie
s_2019.5.281/linux/tbb/include -O0
LD flags (DEBUG): -Wl,--as-needed -shared-intel -qopenmp -rdynamic
-Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker
/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/i
ntel64/lib/release -Xlinker -rpath -Xlinker
/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib -lpthread
LIBRARIES (DEBUG):
/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib/libmpicxx.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_iostreams.so;/opt/apps/inte
l19/python2_7/boost/1.69/lib/libboost_serialization.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_system.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_thread.so;-lpthr
ead;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_regex.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_chrono.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_date_t
ime.so;/opt/apps/intel19/python2_7/boost/1.69/lib/libboost_atomic.so;/opt/apps/intel19/metis/5.1.0/lib/libmetis.so;/opt/apps/intel19/gsl/2.5/lib/libgsl.so;/opt/apps/intel19/gsl/2.5/lib/libgslcblas.so;/home1/apps/intel19/impi19_0/p4est/2.2/lib/libp4est.so;/home1/apps/intel19/impi19_0/p4est/2.2/lib/libsc.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmklcore.so;/home1/apps/intel19/impi19_0/slepc/3.11/clx/lib/libslepc.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libpetsc.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libHYPRE.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libcmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libdmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libzmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libmumps_common.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libpord.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libscalapack.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libumfpack.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libklu.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libcholmod.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libbtf.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libccolamd.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libcolamd.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libcamd.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libamd.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsuitesparseconfig.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsuperlu.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsuperlu_dist.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libEl.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libElSuiteSparse.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libpmrrr.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libspai.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsundials_cvode.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsundials_nvecserial.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libsundials_nvecparallel.a;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_sequential.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64/libmkl_def.so;/opt/apps/intel19/impi19_0/phdf5/1.10.4/x86_64/lib/libhdf5hl_fortran.so;/opt/apps/intel19/impi19_0/phdf5/1.10.4/x86_64/lib/libhdf5_fortran.so;/opt/apps/intel19/impi19_0/phdf5/1.10.4/x86_64/lib/libhdf5_hl.so;/opt/apps/intel19/impi19_0/phdf5/1.10.4/x86_64/lib/libhdf5.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libchaco.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libzoltan.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libparmetis.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libmetis.so;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libptesmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libptscotchparmetis.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libptscotch.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libptscotcherr.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libesmumps.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libscotch.a;/home1/apps/intel19/impi19_0/petsc/3.11/clx/lib/libscotcherr.a;/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib/libmpifort.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib/release/libmpi.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libifport.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libifcoremt_pic.a;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libimf.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libsvml.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libipgo.a;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libirc.so;/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin/libirc_s.a;rt;m;pthread;/usr/lib64/libz.so;dl;
> but I would suspect that the problem results from this different spelling.
> Now, I looked into the deal.II sources and I can't find any occurrence where
> we would test with this spelling. What is your setting for CXXFLAGS, LDFLAGS,
> etc?
cmake -VV \
-DCMAKE_INSTALL_PREFIX=%{INSTALL_DIR} \
\
-DDEAL_II_WITH_CXX11=ON \
-DDEAL_II_WITH_CXX17=OFF \
-DDEAL_II_CXX_FLAGS_DEBUG="${BASIC_FLAGS} -O0" \
-DDEAL_II_CXX_FLAGS_RELEASE="${BASIC_FLAGS} -O2" \
\
-DDEAL_II_COMPONENT_MESH_CONVERTER=ON \
\
-DDEAL_II_WITH_MPI=ON \
${MPI_SPECIFICATION} \
${LAPACK_SPECIFICATION} \
\
-DBOOST_DIR=${TACC_BOOST_DIR} \
-DDEAL_II_WITH_GSL=ON \
-DGSL_INCLUDE_DIR=${TACC_GSL_INC:-NO_GSL_INC} \
-DGSL_LIBRARY_DIR=${TACC_GSL_LIB:-NO_GSL_LIB} \
-DGSL_LIBRARY=${TACC_GSL_LIB:-NO_GSL_LIB}/libgsl.so\;${TACC_GSL_LIB:-NO_GSL_LIB}/lib\gslcblas.so
\
-DHDF5_DIR=${TACC_HDF5_DIR} \
-DDEAL_II_WITH_METIS=${CMAKE_USE_METIS} \
-DMETIS_DIR=${TACC_METIS_DIR} \
\
` if [ ${TACC_FAMILY_COMPILER} = "intel" ] ; then echo " \
-DMUMPS_DIR=${TACC_MUMPS_DIR} \
" ; fi ` \
-DDEAL_II_WITH_PETSC=${CMAKE_USE_PETSC} \
-DPETSC_DIR=${PETSC_DIR} -DPETSC_ARCH=${PETSC_ARCH} \
-DDEAL_II_WITH_SLEPC=${CMAKE_USE_PETSC} \
-DSLEPC_DIR=${TACC_SLEPC_DIR} \
-DDEAL_II_WITH_P4EST=ON \
-DP4EST_DIR=${P4ESTDIR} \
-DDEAL_II_WITH_TRILINOS=${CMAKE_USE_TRILINOS} \
-DTRILINOS_DIR=${TACC_TRILINOS_DIR} \
${DEALDIR}/dealii-${DEALVERSION} \
\
%{_topdir}/BUILD/dealii-%{version} \
2>&1 | tee ${LOGDIR}/dealii_cmake.log
Where
export BASIC_FLAGS="-g -march=native"
export BASIC_FLAGS="${BASIC_FLAGS} -I${TBBROOT}/include"
(Doesn’t cmake write this stuff to the log files?)
V.
--
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 [email protected].
To view this discussion on the web visit
https://groups.google.com/d/msgid/dealii/49178816-EE96-46EF-86F4-AF74E7EB7471%40tacc.utexas.edu.
