On Sat, Sep 8, 2018 at 8:08 PM Christoph Junghans <[email protected]> wrote:
> > 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 > I am not sure what you mean here: adding the description for the flag omitting hdf5? or the fact that one needs to add non-standard library locations to the LD_LIBRARY_PATH and then recompile everything? Andrey > 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 a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/7Lm_9os7VW4/unsubscribe. > To unsubscribe from this group and all its topics, 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. 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