The output is: /opt/fftw/3.3.0.3/x86_64/lib/libfftw3f.so.mpi30.3.3.0: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, not stripped.
On Mon, Sep 1, 2014 at 12:50 AM, Christoph Junghans <[email protected]> wrote: > 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. -- 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.
