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.
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
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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