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

Jaime Sierra jaisiero at gmail.com
Thu Dec 13 19:08:16 CET 2018 

I suspect CUDA is not linked dinamically. I'm almost 100% sure.

function cuGetExportTable not supported. Please, report this error to <
support at rcuda.net> so that it is supported in future versions of rCUDA.

this function is called when CUDA Runtime is compiled statically.

The ld command is telling me that:
libcudart.so.8.0 => /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcudart.so.8.0

and my environment variables are unset·

Regards,
Jaime.


El jue., 13 dic. 2018 a las 18:27, Szilárd Páll (<pall.szilard at gmail.com>)
escribió:

> On Thu, Dec 13, 2018 at 6:07 PM Jaime Sierra <jaisiero at gmail.com> wrote:
> >
> > My cmake config:
> >
> > ~/cmake-3.13.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > -DCUDA_TOOLKIT_ROOT_DIR=/nfs2/LIBS/x86_64/LIBS/CUDA/8.0
> > -DCMAKE_INSTALL_PREFIX=/nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0
> > -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DBUILD_SHARED_LIBS=ON
> > -DCUDA_NVCC_FLAGS=--cudart=shared
>
> Why pass that flag when the abovecache variable should do the same?
>
> > -DGMX_PREFER_STATIC_LIBS=OFF
> >
> > ldd /nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0/bin/gmx mdrun
> > /nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0/bin/gmx:
> >         linux-vdso.so.1 =>  (0x00007ffc6f6f4000)
> >         libgromacs.so.3 =>
> >
> /nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0/bin/../lib64/libgromacs.so.3(0x00007fb588ed9000)
> >         libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fb588bba000)
> >         libm.so.6 => /lib64/libm.so.6 (0x00007fb5888b8000)
> >         libgomp.so.1 => /lib64/libgomp.so.1 (0x00007fb588692000)
> >         libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fb58847b000)
> >         libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fb58825f000)
> >         libc.so.6 => /lib64/libc.so.6 (0x00007fb587e9e000)
> >         libcudart.so.8.0 =>
> > /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcudart.so.8.0
> (0x00007fb587c37000)
> >         libcufft.so.8.0 =>
> > /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcufft.so.8.0
> (0x00007fb57ede9000)
> >         libdl.so.2 => /lib64/libdl.so.2 (0x00007fb57ebe4000)
> >         librt.so.1 => /lib64/librt.so.1 (0x00007fb57e9dc000)
> >         libmkl_intel_lp64.so =>
> >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_intel_lp64.so
> > (0x00007fb57e2b9000)
> >         libmkl_intel_thread.so =>
> >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_intel_thread.so
> > (0x00007fb57d21e000)
> >         libmkl_core.so =>
> >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_core.so
> > (0x00007fb57bcf0000)
> >         libiomp5.so =>
> > /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/lib/intel64/libiomp5.so
> > (0x00007fb57b9d7000)
> >         libmkl_gf_lp64.so =>
> >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_gf_lp64.so
> > (0x00007fb57b2b4000)
> >         /lib64/ld-linux-x86-64.so.2 (0x00007fb58bf2d000
> >
> >
> >
> > IDK what i'm doing wrong.
>
> You asked for dynamic linking against the CUDA runtime and you got
> that. Please be more specific what the problem is.
>
> --
> Szilárd
>
> >
> > Regards,
> > Jaime.
> >
> > El mar., 11 dic. 2018 a las 22:14, Szilárd Páll (<pall.szilard at gmail.com
> >)
> > escribió:
> >
> > > AFAIK the right way to control RPATH using cmake is:
> > > https://cmake.org/cmake/help/v3.12/variable/CMAKE_SKIP_RPATH.html
> > > no need to poke the binary.
> > >
> > > If you still need to turn off static cudart linking the way to do that
> > > is also via a CMake feature:
> > > https://cmake.org/cmake/help/latest/module/FindCUDA.html
> > > The default is static.
> > >
> > > --
> > > Szilárd
> > > On Tue, Dec 11, 2018 at 10:45 AM Jaime Sierra <jaisiero at gmail.com>
> wrote:
> > > >
> > > > I'm trying to rewrite the RPATH because shared libraries paths used
> by
> > > > GROMACS are hardcoded in the binary.
> > > >
> > > > ldd /nfs2/opt/APPS/x86_64/APPS/GROMACS/2016/CUDA/8.0/bin/gmx
> > > > linux-vdso.so.1 =>  (0x00007ffddf1d3000)
> > > > libgromacs.so.2 =>
> > > >
> > >
> /nfs2/opt/APPS/x86_64/APPS/GROMACS/2016/CUDA/8.0/bin/../lib64/libgromacs.so.2
> > > > (0x00007f0094b25000)
> > > > libcudart.so.8.0 => not found
> > > > libnvidia-ml.so.1 => /lib64/libnvidia-ml.so.1 (0x00007f0094500000)
> > > > libz.so.1 => /lib64/libz.so.1 (0x00007f00942ea000)
> > > > libdl.so.2 => /lib64/libdl.so.2 (0x00007f00940e5000)
> > > > librt.so.1 => /lib64/librt.so.1 (0x00007f0093edd000)
> > > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0093cc1000)
> > > > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f00939b7000)
> > > > libm.so.6 => /lib64/libm.so.6 (0x00007f00936b5000)
> > > > libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f009348f000)
> > > > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0093278000)
> > > > libc.so.6 => /lib64/libc.so.6 (0x00007f0092eb7000)
> > > > libcudart.so.8.0 =>
> > > /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcudart.so.8.0
> > > > (0x00007f0092c50000)
> > > > /lib64/ld-linux-x86-64.so.2 (0x00007f0097ad2000)
> > > >
> > > > ldd /nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0/bin/gmx
> > > > linux-vdso.so.1 =>  (0x00007fff27b8d000)
> > > > libgromacs.so.3 =>
> > > >
> > >
> /nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0/bin/../lib64/libgromacs.so.3
> > > > (0x00007fcb4aa3e000)
> > > > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fcb4a71f000)
> > > > libm.so.6 => /lib64/libm.so.6 (0x00007fcb4a41d000)
> > > > libgomp.so.1 => /lib64/libgomp.so.1 (0x00007fcb4a1f7000)
> > > > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fcb49fe0000)
> > > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fcb49dc4000)
> > > > libc.so.6 => /lib64/libc.so.6 (0x00007fcb49a03000)
> > > > libcudart.so.8.0 =>
> > > /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcudart.so.8.0
> > > > (0x00007fcb4979c000)
> > > > libcufft.so.8.0 =>
> /nfs2/LIBS/x86_64/LIBS/CUDA/8.0/lib64/libcufft.so.8.0
> > > > (0x00007fcb4094e000)
> > > > libdl.so.2 => /lib64/libdl.so.2 (0x00007fcb40749000)
> > > > librt.so.1 => /lib64/librt.so.1 (0x00007fcb40541000)
> > > > libfftw3f.so.3 =>
> > > > /nfs2/LIBS/x86_64/LIBS/FFTW/3.3.3/SINGLE/lib/libfftw3f.so.3
> > > > (0x00007fcb401c8000)
> > > > libmkl_intel_lp64.so =>
> > > >
> > >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_intel_lp64.so
> > > > (0x00007fcb3faa4000)
> > > > libmkl_intel_thread.so =>
> > > >
> > >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_intel_thread.so
> > > > (0x00007fcb3ea0a000)
> > > > libmkl_core.so =>
> > > >
> > >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_core.so
> > > > (0x00007fcb3d4dc000)
> > > > libiomp5.so =>
> > > > /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/lib/intel64/libiomp5.so
> > > > (0x00007fcb3d1c2000)
> > > > libmkl_gf_lp64.so =>
> > > >
> > >
> /nfs2/LIBS/x86_64/LIBS/mkl/l_mkl_11.1.0.080/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_gf_lp64.so
> > > > (0x00007fcb3caa0000)
> > > > /lib64/ld-linux-x86-64.so.2 (0x00007fcb4d785000)
> > > >
> > > > See the differences between the 2016 & 2018 version.
> > > >
> > > > I'm using Cmake 3.13.1.
> > > >
> > > > ~/cmake-3.13.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
> > > > -DCUDA_TOOLKIT_ROOT_DIR=/nfs2/LIBS/x86_64/LIBS/CUDA/8.0
> > > >
> -DCMAKE_INSTALL_PREFIX=/nfs2/opt/APPS/x86_64/APPS/GROMACS/2018/CUDA/8.0
> > > > -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DBUILD_SHARED_LIBS=ON
> > > > -DCUDA_NVCC_FLAGS=--cudart=shared -DGMX_PREFER_STATIC_LIBS=OFF
> > > > -DEXTRA_NVCCFLAGS=--cudart=shared
> > > >
> > > > I think I've tried almost everything.
> > > >
> > > > Regards.
> > > >
> > > > El lun., 10 dic. 2018 a las 16:09, Szilárd Páll (<
> pall.szilard at gmail.com
> > > >)
> > > > escribió:
> > > >
> > > > > 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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