[Dune] A problem with Dune compiling

[Christian Engwer]

Hi,

can you please test the latest dune-common? We believe the problem
should be fixed now.

Cheers
Christian

On Wed, Feb 23, 2011 at 03:23:38PM +0100, arya fallahi wrote:
> Dear Dune team,
> 
> I just updated my dune version and I have problems with compiling the updated svn version. The dune returned messages and the identities of my working environment are as follows:
> 
> pcp042851:dune-trunk fallahi$ svn info dune-common
> Path: dune-common
> URL: https://svn.dune-project.org/svn/dune-common/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-common
> Repository UUID: 419231ca-4411-0410-aba2-fc6cf8c4f609
> Revision: 6353
> Node Kind: directory
> Schedule: normal
> Last Changed Author: christi
> Last Changed Rev: 6353
> Last Changed Date: 2011-02-22 17:27:11 +0100 (Tue, 22 Feb 2011)
> 
> pcp042851:dune-trunk fallahi$ svn info dune-grid
> Path: dune-grid
> URL: https://svn.dune-project.org/svn/dune-grid/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-grid
> Repository UUID: f82f27de-4411-0410-b156-930a902cda50
> Revision: 7451
> Node Kind: directory
> Schedule: normal
> Last Changed Author: mnolte
> Last Changed Rev: 7451
> Last Changed Date: 2011-02-23 14:06:08 +0100 (Wed, 23 Feb 2011)
> 
> pcp042851:dune-trunk fallahi$ svn info dune-istl
> Path: dune-istl
> URL: https://svn.dune-project.org/svn/dune-istl/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-istl
> Repository UUID: 8c7282f0-4411-0410-8e4f-cdd3e049afb8
> Revision: 1455
> Node Kind: directory
> Schedule: normal
> Last Changed Author: sander
> Last Changed Rev: 1453
> Last Changed Date: 2011-02-14 15:30:19 +0100 (Mon, 14 Feb 2011)
> 
> pcp042851:dune-trunk fallahi$ time ./dune-common/bin/dunecontrol --opts=arya.imac.opts all
> --- going to build dune-common dune-grid dune-istl dune-grid-howto hades  ---
> --- calling all for dune-common ---
> --- calling autogen for dune-common ---
> Found am directory /Users/fallahi/svnwork/dune-trunk/dune-common/am
> --> dunedoxynize...
> Generating doc/doxygen/Doxyfile.in from 
>     global style
>     and dune-common config
>     ... done
> --> libtoolize...
> glibtoolize: putting auxiliary files in `.'.
> glibtoolize: linking file `./ltmain.sh'
> glibtoolize: Remember to add `LT_INIT' to configure.ac.
> glibtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
> glibtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
> glibtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
> --> writing dependencies.m4
>     for dune-common 2.1-svn dune at dune-project.org
>         requires 
> --> aclocal...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune_all.m4:51: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune_common.m4:71: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:18: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> --> autoheader...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:9785: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:9970: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:18: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> --> automake...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:9785: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:9970: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:18: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> configure.ac:13: installing `./config.sub'
> configure.ac:13: installing `./config.guess'
> am/documentation:12: doc-local was already defined in condition DUNEWEB, which is included in condition TRUE ...
> Makefile.am:16:   `am/global-rules' included from here
> am/global-rules:19:   `am/documentation' included from here
> am/top-rules:30: ... `doc-local' previously defined here
> Makefile.am:15:   `am/top-rules' included from here
> am/documentation:18: doc-clean was already defined in condition DUNEWEB, which is included in condition TRUE ...
> Makefile.am:16:   `am/global-rules' included from here
> am/global-rules:19:   `am/documentation' included from here
> am/top-rules:31: ... `doc-clean' previously defined here
> Makefile.am:15:   `am/top-rules' included from here
> am/top-rules:22: user target `distclean-libtool' defined here...
> Makefile.am:15:   `am/top-rules' included from here
> /usr/bin/../share/automake-1.10/am/libtool.am: ... overrides Automake target `distclean-libtool' defined here
> --> autoconf...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:9785: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:9970: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:18: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> Now run ./configure to setup dune-common
> --- calling configure for dune-common ---
> ----- using default flags $CONFIGURE_FLAGS from /Users/fallahi/svnwork/dune-trunk/arya.imac.opts -----
> ./configure CXX='mpicxx' CC='mpicc' LD='mpicxx' CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2' CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2' LDFLAGS=' ' --enable-hades3deltd --enable-hades3dfetd --enable-hades3ddges --enable-hades3dfefd --disable-documentation --enable-parallel --enable-debug-output --prefix='/Users/fallahi/ownlib/hades' --with-boost='/Users/fallahi/extlib/boost-trunk' --with-metis='/Users/fallahi/extlib/metis-4.0' --with-rlog='/Users/fallahi/extlib/rlog-trunk' --with-alugrid='/Users/fallahi/extlib/ALUGrid-1.23' ACLOCAL_AMFLAGS="-I . -I 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... ./install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> checking whether make sets $(MAKE)... yes
> checking how to create a pax tar archive... gnutar
> checking how to create a pax tar archive... (cached) gnutar
> checking for inkscape... no
> checking for doxygen... no
> checking for latex... latex
> checking for bibtex... bibtex
> checking for dvipdf... dvipdf
> checking for dvips... dvips
> checking for wml... no
> checking for dot... no
> checking for perl... perl
> checking for convert... convert
> ./configure: line 3638: PKG_PROG_PKG_CONFIG: command not found
> checking for style of include used by make... GNU
> checking for gcc... mpicc
> 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 mpicc accepts -g... yes
> checking for mpicc option to accept ISO C89... none needed
> checking dependency style of mpicc... gcc3
> checking dependency style of mpicc... (cached) gcc3
> checking how to run the C preprocessor... mpicc -E
> checking whether we are using the GNU C++ compiler... yes
> checking whether mpicxx accepts -g... yes
> checking dependency style of mpicxx... gcc3
> checking dependency style of mpicxx... (cached) gcc3
> checking how to run the C++ preprocessor... mpicxx -E
> checking for g77... no
> checking for xlf... no
> checking for f77... no
> checking for frt... no
> checking for pgf77... no
> checking for cf77... no
> checking for fort77... no
> checking for fl32... no
> checking for af77... no
> checking for xlf90... no
> checking for f90... no
> checking for pgf90... no
> checking for pghpf... no
> checking for epcf90... no
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran accepts -g... yes
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran accepts -g... yes
> checking build system type... i386-apple-darwin10.6.0
> checking host system type... i386-apple-darwin10.6.0
> checking for a sed that does not truncate output... /usr/bin/sed
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for fgrep... /usr/bin/grep -F
> checking for ld used by mpicc... mpicxx
> checking if the linker (mpicxx) is GNU ld... no
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
> checking the name lister (/usr/bin/nm) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 196608
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking for mpicxx option to reload object files... -r
> checking how to recognize dependent libraries... pass_all
> checking for ar... ar
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm output from mpicc object... ok
> checking for dsymutil... dsymutil
> checking for nmedit... nmedit
> checking for lipo... lipo
> checking for otool... otool
> checking for otool64... no
> checking for -single_module linker flag... yes
> checking for -exported_symbols_list linker flag... yes
> 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 whether we are using the GNU C++ compiler... (cached) yes
> checking whether mpicxx accepts -g... (cached) yes
> checking dependency style of mpicxx... (cached) gcc3
> checking dependency style of mpicxx... (cached) gcc3
> checking how to run the C++ preprocessor... mpicxx -E
> checking whether we are using the GNU Fortran 77 compiler... (cached) yes
> checking whether gfortran accepts -g... (cached) yes
> checking whether we are using the GNU Fortran compiler... (cached) yes
> checking whether gfortran accepts -g... (cached) yes
> checking for objdir... .libs
> checking if mpicc supports -fno-rtti -fno-exceptions... no
> checking for mpicc option to produce PIC... -fno-common -DPIC
> checking if mpicc PIC flag -fno-common -DPIC works... yes
> checking if mpicc static flag -static works... no
> checking if mpicc supports -c -o file.o... yes
> checking if mpicc supports -c -o file.o... (cached) yes
> checking whether the mpicc linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 for ld used by mpicxx... mpicxx
> checking if the linker (mpicxx) is GNU ld... no
> checking whether the mpicxx linker (mpicxx) supports shared libraries... yes
> checking for mpicxx option to produce PIC... -fno-common -DPIC
> checking if mpicxx PIC flag -fno-common -DPIC works... yes
> checking if mpicxx static flag -static works... no
> checking if mpicxx supports -c -o file.o... yes
> checking if mpicxx supports -c -o file.o... (cached) yes
> checking whether the mpicxx linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 option to produce PIC... -fno-common
> checking if gfortran PIC flag -fno-common works... yes
> checking if gfortran static flag -static works... no
> checking if gfortran supports -c -o file.o... yes
> checking if gfortran supports -c -o file.o... (cached) yes
> checking whether the gfortran linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 option to produce PIC... -fno-common
> checking if gfortran PIC flag -fno-common works... yes
> checking if gfortran static flag -static works... no
> checking if gfortran supports -c -o file.o... yes
> checking if gfortran supports -c -o file.o... (cached) yes
> checking whether the gfortran linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> checking how to hardcode library paths into programs... immediate
> ./configure: line 22928: PKG_PROG_PKG_CONFIG: command not found
> checking for ranlib... (cached) ranlib
> checking how to get verbose linking output from gfortran... -v
> checking for Fortran 77 libraries of gfortran...  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../.. -lgfortranbegin -lgfortran
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... unknown
> checking for unknown... no
> checking for ATL_xerbla in -latlas... no
> checking for unknown in -lblas... no
> checking for unknown in -lcxml... no
> checking for unknown in -ldxml... no
> checking for unknown in -lscs... no
> checking for unknown in -lcomplib.sgimath... no
> checking for unknown in -lblas... (cached) no
> checking for unknown in -lblas... (cached) no
> checking how to get verbose linking output from gfortran... -v
> checking for Fortran libraries of gfortran...  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../.. -lgfortranbegin -lgfortran
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... unknown
> configure: WARNING: unknown Fortran name-mangling scheme
> checking whether compiler is officially supported by DUNE... yes
> checking whether g++ accepts -std=c++0x... no
> checking whether static_assert is supported... no
> checking whether nullptr is supported... no
> checking type_traits usability... no
> checking type_traits presence... no
> checking for type_traits... no
> checking tr1/type_traits usability... yes
> checking tr1/type_traits presence... yes
> checking for tr1/type_traits... yes
> checking tuple usability... no
> checking tuple presence... no
> checking for tuple... no
> checking tr1/tuple usability... yes
> checking tr1/tuple presence... yes
> checking for tr1/tuple... 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 boost/make_shared.hpp usability... no
> checking boost/make_shared.hpp presence... no
> checking for boost/make_shared.hpp... no
> checking whether compiling C++ code works... yes
> checking whether linking C++ objects works... yes
> checking for __attribute__((deprecated))... yes
> checking rpc/rpc.h usability... yes
> checking rpc/rpc.h presence... yes
> checking for rpc/rpc.h... yes
> checking for mpicc... mpicc
> checking for MPI_Init... yes
> checking for mpi.h... yes
> configure: Trying to identify the version of MPI compiler mpicc
> checking for lam... rm: conftest.dSYM: is a directory
> no
> checking for mpich... rm: conftest.dSYM: is a directory
> no
> checking for OpenMPI... yes
> rm: conftest.dSYM: is a directory
> checking whether compiling with OpenMPI works... yes
> configure: WARNING: Disabled test whether running with OpenMPI works.
> checking for MPI_Finalized in -lm... 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 malloc.h usability... no
> checking malloc.h presence... no
> checking for malloc.h... no
> 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/exprtmpl/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: 
> 
> ----------------------------------------
> 
> MPI.....................: yes (OpenMPI)
> 
> ----------------------------------------
> 
> See ./configure --help and config.log for reasons why a component wasn't found
> 
> --- calling make for dune-common ---
> make 
> cd . && /bin/sh /Users/fallahi/svnwork/dune-trunk/dune-common/missing --run autoheader
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:9785: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:9970: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:18: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> rm -f stamp-h1
> touch config.h.in
> make  all-recursive
> Making all in dune
> Making all in common
> Making all in .
> make[4]: Nothing to be done for `all-am'.
> Making all in test
> make[4]: Nothing to be done for `all'.
> Making all in exprtmpl
> make[4]: Nothing to be done for `all'.
> Making all in parallel
> Making all in test
> make[5]: Nothing to be done for `all'.
> make[5]: Nothing to be done for `all-am'.
> make[3]: Nothing to be done for `all-am'.
> Making all in lib
> make[2]: Nothing to be done for `all'.
> Making all in doc
> Making all in doxygen
> make[3]: Nothing to be done for `all'.
> Making all in buildsystem
> make[3]: Nothing to be done for `all'.
> make[3]: Nothing to be done for `all-am'.
> Making all in bin
> make[2]: Nothing to be done for `all'.
> Making all in m4
> make[2]: Nothing to be done for `all'.
> Making all in am
> cd . && /bin/sh ./config.status config.h
> config.status: creating config.h
> config.status: config.h is unchanged
> --- dune-common done ---
> --- calling all for dune-grid ---
> --- calling autogen for dune-grid ---
> Found am directory /Users/fallahi/svnwork/dune-trunk/dune-common/am
> --> dunedoxynize...
> Generating doc/doxygen/Doxyfile.in from 
>     global style
>     and dune-grid config
>     ... done
> --> libtoolize...
> glibtoolize: putting auxiliary files in `.'.
> glibtoolize: linking file `./ltmain.sh'
> glibtoolize: Remember to add `LT_INIT' to configure.ac.
> glibtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
> glibtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
> glibtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
> --> writing dependencies.m4
>     for dune-grid 2.1-svn dune at dune-project.org
>         requires  dune-common >= 2.1 
> --> aclocal...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune_all.m4:51: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune_common.m4:71: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:26: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune.m4:489: DUNE_CHECK_MODULES is expanded from...
> /Users/fallahi/svnwork/dune-trunk/dune-common/m4/dune_common.m4:80: DUNE_COMMON_CHECK_MODULE is expanded from...
> --> linking dune-common/am...
> --> autoheader...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:11456: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:11691: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:26: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> aclocal.m4:11367: DUNE_CHECK_MODULES is expanded from...
> aclocal.m4:11700: DUNE_COMMON_CHECK_MODULE is expanded from...
> --> automake...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:11456: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:11691: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:26: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> aclocal.m4:11367: DUNE_CHECK_MODULES is expanded from...
> aclocal.m4:11700: DUNE_COMMON_CHECK_MODULE is expanded from...
> configure.ac:13: installing `./config.sub'
> configure.ac:13: installing `./config.guess'
> am/top-rules:30: doc-local was already defined in condition TRUE, which includes condition DUNEWEB ...
> Makefile.am:30:   `am/top-rules' included from here
> am/documentation:12: ... `doc-local' previously defined here
> Makefile.am:29:   `am/global-rules' included from here
> am/global-rules:19:   `am/documentation' included from here
> am/top-rules:31: doc-clean was already defined in condition TRUE, which includes condition DUNEWEB ...
> Makefile.am:30:   `am/top-rules' included from here
> am/documentation:18: ... `doc-clean' previously defined here
> Makefile.am:29:   `am/global-rules' included from here
> am/global-rules:19:   `am/documentation' included from here
> am/top-rules:22: user target `distclean-libtool' defined here...
> Makefile.am:30:   `am/top-rules' included from here
> /usr/bin/../share/automake-1.10/am/libtool.am: ... overrides Automake target `distclean-libtool' defined here
> --> autoconf...
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:11456: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:11691: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:26: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> aclocal.m4:11367: DUNE_CHECK_MODULES is expanded from...
> aclocal.m4:11700: DUNE_COMMON_CHECK_MODULE is expanded from...
> Now run ./configure to setup dune-grid
> --- calling configure for dune-grid ---
> ----- using default flags $CONFIGURE_FLAGS from /Users/fallahi/svnwork/dune-trunk/arya.imac.opts -----
> ./configure CXX='mpicxx' CC='mpicc' LD='mpicxx' CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2' CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2' LDFLAGS=' ' --enable-hades3deltd --enable-hades3dfetd --enable-hades3ddges --enable-hades3dfefd --disable-documentation --enable-parallel --enable-debug-output --prefix='/Users/fallahi/ownlib/hades' --with-boost='/Users/fallahi/extlib/boost-trunk' --with-metis='/Users/fallahi/extlib/metis-4.0' --with-rlog='/Users/fallahi/extlib/rlog-trunk' --with-alugrid='/Users/fallahi/extlib/ALUGrid-1.23' "--with-dune-common=/Users/fallahi/svnwork/dune-trunk/dune-common/" ACLOCAL_AMFLAGS="-I . -I m4 -I /Users/fallahi/svnwork/dune-trunk/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... ./install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> checking whether make sets $(MAKE)... yes
> checking how to create a pax tar archive... gnutar
> checking how to create a pax tar archive... (cached) gnutar
> checking for inkscape... no
> checking for doxygen... no
> checking for latex... latex
> checking for bibtex... bibtex
> checking for dvipdf... dvipdf
> checking for dvips... dvips
> checking for wml... no
> checking for dot... no
> checking for perl... perl
> checking for convert... convert
> ./configure: line 3785: PKG_PROG_PKG_CONFIG: command not found
> checking for style of include used by make... GNU
> checking for gcc... mpicc
> 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 mpicc accepts -g... yes
> checking for mpicc option to accept ISO C89... none needed
> checking dependency style of mpicc... gcc3
> checking dependency style of mpicc... (cached) gcc3
> checking how to run the C preprocessor... mpicc -E
> checking whether we are using the GNU C++ compiler... yes
> checking whether mpicxx accepts -g... yes
> checking dependency style of mpicxx... gcc3
> checking dependency style of mpicxx... (cached) gcc3
> checking how to run the C++ preprocessor... mpicxx -E
> checking for g77... no
> checking for xlf... no
> checking for f77... no
> checking for frt... no
> checking for pgf77... no
> checking for cf77... no
> checking for fort77... no
> checking for fl32... no
> checking for af77... no
> checking for xlf90... no
> checking for f90... no
> checking for pgf90... no
> checking for pghpf... no
> checking for epcf90... no
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran accepts -g... yes
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran accepts -g... yes
> checking build system type... i386-apple-darwin10.6.0
> checking host system type... i386-apple-darwin10.6.0
> checking for a sed that does not truncate output... /usr/bin/sed
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for fgrep... /usr/bin/grep -F
> checking for ld used by mpicc... mpicxx
> checking if the linker (mpicxx) is GNU ld... no
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
> checking the name lister (/usr/bin/nm) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 196608
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking for mpicxx option to reload object files... -r
> checking how to recognize dependent libraries... pass_all
> checking for ar... ar
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm output from mpicc object... ok
> checking for dsymutil... dsymutil
> checking for nmedit... nmedit
> checking for lipo... lipo
> checking for otool... otool
> checking for otool64... no
> checking for -single_module linker flag... yes
> checking for -exported_symbols_list linker flag... yes
> 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 whether we are using the GNU C++ compiler... (cached) yes
> checking whether mpicxx accepts -g... (cached) yes
> checking dependency style of mpicxx... (cached) gcc3
> checking dependency style of mpicxx... (cached) gcc3
> checking how to run the C++ preprocessor... mpicxx -E
> checking whether we are using the GNU Fortran 77 compiler... (cached) yes
> checking whether gfortran accepts -g... (cached) yes
> checking whether we are using the GNU Fortran compiler... (cached) yes
> checking whether gfortran accepts -g... (cached) yes
> checking for objdir... .libs
> checking if mpicc supports -fno-rtti -fno-exceptions... no
> checking for mpicc option to produce PIC... -fno-common -DPIC
> checking if mpicc PIC flag -fno-common -DPIC works... yes
> checking if mpicc static flag -static works... no
> checking if mpicc supports -c -o file.o... yes
> checking if mpicc supports -c -o file.o... (cached) yes
> checking whether the mpicc linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 for ld used by mpicxx... mpicxx
> checking if the linker (mpicxx) is GNU ld... no
> checking whether the mpicxx linker (mpicxx) supports shared libraries... yes
> checking for mpicxx option to produce PIC... -fno-common -DPIC
> checking if mpicxx PIC flag -fno-common -DPIC works... yes
> checking if mpicxx static flag -static works... no
> checking if mpicxx supports -c -o file.o... yes
> checking if mpicxx supports -c -o file.o... (cached) yes
> checking whether the mpicxx linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 option to produce PIC... -fno-common
> checking if gfortran PIC flag -fno-common works... yes
> checking if gfortran static flag -static works... no
> checking if gfortran supports -c -o file.o... yes
> checking if gfortran supports -c -o file.o... (cached) yes
> checking whether the gfortran linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> 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 option to produce PIC... -fno-common
> checking if gfortran PIC flag -fno-common works... yes
> checking if gfortran static flag -static works... no
> checking if gfortran supports -c -o file.o... yes
> checking if gfortran supports -c -o file.o... (cached) yes
> checking whether the gfortran linker (mpicxx) supports shared libraries... yes
> checking dynamic linker characteristics... darwin10.6.0 dyld
> checking how to hardcode library paths into programs... immediate
> ./configure: line 23075: PKG_PROG_PKG_CONFIG: command not found
> checking for ranlib... (cached) ranlib
> checking how to get verbose linking output from gfortran... -v
> checking for Fortran 77 libraries of gfortran...  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../.. -lgfortranbegin -lgfortran
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... unknown
> checking for unknown... no
> checking for ATL_xerbla in -latlas... no
> checking for unknown in -lblas... no
> checking for unknown in -lcxml... no
> checking for unknown in -ldxml... no
> checking for unknown in -lscs... no
> checking for unknown in -lcomplib.sgimath... no
> checking for unknown in -lblas... (cached) no
> checking for unknown in -lblas... (cached) no
> checking how to get verbose linking output from gfortran... -v
> checking for Fortran libraries of gfortran...  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../.. -lgfortranbegin -lgfortran
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... unknown
> configure: WARNING: unknown Fortran name-mangling scheme
> checking whether compiler is officially supported by DUNE... yes
> checking whether g++ accepts -std=c++0x... no
> checking whether static_assert is supported... no
> checking whether nullptr is supported... no
> checking type_traits usability... no
> checking type_traits presence... no
> checking for type_traits... no
> checking tr1/type_traits usability... yes
> checking tr1/type_traits presence... yes
> checking for tr1/type_traits... yes
> checking tuple usability... no
> checking tuple presence... no
> checking for tuple... no
> checking tr1/tuple usability... yes
> checking tr1/tuple presence... yes
> checking for tr1/tuple... 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 boost/make_shared.hpp usability... no
> checking boost/make_shared.hpp presence... no
> checking for boost/make_shared.hpp... no
> checking whether compiling C++ code works... yes
> checking whether linking C++ objects works... yes
> checking for __attribute__((deprecated))... yes
> checking rpc/rpc.h usability... yes
> checking rpc/rpc.h presence... yes
> checking for rpc/rpc.h... yes
> checking for mpicc... mpicc
> checking for MPI_Init... yes
> checking for mpi.h... yes
> configure: Trying to identify the version of MPI compiler mpicc
> checking for lam... rm: conftest.dSYM: is a directory
> no
> checking for mpich... rm: conftest.dSYM: is a directory
> no
> checking for OpenMPI... yes
> rm: conftest.dSYM: is a directory
> checking whether compiling with OpenMPI works... yes
> configure: WARNING: Disabled test whether running with OpenMPI works.
> checking for MPI_Finalized in -lm... 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 malloc.h usability... no
> checking malloc.h presence... no
> checking for malloc.h... no
> checking for string.h... (cached) yes
> checking for pow in -lm... yes
> checking for sqrt... yes
> checking for strchr... yes
> ./configure: line 30216: PKG_PROG_PKG_CONFIG: command not found
> configure: creating ./config.lt
> config.lt: creating libtool
> checking for dune-common installation or source tree... found in /Users/fallahi/svnwork/dune-trunk/dune-common
> checking dune/common/stdstreams.hh usability... yes
> checking dune/common/stdstreams.hh presence... yes
> checking for dune/common/stdstreams.hh... yes
> checking for libdunecommon... yes
> checking for X... libraries /usr/X11/lib, headers 
> checking whether -R must be followed by a space... no
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for the pthreads library -lpthreads... no
> checking whether pthreads work without any flags... yes
> checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
> checking if more special flags are required for pthreads... -D_THREAD_SAFE
> checking for cc_r... mpicc
> checking whether we are using the Microsoft C compiler... no
> checking windows.h usability... no
> checking windows.h presence... no
> checking for windows.h... no
> checking for OpenGL library... no
> checking grape.h usability... no
> checking grape.h presence... no
> checking for grape.h... no
> configure: searching for ALBERTA in /usr...
> configure: searching for ALBERTA in /usr/local...
> configure: searching for ALBERTA in /usr/local/alberta...
> configure: searching for ALBERTA in /opt/alberta...
> checking alberta.h usability... no
> checking alberta.h presence... no
> checking for alberta.h... no
> configure: WARNING: alberta.h not found in -I/include/alberta
> ./configure: line 36577: --libs-only-L: command not found
> ./configure: line 36578: --libs-only-L: command not found
> checking for UG... ./configure: line 36585: --exists: command not found
> no
> configure: WARNING: UG not found
> checking for amiramesh/AmiraMesh.h... no
> configure: WARNING: AmiraMesh.h not found in /usr/local/amiramesh/include/amiramesh
> checking psurface/PSurface.h usability... no
> checking psurface/PSurface.h presence... no
> checking for psurface/PSurface.h... no
> checking ALUGrid version >= 1.23... ./configure: line 37436: --atleast-version=1.23: command not found
> yes (ALUGrid-1.23)
> checking alugrid_serial.h usability... yes
> checking alugrid_serial.h presence... yes
> checking for alugrid_serial.h... yes
> checking alugrid_parallel.h usability... yes
> checking alugrid_parallel.h presence... yes
> checking for alugrid_parallel.h... yes
> checking for malloc in -lalugrid... yes
> configure: searching for GMP in /usr...
> checking gmpxx.h usability... no
> checking gmpxx.h presence... no
> checking for gmpxx.h... no
> configure: WARNING: gmpxx.h not found in /usr
> configure: searching for GMP in /usr/local...
> checking for gmpxx.h... (cached) no
> configure: WARNING: gmpxx.h not found in /usr/local
> checking for alglib4dune (>=1.0) via pkgconfig... ./configure: line 38736: pkg-config: command not found
> no
> 
> Found the following Dune-components: 
> 
> ----------------------------------------
> 
> dune-common.............: version 2.1-svn
> ALBERTA.................: no
> ALUGrid.................: version 1.23 (parallel)
> AlgLib for DUNE.........: no
> AmiraMesh...............: no
> Extra utils enabled.....: no
> GMP.....................: no
> Grape...................: no
> MPI.....................: yes (OpenMPI)
> OpenGL..................: no
> UG......................: no
> psurface................: no
> 
> ----------------------------------------
> 
> See ./configure --help and config.log for reasons why a component wasn't found
> 
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating lib/Makefile
> config.status: creating doc/appl/refelements/Makefile
> config.status: creating doc/appl/Makefile
> config.status: creating doc/refinement/Makefile
> config.status: creating doc/doxygen/Makefile
> config.status: creating doc/doxygen/Doxyfile
> config.status: creating doc/grids/Makefile
> config.status: creating doc/grids/amc/Makefile
> config.status: creating doc/grids/amiramesh/Makefile
> config.status: creating doc/grids/dgf/Makefile
> config.status: creating doc/grids/gridfactory/Makefile
> config.status: creating doc/grids/gmsh/Makefile
> config.status: creating doc/grids/starcd/Makefile
> config.status: creating doc/Makefile
> config.status: creating dune/Makefile
> config.status: creating dune/grid/Makefile
> config.status: creating dune/grid/test/Makefile
> config.status: creating dune/grid/common/test/Makefile
> config.status: creating dune/grid/common/quadraturerules/Makefile
> config.status: creating dune/grid/common/refinement/Makefile
> config.status: creating dune/grid/common/Makefile
> config.status: creating dune/grid/uggrid/Makefile
> config.status: creating dune/grid/sgrid/Makefile
> config.status: creating dune/grid/albertagrid/Makefile
> config.status: creating dune/grid/albertagrid/test/Makefile
> config.status: creating dune/grid/yaspgrid/Makefile
> config.status: creating dune/grid/onedgrid/Makefile
> config.status: creating dune/grid/utility/Makefile
> config.status: creating dune/grid/utility/test/Makefile
> config.status: creating dune/grid/alugrid/common/Makefile
> config.status: creating dune/grid/alugrid/2d/Makefile
> config.status: creating dune/grid/alugrid/3d/Makefile
> config.status: creating dune/grid/alugrid/Makefile
> config.status: creating dune/grid/io/file/test/Makefile
> config.status: creating dune/grid/io/file/amiramesh/Makefile
> config.status: creating dune/grid/io/file/dgfparser/Makefile
> config.status: creating dune/grid/io/file/dgfparser/test/Makefile
> config.status: creating dune/grid/io/file/dgfparser/utils/Makefile
> config.status: creating dune/grid/io/file/gnuplot/Makefile
> config.status: creating dune/grid/io/file/vtk/Makefile
> config.status: creating dune/grid/io/file/Makefile
> config.status: creating dune/grid/io/visual/grape/Makefile
> config.status: creating dune/grid/io/visual/Makefile
> config.status: creating dune/grid/io/Makefile
> config.status: creating dune/grid/genericgeometry/Makefile
> config.status: creating dune/grid/genericgeometry/test/Makefile
> config.status: creating dune/grid/geometrygrid/Makefile
> config.status: creating m4/Makefile
> config.status: creating dune-grid.pc
> config.status: creating utility/Makefile
> config.status: creating utility/alu-to-vtk/Makefile
> config.status: creating utility/gmsh-to-alu/Makefile
> config.status: creating utility/gridinfo-gmsh/Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: executing depfiles commands
> config.status: executing libtool commands
> --- calling make for dune-grid ---
> make 
> cd . && /bin/sh /Users/fallahi/svnwork/dune-trunk/dune-grid/missing --run autoheader
> configure.ac:13: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
> aclocal.m4:11456: DUNE_CHECK_ALL is expanded from...
> configure.ac:13: the top level
> aclocal.m4:11691: DUNE_COMMON_CHECKS is expanded from...
> dependencies.m4:26: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
> aclocal.m4:11367: DUNE_CHECK_MODULES is expanded from...
> aclocal.m4:11700: DUNE_COMMON_CHECK_MODULE is expanded from...
> rm -f stamp-h1
> touch config.h.in
> cd . && /bin/sh ./config.status config.h
> config.status: creating config.h
> config.status: config.h is unchanged
> make  all-recursive
> Making all in doc
> Making all in appl
> Making all in refelements
> make[4]: Nothing to be done for `all'.
> make[4]: Nothing to be done for `all-am'.
> Making all in doxygen
> make[3]: Nothing to be done for `all'.
> Making all in grids
> Making all in amc
> make[4]: Nothing to be done for `all'.
> Making all in amiramesh
> make[4]: Nothing to be done for `all'.
> Making all in gridfactory
> make[4]: Nothing to be done for `all'.
> Making all in gmsh
> make[4]: Nothing to be done for `all'.
> Making all in starcd
> make[4]: Nothing to be done for `all'.
> Making all in dgf
> make[4]: Nothing to be done for `all'.
> make[4]: Nothing to be done for `all-am'.
> make[3]: Nothing to be done for `all-am'.
> Making all in dune
> Making all in grid
> Making all in genericgeometry
> Making all in test
> make[5]: Nothing to be done for `all'.
> make[5]: Nothing to be done for `all-am'.
> Making all in common
> Making all in refinement
> make[5]: Nothing to be done for `all'.
> Making all in test
> make[5]: Nothing to be done for `all'.
> Making all in quadraturerules
> make[5]: Nothing to be done for `all'.
> make[5]: Nothing to be done for `all-am'.
> Making all in alugrid
> Making all in common
> make[5]: Nothing to be done for `all'.
> Making all in 2d
> /bin/sh ../../../../libtool --tag=CXX   --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../../../..  -I/Users/fallahi/svnwork/dune-trunk/dune-common -I../../../.. -D_REENTRANT -I/Users/fallahi/extlib/openmpi-1.4.1/include -DMPIPP_H -DENABLE_MPI=1 -I/Users/fallahi/extlib/ALUGrid-1.23/include -I/Users/fallahi/extlib/ALUGrid-1.23/include/serial -I/Users/fallahi/extlib/ALUGrid-1.23/include/duneinterface -DENABLE_ALUGRID -I/Users/fallahi/extlib/ALUGrid-1.23/include/parallel -DMPICH_IGNORE_CXX_SEEK -O2  -DMPICH_IGNORE_CXX_SEEK -O2 -MT libalu2d_la-intersection.lo -MD -MP -MF .deps/libalu2d_la-intersection.Tpo -c -o libalu2d_la-intersection.lo `test -f 'intersection.cc' || echo './'`intersection.cc
> libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../../../.. -I/Users/fallahi/svnwork/dune-trunk/dune-common -I../../../.. -D_REENTRANT -I/Users/fallahi/extlib/openmpi-1.4.1/include -DMPIPP_H -DENABLE_MPI=1 -I/Users/fallahi/extlib/ALUGrid-1.23/include -I/Users/fallahi/extlib/ALUGrid-1.23/include/serial -I/Users/fallahi/extlib/ALUGrid-1.23/include/duneinterface -DENABLE_ALUGRID -I/Users/fallahi/extlib/ALUGrid-1.23/include/parallel -DMPICH_IGNORE_CXX_SEEK -O2 -DMPICH_IGNORE_CXX_SEEK -O2 -MT libalu2d_la-intersection.lo -MD -MP -MF .deps/libalu2d_la-intersection.Tpo -c intersection.cc -o libalu2d_la-intersection.o
> In file included from /Users/fallahi/svnwork/dune-trunk/dune-common/dune/common/mpicollectivecommunication.hh:19,
>                  from ../../../../dune/grid/alugrid/3d/alu3dinclude.hh:26,
>                  from ../../../../dune/grid/alugrid/3d/mappings.hh:14,
>                  from ../../../../dune/grid/alugrid/2d/geometry.hh:10,
>                  from intersection.cc:8:
> /Users/fallahi/svnwork/dune-trunk/dune-common/dune/common/shared_ptr.hh:307: error: ‘std::tr1::make_shared’ has not been declared
> make[5]: *** [libalu2d_la-intersection.lo] Error 1
> make[4]: *** [all-recursive] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
> --- Failed to build dune-grid ---
> Terminating dunecontrol due to previous errors!
> 
> real	1m3.644s
> user	0m40.626s
> sys	0m23.319s
> 
> Thank you very much for your help.
> 
> Arya Fallahi, 
> Dr. sc. techn.  ETH, 
> Computational Accelerator Scientist 
> Paul Scherrer Institute (PSI), 
> CH-5232 Villigen, Switzerland, 
> arya.fallahi at psi.ch, 
> +41(0)56 310 50 17
> 
> 
> 
> _______________________________________________
> Dune mailing list
> Dune at dune-project.org
> http://lists.dune-project.org/mailman/listinfo/dune
>