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

[Szilárd Páll]

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Those binaries are extremely outdated.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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