[Dune] Dune Release 1.2 configure crashes early on in dune-common

Benedikt Oswald benedikt.oswald at psi.ch
Mon Feb 16 11:08:41 CET 2009


Dear Dune, the configure of Dune Release 1.2 crashes with the following error message, cf. end of output:

=================================================
[oswald at merlin00 dune-1.2]$ uname -a
Linux merlin00 2.6.9-78.0.1.ELsmp #1 SMP Tue Aug 5 13:53:03 CDT 2008 x86_64 x86_64 x86_64 GNU/Linux
===================================================

I am not sure on where to search for the error:

I have installed the following versions of autoconf and automake:

=====================================================================
[oswald at merlin00 dune-1.2]$ autoconf --version
autoconf (GNU Autoconf) 2.63
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later
<http://gnu.org/licenses/old-licenses/gpl-2.0.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
=====================================================================



===================================================
[oswald at merlin00 dune-1.2]$ automake --version
automake (GNU automake) 1.9.2
Written by Tom Tromey <tromey at redhat.com>.
==================================================



[oswald at merlin00 dune-1.2]$ ./dune-common/bin/dunecontrol --opts=dune.psi.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 /home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-common/am
--> libtoolize...
Remember to add `AC_PROG_LIBTOOL' to `configure.ac'.
--> writing dependencies.m4
    for dune-common 1.2 dune at dune-project.org
        requires
--> aclocal...
/usr/share/aclocal/libgcrypt.m4:23: warning: underquoted definition of AM_PATH_LIBGCRYPT
  run info '(automake)Extending aclocal'
  or see http://sources.redhat.com/automake/automake.html#Extending-aclocal
configure.ac:15: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
dependencies.m4:17: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-common/m4/dune_all.m4:19: DUNE_CHECK_ALL is expanded from...
configure.ac:15: the top level
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:1994: AC_CACHE_CHECK is expanded from...
/usr/share/aclocal/libtool.m4:609: AC_LIBTOOL_LINKER_OPTION is expanded from...
/usr/share/aclocal/libtool.m4:2486: _LT_AC_LANG_C_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:2485: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:95: AC_LIBTOOL_SETUP is expanded from...
/usr/share/aclocal/libtool.m4:75: _AC_PROG_LIBTOOL is expanded from...
/usr/share/aclocal/libtool.m4:40: AC_PROG_LIBTOOL is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
/usr/share/aclocal/libtool.m4:566: AC_LIBTOOL_COMPILER_OPTION is expanded from...
/usr/share/aclocal/libtool.m4:4540: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
/usr/share/aclocal/libtool.m4:2631: _LT_AC_LANG_CXX_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:2630: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:1647: _LT_AC_TAGCONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
/usr/share/aclocal/libtool.m4:3661: _LT_AC_LANG_F77_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:3660: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
/usr/share/aclocal/libtool.m4:3761: _LT_AC_LANG_GCJ_CONFIG is expanded from...
/usr/share/aclocal/libtool.m4:3760: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-common/m4/dune_common.m4:1: DUNE_COMMON_CHECKS is expanded from...
--> autoheader...
configure.ac:15: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
dependencies.m4:17: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
aclocal.m4:7435: DUNE_CHECK_ALL is expanded from...
configure.ac:15: the top level
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:1994: AC_CACHE_CHECK is expanded from...
aclocal.m4:600: AC_LIBTOOL_LINKER_OPTION is expanded from...
aclocal.m4:2477: _LT_AC_LANG_C_CONFIG is expanded from...
aclocal.m4:2476: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
aclocal.m4:86: AC_LIBTOOL_SETUP is expanded from...
aclocal.m4:66: _AC_PROG_LIBTOOL is expanded from...
aclocal.m4:31: AC_PROG_LIBTOOL is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:557: AC_LIBTOOL_COMPILER_OPTION is expanded from...
aclocal.m4:4519: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:2618: _LT_AC_LANG_CXX_CONFIG is expanded from...
aclocal.m4:2617: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
aclocal.m4:1638: _LT_AC_TAGCONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3644: _LT_AC_LANG_F77_CONFIG is expanded from...
aclocal.m4:3643: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3744: _LT_AC_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:3743: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:7530: DUNE_COMMON_CHECKS is expanded from...
--> automake...
configure.ac:15: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
dependencies.m4:17: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
aclocal.m4:7435: DUNE_CHECK_ALL is expanded from...
configure.ac:15: the top level
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:1994: AC_CACHE_CHECK is expanded from...
aclocal.m4:600: AC_LIBTOOL_LINKER_OPTION is expanded from...
aclocal.m4:2477: _LT_AC_LANG_C_CONFIG is expanded from...
aclocal.m4:2476: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
aclocal.m4:86: AC_LIBTOOL_SETUP is expanded from...
aclocal.m4:66: _AC_PROG_LIBTOOL is expanded from...
aclocal.m4:31: AC_PROG_LIBTOOL is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:557: AC_LIBTOOL_COMPILER_OPTION is expanded from...
aclocal.m4:4519: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:2618: _LT_AC_LANG_CXX_CONFIG is expanded from...
aclocal.m4:2617: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
aclocal.m4:1638: _LT_AC_TAGCONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3644: _LT_AC_LANG_F77_CONFIG is expanded from...
aclocal.m4:3643: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3744: _LT_AC_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:3743: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:7530: DUNE_COMMON_CHECKS is expanded from...
doc/doxygen/Makefile.am:10: WHAT was already defined in condition TRUE, which includes condition BUILD_DOCS and WML ...
doc/doxygen/Makefile.am:6: ... `WHAT' previously defined here
am/doxygen:70: user target `html' defined here...
doc/doxygen/Makefile.am:22:   `am/doxygen' included from here
automake: ... overrides Automake target `html' defined here
am/doxygen:70: consider using html-local instead of html
doc/doxygen/Makefile.am:22:   `am/doxygen' included from here
--> autoconf...
configure.ac:15: warning: PKG_PROG_PKG_CONFIG is m4_require'd but not m4_defun'd
dependencies.m4:17: DUNE_CHECK_MOD_DEPENDENCIES is expanded from...
aclocal.m4:7435: DUNE_CHECK_ALL is expanded from...
configure.ac:15: the top level
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:1994: AC_CACHE_CHECK is expanded from...
aclocal.m4:600: AC_LIBTOOL_LINKER_OPTION is expanded from...
aclocal.m4:2477: _LT_AC_LANG_C_CONFIG is expanded from...
aclocal.m4:2476: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
aclocal.m4:86: AC_LIBTOOL_SETUP is expanded from...
aclocal.m4:66: _AC_PROG_LIBTOOL is expanded from...
aclocal.m4:31: AC_PROG_LIBTOOL is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:557: AC_LIBTOOL_COMPILER_OPTION is expanded from...
aclocal.m4:4519: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:2618: _LT_AC_LANG_CXX_CONFIG is expanded from...
aclocal.m4:2617: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
aclocal.m4:1638: _LT_AC_TAGCONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3644: _LT_AC_LANG_F77_CONFIG is expanded from...
aclocal.m4:3643: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:15: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
aclocal.m4:3744: _LT_AC_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:3743: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
aclocal.m4:7530: DUNE_COMMON_CHECKS is expanded from...
Now run ./configure to setup dune-common
--- calling configure for dune-common ---
----- using default flags $CONFIGURE_FLAGS from /home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune.psi.opts -----
./configure CXX='mpicxx' CC='mpicxx' LD='mpicxx' CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK ' CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK ' LDFLAGS='-lgfortran /usr/lib64/libblas.so.3.1.1 '
LTFLAGS='-all-static ' --enable-experimental-hades3deld --disable-shared --enable-static --disable-documentation --enable-parallel --enable-boost
--with-boost='/scratch2/amas/oswald/extlib/merlin/boost-1.37.0' --enable-debug-high --enable-message-high
--with-trilinos='/scratch2/amas/oswald/extlib/merlin/trilinos-9.0.1-openmpi-1.2.5' --enable-trilinos-solver --with-geoexporter='/scratch2/amas/oswald/ownlib/merlin/faraday/euklid'
--prefix='/scratch2/amas/oswald/ownlib/merlin/hades' --with-metis='/scratch2/amas/oswald/extlib/merlin/metis-4.0'
--with-alugrid='/scratch2/amas/oswald/extlib/merlin/ALUGrid-1.14-openmpi-1.2.5' --with-rlog='/scratch2/amas/oswald/extlib/merlin/rlog-1.4'
"--with-dune-common=/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-common" "--with-dune-grid=/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-grid"
"--with-dune-istl=/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-istl" "--with-dune-grid-howto=/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-grid-howto"
"--with-hades=/home2/oswald/scratch2-svnwork-merlin/dune-1.2/hades" ACLOCAL_AMFLAGS="-I . -I /home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-common/m4 -I
/home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-grid/m4 -I /home2/oswald/scratch2-svnwork-merlin/dune-1.2/dune-istl/m4"
configure: WARNING: unrecognized options: --enable-experimental-hades3deld, --enable-boost, --with-boost, --enable-debug-high, --enable-message-high, --with-trilinos,
--enable-trilinos-solver, --with-geoexporter, --with-metis, --with-alugrid, --with-rlog, --with-dune-common, --with-dune-grid, --with-dune-istl, --with-dune-grid-howto, --with-hades
checking for gawk... gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets $(MAKE)... yes
checking whether ln -s works... yes
HOSTID:
./configure: line 2849: PKG_PROG_PKG_CONFIG: command not found
checking for style of include used by make... GNU
checking for gcc... mpicxx
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 mpicxx accepts -g... yes
checking for mpicxx option to accept ISO C89... unsupported
checking dependency style of mpicxx... gcc3
checking how to run the C preprocessor... mpicxx -E
checking whether we are using the GNU C++ compiler... yes
checking whether mpicxx accepts -g... yes
checking dependency style of mpicxx... gcc3
checking how to run the C++ preprocessor... mpicxx -E
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
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 ld used by mpicxx... mpicxx
checking if the linker (mpicxx) is GNU ld... no
checking for mpicxx option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether mpif77 accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicxx object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicxx static flag  works... no
checking if mpicxx supports -fno-rtti -fno-exceptions... yes
checking for mpicxx option to produce PIC... -fPIC
checking if mpicxx PIC flag -fPIC works... yes
checking if mpicxx supports -c -o file.o... yes
checking whether the mpicxx linker (mpicxx -m elf_x86_64) supports shared libraries... no
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... no
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by mpicxx... mpicxx -m elf_x86_64
checking if the linker (mpicxx -m elf_x86_64) is GNU ld... no
checking whether the mpicxx linker (mpicxx -m elf_x86_64) supports shared libraries... yes
checking for mpicxx option to produce PIC... -fPIC
checking if mpicxx PIC flag -fPIC works... yes
checking if mpicxx supports -c -o file.o... yes
checking whether the mpicxx linker (mpicxx -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
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... no
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for mpif77 option to produce PIC... -fPIC
checking if mpif77 PIC flag -fPIC works... yes
checking if mpif77 supports -c -o file.o... yes
checking whether the mpif77 linker (mpicxx -m elf_x86_64) supports shared libraries... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
./configure: line 20252: PKG_PROG_PKG_CONFIG: command not found
checking for ranlib... (cached) ranlib
checking whether g++ accepts -std=c++0x... no
checking whether static_assert is supported... no
checking whether nullptr is supported... 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... no
checking for mpich... no
checking for OpenMPI... yes
checking whether compiling with OpenMPI works... yes
checking whether running with OpenMPI works... yes
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 for inkscape... no
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for string.h... (cached) yes
./configure: line 22904: syntax error near unexpected token `array'
./configure: line 22904: `                        array tr1/array tuple tr1/tuple'
--- Failed to build dune-common ---
Execution of dunecontrol terminated due to errors!








-- 
------------------------------------------------------------------------------------------------------------------
Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch, Computational Accelerator Scientist,
Paul Scherrer  Institute (PSI), CH-5232 Villigen, Suisse, benedikt.oswald at psi.ch, +41(0)56 310 32 12
http://amas.web.psi.ch/people/boswald/index.html
------------------------------------------------------------------------------------------------------------------




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