QVina-W-GPU is proposed to parallelize the efficient QVina-W docking software, which can exploit the highly-parallel hardware architecture to speed up the process of molecule docking.
Note: at least one GPU card is required and make sure the version of GPU driver is up to date
Run on the executable file
-
For the first time to use QVina-GPU, please run
QVina-W-GPU-K.exe
with command./Qvina-W-GPU-K.exe --config ./input_file_example/2bm2_config.txt
You are supposed to have the docking results2bm2_out.pdbqt
of our example complex and aKernel2_Opt.bin
file -
Once you have the
Kernel2_Opt.bin
file, you can runQvina-W-GPU.exe
without compiling the kernel files (thus to save more runtime)When you run
Qvina-W-GPU.exe
, please make sureKernel2_Opt.bin
file are in the same directory
Visual Studio 2019 is recommended for build Vina-GPU from source
-
install boost library (current version is 1.77.0)
-
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
-
add
./lib
./OpenCL/inc
$(YOUR_BOOST_LIBRARY_PATH)/boost
$(YOUR_CUDA_TOOLKIT_LIBRARY_PATH)/CUDA/v11.5/include
in the include directories -
add
$(YOUR_BOOST_LIBRARY_PATH)/stage/lib
$(YOUR_CUDA_TOOLKIT_PATH)/CUDA/lib/Win32
in the addtional library -
add
OpenCL.lib
in the additional dependencies -
add
--config ./input_file_example/2bm2_config.txt
in the command arguments -
add
WIN32
in the preprocessor definitions if necessary -
if you want to compile the binary kernel file on the fly, add
BUILD_KERNEL_FROM_SOURCE
in the preprocessor definitions -
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
.
-
install boost library (current version is 1.77.0)
-
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) -
change the
BOOST_LIB_PATH
andOPENCL_LIB_PATH
accordingly inMakefile
-
set GPU platform
GPU_PLATFORM
and OpenCL versionOPENCL_VERSION
inMakefile
. 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
.
Macros | Options | Descriptions |
---|---|---|
GPU_PLATFORM | -DNVIDIA_PLATFORM / -DAMD_PLATFORM | NVIDIA / AMD GPU platform |
OPENCL_VERSION | -DOPENCL_3_0 / -DOPENCL_1_2 | OpenCL version 3.0 / 1.2 |
-
type
make clean
andmake source
to build Vina-GPU that compile the kernel files on the fly (this would take some time at the first use) -
after a successful compiling,
Vina-GPU
can be seen in the directory -
type
./QVina-W-GPU --config ./input_file_example/2bm2_config.txt
to run QVina-W-GPU -
once you successfully run QVina-W-GPU, its runtime can be further reduced by typing
make clean
andmake
to build it without compiling kernel files (but make sure theKernel2_Opt.bin
file is unchanged) -
other compile options:
Options | Description |
---|---|
-g | debug |
-DDISPLAY_ADDITION_INFO | print addition information |