[Dune] problem compiling dune from trunk
Oswald Benedikt
Benedikt.Oswald at psi.ch
Tue Mar 26 21:41:14 CET 2013
Dear Christian,
thanks for looking and sorry for the insufficient information.
I had a look at the config.log in the dune-geometry module and found this, cf. below.
since this happens on the Cray I suspect that something goes wrong when ordering the
compiler / linker to do everything static. The cray requires everything to be linked static.
I now remember that I had this problem before, that I solved it but it now reappears.
I have to investigate why the configure tries to link to a shared fortran library.
Thanks again for pointing me to have a look at config,log ... in fact, I should have done this
right from the start.
Greetings, Benedikt
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_
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 --static -L/users/b
oswald/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 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 --static -DMPICH_IGNORE_CXX_SEEK -O2 -DNDEBUG -DHAVE_SUPERLU_DIST -DHAVE_PASTIX -I/users/boswald/extlib/superl
udist/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 --static conftest.cpp -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 /scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib/.libs/libdunecommon.a -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 ## _
I had a look at this directory:
ela2 dune-common/lib> pwd
/scratch/rosa/boswald/svnwork/dune-trunk/dune-common/lib
ela2 dune-common/lib> ls -lsh
total 92K
16K -rw-r--r-- 1 boswald psi 16K 2013-03-26 17:17 dunemodules.lib
4.0K -rw-r--r-- 1 boswald psi 1.8K 2013-03-26 17:49 libdunecommon.la
36K -rw-r--r-- 1 boswald psi 35K 2013-03-26 17:48 Makefile
4.0K -rw-r--r-- 1 boswald psi 541 2013-03-26 17:17 Makefile.am
32K -rw-r--r-- 1 boswald psi 31K 2013-03-26 17:44 Makefile.in
the contents of the libdunecommon.la is:
# libdunecommon.la - a libtool library file
# Generated by ltmain.sh (GNU libtool) 2.2.6
#
# Please DO NOT delete this file!
# It is necessary for linking the library.
# The name that we can dlopen(3).
dlname=''
# Names of this library.
library_names=''
# The name of the static archive.
old_library='libdunecommon.a'
# Linker flags that can not go in dependency_libs.
inherited_linker_flags=''
# Libraries that this one depends upon.
dependency_libs=' -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 /apps/ela/opt/gcc/
4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64/libquadmath.la /apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64/libgfortran.la /opt/gcc/4.6.2/snos/lib/../lib64/lib
quadmath.la /apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64/libgomp.la /apps/ela/opt/gcc/4.6.2/snos/bin/../lib/gcc/x86_64-suse-linux/4.6.2/../../../../lib64/libstdc++.la'
# Names of additional weak libraries provided by this library
weak_library_names=''
# Version information for libdunecommon.
current=0
age=0
revision=0
# Is this an already installed library?
installed=no
# Should we warn about portability when linking against -modules?
shouldnotlink=no
# Files to dlopen/dlpreopen
dlopen=''
dlpreopen=''
# Directory that this library needs to be installed in:
libdir='/scratch/rosa/boswald/hades3d/lib'
-----Original Message-----
From: Christian Engwer [mailto:christian.engwer at uni-muenster.de]
Sent: Tue 3/26/2013 20:01
To: Oswald Benedikt
Cc: dune at dune-project.org
Subject: Re: [Dune] problem compiling dune from trunk
Dear Benedikt,
without further information it is really hard to guess what you
problem might be. My first questions would be
a) is the a libdunecommon.la in the lib dir of dune-common
b) what is the error (in the config.log)
Cheers
Christian
On Tue, Mar 26, 2013 at 06:01:35PM +0100, Oswald Benedikt wrote:
> Dear Dune,
>
> I just tried to compile the dune trunk version and got the following error message:
>
> checking for strchr... yes
> configure: creating ./config.lt
> config.lt: creating libtool
> checking for dune-common installation or source tree... found in /scratch/rosa/boswald/svnwork/dune-trunk/dune-common
> checking dune/common/stdstreams.hh usability... yes
> checking dune/common/stdstreams.hh presence... yes
> checking for dune/common/stdstreams.hh... yes
> checking for libdunecommon... no
> configure: WARNING: <base-directory>/dune-trunk/dune-common does not seem to contain a valid dune-common (failed to link with libdunecommon.la)
>
>
> The uses dune versions are:
>
> URL: https://svn.dune-project.org/svn/dune-common/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-common
> Repository UUID: 419231ca-4411-0410-aba2-fc6cf8c4f609
> Revision: 7432
> Node Kind: directory
> Schedule: normal
> Last Changed Author: sander
> Last Changed Rev: 7431
> Last Changed Date: 2013-03-20 15:54:17 +0100 (Wed, 20 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-geometry/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-geometry
> Repository UUID: e31b3757-9ccd-424d-b11c-a976522ded21
> Revision: 486
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 478
> Last Changed Date: 2013-03-11 17:25:29 +0100 (Mon, 11 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-grid/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-grid
> Repository UUID: f82f27de-4411-0410-b156-930a902cda50
> Revision: 8921
> Node Kind: directory
> Schedule: normal
> Last Changed Author: sander
> Last Changed Rev: 8921
> Last Changed Date: 2013-03-25 10:09:17 +0100 (Mon, 25 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-istl/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-istl
> Repository UUID: 8c7282f0-4411-0410-8e4f-cdd3e049afb8
> Revision: 1908
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 1908
> Last Changed Date: 2013-03-21 23:18:47 +0100 (Thu, 21 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-grid-howto/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-grid-howto
> Repository UUID: 971b7fa1-7d12-0410-b1b7-9c127676b1f7
> Revision: 429
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 415
> Last Changed Date: 2013-02-02 00:47:51 +0100 (Sat, 02 Feb 2013)
>
> and the used gcc version is:
>
> COLLECT_GCC=/opt/gcc/4.6.2/bin/../snos/bin/g++
>
>
> I seem to remember a similar sounding error a few weeks ago.
>
> Would you have any suggestions on what is going wrong ?
>
> Thanks in advance, greetings, Benedikt
>
>
>
>
>
> _______________________________________________
> Dune mailing list
> Dune at dune-project.org
> http://lists.dune-project.org/mailman/listinfo/dune
>
--
Prof. Dr. Christian Engwer
Institut für Numerische und Angewandte Mathematik
Fachbereich Mathematik und Informatik der Universität Münster
Einsteinstrasse 62
48149 Münster
E-Mail christian.engwer at uni-muenster.de
Telefon +49 251 83-35067
FAX +49 251 83-32729
-----Original Message-----
From: Christian Engwer [mailto:christian.engwer at uni-muenster.de]
Sent: Tue 3/26/2013 20:01
To: Oswald Benedikt
Cc: dune at dune-project.org
Subject: Re: [Dune] problem compiling dune from trunk
Dear Benedikt,
without further information it is really hard to guess what you
problem might be. My first questions would be
a) is the a libdunecommon.la in the lib dir of dune-common
b) what is the error (in the config.log)
Cheers
Christian
On Tue, Mar 26, 2013 at 06:01:35PM +0100, Oswald Benedikt wrote:
> Dear Dune,
>
> I just tried to compile the dune trunk version and got the following error message:
>
> checking for strchr... yes
> configure: creating ./config.lt
> config.lt: creating libtool
> checking for dune-common installation or source tree... found in /scratch/rosa/boswald/svnwork/dune-trunk/dune-common
> checking dune/common/stdstreams.hh usability... yes
> checking dune/common/stdstreams.hh presence... yes
> checking for dune/common/stdstreams.hh... yes
> checking for libdunecommon... no
> configure: WARNING: <base-directory>/dune-trunk/dune-common does not seem to contain a valid dune-common (failed to link with libdunecommon.la)
>
>
> The uses dune versions are:
>
> URL: https://svn.dune-project.org/svn/dune-common/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-common
> Repository UUID: 419231ca-4411-0410-aba2-fc6cf8c4f609
> Revision: 7432
> Node Kind: directory
> Schedule: normal
> Last Changed Author: sander
> Last Changed Rev: 7431
> Last Changed Date: 2013-03-20 15:54:17 +0100 (Wed, 20 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-geometry/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-geometry
> Repository UUID: e31b3757-9ccd-424d-b11c-a976522ded21
> Revision: 486
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 478
> Last Changed Date: 2013-03-11 17:25:29 +0100 (Mon, 11 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-grid/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-grid
> Repository UUID: f82f27de-4411-0410-b156-930a902cda50
> Revision: 8921
> Node Kind: directory
> Schedule: normal
> Last Changed Author: sander
> Last Changed Rev: 8921
> Last Changed Date: 2013-03-25 10:09:17 +0100 (Mon, 25 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-istl/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-istl
> Repository UUID: 8c7282f0-4411-0410-8e4f-cdd3e049afb8
> Revision: 1908
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 1908
> Last Changed Date: 2013-03-21 23:18:47 +0100 (Thu, 21 Mar 2013)
>
> Path: .
> URL: https://svn.dune-project.org/svn/dune-grid-howto/trunk
> Repository Root: https://svn.dune-project.org/svn/dune-grid-howto
> Repository UUID: 971b7fa1-7d12-0410-b1b7-9c127676b1f7
> Revision: 429
> Node Kind: directory
> Schedule: normal
> Last Changed Author: gruenich
> Last Changed Rev: 415
> Last Changed Date: 2013-02-02 00:47:51 +0100 (Sat, 02 Feb 2013)
>
> and the used gcc version is:
>
> COLLECT_GCC=/opt/gcc/4.6.2/bin/../snos/bin/g++
>
>
> I seem to remember a similar sounding error a few weeks ago.
>
> Would you have any suggestions on what is going wrong ?
>
> Thanks in advance, greetings, Benedikt
>
>
>
>
>
> _______________________________________________
> Dune mailing list
> Dune at dune-project.org
> http://lists.dune-project.org/mailman/listinfo/dune
>
--
Prof. Dr. Christian Engwer
Institut für Numerische und Angewandte Mathematik
Fachbereich Mathematik und Informatik der Universität Münster
Einsteinstrasse 62
48149 Münster
E-Mail christian.engwer at uni-muenster.de
Telefon +49 251 83-35067
FAX +49 251 83-32729
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