[Dune] A problem with Dune compiling

[arya fallahi]

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