Re: Libtool adding libraries differently than neededwith compilerwrappers

John R. Cary Fri, 22 Apr 2011 10:00:26 -0700

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' libtoolsed -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' libtoolsed -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 Istill get

the error.

Thx....John



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/1.0-1.0000.7901.22.1.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/1.8.3.1/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
./.libs/libfmcfm.a

-L/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-

r1341-par/lib/pathf

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libglf23mpi.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libmmm95.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libifspppl.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libnclass.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libkapisn.a

-L/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1

96-par/lib/pathf

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libGYRO.a

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libNEO.a

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libTGLF.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.

12-r51-ser/lib

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/liblsode.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/libnlother.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/libr8slatec.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/l

ib

/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/lib

/librfftw.a

/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/lib

/libfftw.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

/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0.4

7-r114-par/lib/libezcdf.a

/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0.4

7-r114-par/lib/libvshdf5.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par

/lib

/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par/l

ib/libnetcdf_c++.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par/l

ib/libnetcdf.a
/opt/fftw/3.2.2.1/lib/libfftw3.so /opt/fftw/3.2.2.1/lib/libfftw3f.so
/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64/libpmi.so -lpthread -ldl
/usr/lib64/gcc/x86_64-suse-linux/4.1.2/libstdc++.so -lm -lc -lgcc_s
-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 -pthread

-Wl,-rpath

-Wl,/opt/fftw/3.2.2.1/lib -Wl,-rpath
-Wl,/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -Wl,-rpath
-Wl,/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -Wl,-rpath
-Wl,/opt/fftw/3.2.2.1/lib -Wl,-rpath
-Wl,/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -Wl,-rpath
-Wl,/usr/lib64/gcc/x86_64-suse-linux/4.1.2

/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/bin

/ld:
attempted static link of dynamic object
`/opt/fftw/3.2.2.1/lib/libfftw3.so'
collect2: ld returned 1 exit status


So one sees that libtool put /opt/fftw/3.2.2.1/lib/libfftw3.so at the
end of
the link line when there was no need.  To get this to work, I remove

any

.so files with full path:
/opt/fftw/3.2.2.1/lib/libfftw3.so /opt/fftw/3.2.2.1/lib/libfftw3f.so
     /opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64/libpmi.so
     /usr/lib64/gcc/x86_64-suse-linux/4.1.2/libstdc++.so

and

     -lgcc_s

from the link line and run it by hand.  Then it works.  (See below):

So is there a way to tell libtool not to add any of these libraries
to the link line?

Thx...John Cary

Working 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

./.libs/libfmcfm.a

-L/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-

r1341-par/lib/pathf

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libglf23mpi.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libmmm95.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libifspppl.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libnclass.a

/project/projectdirs/facets/franklin/internal-path-3.2/ntcc_transport-r1

341-par/lib/pathf/libkapisn.a

-L/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r1

96-par/lib/pathf

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libGYRO.a

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libNEO.a

/project/projectdirs/facets/franklin/internal-path-3.2/ga_transport-r196

-par/lib/pathf/libTGLF.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.

12-r51-ser/lib

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/liblsode.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/libnlother.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netlib_lite-1.0.12

-r51-ser/lib/libr8slatec.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/l

ib

/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/lib

/librfftw.a

/project/projectdirs/facets/franklin/contrib-path-3.2/fftw-2.1.5-ser/lib

/libfftw.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

/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0.4

7-r114-par/lib/libezcdf.a

/project/projectdirs/facets/franklin/contrib-path-3.2/fciowrappers-1.0.4

7-r114-par/lib/libvshdf5.a

-L/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par

/lib

/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par/l

ib/libnetcdf_c++.a

/project/projectdirs/facets/franklin/contrib-path-3.2/netcdf-4.1.1-par/l

ib/libnetcdf.a
-lpthread -ldl -lm -lc
-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 -pthread

-Wl,-rpath

-Wl,/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -Wl,-rpath
-Wl,/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -Wl,-rpath
-Wl,/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -Wl,-rpath
-Wl,/usr/lib64/gcc/x86_64-suse-linux/4.1.2
$



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Re: Libtool adding libraries differently than neededwith compilerwrappers

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