improved Makefile to separately compile .xo krnl objs

ofdock_taskpar_xl/device/Krnl_Conform.cl

+#include "defines_krnls.h"
+
 // --------------------------------------------------------------------------
 // Conform changes the conformation of the ligand according to 
 // the genotype fed by any producer logic/kernel (IC, GG, LSs).

ofdock_taskpar_xl/device/Krnl_GA.cl

-//IC:  initial calculation of energy of populations
-//GG:  genetic generation 
-//LS:  local search
-//OFF: turn off 
-
-#include "../defines.h"
-
-#define PIPE_DEPTH_16  16
-#define PIPE_DEPTH_64  64
-
-// Status of pipe operation
-// Success: 0
-// Failure: negative value, e.g.: -1, -2, etc
-
-// Important: the evaluation of failure of "pipe-expr" 
-// must be done: (pipe-expr != PIPE_STATUS_SUCCESS),
-// as a failure is characterize by any negative integer number.
-typedef int nb_pipe_status;
-#define PIPE_STATUS_SUCCESS      0
-#define PIPE_STATUS_FAILURE	-1
-
-// Send active signal to IGL_Arbiter
-// Resized to valid SDAccel depths: 16, 32, ...
-pipe char    pipe_ga2igl_ic_active			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
-
-// Send genotypes from producer (IC) to Conform
-pipe float  pipe_ic2conf_genotype   			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
-
-// Send ligand-atom positions from Conform to InterE & IntraE
-// Resized to valid SDAccel depths: 16, 32, ...
-pipe float8 pipe_conf2intere_xyz    			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
-pipe char   pipe_conf2intere_actmode			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
-
-pipe float8 pipe_conf2intrae_xyz        		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
-pipe char   pipe_conf2intrae_actmode    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
-
-// Send energy values from InterE & IntraE to genotype-senders (IC, GG, LSs)
-// Resized to valid SDAccel depths: 16, 32, ...
-pipe float  pipe_intere2storeic_intere     		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
-pipe float  pipe_intrae2storeic_intrae     		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
-
-// Send genotype-producer-pipe selector and genotype 
-// from IGL_Arbiter to Conform
-// Resized to valid SDAccel depths: 16, 32, ...
-pipe char   pipe_igl2conform_actmode	    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16))); // active, mode
-
-// Turn-off signal to IGL_Arbiter, Conform, InterE, IntraE
-// Resized to valid SDAccel depths: 16, 32, ...
-pipe int    pipe_iglarbiter_off		    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+#include "defines_krnls.h"
 
 // --------------------------------------------------------------------------
 // Lamarckian Genetic-Algorithm (GA): GA + LS (Local Search) 
@@ -200,7 +152,7 @@ void Krnl_GA(
 // --------------------------------------------------------------------------
 // --------------------------------------------------------------------------
 
-#include "Krnl_Conform.cl"
-#include "Krnl_InterE.cl"
-#include "Krnl_IntraE.cl"
+//#include "Krnl_Conform.cl"
+//#include "Krnl_InterE.cl"
+//#include "Krnl_IntraE.cl"
 

ofdock_taskpar_xl/device/Krnl_InterE.cl

+#include "defines_krnls.h"
+
 // --------------------------------------------------------------------------
 // InterE calculates the intermolecular energy of a ligand given by 
 // ligand xyz-positions, and a receptor represented as a grid. 

ofdock_taskpar_xl/device/Krnl_IntraE.cl

+#include "defines_krnls.h"
+
 // sqrt7 ////https://www.codeproject.com/Articles/69941/Best-Square-Root-Method-Algorithm-Function-Precisi
 __attribute__((always_inline))
 float sqrt_custom(const float x) 

ofdock_taskpar_xl/device/defines_krnls.h

+//IC:  initial calculation of energy of populations
+//GG:  genetic generation 
+//LS:  local search
+//OFF: turn off 
+
+#include "../defines.h"
+
+#define PIPE_DEPTH_16  16
+#define PIPE_DEPTH_64  64
+
+// Status of pipe operation
+// Success: 0
+// Failure: negative value, e.g.: -1, -2, etc
+
+// Important: the evaluation of failure of "pipe-expr" 
+// must be done: (pipe-expr != PIPE_STATUS_SUCCESS),
+// as a failure is characterize by any negative integer number.
+typedef int nb_pipe_status;
+#define PIPE_STATUS_SUCCESS      0
+#define PIPE_STATUS_FAILURE	-1
+
+// Send active signal to IGL_Arbiter
+// Resized to valid SDAccel depths: 16, 32, ...
+pipe char    pipe_ga2igl_ic_active			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+
+// Send genotypes from producer (IC) to Conform
+pipe float  pipe_ic2conf_genotype   			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
+
+// Send ligand-atom positions from Conform to InterE & IntraE
+// Resized to valid SDAccel depths: 16, 32, ...
+pipe float8 pipe_conf2intere_xyz    			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
+pipe char   pipe_conf2intere_actmode			__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+
+pipe float8 pipe_conf2intrae_xyz        		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_64)));
+pipe char   pipe_conf2intrae_actmode    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+
+// Send energy values from InterE & IntraE to genotype-senders (IC, GG, LSs)
+// Resized to valid SDAccel depths: 16, 32, ...
+pipe float  pipe_intere2storeic_intere     		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+pipe float  pipe_intrae2storeic_intrae     		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));
+
+// Send genotype-producer-pipe selector and genotype 
+// from IGL_Arbiter to Conform
+// Resized to valid SDAccel depths: 16, 32, ...
+pipe char   pipe_igl2conform_actmode	    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16))); // active, mode
+
+// Turn-off signal to IGL_Arbiter, Conform, InterE, IntraE
+// Resized to valid SDAccel depths: 16, 32, ...
+pipe int    pipe_iglarbiter_off		    		__attribute__((xcl_reqd_pipe_depth(PIPE_DEPTH_16)));

ofdock_taskpar_xl/host/src/performdocking.cpp

@@ -76,7 +76,7 @@ filled with clock() */
     	// xocc compiler load into OpenCL Binary and return as Binaries
     	// OpenCL and it can contain many functions which can be executed on the
    	// device.
-    	std::string binaryFile = xcl::find_binary_file(device_name,"Krnl_GA");
+    	std::string binaryFile = xcl::find_binary_file(device_name,"docking");
     	cl::Program::Binaries bins = xcl::import_binary_file(binaryFile);
     	devices.resize(1);
     	cl::Program program(context, devices, bins);

[Leonardo Solis]

Runtime on AWS after xclbin was already loaded in a previous run (other parameters were not modified):

#runs	Runtime (s)
10	6.285
20	6.755
40	7.975
80	10.568
100	11.999