On Sat, Sep 8, 2018, 09:43 'Andrey Brukhno' via votca < [email protected]> 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 >>> <[email protected]> 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 [email protected]. >>> > To post to this group, send email to [email protected]. >>> > 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
