2014-09-01 10:34 GMT-06:00 Animesh Agarwal <[email protected]>: > 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"""" Something is screwed up with the system, 32 and 64-bit LSB shared object cannot be combined.
Maybe you could set Boost_LIBRARIES (using -DBoost_LIBRARIES="/path/to/libprogram_options.so;/path/to/libfilesystem.so") yourself. Christoph > > 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. -- 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.
