[Dune] dune installation problem

Wed Jun 3 04:58:35 CEST 2015

By the way, the opt file is as follows:

CONFIGURE_FLAGS="     MPICC='$HOME/extlib/openmpi-1.8/bin/mpicc'
            CC=gcc-4.7
            CFLAGS='-O3 -g0 --no-strict-aliasing'
            CPP=cpp-4.7
            CPPFLAGS='-O3 -g0 --no-strict-aliasing'
            CXX=g++-4.7
            CXXFLAGS='-O3 -g0 --no-strict-aliasing'
            F77=gfortran-4.7
            FFLAGS='-O3 -g0 --no-strict-aliasing'
            FC=gfortran-4.7
            #FCFLAGS='-O3 -g0 --no-strict-aliasing'
            --enable-parallel
            --prefix='$HOME/extlib/cyrus'
            --with-metis='$HOME/extlib/metis-5.1'
            --with-alugrid='$HOME/extlib/alugrid-1.52' "

On Wed, Jun 3, 2015 at 4:57 AM, Arya Fallahi <arya.fallahi at gmail.com> wrote:

> Dear dune,
>
> I have faced with some serious troubles with upgrading my mpi
> installation. After the new released mpi (v1.8) is installed, I could never
> compile the dune package. I checked very many solutions even going to
> previous versions of dune. But, none of them worked. I wonder if you can
> help me with the problem.
>
> Surprisingly, after dune-common is compiled, dune-geometry returns an
> error that there is no dune-common module in the domain. The following is
> the output in the terminal. I have also attached the log files for the
> dune-common and dune-geometry.
>
> I will be very thankful if you help me on this matter,
>
> Regards,
> Arya
>
>
> [cfel-kaert-lx1] ~/workspace $ sudo ./dune-common/bin/dunecontrol
> --opts=cyrus.opts all
> --- going to build dune-common dune-geometry dune-grid cyrus  ---
> --- calling all for dune-common ---
> --- calling autogen for dune-common ---
> Skipping dune-autogen
> --- calling configure for dune-common ---
> ----- using default flags $CONFIGURE_FLAGS from /afs/
> desy.de/user/a/afallahi/workspace/cyrus.opts -----
> ./configure MPICC='/afs/
> desy.de/user/a/afallahi/extlib/openmpi-1.8/bin/mpicc' CC=gcc-4.7
> CFLAGS='-O3 -g0 --no-strict-aliasing' CPP=cpp-4.7 CPPFLAGS='-O3 -g0
> --no-strict-aliasing' CXX=g++-4.7 CXXFLAGS='-O3 -g0 --no-strict-aliasing'
> F77=gfortran-4.7 FFLAGS='-O3 -g0 --no-strict-aliasing' FC=gfortran-4.7
> #FCFLAGS='-O3 -g0 --no-strict-aliasing' --enable-parallel --prefix='/afs/
> desy.de/user/a/afallahi/extlib/cyrus' --with-metis='/afs/
> desy.de/user/a/afallahi/extlib/metis-5.1'  ACLOCAL_AMFLAGS="-I . -I
> m4"user/a/afallahi/extlib/alugrid-1.52'
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a pax tar archive... gnutar
> checking whether make supports nested variables... yes
> checking how to create a pax tar archive... (cached) gnutar
> checking for inkscape... inkscape
> checking for doxygen... doxygen
> checking for latex... latex
> checking for bibtex... bibtex
> checking for dvipdf... dvipdf
> checking for dvips... dvips
> checking for wml... no
> checking for dot... dot
> checking for perl... perl
> checking for convert... convert
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for style of include used by make... GNU
> checking for gcc... gcc-4.7
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc-4.7 accepts -g... yes
> checking for gcc-4.7 option to accept ISO C89... none needed
> checking dependency style of gcc-4.7... gcc3
> checking dependency style of gcc-4.7... (cached) gcc3
> checking how to run the C preprocessor... cpp-4.7
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++-4.7 accepts -g... yes
> checking dependency style of g++-4.7... gcc3
> checking dependency style of g++-4.7... (cached) gcc3
> checking how to run the C++ preprocessor... g++-4.7 -E
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran-4.7 accepts -g... yes
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran-4.7 accepts -g... yes
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking how to print strings... printf
> checking for a sed that does not truncate output... /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by gcc-4.7... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 98304
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking how to convert x86_64-unknown-linux-gnu file names to
> x86_64-unknown-linux-gnu format... func_convert_file_noop
> checking how to convert x86_64-unknown-linux-gnu file names to toolchain
> format... func_convert_file_noop
> checking for /usr/bin/ld option to reload object files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for dlltool... no
> checking how to associate runtime and link libraries... printf %s\n
> checking for ar... ar
> checking for archiver @FILE support... @
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc-4.7 object... ok
> checking for sysroot... no
> checking for mt... no
> checking if : is a manifest tool... no
> 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 dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc-4.7 supports -fno-rtti -fno-exceptions... no
> checking for gcc-4.7 option to produce PIC... -fPIC -DPIC
> checking if gcc-4.7 PIC flag -fPIC -DPIC works... yes
> checking if gcc-4.7 static flag -static works... yes
> checking if gcc-4.7 supports -c -o file.o... yes
> checking if gcc-4.7 supports -c -o file.o... (cached) yes
> checking whether the gcc-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking how to run the C++ preprocessor... g++-4.7 -E
> checking for ld used by g++-4.7... /usr/bin/ld -m elf_x86_64
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> checking whether the g++-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking for g++-4.7 option to produce PIC... -fPIC -DPIC
> checking if g++-4.7 PIC flag -fPIC -DPIC works... yes
> checking if g++-4.7 static flag -static works... yes
> checking if g++-4.7 supports -c -o file.o... yes
> checking if g++-4.7 supports -c -o file.o... (cached) yes
> checking whether the g++-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for gfortran-4.7 option to produce PIC... -fPIC
> checking if gfortran-4.7 PIC flag -fPIC works... yes
> checking if gfortran-4.7 static flag -static works... yes
> checking if gfortran-4.7 supports -c -o file.o... yes
> checking if gfortran-4.7 supports -c -o file.o... (cached) yes
> checking whether the gfortran-4.7 linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for gfortran-4.7 option to produce PIC... -fPIC
> checking if gfortran-4.7 PIC flag -fPIC works... yes
> checking if gfortran-4.7 static flag -static works... yes
> checking if gfortran-4.7 supports -c -o file.o... yes
> checking if gfortran-4.7 supports -c -o file.o... (cached) yes
> checking whether the gfortran-4.7 linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for ranlib... (cached) ranlib
> checking how to get verbose linking output from gfortran-4.7... -v
> checking for Fortran 77 libraries of gfortran-4.7...  -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2
> -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../..
> -lgfortran -lm -lquadmath
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... lower case, underscore, no
> extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -lblas... yes
> checking for dgemm_ in -ldgemm... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for sgemm_ in -lscs... no
> checking for sgemm_ in -lcomplib.sgimath... no
> checking for sgemm_ in -lblas... (cached) yes
> checking for sgemm_ in -lessl... no
> checking for sgemm_ in -lblas... (cached) yes
> checking for cheev_... no
> checking for cheev_ in -llapack... yes
> checking how to get verbose linking output from gfortran-4.7... -v
> checking for Fortran libraries of gfortran-4.7...  -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2
> -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../..
> -lgfortran -lm -lquadmath
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, no
> extra underscore
> checking whether compiler is officially supported by DUNE... yes
> checking whether g++ accepts -std=c++0x... yes
> checking whether static_assert is supported... yes
> checking whether nullptr is supported... yes
> checking type_traits usability... yes
> checking type_traits presence... yes
> checking for type_traits... yes
> checking tr1/type_traits usability... yes
> checking tr1/type_traits presence... yes
> checking for tr1/type_traits... yes
> checking tuple usability... yes
> checking tuple presence... yes
> checking for tuple... yes
> checking tr1/tuple usability... yes
> checking tr1/tuple presence... yes
> checking for tr1/tuple... yes
> checking whether <array> C++0x is supported... yes
> checking memory usability... yes
> checking memory presence... yes
> checking for memory... yes
> checking tr1/memory usability... yes
> checking tr1/memory presence... yes
> checking for tr1/memory... yes
> checking boost/shared_ptr.hpp usability... no
> checking boost/shared_ptr.hpp presence... no
> checking for boost/shared_ptr.hpp... no
> checking the location of shared_ptr header file...
> checking whether SHARED_PTR_NAMESPACE (std) provides make_shared... yes
> checking whether compiling C++ code works... yes
> checking whether linking C++ objects works... yes
> checking for __attribute__((deprecated))... yes
> checking for __attribute__((deprecated("message")))... yes
> checking for __attribute__((unused))... yes
> checking rpc/rpc.h usability... yes
> checking rpc/rpc.h presence... yes
> checking for rpc/rpc.h... yes
> checking for an ANSI C-conforming const... yes
> checking for inline... inline
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking for stdlib.h... (cached) yes
> checking for GNU libc compatible malloc... yes
> checking for GMP... configure: searching for GMP in /usr...
> checking gmpxx.h usability... yes
> checking gmpxx.h presence... yes
> checking for gmpxx.h... yes
> checking for __gmpz_abs in -L/usr/lib -lgmp... yes
> checking for __gmpz_abs in -L/usr/lib -lgmpxx... yes
> /usr
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for string.h... (cached) yes
> checking for pow in -lm... yes
> checking for sqrt... yes
> checking for strchr... yes
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating lib/Makefile
> config.status: creating bin/Makefile
> config.status: creating dune/Makefile
> config.status: creating dune/common/Makefile
> config.status: creating dune/common/test/Makefile
> config.status: creating dune/common/parallel/Makefile
> config.status: creating dune/common/parallel/test/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/doxygen/Makefile
> config.status: creating doc/doxygen/Doxyfile
> config.status: creating doc/buildsystem/Makefile
> config.status: creating m4/Makefile
> config.status: creating am/Makefile
> config.status: creating bin/check-log-store
> config.status: creating dune-common.pc
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: executing depfiles commands
> config.status: executing libtool commands
>
> Found the following Dune-components:
>
> ----------------------------------------
>
> GMP.....................: yes
> MPI.....................: no
>
> ----------------------------------------
>
> See ./configure --help and config.log for reasons why a component wasn't
> found
>
> --- calling make for dune-common ---
> make
> make  all-recursive
> make[1]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common'
> Making all in dune
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune'
> Making all in common
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common'
> Making all in .
> make[4]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common'
> make[4]: Nothing to be done for `all-am'.
> make[4]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common'
> Making all in test
> make[4]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/test'
> make[4]: Nothing to be done for `all'.
> make[4]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/test'
> Making all in parallel
> make[4]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel'
> Making all in test
> make[5]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel/test'
> make[5]: Nothing to be done for `all'.
> make[5]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel/test'
> make[5]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel'
> make[5]: Nothing to be done for `all-am'.
> make[5]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel'
> make[4]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common/parallel'
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune/common'
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune'
> make[3]: Nothing to be done for `all-am'.
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune'
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/dune'
> Making all in lib
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/lib'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/lib'
> Making all in doc
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc'
> Making all in doxygen
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc/doxygen'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc/doxygen'
> Making all in buildsystem
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc/buildsystem'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc/buildsystem'
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc'
> make[3]: Nothing to be done for `all-am'.
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc'
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/doc'
> Making all in bin
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/bin'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/bin'
> Making all in m4
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/m4'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/m4'
> Making all in am
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[3]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[4]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[4]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[3]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common/am'
> make[2]: Entering directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common'
> make[2]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common'
> make[1]: Leaving directory `/afs/
> desy.de/user/a/afallahi/workspace/dune-common'
> --- dune-common done ---
> --- calling all for dune-geometry ---
> --- calling autogen for dune-geometry ---
> Skipping dune-autogen
> --- calling configure for dune-geometry ---
> ----- using default flags $CONFIGURE_FLAGS from /afs/
> desy.de/user/a/afallahi/workspace/cyrus.opts -----
> ./configure MPICC='/afs/
> desy.de/user/a/afallahi/extlib/openmpi-1.8/bin/mpicc' CC=gcc-4.7
> CFLAGS='-O3 -g0 --no-strict-aliasing' CPP=cpp-4.7 CPPFLAGS='-O3 -g0
> --no-strict-aliasing' CXX=g++-4.7 CXXFLAGS='-O3 -g0 --no-strict-aliasing'
> F77=gfortran-4.7 FFLAGS='-O3 -g0 --no-strict-aliasing' FC=gfortran-4.7
> #FCFLAGS='-O3 -g0 --no-strict-aliasing' --enable-parallel --prefix='/afs/
> desy.de/user/a/afallahi/extlib/cyrus' --with-metis='/afs/
> desy.de/user/a/afallahi/extlib/metis-5.1'  "--with-dune-common=/afs/
> desy.de/user/a/afallahi/workspace/dune-common/" ACLOCAL_AMFLAGS="-I . -I
> m4 -I /afs/desy.de/user/a/afallahi/workspace/dune-common/m4"
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a pax tar archive... gnutar
> checking whether make supports nested variables... yes
> checking how to create a pax tar archive... (cached) gnutar
> checking for inkscape... inkscape
> checking for doxygen... doxygen
> checking for latex... latex
> checking for bibtex... bibtex
> checking for dvipdf... dvipdf
> checking for dvips... dvips
> checking for wml... no
> checking for dot... dot
> checking for perl... perl
> checking for convert... convert
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for style of include used by make... GNU
> checking for gcc... gcc-4.7
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc-4.7 accepts -g... yes
> checking for gcc-4.7 option to accept ISO C89... none needed
> checking dependency style of gcc-4.7... gcc3
> checking dependency style of gcc-4.7... (cached) gcc3
> checking how to run the C preprocessor... cpp-4.7
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++-4.7 accepts -g... yes
> checking dependency style of g++-4.7... gcc3
> checking dependency style of g++-4.7... (cached) gcc3
> checking how to run the C++ preprocessor... g++-4.7 -E
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran-4.7 accepts -g... yes
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran-4.7 accepts -g... yes
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking how to print strings... printf
> checking for a sed that does not truncate output... /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by gcc-4.7... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 98304
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking how to convert x86_64-unknown-linux-gnu file names to
> x86_64-unknown-linux-gnu format... func_convert_file_noop
> checking how to convert x86_64-unknown-linux-gnu file names to toolchain
> format... func_convert_file_noop
> checking for /usr/bin/ld option to reload object files... -r
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for dlltool... no
> checking how to associate runtime and link libraries... printf %s\n
> checking for ar... ar
> checking for archiver @FILE support... @
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc-4.7 object... ok
> checking for sysroot... no
> checking for mt... no
> checking if : is a manifest tool... no
> 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 dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc-4.7 supports -fno-rtti -fno-exceptions... no
> checking for gcc-4.7 option to produce PIC... -fPIC -DPIC
> checking if gcc-4.7 PIC flag -fPIC -DPIC works... yes
> checking if gcc-4.7 static flag -static works... yes
> checking if gcc-4.7 supports -c -o file.o... yes
> checking if gcc-4.7 supports -c -o file.o... (cached) yes
> checking whether the gcc-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking how to run the C++ preprocessor... g++-4.7 -E
> checking for ld used by g++-4.7... /usr/bin/ld -m elf_x86_64
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> checking whether the g++-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking for g++-4.7 option to produce PIC... -fPIC -DPIC
> checking if g++-4.7 PIC flag -fPIC -DPIC works... yes
> checking if g++-4.7 static flag -static works... yes
> checking if g++-4.7 supports -c -o file.o... yes
> checking if g++-4.7 supports -c -o file.o... (cached) yes
> checking whether the g++-4.7 linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for gfortran-4.7 option to produce PIC... -fPIC
> checking if gfortran-4.7 PIC flag -fPIC works... yes
> checking if gfortran-4.7 static flag -static works... yes
> checking if gfortran-4.7 supports -c -o file.o... yes
> checking if gfortran-4.7 supports -c -o file.o... (cached) yes
> checking whether the gfortran-4.7 linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for gfortran-4.7 option to produce PIC... -fPIC
> checking if gfortran-4.7 PIC flag -fPIC works... yes
> checking if gfortran-4.7 static flag -static works... yes
> checking if gfortran-4.7 supports -c -o file.o... yes
> checking if gfortran-4.7 supports -c -o file.o... (cached) yes
> checking whether the gfortran-4.7 linker (/usr/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for ranlib... (cached) ranlib
> checking how to get verbose linking output from gfortran-4.7... -v
> checking for Fortran 77 libraries of gfortran-4.7...  -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2
> -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../..
> -lgfortran -lm -lquadmath
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... lower case, underscore, no
> extra underscore
> checking for sgemm_... no
> checking for ATL_xerbla in -latlas... no
> checking for sgemm_ in -lblas... yes
> checking for dgemm_ in -ldgemm... no
> checking for sgemm_ in -lcxml... no
> checking for sgemm_ in -ldxml... no
> checking for sgemm_ in -lscs... no
> checking for sgemm_ in -lcomplib.sgimath... no
> checking for sgemm_ in -lblas... (cached) yes
> checking for sgemm_ in -lessl... no
> checking for sgemm_ in -lblas... (cached) yes
> checking for cheev_... no
> checking for cheev_ in -llapack... yes
> checking how to get verbose linking output from gfortran-4.7... -v
> checking for Fortran libraries of gfortran-4.7...  -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2
> -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -L/afs/
> desy.de/user/a/afallahi/extlib/gcc-4.7/lib/gcc/x86_64-linux-gnu/4.7.2/../../..
> -lgfortran -lm -lquadmath
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, no
> extra underscore
> checking whether compiler is officially supported by DUNE... yes
> checking whether g++ accepts -std=c++0x... yes
> checking whether static_assert is supported... yes
> checking whether nullptr is supported... yes
> checking type_traits usability... yes
> checking type_traits presence... yes
> checking for type_traits... yes
> checking tr1/type_traits usability... yes
> checking tr1/type_traits presence... yes
> checking for tr1/type_traits... yes
> checking tuple usability... yes
> checking tuple presence... yes
> checking for tuple... yes
> checking tr1/tuple usability... yes
> checking tr1/tuple presence... yes
> checking for tr1/tuple... yes
> checking whether <array> C++0x is supported... yes
> checking memory usability... yes
> checking memory presence... yes
> checking for memory... yes
> checking tr1/memory usability... yes
> checking tr1/memory presence... yes
> checking for tr1/memory... yes
> checking boost/shared_ptr.hpp usability... no
> checking boost/shared_ptr.hpp presence... no
> checking for boost/shared_ptr.hpp... no
> checking the location of shared_ptr header file...
> checking whether SHARED_PTR_NAMESPACE (std) provides make_shared... yes
> checking whether compiling C++ code works... yes
> checking whether linking C++ objects works... yes
> checking for __attribute__((deprecated))... yes
> checking for __attribute__((deprecated("message")))... yes
> checking for __attribute__((unused))... yes
> checking rpc/rpc.h usability... yes
> checking rpc/rpc.h presence... yes
> checking for rpc/rpc.h... yes
> checking for an ANSI C-conforming const... yes
> checking for inline... inline
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking for stdlib.h... (cached) yes
> checking for GNU libc compatible malloc... yes
> checking for GMP... configure: searching for GMP in /usr...
> checking gmpxx.h usability... yes
> checking gmpxx.h presence... yes
> checking for gmpxx.h... yes
> checking for __gmpz_abs in -L/usr/lib -lgmp... yes
> checking for __gmpz_abs in -L/usr/lib -lgmpxx... yes
> /usr
> checking malloc.h usability... yes
> checking malloc.h presence... yes
> checking for malloc.h... yes
> checking for string.h... (cached) yes
> checking for pow in -lm... yes
> checking for sqrt... yes
> checking for strchr... yes
> configure: creating ./config.lt
> config.lt: creating libtool
> checking for dune-common installation or source tree... not found
> checking dune/common/stdstreams.hh usability... no
> checking dune/common/stdstreams.hh presence... no
> checking for dune/common/stdstreams.hh... no
> checking for alglib4dune (>=1.0) via pkgconfig... no
> configure: error: could not find required module dune-common
> --- Failed to build dune-geometry ---
> Terminating dunecontrol due to previous errors!
>
>
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