[Dune] beta5 configuration problem

[Christian May]

Dear Christian,

thanks for the quick reply. I'm using Linux 2.6.8 under an x86_64
platform. When I run dunecontrol with parameter all, I end up
with the attached error. The problem seems to be during make in
dune-common even though libdunecommon.a was created.

Thanks a lot
Christian




On Mon, 16 Jul 2007, Christian Engwer wrote:

> Dear Christian,
>
> > I have some trouble configuring the beta5 version.
> > Calling
> > $ ./dune-common-1.0beta5/bin/dunecontrol autogen
> > works fine, but upon invoking
> > $ ./dune-common-1.0beta5/bin/dunecontrol configure --prefix=/home2/phys/cmay/ --disable-mpiruntest
> > I get the following error:
> >
> > >configure: error: /home2/phys/cmay/dune/dune-common-1.0beta5 does not
> > >seem to contain a valid dune-common (failed to link with
> > >libdunecommon.la)
>
> Are you building several dune modules, or just dune-common? If you are
> building more modules, please take the time to read installation notes
> on the web page.
>
> > I attached the config.log file.
>
> Your log file is the log file written in dune-common. This log file
> suggests that dune-common is configured properly. Before you configure
> other modules, you have to fully build dune-common. Usually you will
> want to write an options files and call:
> ./dune-common/bin/dunecontrol --opts=optionsfile all
>
> the all target will call (for each module) autogen, configure and
> make.
>
> When building i.e. dune-grid you will need a libdunecommon. This lib
> is not available before calling make in dune-common. Therefor we
> introduced the extra dunecontrol target "all".
>
> If you did follow the instructions and the problem is a different one,
> please provide the log file from the modules that fails to run
> configure and please tell in detail which architecture and which
> configuration you are using.
>
> CU Christian
>
-------------- next part --------------
cmay at gonzales2-c:~/dune> ./dune-common-1.0beta5/bin/dunecontrol --opts=options all
--- going to build dune-common dune-grid dune-grid-howto dune-istl  ---
----- loading default flags $ALL_FLAGS from /home2/phys/cmay/dune/options -----
--- calling all for dune-common ---
----- loading default flags $AUTOGEN_FLAGS from /home2/phys/cmay/dune/options -----
----- loading default flags $CONFIGURE_FLAGS from /home2/phys/cmay/dune/options -----
./configure --prefix='/home2/phys/cmay/' --disable-mpiruntest "--with-dune-common=/home2/phys/cmay/dune/dune-common-1.0beta5" "--with-dune-grid=/home2/phys/cmay/dune/dune-grid-1.0beta5" "--with-dune-istl=/home2/phys/cmay/dune/dune-istl-1.0beta5"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether ln -s works... yes
checking for style of include used by make... GNU
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -E
checking whether compiling C++ code works... yes
checking whether linking C++ objects works... yes
checking for __attribute__((deprecated))... yes
checking for ranlib... ranlib
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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 ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld 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 how to run the C++ preprocessor... g++ -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... cat: /etc/ld.so.conf.d/*.conf: No such file or directory
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... cat: /etc/ld.so.conf.d/*.conf: No such file or directory
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 static flag -static works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... cat: /etc/ld.so.conf.d/*.conf: No such file or directory
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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 rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for X... libraries /usr/X11R6/lib64, headers /usr/X11R6/include
checking whether -R must be followed by a space... neither works
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... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
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... -lGL
checking grape.h usability... no
checking grape.h presence... no
checking for grape.h... no
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... no
checking for IBM MPI... checking whether compiling with  works... yes
configure: WARNING: Diabled test whether running with  works.
checking /usr/local/ug/include/gm.h usability... no
checking /usr/local/ug/include/gm.h presence... no
checking for /usr/local/ug/include/gm.h... no
configure: WARNING: gm.h not found in /usr/local/ug/include
checking amiramesh/AmiraMesh.h usability... no
checking amiramesh/AmiraMesh.h presence... no
checking for amiramesh/AmiraMesh.h... no
configure: WARNING: AmiraMesh.h not found in /usr/local/amiramesh/include/amiramesh
checking psurface.h usability... no
checking psurface.h presence... no
checking for psurface.h... no
configure: Check for psurface library aborted because AmiraMesh is unavailable!
checking for ParMETIS library... failed
checking how to get verbose linking output from g77... -v
checking for Fortran 77 libraries of g77...  -L/home2/phys/cmay/acml3.6.0/gfortran/lib/:-L/home2/phys/cmay/lib/ -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4 -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../lib64 -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking for SuperLU library... failed
checking for SuperLUDist library... failed
checking whether H5_HAVE_PARALLEL is declared... no
checking hdf5.h usability... no
checking hdf5.h presence... no
checking for hdf5.h... no
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for string.h... (cached) yes
checking for pow in -lm... yes
checking for sqrt... yes
checking for strchr... yes
checking for doxygen... doxygen
checking for latex... no
checking for bibtex... no
checking for dvipdf... no
checking for dvips... no
checking for wml... no
checking for perl... perl
checking for inkscape... no
checking for convert... convert
checking for METIS library... failed
checking dune-common requirements...

Found the following Dune-components:

-----------------------------

ALBERTA..........: no
ALUGrid..........: no
AmiraMesh........: no
BLAS.............: no
Grape............: no
HDF5.............: no
MPI..............: yes ()
METIS............: no
ParMETIS.........: no
SuperLU..........: no
SuperLU-DIST.....: no
OpenGL...........: yes
UG...............: no

-----------------------------

See ./configure --help and config.log for reasons why a component wasn't found


Note: Most of the libraries checked for above are only used for the self-test
of Dune. The library itself will build and the headers will work even if
ALBERTA, MPI, etc. cannot be found. An exception to this are UG and AmiraMesh
which need to be found right now if you want to use them later.

configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating bin/Makefile
config.status: creating common/Makefile
config.status: creating common/test/Makefile
config.status: creating common/exprtmpl/Makefile
config.status: creating doc/Makefile
config.status: creating doc/devel/Makefile
config.status: creating doc/layout/Makefile
config.status: creating doc/doxygen/Makefile
config.status: creating doc/buildsystem/Makefile
config.status: creating m4/Makefile
config.status: creating am/Makefile
config.status: creating bin/wmlwrap
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
----- loading default flags $MAKE_FLAGS from /home2/phys/cmay/dune/options -----
make install
Making install in lib
make[1]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/lib'
cd $(dirname ../common/libcommon.la) && make $(basename ../common/libcommon.la)
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[2]: `libcommon.la' is up to date.
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/lib'
cd $(dirname ../common/libcommon.la) && make $(basename ../common/libcommon.la)
make[3]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[3]: `libcommon.la' is up to date.
make[3]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
test -z "/home2/phys/cmay//lib" || mkdir -p -- "/home2/phys/cmay//lib"
 /bin/sh ../libtool --mode=install /usr/bin/install -c  'libdunecommon.la' '/home2/phys/cmay//lib/libdunecommon.la'
/usr/bin/install -c .libs/libdunecommon.lai /home2/phys/cmay//lib/libdunecommon.la
/usr/bin/install -c .libs/libdunecommon.a /home2/phys/cmay//lib/libdunecommon.a
chmod 644 /home2/phys/cmay//lib/libdunecommon.a
ranlib /home2/phys/cmay//lib/libdunecommon.a
PATH="$PATH:/sbin" ldconfig -n /home2/phys/cmay//lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home2/phys/cmay//lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/lib'
make[1]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/lib'
Making install in common
make[1]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
Making install in .
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[3]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/home2/phys/cmay//include/dune/common" || mkdir -p -- "/home2/phys/cmay//include/dune/common"
 /usr/bin/install -c -m 644 'dlist.cc' '/home2/phys/cmay//include/dune/common/dlist.cc'
 /usr/bin/install -c -m 644 'stdstreams.cc' '/home2/phys/cmay//include/dune/common/stdstreams.cc'
 /usr/bin/install -c -m 644 'alignment.hh' '/home2/phys/cmay//include/dune/common/alignment.hh'
 /usr/bin/install -c -m 644 'array.hh' '/home2/phys/cmay//include/dune/common/array.hh'
 /usr/bin/install -c -m 644 'arraylist.hh' '/home2/phys/cmay//include/dune/common/arraylist.hh'
 /usr/bin/install -c -m 644 'bitfield.hh' '/home2/phys/cmay//include/dune/common/bitfield.hh'
 /usr/bin/install -c -m 644 'debugstream.hh' '/home2/phys/cmay//include/dune/common/debugstream.hh'
 /usr/bin/install -c -m 644 'dlist.hh' '/home2/phys/cmay//include/dune/common/dlist.hh'
 /usr/bin/install -c -m 644 'enumset.hh' '/home2/phys/cmay//include/dune/common/enumset.hh'
 /usr/bin/install -c -m 644 'exceptions.hh' '/home2/phys/cmay//include/dune/common/exceptions.hh'
 /usr/bin/install -c -m 644 'fixedarray.hh' '/home2/phys/cmay//include/dune/common/fixedarray.hh'
 /usr/bin/install -c -m 644 'fmatrix.hh' '/home2/phys/cmay//include/dune/common/fmatrix.hh'
 /usr/bin/install -c -m 644 'fvector.hh' '/home2/phys/cmay//include/dune/common/fvector.hh'
 /usr/bin/install -c -m 644 'genericiterator.hh' '/home2/phys/cmay//include/dune/common/genericiterator.hh'
 /usr/bin/install -c -m 644 'helpertemplates.hh' '/home2/phys/cmay//include/dune/common/helpertemplates.hh'
 /usr/bin/install -c -m 644 'interfaces.hh' '/home2/phys/cmay//include/dune/common/interfaces.hh'
 /usr/bin/install -c -m 644 'iteratorfacades.hh' '/home2/phys/cmay//include/dune/common/iteratorfacades.hh'
 /usr/bin/install -c -m 644 'logictraits.hh' '/home2/phys/cmay//include/dune/common/logictraits.hh'
 /usr/bin/install -c -m 644 'misc.hh' '/home2/phys/cmay//include/dune/common/misc.hh'
 /usr/bin/install -c -m 644 'poolallocator.hh' '/home2/phys/cmay//include/dune/common/poolallocator.hh'
 /usr/bin/install -c -m 644 'sllist.hh' '/home2/phys/cmay//include/dune/common/sllist.hh'
 /usr/bin/install -c -m 644 'smartpointer.hh' '/home2/phys/cmay//include/dune/common/smartpointer.hh'
 /usr/bin/install -c -m 644 'stack.hh' '/home2/phys/cmay//include/dune/common/stack.hh'
 /usr/bin/install -c -m 644 'stdstreams.hh' '/home2/phys/cmay//include/dune/common/stdstreams.hh'
 /usr/bin/install -c -m 644 'timer.hh' '/home2/phys/cmay//include/dune/common/timer.hh'
 /usr/bin/install -c -m 644 'tuples.hh' '/home2/phys/cmay//include/dune/common/tuples.hh'
 /usr/bin/install -c -m 644 'typetraits.hh' '/home2/phys/cmay//include/dune/common/typetraits.hh'
 /usr/bin/install -c -m 644 'precision.hh' '/home2/phys/cmay//include/dune/common/precision.hh'
 /usr/bin/install -c -m 644 'bigunsignedint.hh' '/home2/phys/cmay//include/dune/common/bigunsignedint.hh'
 /usr/bin/install -c -m 644 'gcd.hh' '/home2/phys/cmay//include/dune/common/gcd.hh'
 /usr/bin/install -c -m 644 'lcm.hh' '/home2/phys/cmay//include/dune/common/lcm.hh'
 /usr/bin/install -c -m 644 'configparser.hh' '/home2/phys/cmay//include/dune/common/configparser.hh'
 /usr/bin/install -c -m 644 'propertymap.hh' '/home2/phys/cmay//include/dune/common/propertymap.hh'
 /usr/bin/install -c -m 644 'collectivecommunication.hh' '/home2/phys/cmay//include/dune/common/collectivecommunication.hh'
 /usr/bin/install -c -m 644 'mpihelper.hh' '/home2/phys/cmay//include/dune/common/mpihelper.hh'
 /usr/bin/install -c -m 644 'singleton.hh' '/home2/phys/cmay//include/dune/common/singleton.hh'
 /usr/bin/install -c -m 644 'mpicollectivecommunication.hh' '/home2/phys/cmay//include/dune/common/mpicollectivecommunication.hh'
 /usr/bin/install -c -m 644 'geometrytype.hh' '/home2/phys/cmay//include/dune/common/geometrytype.hh'
 /usr/bin/install -c -m 644 'tripel.hh' '/home2/phys/cmay//include/dune/common/tripel.hh'
 /usr/bin/install -c -m 644 'utility.hh' '/home2/phys/cmay//include/dune/common/utility.hh'
 /usr/bin/install -c -m 644 'bartonnackmanifcheck.hh' '/home2/phys/cmay//include/dune/common/bartonnackmanifcheck.hh'
 /usr/bin/install -c -m 644 'binaryfunctions.hh' '/home2/phys/cmay//include/dune/common/binaryfunctions.hh'
make[3]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
Making install in test
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/test'
make[3]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/test'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/test'
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/test'
Making install in exprtmpl
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/exprtmpl'
make[3]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/exprtmpl'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/home2/phys/cmay//include/dune/common/exprtmpl" || mkdir -p -- "/home2/phys/cmay//include/dune/common/exprtmpl"
 /usr/bin/install -c -m 644 'exprexpr.inc' '/home2/phys/cmay//include/dune/common/exprtmpl/exprexpr.inc'
 /usr/bin/install -c -m 644 'norm.inc' '/home2/phys/cmay//include/dune/common/exprtmpl/norm.inc'
 /usr/bin/install -c -m 644 'scalar.inc' '/home2/phys/cmay//include/dune/common/exprtmpl/scalar.inc'
make[3]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/exprtmpl'
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common/exprtmpl'
make[1]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/common'
Making install in doc
make[1]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/doc'
Making install in devel
make[2]: Entering directory `/home2/phys/cmay/dune/dune-common-1.0beta5/doc/devel'
make[2]: *** No rule to make target `codingstyle.html', needed by `all-am'.  Stop.
make[2]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/doc/devel'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home2/phys/cmay/dune/dune-common-1.0beta5/doc'
make: *** [install-recursive] Error 1
--- Failed to build dune_common ---
Execution of dunecontrol terminated due to errors!