On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca < votca@googlegroups.com> wrote:
> 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 - ?). > HDF5 is used to read H5MD files! > Anyway, what is the cmake option to switch it off (I could not find it)? > -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON Christoph > > > 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> 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. >>> 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. >>> >> -- > 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+unsubscr...@googlegroups.com. > To post to this group, send email to votca@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. 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