Re: Libtool adding libraries differently than neededwith compilerwrappers
Hi Nitin,
I did go down this path before.
I added
AC_CONFIG_COMMANDS(rminterlibdeps,
[
echo Executing rminterlibdeps
os_fc=`uname`-${FC};
case $os_fc in
Linux-ftn)
echo Removing the inter-library dependencies;
sed -i.bak -e 's/postdeps=.*$/postdeps=/g' -e
's/postdep_objects=.*$/postdep_objects=/g' -e
's/link_all_deplibs=.*$/link_all_deplibs=no/g' libtool
sed -i.bak -e 's? -L/opt/fftw/3.2.[0-9]/lib ? ?g' -e 's?
/opt/fftw/3.2.[0-9]/lib ? ?g' libtool
# The general one does not seem to work?
# sed -i.bak -e 's? -L/opt/fftw/3.2.[0-9].[0-9]/lib ? ?g' -e
's? /opt/fftw/3.2.[0-9].[0-9]/lib ? ?g' libtool
sed -i.bak -e 's? -L/opt/fftw/3.2.2.1/lib ? ?g' -e 's?
/opt/fftw/3.2.2.1/lib ? ?g' libtool
;;
esac
rm -f libtool.bak;
]
)
to my configure.ac, and I have:
nid00163.franklin$ grep fftw libtool
nid00163.franklin$
showing that all references to fftw in libtool have been removed, but I
still get
the error.
ThxJohn
On 4/22/2011 10:38 AM, Kapoor, Nitin wrote:
I am having a similar issue where libtool is passing
(/usr/sfw/lib/libstdc++.so) to the linker.
libtool: link: g++ -g -O2 -D_REENTRANT -pthreads -o .libs/EnumVal
src/EnumVal/EnumVal.o ../src/.libs/libxerces-c.so
/usr/sfw/lib/libstdc++.so -L/usr/sfw/lib -lnsl -lsocket -licuuc
-licudata -pthreads -Wl,-R -Wl,/usr/local/lib -Wl,-R -Wl,/usr/sfw/lib
ld: warning: file /usr/sfw/lib/libstdc++.so: attempted multiple
inclusion of file
I found out that it is because of the postdeps variable in the libtool
script. If you search the libtool script, you will find a similar entry
to this:-
postdeps="-lstdc++ -lm -lgcc_s -lgcc_s". If I remove -lstdc++, then I
get clean compile ( no multiple inclusion warning).
I do not know how to configure libtool to remove it by itself. This may
be your issue as well.
Thanks,
Nitin.
-Original Message-
From: libtool-bounces+nkapoor=sensis@gnu.org
[mailto:libtool-bounces+nkapoor=sensis@gnu.org] On Behalf Of John R.
Cary
Sent: Friday, April 22, 2011 12:28 PM
To: libtool@gnu.org
Subject: Re: Libtool adding libraries differently than neededwith
compilerwrappers
Hi Nitin,
I take the link line output from libtool and throw it into a shell
script, then
I remove those entries and run the script.
Thx...John
On 4/22/2011 10:25 AM, Kapoor, Nitin wrote:
Hi John,
How are you removing the following paths from you link:
/opt/fftw/3.2.2.1/lib/libfftw3.so /opt/fftw/3.2.2.1/lib/libfftw3f.so
/opt/cray/pmi/1.0-1..7901.22.1.ss/lib64/libpmi.so
/usr/lib64/gcc/x86_64-suse-linux/4.1.2/libstdc++.so
and
-lgcc_s
Are you hand editing the libtool script ?
Thanks
Nitin.
-Original Message-
From: libtool-bounces+nkapoor=sensis@gnu.org
[mailto:libtool-bounces+nkapoor=sensis@gnu.org] On Behalf Of John
R.
Cary
Sent: Friday, April 22, 2011 9:17 AM
To: libtool@gnu.org
Subject: Libtool adding libraries differently than needed with
compilerwrappers
We have a project using libtool on a Cray-XT4 using pathscale.
For compiling in parallel, we are supposed to use the compiler
wrapper, in this case ftn, that adds various libraries. A particular
complexity is that one has to switch libraries between front and
back end nodes, and this is done with LD_LIBRARY_PATH. We have
a problem, in that libtool seems to extract libraries from
the wrapper and put them at the end of the link line in a way
that the linker exits with an error.
System information
x86_64-unknown-linux-gnu
bash
ftn (wrapping pathf90)
-extend-source -byteswapio -fno-second-underscore -r8 -O2
-fno-second-underscore
/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/bin
/ld
libtool (GNU libtool) 2.4
autoconf (GNU Autoconf) 2.68
automake (GNU automake) 1.11.1
The failure is
/bin/sh ../../libtool --tag=FC --tag=FC --mode=link ftn
-I../../interfaces/wrap -I../../interfaces/src
-I/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1
96-par/include
-I/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-
r1341-par/include
-I/opt/cray/hdf5-parallel/1.8.3.1/hdf5-parallel-pathscale/include
-I/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0
.47-r114-par/include
-extend-source -byteswapio -fno-second-underscore -r8 -O2
-fno-second-underscore -o runFlowShear runFlowShear.o libfmcfm.la
-L/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-
r1341-par/lib/pathf
-lglf23mpi -lmmm95 -lifspppl -lnclass -lkapisn
-L/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1
96-par/lib/pathf
-lGYRO -lNEO -lTGLF
-L/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.
12-r51-ser/lib
-llsode -lnlother -lr8slatec
-L/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/l
ib
-lrfftw -lfftw /opt/acml/4.2.0/pathscale64/
RE: Libtool adding libraries differently than neededwith compilerwrappers
I am having a similar issue where libtool is passing (/usr/sfw/lib/libstdc++.so) to the linker. libtool: link: g++ -g -O2 -D_REENTRANT -pthreads -o .libs/EnumVal src/EnumVal/EnumVal.o ../src/.libs/libxerces-c.so /usr/sfw/lib/libstdc++.so -L/usr/sfw/lib -lnsl -lsocket -licuuc -licudata -pthreads -Wl,-R -Wl,/usr/local/lib -Wl,-R -Wl,/usr/sfw/lib ld: warning: file /usr/sfw/lib/libstdc++.so: attempted multiple inclusion of file I found out that it is because of the postdeps variable in the libtool script. If you search the libtool script, you will find a similar entry to this:- postdeps="-lstdc++ -lm -lgcc_s -lgcc_s". If I remove -lstdc++, then I get clean compile ( no multiple inclusion warning). I do not know how to configure libtool to remove it by itself. This may be your issue as well. Thanks, Nitin. -Original Message- From: libtool-bounces+nkapoor=sensis@gnu.org [mailto:libtool-bounces+nkapoor=sensis@gnu.org] On Behalf Of John R. Cary Sent: Friday, April 22, 2011 12:28 PM To: libtool@gnu.org Subject: Re: Libtool adding libraries differently than neededwith compilerwrappers Hi Nitin, I take the link line output from libtool and throw it into a shell script, then I remove those entries and run the script. Thx...John On 4/22/2011 10:25 AM, Kapoor, Nitin wrote: > Hi John, > > How are you removing the following paths from you link: > > /opt/fftw/3.2.2.1/lib/libfftw3.so /opt/fftw/3.2.2.1/lib/libfftw3f.so > /opt/cray/pmi/1.0-1..7901.22.1.ss/lib64/libpmi.so > /usr/lib64/gcc/x86_64-suse-linux/4.1.2/libstdc++.so > > and > > -lgcc_s > > > Are you hand editing the libtool script ? > > > Thanks > > Nitin. > > -Original Message- > From: libtool-bounces+nkapoor=sensis@gnu.org > [mailto:libtool-bounces+nkapoor=sensis@gnu.org] On Behalf Of John R. > Cary > Sent: Friday, April 22, 2011 9:17 AM > To: libtool@gnu.org > Subject: Libtool adding libraries differently than needed with > compilerwrappers > > We have a project using libtool on a Cray-XT4 using pathscale. > For compiling in parallel, we are supposed to use the compiler > wrapper, in this case ftn, that adds various libraries. A particular > complexity is that one has to switch libraries between front and > back end nodes, and this is done with LD_LIBRARY_PATH. We have > a problem, in that libtool seems to extract libraries from > the wrapper and put them at the end of the link line in a way > that the linker exits with an error. > > System information > x86_64-unknown-linux-gnu > bash > ftn (wrapping pathf90) > -extend-source -byteswapio -fno-second-underscore -r8 -O2 > -fno-second-underscore > /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/bin > /ld > libtool (GNU libtool) 2.4 > autoconf (GNU Autoconf) 2.68 > automake (GNU automake) 1.11.1 > > The failure is > > /bin/sh ../../libtool --tag=FC --tag=FC --mode=link ftn > -I../../interfaces/wrap -I../../interfaces/src > -I/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1 > 96-par/include > -I/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport- > r1341-par/include > -I/opt/cray/hdf5-parallel/1.8.3.1/hdf5-parallel-pathscale/include > -I/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0 > .47-r114-par/include > -extend-source -byteswapio -fno-second-underscore -r8 -O2 > -fno-second-underscore -o runFlowShear runFlowShear.o libfmcfm.la > -L/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport- > r1341-par/lib/pathf > -lglf23mpi -lmmm95 -lifspppl -lnclass -lkapisn > -L/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1 > 96-par/lib/pathf > -lGYRO -lNEO -lTGLF > -L/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0. > 12-r51-ser/lib > -llsode -lnlother -lr8slatec > -L/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/l > ib > -lrfftw -lfftw /opt/acml/4.2.0/pathscale64/lib/libacml.a > /opt/acml/4.2.0/pathscale64/lib/libacml.a > /opt/acml/4.2.0/pathscale64/lib/libacml_mv.a > -L/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0 > .47-r114-par/lib > -lezcdf -lvshdf5 > -L/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par > /lib > -lnetcdf -lnetcdf_c++ > -L/opt/cray/hdf5-parallel/1.8.3.1/hdf5-parallel-pathscale/lib > -lhdf5_fortran -lhdf5_hl -lhdf5 > /global/common/franklin/usg/szip/2.1/lib/libsz.a -lz > libtool: link: ftn -I../../interfaces/wrap -I../../interfaces/src > -I/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1 > 96-par/include > -I/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport- > r1341-par/include > -I/opt/cray/hdf5-parallel/1
