[Dune] Problems compiling dune trunk on Cray XT6

Benedikt Oswald benedikt.oswald at psi.ch
Mon Nov 12 14:08:10 CET 2012 

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, GFA
> Paul Scherrer  Institute (PSI), CH-5232 Villigen, Suisse, 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

--------------------------------------------------------------------------------------------------------------------------------------------------------------------
Benedikt Oswald, Dr. sc. techn., dipl. El. Ing. ETH, www.psi.ch, GFA
Paul Scherrer  Institute (PSI), CH-5232 Villigen, Suisse, 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.
--------------------------------------------------------------------------------------------------------------------------------------------------------------------

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