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
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.
