[gmx-users] Install GROMACS 2018 with CUDA features in dynamic linking way

[Jaime Sierra]

Hi pall,

thanks for your answer,
I have my own "HOW_TO_INSTALL" guide like:

$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.4.tar.gz
$ tar xzf gromacs-5.1.4.tar.gz
$ cd gromacs-5.1.4.tar.gz
$ mkdir build
$ cd build
$ export EXTRA_NVCCFLAGS=--cudart=shared
$ export PATH=$APPS/CMAKE/2.8.12.2/bin/:$PATH
$ cmake .. -DCMAKE_INSTALL_PREFIX=$APPS/GROMACS/5.1.4/CUDA8.0/GPU
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=$LIBS/FFTW/3.3.3/SINGLE/
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=$LIBS/CUDA/8.0/
$ make -j $(nproc)
$ make install
$ chrpath -r '$ORIGIN/../lib64' $APPS/GROMACS/5.1.4/GPU/bin/gmx

that works until GROMACS 2016, I couldn't make it work for GROMACS 2018.

Regards,

Jaime.

El vie., 7 dic. 2018 a las 15:49, Szilárd Páll (<pall.szilard at gmail.com>)
escribió:

> Hi Jaime,
>
> Have you tried passing that variable to nvcc? Does it not work?
>
> Note that GROMACS makes up to a dozen of CUDA runtime calls (kernels
> and transfers) per iteration with iteration times in the range of
> milliseconds at longest and peak in the hundreds of nanoseconds and
> the CPU needs to sync up every iteration with the GPU. Hence, I
> suspect GROMACS may be a challenging use-case for rCUDA, but I'm very
> interested in your observations and benchmarks results when you have
> some.
>
> Cheers,
> On Fri, Dec 7, 2018 at 10:39 AM Jaime Sierra <jaisiero at gmail.com> wrote:
> >
> > Hi,
> >
> > my name is Jaime Sierra, a researcher from Polytechnic University of
> > Valencia, Spain. I would like to know how to compile & install GROMACS
> > 2018 with CUDA features with the "--cudart=shared" compilation option to
> > use it with our rCUDA software.
> >
> >
> > We haven't had this problem in previous releases of GROMACS like 2016,
> > 5.1.4 and so on.
> >
> >
> > Regards,
> >
> > Jaime.
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