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

[Jaime Sierra]

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.

[Szilárd Páll]

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,

Post by Jaime Sierra
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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[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.

Post by Szilárd Páll
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,

Post by Jaime Sierra
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.
--
Gromacs Users mailing list
* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

Post by Jaime Sierra
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[Mark Abraham]

Hi,

Your final line doesn't match your CMAKE_INSTALL_PREFIX

Mark

Post by Jaime Sierra
Hi pall,
thanks for your answer,
$ 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.

Post by Szilárd Páll
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,

Post by Jaime Sierra
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

Post by Szilárd Páll

Post by Jaime Sierra
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.
--
Gromacs Users mailing list
* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

Post by Jaime Sierra
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[Gmail]

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.

Post by Mark Abraham
Hi,
Your final line doesn't match your CMAKE_INSTALL_PREFIX
Mark

Post by Jaime Sierra
Hi pall,
thanks for your answer,
$ 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.

Post by Szilárd Páll
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,

Post by Jaime Sierra
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

Post by Szilárd Páll

Post by Jaime Sierra
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.
--
Gromacs Users mailing list
* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

Post by Jaime Sierra
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