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] <javascript:>> 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. 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
