After all, it did work and now I get no error when I tried csg_call, csg_map, csg_stat or csg_reupdate etc. However it did complain all the way during installation:
cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4) cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4) cmake: /home/andrey/anaconda2/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4) cmake: /home/andrey/anaconda2/lib/libcrypto.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4) Not sure how important it is though. Thanks for your help! Andrey On Saturday, September 8, 2018 at 6:58:49 PM UTC+1, Andrey Brukhno wrote: > > > On Saturday, September 8, 2018 at 6:42:03 PM UTC+1, Christoph Junghans > wrote: >> >> >> >> On Sat, Sep 8, 2018 at 11:24 'Andrey Brukhno' via votca < >> [email protected]> 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! >> > > Alright, whatever.. I suppose it is from here: > https://support.hdfgroup.org/HDF5/Tutor/ > > >> >> >>> Anyway, what is the cmake option to switch it off (I could not find it)? >>> >> -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=ON >> > > OK, thanks a lot! > > 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? > > 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) > > 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.
