Thanks. The version I had installed manually or one available in my cluster doesn't seem to work. Would you suggest any specific boost installation?
On Sat, Apr 25, 2020 at 4:58 PM Christoph Junghans <[email protected]> wrote: > On Sat, Apr 25, 2020 at 2:03 PM Salman Bin Kashif <[email protected]> > wrote: > > > > Thank you. I tried the seI guess there may be another issue. I used the > following command: > > > > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_GMX=ON > -DGROMACS_INCLUDE_DIR=/home/sbinkas/software/gromacs-2018.3/include > -DGROMACS_LIBRARY=/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so > -DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=ON > -DCMAKE_PREFIX_PATH=/home/sbinkas/software .. > > > > cmake command runs fine. > > > > make -j5 throws the error > > > > Error looks like: > > > > ../libtools/libvotca_tools.so.6: undefined reference to > `boost::program_options::option_description::format_name[abi:cxx11][ 66%] > Built target votca_csg > This error means your boost was compiled with a different compiler and > possibly has no C++-11 support enabled. > > Christoph > > > make: *** [all] Error 2 > > > > Am I missing something? > > > > In the meanwhile, I will try with option 1. > > > > On Sat, Apr 25, 2020 at 3:46 PM Salman Bin Kashif <[email protected]> > wrote: > >> > >> Thanks so much. I wiil try using the disable package option first. > >> > >> On Sat, Apr 25, 2020 at 2:09 PM Salman Bin Kashif <[email protected]> > wrote: > >>> > >>> Following is the output of make VERBOSE-1 > >>> > >>> [sbinkas@node0170 build]$ make VERBOSE=1 > >>> /software/cmake/3.10.0/bin/cmake -H/home/sbinkas/software/votca > -B/home/sbinkas/software/votca/build --check-build-system > CMakeFiles/Makefile.cmake 0 > >>> /software/cmake/3.10.0/bin/cmake -E cmake_progress_start > /home/sbinkas/software/votca/build/CMakeFiles > /home/sbinkas/software/votca/build/CMakeFiles/progress.marks > >>> make -f CMakeFiles/Makefile2 all > >>> make[1]: Entering directory `/home/sbinkas/software/votca/build' > >>> make -f tools/share/man/CMakeFiles/votca_tools_manpages.dir/build.make > tools/share/man/CMakeFiles/votca_tools_manpages.dir/depend > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> cd /home/sbinkas/software/votca/build && > /software/cmake/3.10.0/bin/cmake -E cmake_depends "Unix Makefiles" > /home/sbinkas/software/votca /home/sbinkas/software/votca/tools/share/man > /home/sbinkas/software/votca/build > /home/sbinkas/software/votca/build/tools/share/man > /home/sbinkas/software/votca/build/tools/share/man/CMakeFiles/votca_tools_manpages.dir/DependInfo.cmake > --color= > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make -f tools/share/man/CMakeFiles/votca_tools_manpages.dir/build.make > tools/share/man/CMakeFiles/votca_tools_manpages.dir/build > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> make[2]: Nothing to be done for > `tools/share/man/CMakeFiles/votca_tools_manpages.dir/build'. > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> [ 0%] Built target votca_tools_manpages > >>> make -f tools/src/libtools/CMakeFiles/gitversion.dir/build.make > tools/src/libtools/CMakeFiles/gitversion.dir/depend > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> cd /home/sbinkas/software/votca/build && > /software/cmake/3.10.0/bin/cmake -E cmake_depends "Unix Makefiles" > /home/sbinkas/software/votca > /home/sbinkas/software/votca/tools/src/libtools > /home/sbinkas/software/votca/build > /home/sbinkas/software/votca/build/tools/src/libtools > /home/sbinkas/software/votca/build/tools/src/libtools/CMakeFiles/gitversion.dir/DependInfo.cmake > --color= > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make -f tools/src/libtools/CMakeFiles/gitversion.dir/build.make > tools/src/libtools/CMakeFiles/gitversion.dir/build > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> cd /home/sbinkas/software/votca/build/tools/src/libtools && > /software/cmake/3.10.0/bin/cmake > -DTOP_SOURCE_DIR="/home/sbinkas/software/votca" -DGIT_EXECUTABLE="/bin/git" > -P /home/sbinkas/software/votca/tools/CMakeModules/gitversion.cmake > >>> Current git revision is 98e27cd > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> [ 0%] Built target gitversion > >>> make -f tools/src/libtools/CMakeFiles/votca_tools.dir/build.make > tools/src/libtools/CMakeFiles/votca_tools.dir/depend > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> cd /home/sbinkas/software/votca/build && > /software/cmake/3.10.0/bin/cmake -E cmake_depends "Unix Makefiles" > /home/sbinkas/software/votca > /home/sbinkas/software/votca/tools/src/libtools > /home/sbinkas/software/votca/build > /home/sbinkas/software/votca/build/tools/src/libtools > /home/sbinkas/software/votca/build/tools/src/libtools/CMakeFiles/votca_tools.dir/DependInfo.cmake > --color= > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make -f tools/src/libtools/CMakeFiles/votca_tools.dir/build.make > tools/src/libtools/CMakeFiles/votca_tools.dir/build > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> make[2]: Nothing to be done for > `tools/src/libtools/CMakeFiles/votca_tools.dir/build'. > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> [ 27%] Built target votca_tools > >>> make -f tools/src/tools/CMakeFiles/votca_property.dir/build.make > tools/src/tools/CMakeFiles/votca_property.dir/depend > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> cd /home/sbinkas/software/votca/build && > /software/cmake/3.10.0/bin/cmake -E cmake_depends "Unix Makefiles" > /home/sbinkas/software/votca /home/sbinkas/software/votca/tools/src/tools > /home/sbinkas/software/votca/build > /home/sbinkas/software/votca/build/tools/src/tools > /home/sbinkas/software/votca/build/tools/src/tools/CMakeFiles/votca_property.dir/DependInfo.cmake > --color= > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make -f tools/src/tools/CMakeFiles/votca_property.dir/build.make > tools/src/tools/CMakeFiles/votca_property.dir/build > >>> make[2]: Entering directory `/home/sbinkas/software/votca/build' > >>> [ 28%] Building CXX object > tools/src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o > >>> cd /home/sbinkas/software/votca/build/tools/src/tools && > /software/gcc/5.4.0/bin/g++ -I/home/sbinkas/software/votca/tools/include > -I/home/sbinkas/software/votca/build/tools/include -isystem > /home/sbinkas/software/include/eigen3 -Wall -Wextra -Wpedantic -Wshadow > -Wconversion -O3 -DNDEBUG -std=c++14 -o > CMakeFiles/votca_property.dir/votca_property.cc.o -c > /home/sbinkas/software/votca/tools/src/tools/votca_property.cc > >>> In file included from > /home/sbinkas/software/votca/tools/include/votca/tools/eigen.h:52:0, > >>> from > /home/sbinkas/software/votca/tools/include/votca/tools/property.h:21, > >>> from > /home/sbinkas/software/votca/tools/include/votca/tools/application.h:21, > >>> from > /home/sbinkas/software/votca/tools/src/tools/votca_property.cc:22: > >>> /home/sbinkas/software/include/eigen3/unsupported/Eigen/FFT:75:21: > fatal error: fftw3.h: No such file or directory > >>> compilation terminated. > >>> make[2]: *** > [tools/src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o] Error 1 > >>> make[2]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make[1]: *** [tools/src/tools/CMakeFiles/votca_property.dir/all] Error > 2 > >>> make[1]: Leaving directory `/home/sbinkas/software/votca/build' > >>> make: *** [all] Error 2 > >>> > >>> On Sat, Apr 25, 2020 at 1:59 PM Christoph Junghans <[email protected]> > wrote: > >>>> > >>>> > >>>> > >>>> On Sat, Apr 25, 2020 at 11:45 Salman Bin Kashif <[email protected]> > wrote: > >>>>> > >>>>> I have attached the printed output from cmake command herewith > >>>> > >>>> thanks, please do me a favor and also attach the output of “make > VERBOSE=1”. > >>>>> > >>>>> > >>>>> On Sat, Apr 25, 2020 at 1:41 PM Christoph Junghans < > [email protected]> wrote: > >>>>>> > >>>>>> > >>>>>> > >>>>>> On Sat, Apr 25, 2020 at 11:25 Salman Bin Kashif < > [email protected]> wrote: > >>>>>>> > >>>>>>> Thank you. That works too. Next error was encountered in make -j5 > command. > >>>>>>> > >>>>>>> > >>>>>>> /home/sbinkas/software/include/eigen3/unsupported/Eigen/FFT:75:21: > fatal error: fftw3.h: No such file or directory > >>>>>> > >>>>>> it seems the fftw3 dev package is missing! > >>>>>> > >>>>>> Can you post the output of your CMake execution, what fftw3 found? > >>>>>> > >>>>>> Christoph > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> I didn't find fftw.h in the entire eigen folder though. I am not > sure which path should I provide then. > >>>>>>> > >>>>>>> On Sat, Apr 25, 2020 at 1:03 PM Christoph Junghans < > [email protected]> wrote: > >>>>>>>> > >>>>>>>> On Sat, Apr 25, 2020 at 10:52 AM Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> > > >>>>>>>> > Thank you. This suggestion works. The cmake command did not > throw any fatal error this time. > >>>>>>>> > > >>>>>>>> > However, I would like to discuss some caveats: > >>>>>>>> > > >>>>>>>> > 1. Would TXT2TAGS not being found be an issue in later steps? > Like when running the simulation? It does suggest optional. But I assume it > may be used for generating xml files during run. > >>>>>>>> txt2tags is only used to build the manpage (documentation), so no > issue here. > >>>>>>>> > > >>>>>>>> > 2. Warning with run time library: > >>>>>>>> > > >>>>>>>> > Cannot generate a safe runtime search path for target > votca_tools because > >>>>>>>> > files in some directories may conflict with libraries in > implicit > >>>>>>>> > directories: > >>>>>>>> > > >>>>>>>> > runtime library [libexpat.so.1] in /usr/lib64 may be hidden > by files in: > >>>>>>>> > /home/sbinkas/software/lib > >>>>>>>> This error basically means there are two libexpat in your > LD_LIBRARY_PATH. > >>>>>>>> You tell CMake to explicitly use the one from > >>>>>>>> /home/sbinkas/software/lib by add > >>>>>>>> -DCMAKE_PREFIX_PATH=/home/sbinkas/software. > >>>>>>>> > >>>>>>>> Christoph > >>>>>>>> > > >>>>>>>> > I kind of get where is it coming from. This > /home/sbinkas/software/lib got added while installing one of the > dependencies. I don't remember which one to be exact, but possibly it was > from eigen3. So a conflict may have arisen. Should I worry about it? > >>>>>>>> > > >>>>>>>> > Again, I very much appreciate your help. > >>>>>>>> > > >>>>>>>> > -Salman > >>>>>>>> > > >>>>>>>> > > >>>>>>>> > Output: > >>>>>>>> > > >>>>>>>> > > >>>>>>>> > - The following OPTIONAL packages have been found: > >>>>>>>> > > >>>>>>>> > * Git > >>>>>>>> > * FFTW3 > >>>>>>>> > * UnixCommands > >>>>>>>> > * PkgConfig > >>>>>>>> > * HDF5 > >>>>>>>> > * Doxygen > >>>>>>>> > > >>>>>>>> > -- The following REQUIRED packages have been found: > >>>>>>>> > > >>>>>>>> > * EXPAT > >>>>>>>> > * Threads > >>>>>>>> > * Boost (required version >= 1.53.0) > >>>>>>>> > * Eigen3 (required version >= 3.3.0) > >>>>>>>> > * GROMACS (required version >= 2016) > >>>>>>>> > > >>>>>>>> > -- The following OPTIONAL packages have not been found: > >>>>>>>> > > >>>>>>>> > * MKL > >>>>>>>> > * TXT2TAGS > >>>>>>>> > * CLANG_FORMAT (required version >= 7.0.1) > >>>>>>>> > > >>>>>>>> > -- Configuring done > >>>>>>>> > CMake Warning at tools/src/libtools/CMakeLists.txt:5 > (add_library): > >>>>>>>> > Cannot generate a safe runtime search path for target > votca_tools because > >>>>>>>> > files in some directories may conflict with libraries in > implicit > >>>>>>>> > directories: > >>>>>>>> > > >>>>>>>> > runtime library [libexpat.so.1] in /usr/lib64 may be hidden > by files in: > >>>>>>>> > /home/sbinkas/software/lib > >>>>>>>> > > >>>>>>>> > Some of these libraries may not be found correctly. > >>>>>>>> > > >>>>>>>> > > >>>>>>>> > -- Generating done > >>>>>>>> > -- Build files have been written to: > /home/sbinkas/software/votca/build > >>>>>>>> > > >>>>>>>> > On Sat, Apr 25, 2020 at 12:31 PM Christoph Junghans < > [email protected]> wrote: > >>>>>>>> >> > >>>>>>>> >> On Sat, Apr 25, 2020 at 10:26 AM Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> >> > > >>>>>>>> >> > This is the error associated with libgromacs: > >>>>>>>> >> > > >>>>>>>> >> > gmake[1]: *** No rule to make target > `/home/sbinkas/gromacs/lib/libgromacs.so', needed by `cmTC_b3327 '. > Stop. > >>>>>>>> >> > 101 gmake[1]: Leaving directory > `/home/sbinkas/software/votca/build/CMakeFiles/CMakeTmp' > >>>>>>>> >> > 102 gmake: *** [cmTC_b3327/fast] Error 2 > >>>>>>>> >> In the CMake output it says, it is using > >>>>>>>> >> /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so, but > now it > >>>>>>>> >> is looking for > >>>>>>>> >> `/home/sbinkas/gromacs/lib/libgromacs.so, you might want to > help CMake > >>>>>>>> >> by setting > -DGROMACS_LIBRARY=/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so. > >>>>>>>> >> > >>>>>>>> >> Christoph > >>>>>>>> >> > > >>>>>>>> >> > On Sat, Apr 25, 2020 at 12:12 PM Christoph Junghans < > [email protected]> wrote: > >>>>>>>> >> >> > >>>>>>>> >> >> On Sat, Apr 25, 2020 at 8:53 AM Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> >> >> > > >>>>>>>> >> >> > Thanks very much for being patient with me. > >>>>>>>> >> >> > > >>>>>>>> >> >> > I had installed eigen3 easier which incidentally happen > to be from the same source you pointed out. Eigen is being read properly I > assume. > >>>>>>>> >> >> > > >>>>>>>> >> >> > -- Found Eigen3: > /home/sbinkas/software/eigen-eigen-67e894c6cd8f/build_dir > >>>>>>>> >> >> > > >>>>>>>> >> >> > However, there are two more issues: > >>>>>>>> >> >> > > >>>>>>>> >> >> > -- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE) > >>>>>>>> >> >> > txt2tags not found, help cmake to find it by setting > TXT2TAGS_EXECUTABLE > >>>>>>>> >> >> > > >>>>>>>> >> >> > > >>>>>>>> >> >> > I have provided the path to executable txt2tags file in > /home/software/txt2tags-2.6/txt2tags but it still is not fould. However, > the error was not fatal due to it. > >>>>>>>> >> >> Don't worry this one is optional. > >>>>>>>> >> >> > >>>>>>>> >> >> > > >>>>>>>> >> >> > The error was fatal due to not having been able to read > c++ version in gromacs library. It is reaching to the libgromacs.so file > though. > >>>>>>>> >> >> > > >>>>>>>> >> >> > The error message is as follows: > >>>>>>>> >> >> > > >>>>>>>> >> >> > -- Looking for c++ gmx_version in > /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so > >>>>>>>> >> >> > -- Looking for c++ gmx_version in > /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so - not found > >>>>>>>> >> >> > CMake Error at csg/CMakeModules/FindGROMACS.cmake:57 > (message): > >>>>>>>> >> >> > Could not find a suitable gromacs library. gmx_version > is not defined in > >>>>>>>> >> >> > the gromacs library, that is very very strange, take a > look at the error > >>>>>>>> >> >> > message in > /home/sbinkas/software/votca/build/CMakeFiles/CMakeError.log to > >>>>>>>> >> >> > find out what was going wrong. This most likely means > that your gromacs > >>>>>>>> >> >> > version is too old, we need at least gromacs 2016! > >>>>>>>> >> >> > > >>>>>>>> >> >> > My version is 2018.3 > >>>>>>>> >> >> > > >>>>>>>> >> >> > I have used this command for cmake: > >>>>>>>> >> >> > > >>>>>>>> >> >> > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} > -DWITH_GMX=ON .. > >>>>>>>> >> >> > > >>>>>>>> >> >> > Providing the path to include directory and library also > makes no difference. > >>>>>>>> >> >> > > >>>>>>>> >> >> > However, I would note a caveat. The gromacs version I > installed manually on cluster was installed with -DGMX_MPI=OFF. > >>>>>>>> >> >> > > >>>>>>>> >> >> > But, the dependencies requirement suggests > gromacs-openmpi. Can that be a reason? > >>>>>>>> >> >> Votca needs a non-mpi version, so that should be fine. You > only need > >>>>>>>> >> >> gromacs with mpi at runtime to do parallel simulations. > >>>>>>>> >> >> Have a look at the end of > >>>>>>>> >> >> > /home/sbinkas/software/votca/build/CMakeFiles/CMakeError.log to see > >>>>>>>> >> >> what is wrong with your libgromacs. > >>>>>>>> >> >> > >>>>>>>> >> >> > >>>>>>>> >> >> > PS: I am talking about installation on cluster now. On > local machine Votca package got installed using apt-get but as expected, > the simulations were super slow. > >>>>>>>> >> >> Usually you can speed up the gromacs simulation part by > running on all cores. > >>>>>>>> >> >> > >>>>>>>> >> >> Christoph > >>>>>>>> >> >> > > >>>>>>>> >> >> > Thanks for all your help again. > >>>>>>>> >> >> > > >>>>>>>> >> >> > On Sat, Apr 25, 2020 at 9:41 AM Christoph Junghans < > [email protected]> wrote: > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> On Sat, Apr 25, 2020 at 7:15 AM Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> >> >> >> > > >>>>>>>> >> >> >> > Okay. I will install a newer version manually and > apt-get consider the 3.3-beta1 version to be the latest. > >>>>>>>> >> >> >> That might help: > >>>>>>>> >> >> >> > https://askubuntu.com/questions/1068232/how-to-update-libeigen3-to-version-3-3-on-16-04-xenial > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> > > >>>>>>>> >> >> >> > My linux version is: > >>>>>>>> >> >> >> > > >>>>>>>> >> >> >> > Ubuntu 16.04.4 LTS > >>>>>>>> >> >> >> Hmm, as the name suggests that Ubuntu is from 2016 and > we will only > >>>>>>>> >> >> >> support the latest LTS version, which currently is 18.04 > (until later > >>>>>>>> >> >> >> this month when 20.04 LTS is released). We just don't > have the > >>>>>>>> >> >> >> manpower to support anything but the latest versions of > most Linux > >>>>>>>> >> >> >> distributions. > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> Plus, the gromacs version in 16.04 might be also too old > to be used > >>>>>>>> >> >> >> with VOTCA-1.6. > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> Christoph > >>>>>>>> >> >> >> > > >>>>>>>> >> >> >> > On Sat, Apr 25, 2020 at 9:10 AM Christoph Junghans < > [email protected]> wrote: > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> On Fri, Apr 24, 2020 at 10:07 PM Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > Thanks again for answering my questions. > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > "What version do you have installed?" > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > For eigen3, I have installed the version > libeigen3-dev which is mentioned in the dependencies section. The version > information for eigen3 is as follows: > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > libeigen3-dev is already the newest version > (3.3~beta1-2) > >>>>>>>> >> >> >> >> Yes, and 3.3-beta1 is older than 3.3.0, so you need a > newer version of eigen3. > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> What Linux distribution are you using? > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> Christoph > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > -Salman > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > On Sat, Apr 25, 2020 at 12:00 AM Christoph Junghans > <[email protected]> wrote: > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> On Fri, Apr 24, 2020, 21:00 Salman Bin Kashif < > [email protected]> wrote: > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> Thank you, Christoph. I now tried installing v > 1.6. I am trying on local machine for now since it is easier to install all > the dependencies. > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> Initially, my cmake version was old which was > 3.5.1 and on installing votca it was throwing an error that minimum 3.10 > version is required for cmake. Hence I manually installed cmake version > 3.16.5 > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> I verified cmake installation by checking the > cmake --version > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> However, on installing the votca back I got the > following error: > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> Could not find a configuration file for package > "Eigen3" that is compatible > >>>>>>>> >> >> >> >> >>> with requested version "3.3.0". > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> The following configuration files were > considered but not accepted: > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> /usr/lib/cmake/eigen3/Eigen3Config.cmake, > version: unknown > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> This error means the Eigen3 you have installed is > too old. Eigen-3.3.0 got released back in Nov. 2016, so that isn't very new > either. > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> What version do you have installed? > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> Christoph > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> Would I have to install specific cmake version? > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> On Fri, Apr 24, 2020 at 9:10 PM Christoph > Junghans <[email protected]> wrote: > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> Votca-1.4.1 was released back in Sept. 2017 and > we don't really > >>>>>>>> >> >> >> >> >>>> support such old versions anymore. > >>>>>>>> >> >> >> >> >>>> If you don't have a strong reason to use v1.4.1 > try to use Votca-1.6. > >>>>>>>> >> >> >> >> >>>> see > https://github.com/votca/votca/blob/master/README.md > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> On Fri, Apr 24, 2020 at 6:59 PM Salman Bin > Kashif <[email protected]> wrote: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > I am trying to Install Votca on cluster. In > have loaded the required modules there. However, I am getting an error in > terms of finding the package.I used the following command: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > cmake -DCMAKE_INSTALL_PREFIX=${prefix} > -DWITH_FFTW=OFF -DWITH_SQLITE3=OFF .. > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > The error message I get is: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- Boost version: 1.53.0 > >>>>>>>> >> >> >> >> >>>> > -- Found the following Boost libraries: > >>>>>>>> >> >> >> >> >>>> > -- program_options > >>>>>>>> >> >> >> >> >>>> > -- filesystem > >>>>>>>> >> >> >> >> >>>> > -- system > >>>>>>>> >> >> >> >> >>>> > -- checking for module 'gsl' > >>>>>>>> >> >> >> >> >>>> > -- package 'gsl' not found > >>>>>>>> >> >> >> >> >>>> > -- Could NOT find GSL (missing: GSL_LIBRARY > GSL_INCLUDE_DIR) > >>>>>>>> >> >> >> >> >>>> > -- Intel(R) MKL could not be found. > >>>>>>>> >> >> >> >> >>>> > -- > >>>>>>>> >> >> >> >> >>>> > -- The following OPTIONAL packages have been > found: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > * PkgConfig > >>>>>>>> >> >> >> >> >>>> > * EXPAT > >>>>>>>> >> >> >> >> >>>> > * Doxygen > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- The following REQUIRED packages have been > found: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > * Threads > >>>>>>>> >> >> >> >> >>>> > * Boost (required version >= 1.39.0) > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- The following OPTIONAL packages have not > been found: > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > * GSL > >>>>>>>> >> >> >> >> >>>> > * MKL > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- Could NOT find TXT2TAGS (missing: > TXT2TAGS_EXECUTABLE) > >>>>>>>> >> >> >> >> >>>> > txt2tags not found, help cmake to find it by > setting TXT2TAGS_EXECUTABLE > >>>>>>>> >> >> >> >> >>>> > -- Boost version: 1.53.0 > >>>>>>>> >> >> >> >> >>>> > -- Found the following Boost libraries: > >>>>>>>> >> >> >> >> >>>> > -- program_options > >>>>>>>> >> >> >> >> >>>> > -- filesystem > >>>>>>>> >> >> >> >> >>>> > -- system > >>>>>>>> >> >> >> >> >>>> > -- checking for module 'libvotca_tools' > >>>>>>>> >> >> >> >> >>>> > -- package 'libvotca_tools' not found > >>>>>>>> >> >> >> >> >>>> > CMake Error at > /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:108 (message): > >>>>>>>> >> >> >> >> >>>> > Could NOT find SQLITE3 (missing: > SQLITE3_INCLUDE_DIR) > >>>>>>>> >> >> >> >> >>>> > Call Stack (most recent call first): > >>>>>>>> >> >> >> >> >>>> > > /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:315 > (_FPHSA_FAILURE_MESSAGE) > >>>>>>>> >> >> >> >> >>>> > csg/CMakeModules/FindSQLITE3.cmake:34 > (find_package_handle_standard_args) > >>>>>>>> >> >> >> >> >>>> > csg/CMakeModules/FindVOTCA_TOOLS.cmake:32 > (find_package) > >>>>>>>> >> >> >> >> >>>> > csg/CMakeLists.txt:83 (find_package) > >>>>>>>> >> >> >> >> >>>> Usually WITH_SQLITE3=OFF should disable the > search for sqlite3, > >>>>>>>> >> >> >> >> >>>> something funky is going on here as L32 in > v1.4.1 isn't actually > >>>>>>>> >> >> >> >> >>>> checking for sqlite3: > >>>>>>>> >> >> >> >> >>>> > https://github.com/votca/csg/blob/v1.4.1/CMakeModules/FindVOTCA_CSG.cmake > >>>>>>>> >> >> >> >> >>>> Please check you are using the correct version > of csg. > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> Christoph > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- Configuring incomplete, errors occurred! > >>>>>>>> >> >> >> >> >>>> > See also > "/home/sbinkas/votca/build/CMakeFiles/CMakeOutput.log". > >>>>>>>> >> >> >> >> >>>> > See also > "/home/sbinkas/votca/build/CMakeFiles/CMakeError.log". > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > > >>>>>>>> >> >> >> >> >>>> > -- > >>>>>>>> >> >> >> >> >>>> > Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> >>>> > --- > >>>>>>>> >> >> >> >> >>>> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/187cdc4c-6526-4716-8532-d60341aec7a1%40googlegroups.com > . > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> -- > >>>>>>>> >> >> >> >> >>>> Christoph Junghans > >>>>>>>> >> >> >> >> >>>> Web: http://www.compphys.de > >>>>>>>> >> >> >> >> >>>> > >>>>>>>> >> >> >> >> >>>> -- > >>>>>>>> >> >> >> >> >>>> Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> >>>> --- > >>>>>>>> >> >> >> >> >>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e5T9%2BYxURMfUrr8nVyERKqD1yMGGRMONw09eNeUggHNew%40mail.gmail.com > . > >>>>>>>> >> >> >> >> >>> > >>>>>>>> >> >> >> >> >>> -- > >>>>>>>> >> >> >> >> >>> Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> >>> --- > >>>>>>>> >> >> >> >> >>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHy-N%3DpNKX4tQ-KXSU6Aghh23Af%2Bg_M1pJiAB8KsQAi-UQ%40mail.gmail.com > . > >>>>>>>> >> >> >> >> >> > >>>>>>>> >> >> >> >> >> -- > >>>>>>>> >> >> >> >> >> Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> >> --- > >>>>>>>> >> >> >> >> >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e4RwoWm-NDRSYAZPzycT%3DKAoOnK-HZ8JYVCC0Ej5X_%2BEA%40mail.gmail.com > . > >>>>>>>> >> >> >> >> > > >>>>>>>> >> >> >> >> > -- > >>>>>>>> >> >> >> >> > Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> > --- > >>>>>>>> >> >> >> >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHwpcxE%3D%3DZK%3D2Udw9fSFpn3d2rkCk1COVSpY5MaDQ_TpCw%40mail.gmail.com > . > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> -- > >>>>>>>> >> >> >> >> Christoph Junghans > >>>>>>>> >> >> >> >> Web: http://www.compphys.de > >>>>>>>> >> >> >> >> > >>>>>>>> >> >> >> >> -- > >>>>>>>> >> >> >> >> Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> >> --- > >>>>>>>> >> >> >> >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7T7i1nF%3DJj_O4aPEJh6JmEomSn_mLn2kRXW9Q_N7fq%2Bg%40mail.gmail.com > . > >>>>>>>> >> >> >> > > >>>>>>>> >> >> >> > -- > >>>>>>>> >> >> >> > Join us on Slack: > https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> > --- > >>>>>>>> >> >> >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHzzXw%2ByX-ggrOJpXS7p1y0NoWpYrT658Bky%2B9_UW3Kneg%40mail.gmail.com > . > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> -- > >>>>>>>> >> >> >> Christoph Junghans > >>>>>>>> >> >> >> Web: http://www.compphys.de > >>>>>>>> >> >> >> > >>>>>>>> >> >> >> -- > >>>>>>>> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> >> >> >> --- > >>>>>>>> >> >> >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e5bXjZrLsJQUBTRAE3T%2BMs4Unrk3SzCzUp_ZZYCHXXnCA%40mail.gmail.com > . > >>>>>>>> >> >> > > >>>>>>>> >> >> > -- > >>>>>>>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> >> >> > --- > >>>>>>>> >> >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHy91W4YdUGKiYrispvdjrfSQhSFHKrWMubs4X8uDGexTQ%40mail.gmail.com > . > >>>>>>>> >> >> > >>>>>>>> >> >> > >>>>>>>> >> >> > >>>>>>>> >> >> -- > >>>>>>>> >> >> Christoph Junghans > >>>>>>>> >> >> Web: http://www.compphys.de > >>>>>>>> >> >> > >>>>>>>> >> >> -- > >>>>>>>> >> >> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> >> >> --- > >>>>>>>> >> >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7KT6hGWYuOTO%3DwVTkgpBG9DWQWes7FQ8DmB%3DexmZ0x0g%40mail.gmail.com > . > >>>>>>>> >> > > >>>>>>>> >> > -- > >>>>>>>> >> > Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> >> > --- > >>>>>>>> >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHzq6TrBChPWMEdpKKid8CoLLbb555weSia_SHzx4tX%3D5A%40mail.gmail.com > . > >>>>>>>> >> > >>>>>>>> >> > >>>>>>>> >> > >>>>>>>> >> -- > >>>>>>>> >> Christoph Junghans > >>>>>>>> >> Web: http://www.compphys.de > >>>>>>>> >> > >>>>>>>> >> -- > >>>>>>>> >> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> >> --- > >>>>>>>> >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7mfQb%2BC5Cfq2RtFtzZiNDHXNeAR8rFqzYq%2BbAg1SGjqw%40mail.gmail.com > . > >>>>>>>> > > >>>>>>>> > -- > >>>>>>>> > Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> > --- > >>>>>>>> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHy4vWM9Ceaw5scKKeY-fJd0kMBPYziKsLw6qarkNS%3DR9w%40mail.gmail.com > . > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> -- > >>>>>>>> Christoph Junghans > >>>>>>>> Web: http://www.compphys.de > >>>>>>>> > >>>>>>>> -- > >>>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>>> --- > >>>>>>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e4dei82q8VEfajeWidKeRE4m%2BC0h9haLw6j_7qdQ60ixQ%40mail.gmail.com > . > >>>>>>> > >>>>>>> -- > >>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>>> --- > >>>>>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHyvibXKzOp4e4ig-Lv331HkdZ2X9Titsjvt_ooMiqrQPg%40mail.gmail.com > . > >>>>>> > >>>>>> -- > >>>>>> Christoph Junghans > >>>>>> Web: http://www.compphys.de > >>>>>> > >>>>>> -- > >>>>>> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>>> --- > >>>>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7MxFV6fc2WDU0%3D8%2BL%3D%2B4mgaZr4LZ6APYdEqYmtsmmJpA%40mail.gmail.com > . > >>>>> > >>>>> -- > >>>>> Join us on Slack: https://join.slack.com/t/votca/signup > >>>>> --- > >>>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHym1V1DDWnoqELvtNPbFE%3D%2B7KSTE-RCKM2aVArgF5YdRw%40mail.gmail.com > . > >>>> > >>>> -- > >>>> Christoph Junghans > >>>> Web: http://www.compphys.de > >>>> > >>>> -- > >>>> Join us on Slack: https://join.slack.com/t/votca/signup > >>>> --- > >>>> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e4gh80z%3DUPL8nydGrEm3QV0HqRzYm7cozObdZJZR1QZLA%40mail.gmail.com > . > > > > -- > > Join us on Slack: https://join.slack.com/t/votca/signup > > --- > > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFwyQHwt0yXzKSOfqzkxmHsda6x2H5bkUrNqQm-5PyGUNX2Q6w%40mail.gmail.com > . > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e7fxS5eBc3B0%2BY2kNVEquJwkJpF3vkfZSFQDE6aPy-6BQ%40mail.gmail.com > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAFwyQHy8EPGUnz66WC74EXCrpkAyZ4UJjS6gjOcXZu758i-KUQ%40mail.gmail.com.
