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

[Szilárd Páll]

On Sat, Dec 8, 2018 at 10:00 PM Gmail <jaisiero at gmail.com> wrote:
>
> My mistake! It was a typo. Anyway, this is the result before executing
> the chrpath command:
>
> chrpath -l $APPS/GROMACS/2018/CUDA/8.0/bin/gmx
> $APPS/GROMACS/2018/CUDA/8.0/bin/gmx: RPATH=$ORIGIN/../lib64
>
> I'm suspicious that GROMACS 2018 is not being compiled using shared
> libraries, at least, for CUDA.

First of all, what is the goal, why are you trying to manually rewrite
the binary RPATH?

Well, if the binaries not linked against libcudart.so than it clearly
isn't (and the ldd output is a better way to confirm that -- a library
can be linked against gmx even without an RPATH being set).

I have a vague memory that this may have been the default in CMake or
perhaps it changed at some point. What's your CMake version, perhaps
you're using an old CMake?

>
> Jaime.
>
>
> On 8/12/18 21:39, Mark Abraham wrote:
> > 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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