Hello everyone, may I know if there is any expert here who can guide me on enabling the GPU in running GROMACS?
Basically, I am a beginner in running molecular dynamic simulations using GROMACS. I have past experience running MD for a protein-ligand complex, to check if the interactions are stable after the docking. I have been relying on CPU for MD, and therefore to run just a 30 ns simulation, it took about 5 days on my laptop. I have been searching for a solution to enable GPU in GROMACS and all i found is using CUDA. However, CUDA only worked on NVIDIA and my laptop is running Intel iRISXe. Therefore, I wonder if there is any expert here who can guide me the way to enable the GPU. I used Ubuntu to key in all the command lines.
Any video guide or link to a Web page guide? Thank you in advance!
To enable GPU acceleration for running GROMACS, you will need to ensure you have compatible hardware and software. Since GROMACS primarily supports CUDA for NVIDIA GPUs, running it on an Intel iGPU (like Intel Iris Xe) is not feasible as GROMACS does not support OpenCL on Intel GPUs for its GPU-accelerated simulations. However, you can still optimize your performance on your existing setup. Consider compiling GROMACS with the latest version, as newer versions may offer better CPU optimizations. You can install GROMACS using the following steps: first, ensure you have the required dependencies (`cmake`, `gcc`, `g++`, and `git`). Then, download the GROMACS source code from the official GROMACS website. Create a build directory, navigate to it, and run `cmake .. -DGMX_BUILD_OWN_FFTW=ON` to optimize FFT calculations for CPU. After that, compile GROMACS using `make` and install it. While you won’t benefit from GPU acceleration, you can optimize the performance by using parallel processing with MPI (Message Passing Interface) if you have access to a multi-core CPU or a cluster. Look into tutorials like those on the GROMACS website or YouTube channels focusing on molecular dynamics for detailed instructions and video guides. If upgrading your hardware is an option, consider investing in an NVIDIA GPU for significantly faster simulations with GROMACS in the future.
Thank you so much for your reply. I will do the necessary and get back to you if there is any issue. Really appreciate it!
To enable GPU acceleration in GROMACS with Intel iRISXe (which does not support CUDA for GPU acceleration), you're currently limited since GROMACS primarily supports CUDA (NVIDIA GPUs) for GPU acceleration.
However, you can still use CPU-based optimizations such as multi-core parallelism to speed up your simulations. For Intel GPUs, you would need to look into alternative MD software supporting Intel's hardware.
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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