On Thu, Sep 22, 2022 at 6:23 AM Kim Foo <[email protected]> wrote: > > Dear Christoph, > > I am currently in the midst of installing VOTCA on my Ubuntu 18.04 system > which I have already installed GROMACS 2019 on but I encountered an error > when running the following command: > > cmake -B builddir -S votca -DBUILD_XTP=ON > -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.so > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include > > The error shown in the terminal states that I do not have any gromacs_version > when I have already defined the path for it in the command and checked that > the libgromacs.so file does exist in the specified path. The output in the > terminal: > > -- Found Boost: > /home/kimfoo/miniconda3/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found > suitable version "1.74.0", minimum required is "1.71.0") found components: > program_options filesystem system > -- Found Python: /home/kimfoo/miniconda3/bin/python3.9 (found suitable > version "3.9.13", minimum required is "3") found components: Interpreter > -- MKL: Thread Layer(GNU OpenMP) Interface(4-byte Integer) > -- Found OpenMP_CXX: -fopenmp (found version "4.5") > -- Found OpenMP: TRUE (found version "4.5") > -- Could NOT find MKL: Source the compilervars.sh or mklvars.sh scripts > included with your installation of MKL. This script searches for the > libraries in MKLROOT, LIBRARY_PATHS(Linux), and LIB(Windows) environment > variables (missing: MKL_INCLUDE_DIR) > -- Could NOT find MKL: Source the compilervars.sh or mklvars.sh scripts > included with your installation of MKL. This script searches for the > libraries in MKLROOT, LIBRARY_PATHS(Linux), and LIB(Windows) environment > variables (missing: MKL_INCLUDE_DIR MKL_Core_STATIC_LINK_LIBRARY > MKL_Interface_STATIC_LINK_LIBRARY MKL_ThreadLayer_STATIC_LINK_LIBRARY) > -- Found OpenMP_CXX: -fopenmp (found suitable version "4.5", minimum required > is "4.5") > -- Found OpenMP: TRUE (found suitable version "4.5", minimum required is > "4.5") > -- Found Eigen3: /home/kimfoo/miniconda3/share/eigen3/cmake > -- Checking for module 'fftw3' > -- /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or > directory > No package 'fftw3' found > -- Found Python: /home/kimfoo/miniconda3/bin/python3.9 (found suitable > version "3.9.13", minimum required is "3.5") found components: Interpreter > -- Found Boost: > /home/kimfoo/miniconda3/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found > suitable version "1.74.0", minimum required is "1.71.0") found components: > program_options filesystem system regex > -- Found Eigen3: /home/kimfoo/miniconda3/share/eigen3/cmake > -- Found VOTCA_TOOLS: > -- Checking for module 'libgromacs_d' > -- /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or > directory > No package 'libgromacs_d' found > CMake Error at csg/CMakeModules/FindGROMACS.cmake:58 (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/kimfoo/builddir/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! > Call Stack (most recent call first): > CMakeLists.txt:132 (_find_package) > csg/CMakeLists.txt:80 (find_package) > > > -- Configuring incomplete, errors occurred! > See also "/home/kimfoo/builddir/CMakeFiles/CMakeOutput.log". > See also "/home/kimfoo/builddir/CMakeFiles/CMakeError.log". > > I have attached the CMakeError.log file for reference. I checked the error > and there are a two warnings: > > /home/kimfoo/miniconda3/bin/ld: warning: libhwloc.so.15, needed by > /usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or > -rpath-link) > /home/kimfoo/miniconda3/bin/ld: warning: libgomp.so.1, needed by > /usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or > -rpath-link) This is the problem, you will have to look where libhwloc.so.15 and libgomp.so.1 are and then set the LD_LIBRARY_PATH correctly, something like: $ export LD_LIBRARY_PATH=/path/to/lib:${LD_LIBRARY_PATH} There might be a more conda-ish way to do it, but I am not a conda expert. I am CC'ing Jan, who knows much more about conda than I.
Christoph > > I am not sure if these are the reasons for the failure in cmake command. I am > fairly new to cmake so any advice that you have will be greatly appreciated. > Would you suggest that I use -DBUILD_OWN_GROMACS=ON ? However, the version I > would like to install is the 2019 version because I find that the > csg-tutorials can run with the 2019 version but not newer. > > Thank you very much for your time. > > Best regards, > Kimberly > > -- > 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/df5e618e-c383-4d84-bf14-6a13c6d18e28n%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/CAHG27e7USwNdTjO9y2Lsv9hT4btYu84z0ph1yBcyb_P8KYHRdw%40mail.gmail.com.
