On Sat, Sep 8, 2018 at 12:52 'Andrey Brukhno' via votca < [email protected]> wrote:
> > On Saturday, September 8, 2018 at 7:40:43 PM UTC+1, Christoph Junghans > wrote: >> >> >> On Sat, Sep 8, 2018 at 11:58 'Andrey Brukhno' via votca < >> [email protected]> wrote: >> >>> >>> On Saturday, September 8, 2018 at 6:42:03 PM UTC+1, Christoph Junghans >>> wrote: >>> >> >>>> Just for completeness, I did try to update my LD_LIBRARY_PATH including >>>> both standard and non-standard locations for the related lib files. >>>> However, I still see the following in the cmake report, where I flagged all >>>> the supposedly relevant lines with triple asterisk *** >>>> >>> ... >>> *-- 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") **** >>> -- Could NOT find GMX (missing: GMX_EXECUTABLE) >>> -- Boost version: 1.58.0 >>> -- Found the following Boost libraries: >>> -- program_options >>> -- Checking for module 'libvotca_tools' >>> -- No package 'libvotca_tools' found >>> -- Intel(R) MKL could not be found. >>> -- Checking for module 'libvotca_csg' >>> -- No package 'libvotca_csg' found >>> -- Found VOTCA_CSG: votca_csg >>> *-- 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 >>> --- >>> >>> I have two questions regarding the above. >>> >>> 1. Is the line complaining about not found CLANG_FORMAT related in any >>> way to the libhdf5? >>> >> No, that is just another things which didn’t get found, but it is also >> optional! >> > > OK! After reading a bit about HDF5 data objects I thought CLANG_FORMAT > might be an attribute in some data structure or container related to the C > language. > > >> >>> 2. Can it be that at the building time the libraries from different >>> sources are confused or mixed up somehow upon linking? (so that at run time >>> a wrong library is searched for) >>> >> Not sure what you mean! CMake uses the libraries it detects for building >> and linking. However, once you install things the Linux loader, ld, is in >> charge. You can check what it is trying to load by running: “ldd >> <some_binary>”. >> For csg_map that will show a missing libhdf5 in your case. >> LD_LIBRARY_PATH is just a way to help ld find stuff. >> > > I asked this question because merely adding my non-standard location for > libhdf5.so (anaconda2/lib) to LD_LIBRARY_PATH did not resolve the issue. I > had to rebuild and re-install the whole thing, and only then the error > stopped popping up (which implies that it is not that simple as you > describe). > > Anyway it works now. > Cool, if you feel something needs to get added to installation guide, please propose a file change here: https://github.com/votca/votca/blob/master/share/doc/INSTALL.md Christoph > > Andrey > > >> >> Christoph >> >>> >>> Andrey >>> >>> >>>> 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 < >>>>>> [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. >>>>> >>>> -- >>>> 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. >>> >> -- >> 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. > -- 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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