On Sat, Sep 24, 2022 at 3:12 AM Kim Foo <[email protected]> wrote: > > Dear Christoph, > > Thank you for pointing out the reason for the error. I have managed to > install VOTCA successfully. > > I have a question regarding the gmx binary file, that is located inside > /usr/local/gromacs/bin. Everytime i run csg_inverse --options settings.xml, I > get this error: > > ERROR: > # run_gromacs.sh: grompp binary '/usr/bin/gmx_d' not found > # For details see the logfile > /home/kimfoo/votca/csg-tutorials/spce/ibi/inverse.log > > I solved the problem by adding the path to the binary in the settings.xml > file, however, is there any way to allow VOTCA to read the path to the file > (maybe by defining it in .bashrc etc.) without having to define the path in > every settings.xml file? > > I have tried to put the path into .bashrc as follows: > export PATH=$PATH:/usr/local/share/votca > export PATH=$PATH:/usr/local/gromacs/bin > export PATH=$PATH:/usr/local/bin > export PATH=$PATH:/usr/local/lib > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gromacs/lib > > However, I still obtain the same error. > > I am thinking of changing the default path inside csg_defaults.xml, but user > permission is required, and I was wondering if there is a more elegant method. VOTCA detects the gmx binary at CMake time and puts whatever it finds into the defaults. In your case apparently /usr/bin/gmx_d was found. You can change that by setting the path etc BEFORE you run CMake, so the right gmx gets picked up. You can also force CMake to use a certain gmx binary by setting -DGMX_EXECUTABLE=/path/to/gmx as an CMake option. Or as you suggest you can change the default in csg_defaults.xml Or you can overwrite the gmx binary in your settings file as well. (cg.inverse.gromacs.mdrun.command) Or you can also set the CSG_MDRUN_CMD environment variable.
Pick your poison. Christoph > > Any help on this would be greatly appreciated. > > Regards, > Kimberly > > > On Thursday, September 22, 2022 at 10:50:05 PM UTC+9 Christoph Junghans wrote: >> >> 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/3dee86f4-4570-46f8-8a79-8a463a37c60fn%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. 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