[Dune] Problems compiling dune trunk on Cray XT6
Eike Mueller
E.Mueller at bath.ac.uk
Tue Nov 13 11:14:46 CET 2012
Hi Benedikt,
I'm just guessing, but have you tried taking the -static flag out of CFLAGS, CXXFLAGS etc.? I only had to set -all-static in
DUNE_LDFLAGS, and then set --disable-shared and --enable-static in CONFIGURE_FLAGS.
It seems to fall over in the istl-tutorial directory, if you only want to get a working DUNE installation for now and don't need
the tutorial, could you comment this out in dune-istl/dune/istl/Makefile.am in ?
Cheers, Eike
Benedikt Oswald wrote:
> Hello Markus, now it runs until reaching the dune-istl module:
>
> make[1]: Entering directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl'
> Making all in dune
> make[2]: Entering directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl/dune'
> Making all in istl
> make[3]: Entering directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl/dune/istl'
> Making all in .
> make[4]: Entering directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl/dune/istl'
> make[4]: Nothing to be done for `all-am'.
> make[4]: Leaving directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl/dune/istl'
> Making all in tutorial
> make[4]: Entering directory
> `/scratch/rosa/boswald/svnwork/dune-trunk/dune-istl/dune/istl/tutorial'
> CC -std=c++0x -DHAVE_CONFIG_H -I. -I../../..
> -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common -I../../..
> -I/users/boswald/extlib/boost/1.50/gcc/4.6.2/include -DENABLE_BOOST
> -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common
> -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static
> --no-strict-aliasing -DHAVE_SUPERLU_DIST
> -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2
> -lparmetis -lmetis -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer -static --no-strict-aliasing -DHAVE_SUPERLU_DIST
> -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2
> -lparmetis -lmetis -MT example-example.o -MD -MP -MF
> .deps/example-example.Tpo -c -o example-example.o `test -f 'example.cc'
> || echo './'`example.cc
> mv -f .deps/example-example.Tpo .deps/example-example.Po
> /bin/sh ../../../libtool --tag=CXX --mode=link CC -std=c++0x
> -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer -static
> --no-strict-aliasing -DHAVE_SUPERLU_DIST
> -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2
> -lparmetis -lmetis -all-static
> /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/libdunecommon.la
> /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/libdunecommon.la
> -static
> -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2
> -lparmetis -lmetis -o example example-example.o -lm
> libtool: link: CC -std=c++0x -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer --no-strict-aliasing -DHAVE_SUPERLU_DIST
> -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -static -o example example-example.o
> -L/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -L/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2
> -L/apps/ela/alps/4.0.2-2.0400.7033.0/lib/alps
> -L/opt/cray/udreg/2.3.2-1.0400.4691.4.1.gem/lib64
> -L/opt/cray/ugni/2.3-1.0400.4374.4.88.gem/lib64
> -L/opt/cray/pmi/3.0.1-1.0000.8917.33.1.gem/lib64
> -L/opt/cray/dmapp/3.2.1-1.0400.4255.2.159.gem/lib64
> -L/opt/cray/xpmem/0.1-2.0400.31280.3.1.gem/lib64
> -L/opt/cray/mpt/5.5.0/gni/mpich2-gnu/46/lib
> -L/opt/xt-libsci/11.1.00/gnu/46/interlagos/lib -L/usr/lib/alps
> -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2
> -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc
> -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64
> -L/apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../..
> -L/opt/cray/atp/1.4.4/lib/
> /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/.libs/libdunecommon.a
> -lAtpSigHCommData -lAtpSigHandler -lscicpp_gnu -lsci_gnu_mp
> /opt/gcc/4.6.2/snos/lib/../lib64/libstdc++.so
> /opt/gcc/4.6.2/snos/lib/../lib64/libgfortran.so -lmpichf90_gnu_46
> -lmpich_gnu_46 -lmpl -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil
> -ludreg -lpthread /opt/gcc/4.6.2/snos/lib/../lib64/libgomp.so -lrt
> /opt/gcc/4.6.2/snos/lib/../lib64/libquadmath.so -lsuperlu_dist_2.5
> -lparmetis -lmetis -lm
> /apps/ela/system/bin/ld: attempted static link of dynamic object
> `/opt/gcc/4.6.2/snos/lib/../lib64/libstdc++.so'
> collect2: ld returned 1 exit status
>
>
> My configure flags for the Dune Opts file are as follows:
>
>
> CONFIGURE_FLAGS="DUNE_LDFLAGS='-all-static ' MPICXX='CC' CXX='CC'
> CC='cc' F77=ftn LD='CC'
> CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer -static --no-strict-aliasing
> -DHAVE_SUPERLU_DIST
> -I$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L$HOME/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis'
> CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer -static --no-strict-aliasing
> -DHAVE_SUPERLU_DIST
> -I$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L$HOME/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis'
> CFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer -static --no-strict-aliasing
> -DHAVE_SUPERLU_DIST
> -I$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC
> -L$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L$HOME/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis'
> FFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG
> -fomit-frame-pointer -static --no-strict-aliasing'
> LDFLAGS='-static
> -L$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/lib
> -lsuperlu_dist_2.5
> -L$HOME/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 -lparmetis -lmetis'
> LTFLAGS=' '
> --host=x86_64-unknown-linux-gnu
> --enable-static
> --disable-shared
> --disable-mpiruntest
> --enable-hades3deltd
> --enable-hades3dfetd
> --enable-hades3ddges
> --enable-hades3ddgfd
> --enable-hades3dfefd
> --enable-hades3dfeqs
> --disable-documentation
> --enable-parallel
> --enable-boost
> --enable-petsc
> --enable-debug-output
> --without-gmp
> --with-boost='$HOME/extlib/boost/1.50/gcc/4.6.2'
> --with-metis='$HOME/extlib/metis/4.0.3/gcc/4.6.2'
>
> --with-parmetis='$HOME/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2'
> --with-rlog='$HOME/extlib/rlog/svn-rev-21/gcc/4.6.2'
>
> --with-alugrid='$HOME/extlib/ALUGrid/1.94/xt-mpich2/5.5.0/gcc/4.6.2'
>
> --with-petsc='$HOME/extlib/petsc/3.2-p6/xt-mpich2/5.5.0/gcc/4.6.2'
> --prefix='/scratch/rosa/boswald/hades3d'
> "
>
> I have attached the config.log from the dune-istl module.
>
> Why would it now advance further than before but crash with the same
> error message ?
>
> Greetings, Benedikt
>
>
>
> ------------------------------------------------------------------------
>
>
>
>
>
> On Nov 12, 2012, at 12:40 PM, Benedikt Oswald wrote:
>
>> Hello Markus, thanks, compilation is now progressing further, but not
>> yet finished.
>> In fact, there was maintenance on this Cray system last week
>> and it seems that then something was changed...
>> I will report back when it is through.
>>
>> Greetings and thanks again for the quick fix! Benedikt
>>
>>
>> On Nov 12, 2012, at 12:07 PM, Markus Blatt wrote:
>>
>>> On Mon, Nov 12, 2012 at 11:34:33AM +0100, Benedikt Oswald wrote:
>>>> In fact, I think it is a linker error related to dynamic linking
>>>> instead of static.
>>>>
>>>> I am a bit at a loss why this occurrs now ?
>>>>
>>>
>>> You are totally right.
>>>
>>> Have you followed my explanation at
>>> http://www.dr-blatt.de/german/blog-german/2011/11/18/forcing-static-linkage-c-binaries-and-libraries-autoconfautomakelibtool/
>>> , especially on using DUNE_LDFLAGS?
>>>
>>> Hope that it does the trick!
>>>
>>> Markus
>>>
>>> --
>>> Do you need more support with DUNE or HPC in general?
>>>
>>> Dr. Markus Blatt - HPC-Simulation-Software & Services
>>> http://www.dr-blatt.de
>>> Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany
>>> Tel.: +49 (0) 160 97590858 Fax: +49 (0)322 1108991658
>>
>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch
>> <http://www.psi.ch/>, GFA
>> Paul Scherrer Institute (PSI), CH-5232 Villigen, Suisse,
>> benedikt.oswald at psi.ch <mailto:benedikt.oswald at psi.ch>, +41(0)56 310 32 12
>>
>> "Passion is required for any great work, and for the
>> revolution passion and audacity are required in big doses.",
>> Ernesto 'Che' Guevara, Letter to his parents.
>> --------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Dune mailing list
>> Dune at dune-project.org <mailto:Dune at dune-project.org>
>> http://lists.dune-project.org/mailman/listinfo/dune
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------
> Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch
> <http://www.psi.ch>, GFA
> Paul Scherrer Institute (PSI), CH-5232 Villigen, Suisse,
> benedikt.oswald at psi.ch <mailto:benedikt.oswald at psi.ch>, +41(0)56 310 32 12
>
> "Passion is required for any great work, and for the revolution passion
> and audacity are required in big doses.",
> Ernesto 'Che' Guevara, Letter to his parents.
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Dune mailing list
> Dune at dune-project.org
> http://lists.dune-project.org/mailman/listinfo/dune
--
Dr Eike Mueller
Research Officer
Department of Mathematical Sciences
University of Bath
Bath BA2 7AY, United Kingdom
+44 1225 38 5633
e.mueller at bath.ac.uk
http://people.bath.ac.uk/em459/
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