Hi, I am trying to compile libmesh 0.6.1 with petsc2.3.3 and openmpi. I do:
$ PETSC_DIR=/usr/lib/petsc PETSC_ARCH=linux-gnu-c-opt ./configure --prefix=/usr --disable-laspack --disable-slepc --disable-sfc --disable-gzstreams --disable-tecplot --disable-metis --disable-parmetis --disable-tetgen --disable-triangle --with-f77=gfortran --with-mpi=/usr --------------------------------------------- ----------- Configuring libMesh ------------- --------------------------------------------- checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed <<< C++ compiler is gcc-4.2 >>> checking how to run the C++ preprocessor... g++ -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for short int... yes checking size of short int... 2 checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for float... yes checking size of float... 4 checking for double... yes checking size of double... 8 checking for void *... yes checking size of void *... 4 checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking csignal usability... yes checking csignal presence... yes checking for csignal... yes checking whether the compiler implements namespaces... yes checking whether the compiler has locale... yes checking whether the compiler has stringstream... yes checking hash_map usability... no checking hash_map presence... no checking for hash_map... no checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking hash_set usability... no checking hash_set presence... no checking for hash_set... no checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether the compiler supports GCC C++ ABI name demangling... yes checking whether the c++ compiler supports glibc backtrace... yes <<< Configuring library with AMR support >>> <<< Configuring library with periodic BC support >>> <<< Configuring library with higher order p-FEM shapes >>> checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for xdrstdio_create... yes <<< Configuring library with XDR support >>> <<< Configuring library with real number support >>> <<< Configuring library with reference counting support >>> checking for ./contrib/netcdf/lib/i686-pc-linux-gnu/libnetcdf.a... no checking for ./contrib/netcdf/include/netcdf.h... no --------------------------------------------- ----- Configuring for optional packages ----- --------------------------------------------- checking for /usr/lib/petsc/include/petsc.h... yes checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/i486-linux-gnu/4.2.3 -L/usr/lib/gcc/i486-linux-gnu/4.2.3/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i486-linux-gnu/4.2.3/../../.. -lgfortranbegin -lgfortran -lm -lgcc_s <<< Configuring library with PETSc version 2.3.3 support >>> checking for doxygen... no <<< Configuring library with GMV support >>> checking /usr/include/vtk/vtkCommonInstantiator.h usability... no checking /usr/include/vtk/vtkCommonInstantiator.h presence... no checking for /usr/include/vtk/vtkCommonInstantiator.h... no VTK header files not found! ---------------------------------------------- --- Done configuring for optional packages --- ---------------------------------------------- checking for perl... /usr/bin/perl configure: creating ./config.status config.status: creating Make.common config.status: creating doc/Doxyfile config.status: creating contrib/bin/libmesh-config config.status: creating contrib/bin/xda2mgf config.status: creating contrib/bin/create_libmesh_release config.status: creating doc/dot config.status: creating include/base/libmesh_contrib_config.h config.status: creating include/base/libmesh_config.h --------------------------------------------- --------- Done Configuring libMesh ---------- --------------------------------------------- This seems to be allright. Then: $ make -j4 [no errors] $ examples/ex2/ $ make Compiling C++ (in optimized mode) ex2.C... Linking ex2-opt... ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)': ex2.C:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x27): undefined reference to `ompi_mpi_cxx_op_intercept' ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Intracomm::Clone() const': ex2.C:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x44): undefined reference to `MPI::Comm::Comm()' ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Graphcomm::Clone() const': ex2.C:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone() const]+0x41): undefined reference to `MPI::Comm::Comm()' ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const': ex2.C:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const]+0x53): undefined reference to `MPI::Comm::Comm()' ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const': ex2.C:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const]+0x159): undefined reference to `MPI::Comm::Comm()' ex2.i686-pc-linux-gnu.opt.o: In function `MPI::Cartcomm::Clone() const': ex2.C:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone() const]+0x41): undefined reference to `MPI::Comm::Comm()' ex2.i686-pc-linux-gnu.opt.o:ex2.C:(.text._ZN3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*)]+0x8a): more undefined references to `MPI::Comm::Comm()' follow ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI3WinE[vtable for MPI::Win]+0x14): undefined reference to `MPI::Win::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI3WinE[vtable for MPI::Win]+0x24): undefined reference to `MPI::Win::Free()' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI9IntercommE[vtable for MPI::Intercomm]+0xd4): undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI9GraphcommE[vtable for MPI::Graphcomm]+0xd4): undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI8CartcommE[vtable for MPI::Cartcomm]+0xd4): undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI9IntracommE[vtable for MPI::Intracomm]+0xd4): undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI4CommE[vtable for MPI::Comm]+0xd4): undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ex2.i686-pc-linux-gnu.opt.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x3c): undefined reference to `MPI::Datatype::Free()' collect2: ld returned 1 exit status make: *** [ex2-opt] Error 1 Any ideas what could be wrong? Ondrej ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Libmesh-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-devel
