Guideline for developers

Repository description

% tree  -L 1
.
├── bin
├── common
├── device
├── examples
├── host
├── input
├── wrapcl
├── Makefile
├── ...

bin/: Linux binary files are placed here once compiled.

File	Description
`autodock_<type>_<N>wi`	Binary file for `<type>` (cpu, gpu) device with `<N>` (16, 32, 64, 128, 256) work items

common/: common header files for host and device.

File	Description
calcenergy_basic.h	Basic defines and macros for energy calculation
defines.h	Basic defines for energy calculation and kernels optimization

device/: source files containing kernels.

File	Description
auxiliary_genetic.cl	Auxiliary functions for energy calculation
calcenergy.cl	Main function for score (binding energy) calculation
calcgradient.cl	Main function for gradient calculation
calcMergedEneGrad.cl	Score and gradient merged calculation
kernel1.cl	`gpu_calc_initpop`: calculates the scores of initial population
kernel2.cl	`gpu_sum_evals`: sums the evaluation counter states
kernel3.cl	`perform_LS`: performs the Solis-Wets local search
kernel4.cl	`gpu_gen_and_eval_newpops`: performs the genetic generation or global search
kernel_sd.cl	`gradient_minSD`: performs the Steepest-Descent local search
kernel_fire.cl	`gradient_minFire`: performs the Steepest-Descent local search
kernel_ad.cl	`gradient_minAD`: performs the ADADELTA local search

examples/output/: examples of docking log files.

host/: host source files.

File	Description
calcenergy[.h][.cpp]	Auxiliary functions for parallel energy-calculation
getparameters[.h][.cpp]	Functions for processing program input arguments
miscellaneous[.h][.cpp]	General-purpose functions
main.cpp	Main source file
performdocking[.h][.cpp]	Entry point for OpenCL-platform setup and kernels execution
processgrid[.h][.cpp]	Functions for processing and converting the energy grids
processligand[.h][.cpp]	Functions for performing operations in the ligand
processresult[.h][.cpp]	Functions for processing docking results

input/: chemical compounds taken from PDB.

Ligan-receptor complex	Description
1stp	Structural origins of high-affinity biotin binding to streptavidin
3ce3	Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-MET in complex with a Pyrrolopyridinepyridone based inhibitor

For both complexes, the containing folder has a similar structure.

wrapcl/: custom wrapper functions for OpenCL API calls (compliant to OpenCL 1.2).

File	Description
BufferObjects[.h][.cpp]	Functions for allocating, mapping, copying, and querying info of buffers
CommandQueues[.h][.cpp]	Functions for creating and querying info of command queues
commonMacros.h	Header with defines to enable features and display of info of OpenCL elements (platform, devices, etc)
Contexts[.h][.cpp]	Functions for creating and querying info of contexts
Devices[.h][.cpp]	Functions for detecting available devices and querying their attributes
ImportBinary[.h][.cpp]	Functions for loading kernel code and transforming (offline) it into device programs
ImportSource[.h][.cpp]	Functions for loading kernel code and transforming (online) it into device programs
Kernels[.h][.cpp]	Functions for setting kernel arguments, dispatching kernels, and querying kernel attributes
listAttributes[.h][.cpp]	Definitions of OpenCL attributes
Platforms[.h][.cpp]	Functions for detecting installed platforms and querying their attributes
Programs[.h][.cpp]	Functions for querying program's info

make DEVICE=<TYPE>

Parameters	Description	Values
`<TYPE>`	Accelerator chosen	`CPU`, `GPU`

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

Binary-name portion	Description	Values
<type>	Accelerator chosen	`cpu`, `gpu`

make DEVICE=<TYPE> NUMWI=<NWI> CONFIG=<CFG> REPRO=<Y/N>

Argument	Description	Possible values
DEVICE	OpenCL device type	`<TYPE>`: CPU, GPU
NUMWI	Number of work items per work group	`<NWI>` : 16, 32, 64, 128, 256
CONFIG	Host configuration	`<CFG>` : RELEASE, LDEBUG (light), FDEBUG (full)

Check the configurations in the project's Makefile.