On Mon, Dec 21, 2020 at 6:32 AM nancyfor <[email protected]> wrote:
>
> Hi Christoph,
>
> Thanks for your reply. Below my answers/comments
>
>>
>> > In the gromacs installation(in
>> > /mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/share/cmake/gromacs/libgromacs_static.cmake)
>> > I found the libfftw3 that was used (I assume is the one in the following
>> > line)
>> > INTERFACE_LINK_LIBRARIES
>> > "\$<LINK_ONLY:>;\$<LINK_ONLY:rt>;/mpcdf/soft/SLE_12/packages/skylake/fftw/gcc_8-8.4.0-impi_2019.7-2019.7.217/3.3.7/lib/libfftw3f.a;\$<LINK_ONLY:-lpthread>;m;\$<LINK_ONLY:lmfit>"
>>
>> The library is called libfftw3f.a, mind the f as the end, f stands for
>> single precision, while libfftw3.a (no f) is for double precision.
>> So you will need to do something like:
>> -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"
>> and you try to leave -DFFTW3 alone for now as the detecting work previously.
>
>
> I did not see the f. However it did not past the configuration step. It
> seems it is looking for gmx_is_double_precision. That is the line on the
> screen output, related to the error.
>
> 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 tried then for VOTCA to build its own gromacs
>
>>
>> Are you planning to use gromacs for the cg runs or lammps? Otherwise
>> you could also build without gromacs (-DWITH_GMX=OFF
>> -DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=ON
>>
> I use gromacs, but it is useful to know it could be disable for lammps
>
>> > cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
>> > -DBUILD_SHARED_LIBS=OFF -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF
>> > -DBUILD_OWN_GROMACS=ON -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
>> > -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >
>> > and
>> > cmake --build builddir gives me an error: (attached the output with
>> > --verbose)
>> >
>> > Scanning dependencies of target csg_gmxtopol
>> > [ 67%] Building CXX object
>> > csg/src/tools/CMakeFiles/csg_gmxtopol.dir/csg_gmxtopol.cc.o
>> > gmake[2]: *** No rule to make target
>> > 'gromacs/install/lib64/libgromacs.so', needed by
>> > 'csg/src/tools/csg_gmxtopol'. Stop.
>> > CMakeFiles/Makefile2:675: recipe for target
>> > 'csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all' failed
>> > gmake[1]: *** [csg/src/tools/CMakeFiles/csg_gmxtopol.dir/all] Error 2
>> > Makefile:129: recipe for target 'all' failed
>> > gmake: *** [all] Error 2
>> Looking at the log, somehow Gromacs didn't get build, try to start
>> from a fresh checkout and try to run "cmake --build builddir --verbose
>> --target=Gromacs_build" first.
>>
>
> if I used cmake --build builddir --verbose --target=Gromacs_build
> I get
> Unknown argument --target=Gromacs_build
>
> However, using only cmake --build builddir
> It seems in fact the target exits
>
> cmake --build builddir
> Scanning dependencies of target Gromacs_build
> [ 1%] Creating directories for 'Gromacs_build'
> [ 1%] Performing download step (download, verify and extract) for
> 'Gromacs_build'
> -- Downloading...
> dst='/u/forero/src/votca/builddir/gromacs/src/gromacs-2019.6.tar.gz'
>
> Looking at the screen output it installed gromacs, the error appears because
> it is looking for libgromacs.so and because I used -DBUILD_SHARED_LIBS=OFF
> so there was only libgromacs.a. I finally used
ok, yeah, I never thought about that combination.
I added a user error here: https://github.com/votca/votca/pull/552
Thanks for pointing that out!
>
> cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DBUILD_CSGAPPS=ON -DBUILD_XTP=OFF -DBUILD_OWN_GROMACS=ON
> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>
> and finally it was successfully installed :). Is there a way to choose the
> gromacs version to be installed? I am running all my atomistic simulations in
> version 2019.4. I believe this can be changed in the settings.xml file
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.
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.
Christoph
>
> Cheers,
> Nancy
>
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Christoph Junghans
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