[Dune] problem compiling dune from trunk
Oswald Benedikt
Benedikt.Oswald at psi.ch
Wed Mar 27 14:28:43 CET 2013
Hello Markus, thanks. In fact, I have checked and I now use:
CONFIGURE_FLAGS="DUNE_LDFLAGS='-all-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 -L$HOME/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -lpastix -L$HOME/extlib/scotch/6.0.0.rc20/xt-mpich2/5.5.0/gcc/4.6.2/lib -lptscotch -lptscotcherr '
MPICXX='CC' CXX='CC' CC='cc' F77='ftn' LD='CC'
CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing '
CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I$HOME/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I$HOME/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install '
CFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing '
FFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing '
--host=x86_64-unknown-linux-gnu
without further using static related flags in the options
The beginning of the config.log file from dune-geometry looks like this while the error still remains, cf. below:
It seems that this -all-static flag is not passed on to the libtool since the flag does not appear in the command sequence for
the link. and then, the error ocurrs. I am bit confused. Greetings, Benedikt
$ ./configure DUNE_LDFLAGS=-all-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 -L/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -lpastix -L/users/boswald/extlib/scotch/6.0.0.rc20/xt-mpich2/5.5.0/gcc/4.6.2/lib -lptscotch -lptscotcherr MPICXX=CC CXX=CC CC=cc F77=ftn LD=CC CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install CFLAGS=-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing FFLAGS=-DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing --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=/users/boswald/extlib/boost/1.50/gcc/4.6.2 --with-metis=/users/boswald/extlib/metis/4.0.3/gcc/4.6.2 --with-parmetis=/users/boswald/extlib/parmetis/3.2.0/xt-mpich2/5.5.0/gcc/4.6.2 --with-rlog=/users/boswald/extlib/rlog/svn-rev-21/gcc/4.6.2 --with-alugrid=/users/boswald/extlib/ALUGrid/1.94/xt-mpich2/5.5.0/gcc/4.6.2 --with-petsc=/users/boswald/extlib/petsc/3.2-p6/xt-mpich2/5.5.0/gcc/4.6.2 --prefix=/scratch/rosa/boswald/hades3d --with-dune-common=/scratch/rosa/boswald/svnwork/dune-trunk/dune-common/ ACLOCAL_AMFLAGS=-I . -I m4 -I /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/m4
## ------------------ ##
## Running config.lt. ##
## ------------------ ##
config.lt:772: creating libtool
configure:30316: checking for dune-common installation or source tree
configure:30402: result: found in /scratch/rosa/boswald/svnwork/dune-trunk/dune-common
configure:30420: checking dune/common/stdstreams.hh usability
configure:30420: CC -std=c++0x -c -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common conftest.cpp >&5
configure:30420: $? = 0
configure:30420: result: yes
configure:30420: checking dune/common/stdstreams.hh presence
configure:30420: CC -E -std=c++0x -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common conftest.cpp
configure:30420: $? = 0
configure:30420: result: yes
configure:30420: checking for dune/common/stdstreams.hh
configure:30420: result: yes
configure:30451: checking for libdunecommon
configure:30498: ./libtool --tag=CXX --mode=link CC -std=c++0x -o conftest -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common conftest.cpp /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/libdunecommon.la >&5
libtool: link: CC -std=c++0x -o conftest -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superludist/2.5/xt-mpich2/5.5.0/gcc/4.6.2/SRC -I/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -I/scratch/rosa/boswald/svnwork/dune-trunk/dune-common conftest.cpp /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/.libs/libdunecommon.a -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/users/boswald/extlib/pastix/5.2.1/3945/xt-mpich2/5.5.0/gcc/4.6.2/install -L/users/boswald/extlib/scotch/6.0.0.rc20/xt-mpich2/5.5.0/gcc/4.6.2/lib -lsuperlu_dist_2.5 -lparmetis -lmetis -lpastix -lptscotch -lptscotcherr -lmpichf90_gnu_46 -lxpmem -ldmapp -lugni -ludreg /opt/gcc/4.6.2/snos/lib/../lib64/libgfortran.so /opt/gcc/4.6.2/snos/lib/../lib64/libquadmath.so /opt/gcc/4.6.2/snos/lib/../lib64/libgomp.so -lrt /opt/gcc/4.6.2/snos/lib/../lib64/libstdc++.so -lm
/apps/ela/system/bin/ld: attempted static link of dynamic object `/opt/gcc/4.6.2/snos/lib/../lib64/libgfortran.so'
collect2: ld returned 1 exit status
configure:30498: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "dune-geometry"
| #define PACKAGE_TARNAME "dune-geometry"
| #define PACKAGE_VERSION "2.3-svn"
| #define PACKAGE_STRING "dune-geometry 2.3-svn"
| #define PACKAGE_BUGREPORT "dune-devel at dune-project.org"
| #define PACKAGE_URL ""
| #define PACKAGE "dune-geometry"
| #define VERSION "2.3-svn"
| #define DUNE_GEOMETRY_VERSION "2.3-svn"
| #define DUNE_GEOMETRY_VERSION_MAJOR 2
| #define DUNE_GEOMETRY_VERSION_MINOR 3
| #define DUNE_GEOMETRY_VERSION_REVISION 0
| #define PACKAGE "dune-geometry"
| #define VERSION "2.3-svn"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_BLAS 1
| #define HAVE_LAPACK 1
| #define FC_FUNC(name,NAME) name ## _
| #define FC_FUNC_(name,NAME) name ## _
| #define HAVE_STATIC_ASSERT 1
| #define HAVE_NULLPTR 1
| #define HAVE_TYPE_TRAITS 1
| #define HAVE_TR1_TYPE_TRAITS 1
| #define HAVE_TUPLE 1
| #define HAVE_TR1_TUPLE 1
| #define HAVE_ARRAY 1
| #define HAVE_INTEGRAL_CONSTANT 1
| #define HAVE_STD_HASH 1
| #define HAVE_TR1_HASH 1
| #define HAVE_MEMORY 1
| #define HAVE_TR1_MEMORY 1
| #define SHARED_PTR_NAMESPACE std
| #define SHARED_PTR_HEADER <memory>
| #define HAVE_BOOST /**/
| #define HAVE_DUNE_BOOST ENABLE_BOOST
| #define HAVE_MAKE_SHARED 1
| #define HAS_ATTRIBUTE_DEPRECATED 1
| #define HAS_ATTRIBUTE_DEPRECATED_MSG 1
| #define HAS_ATTRIBUTE_UNUSED 1
| #define HAVE_CXA_DEMANGLE 1
| #define DUNE_MINIMAL_DEBUG_LEVEL 4
| #define HAVE_RPC_RPC_H 1
| #define MPI_2 1
| #define HAVE_MPI ENABLE_MPI
| #define HAVE_SYS_MMAN_H 1
| #define HAVE_MPROTECT 1
| #define HAVE_MALLOC_H 1
| #define HAVE_STRING_H 1
| #define HAVE_LIBM 1
| #define HAVE_SQRT 1
| #define HAVE_STRCHR 1
| /* end confdefs.h. */
| #include<dune/common/stdstreams.hh>
| #ifdef F77_DUMMY_MAIN
|
| # ifdef __cplusplus
| extern "C"
| # endif
| int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| #ifdef FC_DUMMY_MAIN
| #ifndef FC_DUMMY_MAIN_EQ_F77
| # ifdef __cplusplus
| extern "C"
| # endif
| int FC_DUMMY_MAIN() { return 1; }
| #endif
| #endif
| int
| main ()
| {
| #ifndef DUNE_MINIMAL_DEBUG_LEVEL
| #define DUNE_MINIMAL_DEBUG_LEVEL 1
| #endif
| Dune::derr.active();
| ;
| return 0;
| }
configure:30507: result: no
configure:30519: WARNING: /scratch/rosa/boswald/svnwork/dune-trunk/dune-common does not seem to contain a valid dune-common (failed to link with libdunecommon.la)
configure:30740: error: could not find required module dune-common
-----Original Message-----
From: dune-bounces+benedikt.oswald=psi.ch at dune-project.org on behalf of Markus Blatt
Sent: Wed 3/27/2013 13:10
To: dune at dune-project.org
Subject: Re: [Dune] problem compiling dune from trunk
On Wed, Mar 27, 2013 at 10:49:04AM +0100, Oswald Benedikt wrote:
> Hello Markus, in fact I use this, is this not equivalent ? Thanks, Benedikt
>
>
>
> CONFIGURE_FLAGS="DUNE_LDFLAGS='-all-static' MPICXX='CC' CXX='CC' CC='cc' F77='ftn' LD='CC -static '
Somehow this contradicts your config.log:
> > configure:30420: result: yes
> > configure:30451: checking for libdunecommon
> > configure:30498: ./libtool --tag=CXX --mode=link CC -std=c++0x -o conftest -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -fomit-frame-pointer --no-strict-aliasing --static -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_
There should be a --all-static right after -std=c++0x with a correcty
set DUNE_LDFLAGS. Please double check.
DUNE_LDFLAGS='-all-static' should be all that is needed. Therfore you
might want to test without redifinition of LD and without any other
static occurrence in the flags.
Markus
--
Do you need more support with DUNE or HPC in general?
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Tel.: +49 (0) 160 97590858 Fax: +49 (0)322 1108991658
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