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

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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.

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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