The question is, what is the significance of this library (libhdf5)? - from what you say I gather, it is not required in general, but it is only necessary if I myself indent to use hdf5 files/data (which obviously I am not currently; unless it is used by VOTCA tools or scripts somewhere under the hood - ?).
Anyway, what is the cmake option to switch it off (I could not find it)? Thanks Andrey On Saturday, September 8, 2018 at 6:01:02 PM UTC+1, Christoph Junghans wrote: > > On Sat, Sep 8, 2018, 09:43 'Andrey Brukhno' via votca < > vo...@googlegroups.com <javascript:>> wrote: > >> Just to make sure, I have done it for the third time now, with the same >> result (error about libhdf5). >> This is strange because the camke log reports it as found: >> >> $ grep HDF master-cmake.log >> -- Found HDF5: >> /home/andrey/anaconda2/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/andrey/anaconda2/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so >> >> (found version "1.10.1") >> * HDF5 >> >> whereas the 'stable' branch does not require it, apparently; at least >> cmake does not report anything about libhdf5. >> > Yeah, in the stable branch the hdf5 I/O backend is off by default, while > it gets enabled automatically in master when an HDF5 library is found! The > code has matured enough since it was added in 1.4! > > There error is due to the fact that your libhdf5 is in non-common place > and hence LD cannot find it at runtime! Either add that directory to your > LD_LIBRARY_PATH or try the new inject rpath option in master. Or you could > also disable the HDF5 backend if you don't need it. > > Christoph > > >> Andrey >> >> On Saturday, September 8, 2018 at 4:05:08 PM UTC+1, Andrey Brukhno wrote: >>> >>> Hi Christoph, thanks for your response. >>> >>> On Friday, September 7, 2018 at 7:05:28 PM UTC+1, Christoph Junghans >>> wrote: >>>> >>>> On Fri, Sep 7, 2018 at 11:03 AM 'Andrey Brukhno' via votca >>>> <vo...@googlegroups.com> wrote: >>>> > >>>> > Hello, >>>> > >>>> > Upon a successful installation of the VOTCA's development (master) >>>> branch I get this error: >>>> > >>>> > ~/votca-dev/bin/csg_map >>>> > /home/andrey/votca-dev/bin/csg_map: error while loading shared >>>> libraries: libvotca_csg.so.5: cannot open shared object file: No such file >>>> or directory >>>> That just means you have to source VOTCARC.bash >>>> >>> >>> Yes, sorry I missed to include that from my terminal output (I meant to >>> show that resulting error): >>> --- >>> build > ~/votca-dev/bin/csg_map >>> /home/andrey/votca-dev/bin/csg_map: error while loading shared >>> libraries: libvotca_csg.so.5: cannot open shared object file: No such file >>> or directory >>> build > . ~/votca-dev/bin/VOTCARC.bash >>> build > ~/votca-dev/bin/csg_map >>> /home/andrey/votca-dev/bin/csg_map: error while loading shared >>> libraries: libhdf5.so.101: cannot open shared object file: No such file or >>> directory >>> --- >>> Note that I tried to install the 'master' twice, repeating the entire >>> process, starting with "git clone -b master ...", both times I ended up >>> with the above error message about missing libhdf5.so.101, whereas it was >>> installed and the installation of 'stable' branch did not complain at all. >>> >>> >>>> We also recently added the option to inject an rpath on Linux, i.e. >>>> -DENABLE_RPATH_INJECT=ON, then the location of libvotca_csg.so.5 will >>>> be stored in csg_map itself. >>>> >>> >>> What does it help? (before it seemed to work fine without it) >>> >>> >>>> >>>> > >>>> > I tried to reinstall libhdf5-dev twice, also checked for all the >>>> other dependencies, everything looks fine, yet the error. >>>> Not sure how this related to libhdf5, the above error refers to >>>> libvotca_csg.so.5, right? >>>> >>>> > >>>> > Meanwhile the 'stable' branch (1.4.1 apparently) did install >>>> correctly and appears to work. >>>> > >>>> > Would appreciate any clues or a fix. >>>> > >>>> > Thanks >>>> > Andrey >>>> > >>>> > PS: for reference, below is the output messages from cmake for my >>>> attempted installation of 'master' >>>> > >>>> > build > cmake -DBUILD_CSGAPPS=ON -DBUILD_TOOLS=ON -DWITH_GMX=ON >>>> -DWITH_SQLITE3=OFF -DCMAKE_INSTALL_PREFIX=$HOME/votca-dev .. >>>> And yeah there is no BUILD_TOOLS option. >>>> >>> >>> Okay, I noticed. I think including it did not affect anything (?). >>> >>> Andrey >>> >>> >>> >>>> >>>> > -- Boost version: 1.58.0 >>>> > -- Found the following Boost libraries: >>>> > -- program_options >>>> > -- filesystem >>>> > -- system >>>> > -- Intel(R) MKL could not be found. >>>> > -- Boost version: 1.58.0 >>>> > -- Found the following Boost libraries: >>>> > -- program_options >>>> > -- filesystem >>>> > -- system >>>> > -- Intel(R) MKL could not be found. >>>> > -- Checking for module 'libgromacs_d' >>>> > -- No package 'libgromacs_d' found >>>> > -- Could NOT find GMX (missing: GMX_EXECUTABLE) >>>> > -- Boost version: 1.58.0 >>>> > -- Found the following Boost libraries: >>>> > -- program_options >>>> > -- Intel(R) MKL could not be found. >>>> > -- Could NOT find CLANG_FORMAT (missing: CLANG_FORMAT_EXECUTABLE) >>>> > -- >>>> > -- The following OPTIONAL packages have been found: >>>> > >>>> > * Git >>>> > * FFTW3 >>>> > * EXPAT >>>> > * TXT2TAGS >>>> > * UnixCommands >>>> > * HDF5 >>>> > * Eigen3 >>>> > * PkgConfig >>>> > * Doxygen >>>> > >>>> > -- The following REQUIRED packages have been found: >>>> > >>>> > * Threads >>>> > * GROMACS (required version >= 20160000) >>>> > * Boost (required version >= 1.57.0) >>>> > * EIGEN3 (required version >= 3.3.0) >>>> > * VOTCA_TOOLS >>>> > * VOTCA_CSG >>>> > >>>> > -- The following OPTIONAL packages have not been found: >>>> > >>>> > * MKL >>>> > >>>> > -- Configuring done >>>> > -- Generating done >>>> > CMake Warning: >>>> > Manually-specified variables were not used by the project: >>>> > >>>> > BUILD_TOOLS >>>> > >>>> > >>>> > -- Build files have been written to: >>>> /home/andrey/Progs/votca-dev/votca-1.5-master/build >>>> > >>>> > [bg:0](st:0) andrey@AndysHome: build > make >>>> > ... >>>> > >>>> > -- >>>> > 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 votca+un...@googlegroups.com. >>>> > To post to this group, send email to vo...@googlegroups.com. >>>> > Visit this group at https://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 votca+un...@googlegroups.com <javascript:>. >> To post to this group, send email to vo...@googlegroups.com <javascript:> >> . >> Visit this group at https://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. 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