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. -- 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