On Mon, Dec 21, 2020 at 10:05 AM nancyfor <[email protected]> wrote: > > > On Monday, 21 December 2020 at 15:35:37 UTC+1 Christoph Junghans wrote: >> >> >> > Looking for c++ gmx_is_double_precision in >> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3f.a >> > - not found >> >> You can look in the CMake error log to see why this test is failing, I >> assume you will need to list libmpi in GROMACS_LIBRARY as well to make >> that work. >> > > I can not located libmpi.a or libm.a. I only found a libmpx.a in > /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a and used > > cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ > -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF > -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/ > > -DGROMACS_LIBRARY="/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3f.a;/mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/lib64/libmpx.a" > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca > > the configuration worked, but when building it I got the same error as before > when linking csg_gmxtopol > ..... > [ 66%] Linking CXX executable csg_gmxtopol > cd /u/forero/src/votca-tmp/votca/builddir/csg/src/tools && > /u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E > cmake_link_script CMakeFiles/csg_gmxtopol.dir/link.txt --verbose=1 > /mpcdf/soft/SLE_12/packages/x86_64/gcc/8.4.0/bin/g++ -Wall -Wextra > -Wpedantic -Wshadow -Wconversion -O3 -DNDEBUG > CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o -o csg_gmxtopol > -Wl,-rpath,/mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib:/mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64:/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib: > ../libcsg/libvotca_csg.a > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a > /mpcdf/soft/SLE_12/packages/skylake/hdf5/gcc_8-8.4.0/1.8.21/lib/libhdf5.so > /usr/lib64/libz.so /usr/lib64/libdl.so -lm > ../../../tools/src/libtools/libvotca_tools.a > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 > > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 > > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 > /usr/lib64/libexpat.so -lm > /mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3.so > > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_program_options.so.1.74.0 > > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_filesystem.so.1.74.0 > > /mpcdf/soft/SLE_12/packages/skylake/boost/gcc_8-8.4.0/1.74.0/lib64/libboost_system.so.1.74.0 > -lpthread > /usr/bin/ld: > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o): > in function `gmx::printBinaryInformation(gmx::TextWriter*, > gmx::IProgramContext const&, gmx::BinaryInformationSettings const&)': > binaryinformation.cpp:(.text+0x706): undefined reference to `fftwf_version' I am running out of ideas....not sure why libfftw3f.a is missing here, even though you had it in GROMACS_LIBRARY above.
> collect2: error: ld returned 1 exit status > csg/src/tools/CMakeFiles/csg_gmxtopol.dir/build.make:98: recipe for target > 'csg/src/tools/csg_gmxtopol' failed > gmake[2]: *** [csg/src/tools/csg_gmxtopol] Error 1 > gmake[2]: Leaving directory '/cobra/u/forero/src/votca-tmp/votca/builddir' > CMakeFiles/Makefile2:644: recipe for target > 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed > gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2 > gmake[1]: Leaving directory '/cobra/u/forero/src/votca-tmp/votca/builddir' > Makefile:129: recipe for target 'all' failed > gmake: *** [all] Error 2 > > >> >> >> > Looking at the screen output it installed gromacs, the error appears >> > because it is looking for libgromacs.so and because I used >> > -DBUILD_SHARED_LIBS=OFF so there was only libgromacs.a. I finally used >> >> ok, yeah, I never thought about that combination. >> I added a user error here: https://github.com/votca/votca/pull/552 >> Thanks for pointing that out! > > > Good! I am glad something useful came out of this long thread :) > >> >> There is no option to select the gromacs version, that would be a case >> of installing with spack. >> VOTCA builds 2019.6 internally, as it is that last version that has >> support for tabulated interactions. >> When you install VOTCA the internally-built gromacs binaries will end >> up in the same directory. > > > Oh, I was not aware this was the case in the new versions of GROMACS. Yeah, gromacs-2020 and higher won't work for coarse-graining, hopefully that feature will be back in gromacs-2022. > >> >> However you can tweak what gromacs version is used at runtime to run >> the simulation with the >> cg.inverse.gromacs.mdrun.command option in the xml files. >> You could set it to something like "mpirun -np 16 mdrun_mpi". >> To tweak the grompp binary use cg.inverse.gromacs.grompp.bin, the >> default is "gmx grompp" for that. > > > Thank you for your help! > Cheers, > Nancy > > -- > 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/fdf5a505-3d77-427c-8811-e461cb5f8f36n%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/CAHG27e6fjjA-bxKmRV8fxBMxs6F9Ea_dZ2vTPy%2BzM0GQboMz2g%40mail.gmail.com.
