[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;

Tue Dec 21 03:43:07 CET 2010

On Mon, Dec 20, 2010 at 8:20 PM, <chris.neale at utoronto.ca> wrote:
>
> Just for completeness, I could not get fftw to compile with --enable-shared
> (although I don't need to any more):
>
> $ ./configure --enable-float --enable-threads --enable-shared
> --prefix=/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2/exec
> $ make
>
> .. <snip> ...
> rm -fr  .libs/libfftw3f.a .libs/libfftw3f.la .libs/libfftw3f.lai
> icc -c99 -shared  -Wl,--whole-archive kernel/.libs/libkernel.a
> dft/.libs/libdft.a dft/codelets/.libs/libdft_codelets.a
> dft/codelets/standard/.libs/libdft_standard.a rdft/.libs/librdft.a
> rdft/codelets/.libs/librdft_codelets.a
> rdft/codelets/r2hc/.libs/librdft_codelets_r2hc.a
> rdft/codelets/hc2r/.libs/librdft_codelets_hc2r.a
> rdft/codelets/r2r/.libs/librdft_codelets_r2r.a reodft/.libs/libreodft.a
> api/.libs/libapi.a -Wl,--no-whole-archive
>  -L/scratch/cneale/GPC/exe/intel/fftw-3.1.2/exec/lib -lm  -pthread
> -Wl,-soname -Wl,libfftw3f.so.3 -o .libs/libfftw3f.so.3.1.2
> icc: command line remark #10010: option '-c99' is deprecated and will be
> removed in a future release. See '-help deprecated'
> ld: kernel/.libs/libkernel.a(alloc.o): relocation R_X86_64_32 against `a
> local symbol' can not be used when making a shared object; recompile with
> -fPIC
> kernel/.libs/libkernel.a(alloc.o): could not read symbols: Bad value
> make[2]: *** [libfftw3f.la] Error 1
> make[2]: Leaving directory
> `/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again'
> make: *** [all] Error 2
>

You need to run "make clean" when you change the configure options.

It will be nice to see some example build instructions on the gromacs site
> as people have time to add them.
>
Please contribute you experience to the wiki pages. Good documentation
requires many people to help. The (main) developers are often too busy too
write detailed documentation.

Roland

 From: Roland Schulz <roland at utk.edu>
>> Subject: Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a
>>        local   symbol' can not be used when making a shared object;
>>  recompile
>>        with -fPIC
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>>        <AANLkTik+V+7738y6EqGy6fNm4ygCVk-Mzh1Aw1sgJaeF at mail.gmail.com<AANLkTik%2BV%2B7738y6EqGy6fNm4ygCVk-Mzh1Aw1sgJaeF at mail.gmail.com>
>> >
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> You want to compile fftw with either --enable-shared or with --with-pic.
>> Or
>> you need to compile a static version of Gromacs. As the message says you
>> can't use fftw without pic with shared libraries in GROMACS.
>>
>> Roland
>>
>> On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale <chris.neale at utoronto.ca
>> >wrote:
>>
>>  Dear Gromacs users:
>>>
>>> I pulled the master version of the source code today at 2pm via:
>>> git clone git://git.gromacs.org/gromacs.git
>>> and I tried to compile it following the instructions posted here:
>>> http://www.gromacs.org/Developer_Zone/Cmake but I was unsuccessful.
>>>  This
>>> is my first attempt at using cmake, but I have been compiling gromacs
>>> successfully with autoconf since version 3.3.1
>>>
>>> I have a recent enough version of cmake:
>>> $ cmake --version
>>> cmake version 2.8.0
>>>
>>> And I have installed fftw:
>>> $ echo $FFTW_LOCATION
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec
>>> $ ls $FFTW_LOCATION/lib
>>> libfftw3f.a  libfftw3f.la  libfftw3f_threads.a   libfftw3f_threads.lapkgconfig
>>>
>>> But then when I try to compile gromacs:
>>> $ cmake ../ -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include
>>> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a
>>> -DCMAKE_INSTALL_PREFIX=$(pwd) -DGMX_X11=OFF
>>> -DCMAKE_CXX_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc
>>> -DCMAKE_C_COMPILER=/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc
>>> $ make -j 4
>>>
>>> I get the error:
>>> ... <snip> ...
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
>>> Linking C shared library libmd.so
>>> ld:
>>>
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a(mapflags.o):
>>> relocation R_X86_64_32S against `a local symbol' can not be used when
>>> making
>>> a shared object; recompile with -fPIC
>>>
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/libfftw3f.a:
>>> could not read symbols: Bad value
>>> make[2]: *** [src/mdlib/libmd.so.6] Error 1
>>> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> Just to be sure, I recompiled my FFTW and also tried a few different
>>> options for FFTW3F_LIBRARIES, all with errors.
>>> This fftw was compiled the same way I did previously, but just in case
>>> our
>>> version of icc was updated and this is causing the problem:
>>> export CC=icc
>>> export CXX=icpc
>>> ./configure --enable-float --enable-threads --prefix=$(pwd)/exec
>>> make
>>> make install
>>>
>>> ############################ USING
>>> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f_threads.a
>>> ... <snip> ...
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_c2r_3d'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_guru_dft_r2c'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_r2c_2d'
>>>
>>> ... <snip> ...
>>>
>>>  78%] Building C object src/kernel/CMakeFiles/g_luck.dir/g_luck.c.o
>>> Linking C executable g_luck
>>> Scanning dependencies of target g_protonate
>>> [ 79%] Building C object
>>> src/kernel/CMakeFiles/g_protonate.dir/g_protonate.c.o
>>> [ 79%] /scinet/gpc/intel/Compiler/11.1/072/lib/intel64//libimf.so:
>>> warning:
>>> warning: feupdateenv is not implemented and will always fail
>>> Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bundle.c.o
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_plan_dft_3d'
>>> ../mdlib/libmd.so.6: undefined reference to `fftwf_execute_dft_r2c'
>>>
>>> ... <snip> ...
>>>
>>> Building C object src/tools/CMakeFiles/gmxana.dir/edittop.c.o
>>> [ 88%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_bar.c.o
>>> [ 89%] Building C object
>>> src/tools/CMakeFiles/gmxana.dir/gmx_pme_error.c.o
>>> Linking C shared library libgmxana.so
>>> [ 89%] Built target gmxana
>>> make: *** [all] Error 2
>>>
>>> ############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
>>> libfftw3f.la
>>> ... <snip> ...
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
>>> Linking C shared library libmd.so
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
>>> libfftw3f.la:
>>> file not recognized: File format not recognized
>>>
>>> ############################ USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/
>>> libfftw3f_threads.la
>>> ... <snip> ...
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
>>> [ 72%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
>>> Linking C shared library libmd.so
>>> /project/pomes/cneale/GPC/exe/intel/fftw-3.1.2_again/exec/lib/
>>> libfftw3f_threads.la: file not recognized: File format not recognized
>>> make[2]: *** [src/mdlib/libmd.so.6] Error 1
>>> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>>
>>> Thank you,
>>> Chris.
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20101220/a6a71aac/attachment.html
>>
>> ------------------------------
>>
>> --
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>
>> End of gmx-users Digest, Vol 80, Issue 135
>> ******************************************
>>
>>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>

-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101220/0a9d1afe/attachment.html>