> 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.