2014-08-31 16:53 GMT-06:00 Animesh Agarwal <[email protected]>: > 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. That is double bad, you want to use libfftw3.so, without "f" and "mpi" at the end.
But if it is a shared object the problem is somewhere else. Please check $ file `readlink -f /gfs1/work/becagarw/expat/lib/libexpat.so` and libm $ ls /usrlib*/libm* > > > > 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. -- 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.
