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: >> >> >> >> 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? > No, that is just another things which didn’t get found, but it is also optional! > 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. 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.
