OCLADock - OpenCL Accelerated Molecular Docking

An OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm.

ocladock-logo

Features

OpenCL-accelerated version of AutoDock 4.2 running a Lamarckian Genetic Algorithm (LGA)
It leverages the LGA paralelism, as entities of multiple docking runs are computed simultaneously
It targets platforms based on multi-core CPU and GPU accelerators
Observed speedups of up to 4x (quad-core CPU) and 56x (GPU) over the original serial AutoDock 4.2 on CPU

Easy Download

The easiest way to download all of OCLADock (source code, prebuilt-binaries for Linux and Windows, sample input data) is to go to our GitLab Repository, and use the Download icon (close to the top right of this webpage, just above the list of files) and use a familiar archive format (e.g., .zip) to fetch everything at once.

download-ocladock-notes

Setup

Requirements

Architecture	Operating system
Intel x86_64	CentOS 6.7 & 6.8
	Ubuntu 16.04
	Windows 7

Prerequisites

Operating system	CPU	GPU
Linux	Intel SDK for OpenCL v1.2	AMD APP SDK v3.0
Windows	Intel SDK for OpenCL 2016 R3	AMD APP SDK v3.0

Other environments/configurations likely work as well, but are untested.

Ready-to-run Executables

We provide ready-to-run executables for Linux and Windows. These executables have been compiled with a fixed number of work-items (wi, basically the degree of parallel processing done). If you are not sure, you should start with the versions using 16 work-items on a quad-core CPU and 64 work-items for a GPU. These values gave the best performance on our target platforms. The best values for your CPU or GPU might be different.

Compilation

You only need to do this if you want to target our sources to a different system or modify the code. This can be configured in the Makefile.

Compilation on Linux

make DEVICE=<TYPE> NUMWI=<NWI>

Parameters	Description	Values
<TYPE>	Accelerator chosen	CPU, GPU
<NWI>	OpenCL work-group size	16, 32, 64

After successful compilation, the host binary ocladock_<type>_<N>wi is placed under bin.

Binary-name portion	Description	Values
*<type>*	Accelerator chosen	cpu, gpu
*<N>*	OpenCL work-group size	16, 32, 64

Compilation on Windows

A Microsoft Visual Studio 2013 solution for two configurations ocladock-cpu-deb and ocladock-gpu-deb can be found in the win folder.

Usage

Basic command

./bin/ocladock_<type>_<N>wi -ffile <protein>.maps.fld -lfile <ligand>.pdbqt -nrun <nruns>

Mandatory options	Description	Value
-ffile	Protein file	<protein>.maps.fld
-lfile	Ligand file	<ligand>.pdbqt

Example

./bin/ocladock_gpu_64wi -ffile ./input/1stp/derived/1stp_protein.maps.fld -lfile ./input/1stp/derived/1stp_ligand.pdbqt -nrun 10

By default the output log file is written in the current working folder. Examples of output logs can be found under examples/output.

Supported arguments

Argument	Description	Default value
-nrun	# Docking runs	1
-nev	# Energy evaluations	2500000
-ngen	# Generations	27000
-lsit	# Local-search iterations (max.)	300
-psize	Population size	150
-mrat	Mutation rate	2 (%)
-crat	Crossover rate	80 (%)
-lsrat	Local-search rate	6 (%)
-trat	Tournament rate	60 (%)
-resnam	Name for docking output log	"docking"

For a complete list of available arguments and their default values, check: getparameters.cpp.

Images

Prebuilt images are provided for Linux and Windows.

Documentation

For more details, go to the Documentation.

Bibliographic information for citing OCLADock

Leonardo Solis-Vasquez and Andreas Koch. 2017. A Performance and Energy Evaluation of OpenCL-accelerated Molecular Docking. In Proceedings of the 5th International Workshop on OpenCL (IWOCL 2017). ACM, New York, NY, USA, Article 3, 11 pages. DOI: https://doi.org/10.1145/3078155.3078167

License

This project is licensed under the MIT License - see the LICENSE file for details.

-- Main.lvs - 26 Jul 2017