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'
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.
> 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
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