jesmin jahan
2012-08-21 16:21:42 UTC
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
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.
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.