2014-08-31 16:27 GMT-06:00 Animesh Agarwal <[email protected]>: >> The error in there is the same as below. > > Please find attached the error log file, when FFTW library is used. The error is still the same: /usr/bin/ld: attempted static link of dynamic object `/opt/fftw/3.3.0.3/x86_64/lib/libfftw3f.so'
can you run $ file `readlink -f /opt/fftw/3.3.0.3/x86_64/lib/libfftw3f.so` and post the output. Also VOTCA needs libfftw3.so (double precision) not libfftw3f.so (single precision) like Gromacs. > > On Mon, Sep 1, 2014 at 12:03 AM, Animesh Agarwal > <[email protected]> wrote: >> Yes, it shows that there is a shared version of boost. I installed the >> libraries using --enable-shared option, so I don't know why there is a >> conflict between static and shared. >> >> On Sun, Aug 31, 2014 at 11:25 PM, Christoph Junghans <[email protected]> >> wrote: >>> 2014-08-31 12:54 GMT-06:00 Animesh Agarwal <[email protected]>: >>>> Please find attached the CMakeError.log file. >>> The error in there is the same as below. >>> /usr/bin/ld: attempted static link of dynamic object >>> `/gfs1/work/becagarw/fftw/lib/libfftw3.so' >>> >>>> >>>> >>>> For the second part, here are the lines above the error: >>>> =============================================================================================================== >>>> [ 0%] Built target hgversion >>>> make -f src/libtools/CMakeFiles/votca_tools.dir/build.make >>>> src/libtools/CMakeFiles/votca_tools.dir/depend >>>> make[2]: Entering directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> cd /gfs1/work/becagarw/VOTCA/src/tools && >>>> /sw/tools/cmake/2.8.11/generic/GNU/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /gfs1/work/becagarw/VOTCA/src/tools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools >>>> /gfs1/work/becagarw/VOTCA/src/tools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools/CMakeFiles/votca_tools.dir/DependInfo.cmake >>>> --color= >>>> make[2]: Leaving directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> make -f src/libtools/CMakeFiles/votca_tools.dir/build.make >>>> src/libtools/CMakeFiles/votca_tools.dir/build >>>> make[2]: Entering directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> make[2]: Nothing to be done for >>>> `src/libtools/CMakeFiles/votca_tools.dir/build'. >>>> make[2]: Leaving directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> /sw/tools/cmake/2.8.11/generic/GNU/bin/cmake -E cmake_progress_report >>>> /gfs1/work/becagarw/VOTCA/src/tools/CMakeFiles 2 3 4 5 6 7 8 9 10 11 >>>> 12 13 14 15 16 17 18 19 20 21 22 23 >>>> [ 95%] Built target votca_tools >>>> make -f src/libtools/CMakeFiles/linktest.dir/build.make >>>> src/libtools/CMakeFiles/linktest.dir/depend >>>> make[2]: Entering directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> cd /gfs1/work/becagarw/VOTCA/src/tools && >>>> /sw/tools/cmake/2.8.11/generic/GNU/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /gfs1/work/becagarw/VOTCA/src/tools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools >>>> /gfs1/work/becagarw/VOTCA/src/tools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools >>>> /gfs1/work/becagarw/VOTCA/src/tools/src/libtools/CMakeFiles/linktest.dir/DependInfo.cmake >>>> --color= >>>> make[2]: Leaving directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> make -f src/libtools/CMakeFiles/linktest.dir/build.make >>>> src/libtools/CMakeFiles/linktest.dir/build >>>> make[2]: Entering directory `/gfs1/work/becagarw/VOTCA/src/tools' >>>> Linking CXX executable linktest >>>> cd /gfs1/work/becagarw/VOTCA/src/tools/src/libtools && >>>> /sw/tools/cmake/2.8.11/generic/GNU/bin/cmake -E cmake_link_script >>>> CMakeFiles/linktest.dir/link.txt --verbose=1 >>>> /opt/cray/craype/2.01/bin/CC -O3 -DNDEBUG >>>> CMakeFiles/linktest.dir/linktest.cc.o -o linktest -rdynamic >>>> libvotca_tools.so.2 -lboost_program_options >>>> /gfs1/work/becagarw/expat/lib/libexpat.so -lpthread -lm >>>> -Wl,-rpath,/gfs1/work/becagarw/VOTCA/src/tools/src/libtools:/gfs1/work/becagarw/expat/lib >>>> /usr/bin/ld: attempted static link of dynamic object `libvotca_tools.so.2' >>> It seems one of your libraries is static (.a file) and mixing of >>> static and shared (.so) is not supported. >>> As expat is explicitly given >>> (gfs1/work/becagarw/expat/lib/libexpat.so) the problem must be your >>> boost installation. >>> Have a look if there is a shared version of boost: >>> $ ls /sw/tools/boost/1.55.0-gcc482/mpp1/lib/*.so >>> I am not 100% sure about the path, but BOOST_ROOT should be >>> /sw/tools/boost/1.55.0-gcc482/mpp1 I guess. >>> >>> Christoph >>>> ================================================================================================================== >>>> >>>> Regards >>>> Animesh >>>> >>>> On Sun, Aug 31, 2014 at 8:36 PM, Christoph Junghans <[email protected]> >>>> wrote: >>>>> 2014-08-31 11:52 GMT-06:00 Animesh Agarwal <[email protected]>: >>>>>> Hi Christoph: >>>>>> >>>>>> I have been trying to install VOTCA on the HLRN >>>>>> cluster, but I am getting some errors. I have installed various >>>>>> libraries needed for the installation. Here is the command: >>>>>> >>>>>> ========================================================================== >>>>>> ./build.sh -DWITH_SQLITE3=NO >>>>>> -DGSL_INCLUDE_DIR=/gfs1/work/becagarw/gsl/include >>>>>> -DGSL_LIBRARY=/gfs1/work/becagarw/gsl/lib/libgsl.so >>>>>> -DGSLCBLAS_LIBRARY=/gfs1/work/becagarw/gsl/lib/libgslcblas.so >>>>>> -DBOOST_ROOT=/sw/tools/boost/1.55.0-gcc482/mpp1/include >>>>>> -DEXPAT_INCLUDE_DIR=/gfs1/work/becagarw/expat/include >>>>>> -DEXPAT_LIBRARY=/gfs1/work/becagarw/expat/lib/libexpat.so >>>>>> -DFFTW3_INCLUDE_DIR=/gfs1/work/becagarw/fftw/include >>>>>> -DFFTW3_LIBRARY=/gfs1/work/becagarw/fftw/lib/libfftw3.so --prefix >>>>>> ${prefix} --latest tools csg >>>>>> =========================================================================== >>>>>> >>>>>> but I get the following error: >>>>>> >>>>>> =========================================================================== >>>>>> Could not find fftw_plan_r2r_1d in >>>>>> /gfs1/work/becagarw/fftw/lib/libfftw3.so, take a look at the error >>>>>> message >>>>>> in /gfs1/work/becagarw/VOTCA/src/tools/CMakeFiles/CMakeError.log to >>>>>> find >>>>>> out what was going wrong. If you are using a static lib (.a) make >>>>>> sure you >>>>>> have specified all dependencies of fftw3 in FFTW3_LIBRARY by hand (i.e. >>>>>> -DFFTW3_LIBRARY='/path/to/libfftw3.so;/path/to/libm.so') ! >>>>>> Call Stack (most recent call first): >>>>>> src/libtools/CMakeLists.txt:11 (find_package) >>>>> To find this error, could you attach your CMakeError.log (from >>>>> /gfs1/work/becagarw/VOTCA/src/tools/CMakeFiles) >>>>> If file is huge, just attach the last ~250 lines. >>>>> >>>>>> ============================================================================= >>>>>> >>>>>> If I switch off the FFTW and GSL libraries, I get the following error: >>>>>> >>>>>> ============================================================================ >>>>>> Linking CXX executable linktest >>>>>> /usr/bin/ld: attempted static link of dynamic object >>>>>> `libvotca_tools.so.2' >>>>>> collect2: error: ld returned 1 exit status >>>>>> make[2]: *** [src/libtools/linktest] Error 1 >>>>>> make[1]: *** [src/libtools/CMakeFiles/linktest.dir/all] Error 2 >>>>>> make: *** [all] Error 2 >>>>> No good idea, could you do >>>>> $ cd tools >>>>> $ make VERBOSE=1 >>>>> and post the last 10 lines above the error. >>>>> >>>>> Christoph >>>>>> ========================================================================== >>>>>> >>>>>> Please let me know how can I fix these errors. >>>>>> >>>>>> Regards >>>>>> Animesh >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "votca" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>>> an email to [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> Visit this group at http://groups.google.com/group/votca. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>>> >>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google Groups >>>>> "votca" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send an >>>>> email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at http://groups.google.com/group/votca. >>>>> For more options, visit https://groups.google.com/d/optout. >>>> >>>> -- >>>> You received this message because you are subscribed to the Google Groups >>>> "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send an >>>> email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/votca. >>>> For more options, visit https://groups.google.com/d/optout. >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
