Dear Jesmin, On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan <shraba...@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Those binaries are extremely outdated.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. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists