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

[Mark Abraham]

Hi,

Your final line doesn't match your CMAKE_INSTALL_PREFIX

Mark

On Sun., 9 Dec. 2018, 07:00 Jaime Sierra <jaisiero at gmail.com wrote:

> 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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