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

[jesmin jahan]

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:
"
* 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.