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.
