[deal.II] Re: Linking error when compiling with Trilinos

2017-09-17 Thread Denis Davydov
You might want to try one of the source-based installers for deal.II, see 
*Source-based 
Installers* https://www.dealii.org/download.html

Regards,
Denis.

On Wednesday, September 13, 2017 at 10:58:10 AM UTC+2, Maxi Miller wrote:
>
> I set up a new dealII-installation on another computer, but when including 
> Trilinos, it fails with (from CMakeError.log):
>
> Performing C++ SOURCE FILE Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG failed 
> with the following output:
> Change Dir: ~/Downloads/dealii/build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTC_b88e6/fast"
> /usr/bin/gmake -f CMakeFiles/cmTC_b88e6.dir/build.make CMakeFiles/
> cmTC_b88e6.dir/build
> gmake[1]: Entering directory 
> `~/Downloads/dealii/build/CMakeFiles/CMakeTmp'
> Building CXX object CMakeFiles/cmTC_b88e6.dir/src.cxx.o
> ~/local_opt/openmpi/bin/mpic++-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++14 
> -fPIC -march=native -fopenmp -Wno-parentheses -Wno-unused-local-typedefs 
> -Og -ggdb -Wa,--compress-debug-sections   -o 
> CMakeFiles/cmTC_b88e6.dir/src.cxx.o -c 
> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx
> Linking CXX executable cmTC_b88e6
> ~/local_opt/cmake/bin/cmake -E cmake_link_script 
> CMakeFiles/cmTC_b88e6.dir/link.txt --verbose=1
> ~/local_opt/openmpi/bin/mpic++   -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++14 
> -fPIC -march=native -fopenmp -Wno-parentheses -Wno-unused-local-typedefs 
> -Og -ggdb -Wa,--compress-debug-sections-rdynamic 
> CMakeFiles/cmTC_b88e6.dir/src.cxx.o  -o cmTC_b88e6 
>  -L~/local_opt/intel/tbb/lib/intel64/gcc4.7 
> -Wl,-rpath,~/local_opt/trilinos/lib:~/local_opt/boost/lib:~/local_opt/intel/tbb/lib/intel64/gcc4.7:~/local_opt/suitesparse/lib:~/local_opt/petsc/lib:~/local_opt/p4est/lib
>  
> -rdynamic -fuse-ld=gold -Wl,-rpath -Wl,~/local_opt/openmpi/lib 
> -Wl,--enable-new-dtags -ggdb /usr/lib64/libbz2.so /usr/lib64/libz.so 
> ~/local_opt/trilinos/lib/libpike-blackbox.so 
> ~/local_opt/trilinos/lib/libtrilinoscouplings.so 
> ~/local_opt/trilinos/lib/libpiro.so ~/local_opt/trilinos/lib/librol.so 
> ~/local_opt/trilinos/lib/libstokhos_muelu.so 
> ~/local_opt/trilinos/lib/libstokhos_ifpack2.so 
> ~/local_opt/trilinos/lib/libstokhos_amesos2.so 
> ~/local_opt/trilinos/lib/libstokhos_tpetra.so 
> ~/local_opt/trilinos/lib/libstokhos_sacado.so 
> ~/local_opt/trilinos/lib/libstokhos.so 
> ~/local_opt/trilinos/lib/libtempus.so 
> ~/local_opt/trilinos/lib/librythmos.so 
> ~/local_opt/trilinos/lib/libmuelu-adapters.so 
> ~/local_opt/trilinos/lib/libmuelu-interface.so 
> ~/local_opt/trilinos/lib/libmuelu.so ~/local_opt/trilinos/lib/libmoertel.so 
> ~/local_opt/trilinos/lib/liblocathyra.so 
> ~/local_opt/trilinos/lib/liblocaepetra.so 
> ~/local_opt/trilinos/lib/liblocalapack.so 
> ~/local_opt/trilinos/lib/libloca.so 
> ~/local_opt/trilinos/lib/libnoxepetra.so 
> ~/local_opt/trilinos/lib/libnoxlapack.so ~/local_opt/trilinos/lib/libnox.so 
> ~/local_opt/trilinos/lib/libphalanx.so 
> ~/local_opt/trilinos/lib/libstk_expreval.so 
> ~/local_opt/trilinos/lib/libstk_mesh_fixtures.so 
> ~/local_opt/trilinos/lib/libstk_tools_lib.so 
> ~/local_opt/trilinos/lib/libstk_transfer_impl.so 
> ~/local_opt/trilinos/lib/libstk_search_util_base.so 
> ~/local_opt/trilinos/lib/libstk_search.so 
> ~/local_opt/trilinos/lib/libstk_unit_main.so 
> ~/local_opt/trilinos/lib/libstk_unit_test_utils.so 
> ~/local_opt/trilinos/lib/libstk_io_util.so 
> ~/local_opt/trilinos/lib/libstk_io.so 
> ~/local_opt/trilinos/lib/libstk_mesh_base.so 
> ~/local_opt/trilinos/lib/libstk_topology.so 
> ~/local_opt/trilinos/lib/libstk_util_use_cases.so 
> ~/local_opt/trilinos/lib/libstk_util_registry.so 
> ~/local_opt/trilinos/lib/libstk_util_diag.so 
> ~/local_opt/trilinos/lib/libstk_util_env.so 
> ~/local_opt/trilinos/lib/libstk_util_parallel.so 
> ~/local_opt/trilinos/lib/libstk_util_util.so 
> ~/local_opt/trilinos/lib/libintrepid2.so 
> ~/local_opt/trilinos/lib/libintrepid.so ~/local_opt/trilinos/lib/libteko.so 
> ~/local_opt/trilinos/lib/libfei_trilinos.so 
> ~/local_opt/trilinos/lib/libfei_base.so 
> ~/local_opt/trilinos/lib/libstratimikos.so 
> ~/local_opt/trilinos/lib/libstratimikosbelos.so 
> ~/local_opt/trilinos/lib/libstratimikosaztecoo.so 
> ~/local_opt/trilinos/lib/libstratimikosamesos.so 
> ~/local_opt/trilinos/lib/libstratimikosml.so 
> ~/local_opt/trilinos/lib/libstratimikosifpack.so 
> ~/local_opt/trilinos/lib/libifpack2-adapters.so 
> ~/local_opt/trilinos/lib/libifpack2.so 
> ~/local_opt/trilinos/lib/libanasazitpetra.so 
> ~/local_opt/trilinos/lib/libModeLaplace.so 
> ~/local_opt/trilinos/lib/libanasaziepetra.so 
> 

[deal.II] Re: Linking error when compiling with Trilinos

2017-09-13 Thread Bruno Turcksin
Hi,

You have several problems.

On Wednesday, September 13, 2017 at 4:58:10 AM UTC-4, Maxi Miller wrote:

>
> ~/local_opt/trilinos/lib/libmuelu-adapters.so: error: undefined reference 
> to 'dmumps_c'
>
You have compile deal or trilinos with MUMPS support but the linker does 
not find it

/petsc/lib/libsuperlu_dist.so ~/local_opt/parmetis/lib/libparmetis.a ~
> /local_opt/metis/lib/libmetis.a /usr/lib64/liblapack.so /usr/lib64/libblas
> .so /usr/lib64/libhwloc.so /usr/lib64/libX11.so /usr/lib64/libssl.so /usr/
> lib64/libcrypto.so ~/local_opt/openmpi/lib/libmpi_usempif08.so ~
> /local_opt/openmpi/lib/libmpi_usempi_ignore_tkr.so ~/local_opt/openmpi/lib
> /libmpi_mpifh.so -ldl -lrt ~/local_opt/p4est/lib/libp4est.so ~/local_opt/
> p4est/lib/libsc.so /usr/lib64/libopenblas.so -lmpi_usempif08 
> -lmpi_usempi_ignore_tkr 
> -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lpthread -lc -lgcc_s -lgcc ~
> /local_opt/openmpi/lib/libmpi.so 
> ~/local_opt/intel/mkl/lib/intel64/libmkl_rt.so: error: undefined 
> reference to 'printf'
> ~/local_opt/intel/mkl/lib/intel64/libmkl_rt.so: error: undefined 
> reference to 'strchr'
>
The error is from MKL which implements Lapack BUT in you are also using 
openblas which implements Lapack and Lapack. So you are mixing three 
different implementation of Lapack (MKL, Openblas, and lapack). That's a 
recipe for disaster make sure all the libraries that you are compiling are 
using the same implementation of Lapack.

Best,

Bruno


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