[gmx-users] Problem with Gromacs installation with GPU.

[jesmin jahan]

Dear  Szilárd

I have downloaded Gromacs 4.6 from git. But I saw that implicit
solvent feature is still not supported.


Features currently not supported by the new GPU and SSE kernels:
Implicit solvent (but this will still be supported on the GPU through OpenMM)

But I need the implicit solvent feature for my experiments. I went to
https://simtk.org/project/ where I found GromacsOpenmm2.0. But that
one is also deprecated!
So, its not clear to me what does it meant by "but this will still be
supported on the GPU through OpenMM"
How to add this feature with Gromacs4.6?

Or is there any version of Gromacs which supports implicit solvent
simulation on GPU? Please let me know.

Thanks,
Jesmin





On Tue, Aug 21, 2012 at 4:24 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
>
> Dear Jesmin,
>
> On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan <shraban03 at gmail.com> wrote:
> > Dear All,
> >
> > I have installed gromacs 4.5.3  on a cluster. I downloaded the
> > gromacs-4.5-GPU-beta2-X86_64 binaries and followed the following
> > instructions:
>
> Those binaries are extremely outdated. Please compile Gromacs form the
> last source release or the latest git version from
> release-4-5-patches.
>
> Cheers,
> --
> Szilárd
>
>
> > "
> > * INSTALLING FROM BINARY DISTRIBUTION:
> >
> > 0. Prerequisites:
> >     - OpenMM (included in the binary release)
> >     - NVIDIA CUDA libraries (version >=3.0);
> >     - NVIDIA driver (for details on compatiblity consult
> >           http://www.nvidia.com/Download/index5.aspx);
> >     - NVIDIA CUDA-enabled GPU (for compatiblity list see
> >           http://www.gromacs.org/gpu).
> >
> >
> > 1. Download and unpack the binary package for the respective
> > OS and architecture. Copy the content of the package to your
> > normal GROMACS installation directory (or to a custom location).
> > Note that as the distributed Gromacs-GPU packages do not contain
> > the entire set of tools and utilities included in a full GROAMCS
> > installation. Therefore, it is recommended to have a ≥v4.5
> > standard Gromacs installation along the GPU accelerated one.
> > e.g. on unix:
> >
> > tar -xvf gromacs-4.5-GPU.tar.gz
> > cp -R gromacs-4.5-GPU/* PATH_TO_GROMACS_INSTALLATION
> >
> >
> > 2. Add the openmm/lib directory to your library path, e.g. in bash:
> >
> > export LD_LIBRARY_PATH=PATH_TO_GROMACS/openmm/lib:$LD_LIBRARY_PATH
> >
> > If there are other OpenMM versions installed, make sure that the
> > supplied libraries have preference when running mdrun-gpu.
> > Also, make sure that the CUDA libraries installed match the version
> > of CUDA with which GROMACS-GPU is compiled.
> >
> >
> > 3. Set the OPENMM_PLUGIN_DIR environment variable to contain the path
> > to the openmm/lib/plugins directory, e.g. in bash:
> >
> > export OPENMM_PLUGIN_DIR=PATH_TO_GROMACS/openmm/lib/plugins
> >
> >
> > 4. At this point, running the command:
> >
> > PATH_TO_GROMACS/bin/mdrun-gpu -h
> >
> > should display the standard mdrun help which means that all the
> > necessary libraries are accessible.
> >
> >
> > "
> >
> > But running the PATH_TO_GROMACS/bin/mdrun-gpu -h command gives me
> >
> > /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-gpu: error while loading
> > shared libraries: libcudart.so.3: cannot open shared object file: No
> > such file or directory
> >
> > So, if I actually look into the cuda library directory I found the
> > following files:
> >
> > libcublas.so        libcudart.so        libcufft.so        libcuinj.so
> >        libcurand.so        libcusparse.so        libnpp.so
> > libcublas.so.4      libcudart.so.4      libcufft.so.4
> > libcuinj.so.4      libcurand.so.4      libcusparse.so.4
> > libnpp.so.4
> > libcublas.so.4.2.9  libcudart.so.4.2.9  libcufft.so.4.2.9
> > libcuinj.so.4.2.9  libcurand.so.4.2.9  libcusparse.so.4.2.9
> > libnpp.so.4.2.9
> >
> > Is there anyone who knows about how to fix this problem?
> >
> > Please let me know.
> >
> >
> > Then, I installed the Gromacs-openmm precompiled version which used
> > cuda 4.1  following the instructions
> > "
> >
> > To install Gromacs-OpenMM, follow these steps.
> >
> > 1. Install Gromacs 4.
> >
> > 2. Install OpenMM.
> >
> > 3. Copy mdrun-openmm to gromacs/bin, where "gromacs" is the root
> > directory of your Gromacs installation (e.g. /usr/local/gromacs).
> >
> > 4. Copy params.agb to gromacs/share/gromacs/top.
> >
> > 5. Add the OpenMM lib directory to your library path (PATH on Windows,
> > DYLD_LIBRARY_PATH on Mac OS X, LD_LIBRARY_PATH on Linux).
> >
> > 6. If you have an Nvidia GPU, install CUDA
> > (http://www.nvidia.com/object/cuda_get.html).  Make sure the CUDA lib
> > directory is in your library path.
> >
> > 7. If you installed OpenMM in the default location (/usr/local/openmm
> > on Mac OS X or Linux, Program Files\OpenMM on Windows), no further
> > steps are required.  If you installed it in a different location, set
> > the environment variable OPENMM_PLUGIN_DIR to point to the OpenMM
> > plugin directory (e.g. /usr/local/openmm/lib/plugins).
> >
> > "
> > Note that I do not have any /usr/local directory. my home is
> > /home1/01945/jesmin.
> >
> > Now if I type
> >
> > mdrun-openmm -h, I get the following error:
> >
> >
> > /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-openmm:
> > /home1/01945/jesmin/cilk/lib64/libstdc++.so.6: version
> > `GLIBCXX_3.4.11' not found (required by
> > /home1/01945/jesmin/Gromacs/4.5.3/openmm/lib/libOpenMM.so)
> >
> > Can anyone help me to about how to solve this problem?
> >
> > Thanks,
> > Jesmin
> > --
> > Jesmin Jahan Tithi
> > PhD Student, CS
> > Stony Brook University, NY-11790.
> > --
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--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.