A heterogeneous OpenCL implementation of AutoDock Vina

[NEWS]: We have released Vina-GPU 2.1, which provides more speed targeting on virtual screening!

[NEWS]: Vina-GPU+: a virtual-screening-accelerated version of Vina-GPU is released together with our Vina-GPU 2.0 toolkit

[NEWS]: A CUDA version of Vina-GPU is avaliable at here

Note: at least one GPU card is required and make sure the version of GPU driver is up to date

1. For the first time to use Vina-GPU, please run Vina-GPU-K.exe with command ./Vina-GPU-K.exe --config=./input_file_example/2bm2_config.txt You are supposed to have the docking results 2bm2_out.pdbqt of our example complex and a Kernel2_Opt.bin file
2. Once you have the Kernel2_Opt.bin file, you can run Vina-GPU.exe without compiling the kernel files (thus to save more runtime)

When you run Vina-GPU.exe, please make sure Kernel2_Opt.bin file are in the same directory

For the usage and limitaiton of Vina-GPU, please check Usage and Limitation. A graphic user interface (GUI) is also provided for Windows users, please check GUI

Visual Studio 2019 is recommended for build Vina-GPU from source

1. install boost library (current version is 1.77.0)

2. install CUDA Toolkit (current version is v11.5) if you are using NVIDIA GPU cards

   Note: the OpenCL library can be found in CUDA installation path for NVIDIA or in the driver installation path for AMD

3. add ./lib ./OpenCL/inc $(YOUR_BOOST_LIBRARY_PATH)/boost $(YOUR_CUDA_TOOLKIT_LIBRARY_PATH)/CUDA/v11.5/include in the include directories

4. add $(YOUR_BOOST_LIBRARY_PATH)/stage/lib $(YOUR_CUDA_TOOLKIT_PATH)/CUDA/lib/Win32in the addtional library

5. add OpenCL.lib in the additional dependencies

6. add --config=./input_file_example/2bm2_config.txt in the command arguments

7. add WIN32 in the preprocessor definitions if necessary

8. if you want to compile the binary kernel file on the fly, add BUILD_KERNEL_FROM_SOURCE in the preprocessor definitions

9. build & run

Note: ensure the line ending are CLRF

Note: At least 8M stack size is needed. To change the stack size, use ulimit -s 8192.

1. install boost library (current version is 1.77.0)

2. install CUDA Toolkit (current version is 11.5) if you are using NVIDIA GPU cards

   note: OpenCL library can be usually in /usr/local/cuda (for NVIDIA GPU cards)

3. change the BOOST_LIB_PATH and OPENCL_LIB_PATH accordingly in Makefile

4. set GPU platform GPU_PLATFORM and OpenCL version OPENCL_VERSIONin Makefile. some options are given below:

   Note: -DOPENCL_3_0 is highly recommended in Linux. To check the OpenCL version on a given platform, use clinfo.

6. type make clean and make source to build Vina-GPU that compile the kernel files on the fly (this would take some time at the first use)

7. after a successful compiling, Vina-GPU can be seen in the directory

8. type ./Vina-GPU --config ./input_file_example/2bm2_config.txt to run Vina-GPU

9. once you successfully run Vina-GPU, its runtime can be further reduced by typing make clean and make to build it without compiling kernel files (but make sure the Kernel2_Opt.bin file is unchanged)

10. other compile options:

Note: The running Vina-GPU on macOS is not recommended and has not fully tested yet

1. install boost library (current version is 1.77.0)

modify Makefile as follows:

2. annotate OPENCL_LIB_PATH, OPENCL_INC_PATH and -L$(OPENCL_LIB_PATH)/lib64
3. add -framework OpenCL in LIB3
4. type make and run

A graphic user interface (GUI) is provided for users on Windows OS

1. first make sure that Vina-GPU.exe can run on a terminal
2. put the Vina-GPU.exe and Kernel2_Opt.bin files in ./Vina-GPU/GUI/exec and overwrite the original files
3. run the Vina-GPU-GUI.exefile within ./Vina-GPU/GUI to start up the Vina-GPU GUI
4. select the input and out output files
5. set the box center, the box size, thread and search_depth
6. click the start button to run Vina-GPU

• Tang, S.; Chen, R.; Lin, M.; Lin, Q.; Zhu, Y.; Ding, J.; Hu, H.; Ling, M.; Wu, J. Accelerating AutoDock Vina with GPUs. Molecules 2022, 27, 3041. https://doi.org/10.3390/molecules27093041

• O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461.