On Wed, Jun 5, 2019 at 10:01 PM Souvik Chakraborty <[email protected]> wrote: > > Thanks a lot, Christoph. It worked when started afresh. One thing to clarify: > if Votca compiles its "own" gromacs, what will be its version? And will it be > compatible with the all-atom trajectory generated by any gromacs version > (2016 and beyond)? Yeah, we just build gromacs-2018.6 internally.
Christoph > > Regards, > Souvik > > > > On Wednesday, 5 June 2019 21:30:26 UTC+8, Christoph Junghans wrote: >> >> >> >> On Wed, Jun 5, 2019, 06:04 Souvik Chakraborty <[email protected]> wrote: >>> >>> Dear members, >>> >>> I am trying to install votca-csg for the first time. I found some error at >>> the 'cmake' step. Please shed light on the issue and if I did something >>> wrong. >>> I have Gromacs 16.03 installed and I am using cmake 3.14.5. >>> >>> ############################################################################## >>> $-> pkg-config --libs libgromacs >>> >>> -L/usr/local/gromacs/lib -lgromacs -lm >> >> If you look at the error message below VOTCA actually picked up a >> libgromacs_d.so from somewhere else. Setting GROMACS_LIBRARY should actually >> overwrite that finding. Please check another time you point CMake to the >> right place and start from a empty build directory again. >> >> Otherwise, you can also have votca compile it's own gromacs by setting >> BUILD_OWN_GROMACS=ON. >> >> Christoph >>> >>> >>> $-> cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} >>> -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include >>> -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.so .. >>> >>> -- Boost version: 1.58.0 >>> -- Found the following Boost libraries: >>> -- program_options >>> -- filesystem >>> -- system >>> -- Intel(R) MKL could not be found. >>> -- Found Eigen3: /usr/local/share/eigen3/cmake >>> -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) >>> -- Boost version: 1.58.0 >>> -- Found the following Boost libraries: >>> -- program_options >>> -- filesystem >>> -- system >>> -- Found Eigen3: /usr/local/share/eigen3/cmake >>> -- Found VOTCA_TOOLS: >>> CMake Error at csg/CMakeModules/FindGROMACS.cmake:52 (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/souvik/Downloads/VOTKA/VOTKA-git/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! >>> Call Stack (most recent call first): >>> CMakeLists.txt:78 (_find_package) >>> csg/CMakeLists.txt:73 (find_package) >>> >>> >>> -- Configuring incomplete, errors occurred! >>> See also >>> "/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeOutput.log". >>> See also >>> "/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeError.log". >>> >>> ######################################################################################### >>> >>> >>> >>> >>> >>> >>> The errors printed on CMakeError.log: >>> >>> CMakeFiles/cmTC_6e721.dir/build.make:65: recipe for target >>> 'CMakeFiles/cmTC_6e721.dir/src.c.o' failed >>> make[1]: *** [CMakeFiles/cmTC_6e721.dir/src.c.o] Error 1 >>> make[1]: Leaving directory >>> '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp' >>> Makefile:121: recipe for target 'cmTC_6e721/fast' failed >>> make: *** [cmTC_6e721/fast] Error 2 >>> >>> Source file was: >>> int main(void) { >>> #ifndef _AIX >>> #error >>> #endif >>> return 0; >>> } >>> Determining if the function gmx_version exists in the >>> /usr/lib/x86_64-linux-gnu/libgromacs_d.so failed with the following output: >>> Change Dir: >>> /home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp >>> >>> Run Build Command(s):/usr/bin/make cmTC_ba1cf/fast >>> /usr/bin/make -f CMakeFiles/cmTC_ba1cf.dir/build.make >>> CMakeFiles/cmTC_ba1cf.dir/build >>> make[1]: Entering directory >>> '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp' >>> Building CXX object CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o >>> /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_version -std=c++14 -o >>> CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o -c >>> /home/souvik/Downloads/VOTKA/VOTKA-git/votca/csg/CMakeModules/CheckFunctionExists.cpp >>> Linking CXX executable cmTC_ba1cf >>> /usr/local/bin/cmake -E cmake_link_script >>> CMakeFiles/cmTC_ba1cf.dir/link.txt --verbose=1 >>> /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_version >>> CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o -o cmTC_ba1cf >>> /usr/lib/x86_64-linux-gnu/libgromacs_d.so >>> CMakeFiles/cmTC_ba1cf.dir/CheckFunctionExists.cpp.o: In function `main': >>> CheckFunctionExists.cpp:(.text+0x10): undefined reference to `gmx_version()' >>> collect2: error: ld returned 1 exit status >>> CMakeFiles/cmTC_ba1cf.dir/build.make:87: recipe for target 'cmTC_ba1cf' >>> failed >>> make[1]: *** [cmTC_ba1cf] Error 1 >>> make[1]: Leaving directory >>> '/home/souvik/Downloads/VOTKA/VOTKA-git/votca/build/CMakeFiles/CMakeTmp' >>> Makefile:121: recipe for target 'cmTC_ba1cf/fast' failed >>> make: *** [cmTC_ba1cf/fast] Error 2 >>> >>> >>> >>> ########################################################################## >>> >>> Regards, >>> >>> Souvik >>> >>> -- >>> 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 post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/votca. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/6e16ab40-7ceb-4d49-9a75-ee17f1f18a39%40googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. > > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/ce9212d2-9329-420a-a949-7a0bdbcf3660%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7DGr_jY-ATH93%3Dx0qPFx8P%3DAPYUPKH2geDyYTUqDbp4g%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
