I am still getting errors in the make -j5 command. I am not sure which branch should I pull the changes from. The modules changed in the above mentioned pull doesn't seem to have changed in my local copy. I am pulling from stable branch.
Initially, I have cloned for version v1.6 On Sat, Apr 25, 2020 at 4:03 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=${prefix} -DWITH_GMX=ON > -DGROMACS_INCLUDE_DIR=/home/sbinkas/software/gromacs-2018.3/include > -DGROMACS_LIBRARY=/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so > -DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=ON > -DCMAKE_PREFIX_PATH=/home/sbinkas/software .. > > cmake command runs fine. > > make -j5 throws the error > > Error looks like: > > ../libtools/libvotca_tools.so.6: undefined reference to > `boost::program_options::option_description::format_name[abi:cxx11][ 66%] > Built target votca_csg > make: *** [all] Error 2 > > Am I missing something? > > In the meanwhile, I will try with option 1. > > On Sat, Apr 25, 2020 at 3:46 PM Salman Bin Kashif <[email protected]> > wrote: > >> Thanks so much. I wiil try using the disable package option first. >> >> On Sat, Apr 25, 2020 at 2:09 PM Salman Bin Kashif <[email protected]> >> wrote: >> >>> Following is the output of make VERBOSE-1 >>> >>> [sbinkas@node0170 build]$ 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 >>>>>>> <https://groups.google.com/d/msgid/votca/CAFwyQHyvibXKzOp4e4ig-Lv331HkdZ2X9Titsjvt_ooMiqrQPg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>>>>> 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 >>>>>> <https://groups.google.com/d/msgid/votca/CAHG27e7MxFV6fc2WDU0%3D8%2BL%3D%2B4mgaZr4LZ6APYdEqYmtsmmJpA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> -- >>>>> 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 >>>>> <https://groups.google.com/d/msgid/votca/CAFwyQHym1V1DDWnoqELvtNPbFE%3D%2B7KSTE-RCKM2aVArgF5YdRw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >>>> 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 >>>> <https://groups.google.com/d/msgid/votca/CAHG27e4gh80z%3DUPL8nydGrEm3QV0HqRzYm7cozObdZJZR1QZLA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- 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/CAFwyQHzhzLokv_xK6rMEcbpTjOgXX1pTrSGq-bQAs8QQu_uKog%40mail.gmail.com.
