This is the output: file `readlink -f /gfs1/work/becagarw/expat/lib/libexpat.so` :::
"""/gfs1/work/becagarw/expat/lib/libexpat.so.1.5.2: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, not stripped""" file `readlink -f /usr/lib/libm.so`:::: """/lib/libm-2.11.3.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.4, dynamically linked (uses shared libs), not stripped"""" Animesh On Mon, Sep 1, 2014 at 3:55 AM, Christoph Junghans <[email protected]> wrote: > 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. -- 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.
