#31, party ported opencl setup: several changes

compiles but errors are detected in swemu

#31, party ported opencl setup: several changes
compiles but errors are detected in swemu
c15a9736 · Leonardo Solis · 12af7ce0 · c15a9736 · c15a9736 · c15a9736
Commit c15a9736 authored Nov 10, 2018 by Leonardo Solis
--- a/ofdock_taskpar_xl/Makefile
+++ b/ofdock_taskpar_xl/Makefile
@@ -113,7 +113,7 @@ CXXFLAGS:=-Wall -O0 -g -std=c++14 $(OTHER_FLAGS)

 # Host Application

-hostbin_SRCS=$(wildcard ../common/src/AOCLUtils/*.cpp wrapcl/src/*.cpp host/src/*.cpp) \
+hostbin_SRCS=$(wildcard ./host/src/*.cpp) \
 		$(oclHelper_SRCS) \
 		$(xcl2_SRCS)

@@ -391,8 +391,8 @@ kerrpt-sw:
 # Compile for sw and hw emulation
 kerswemu:
 	make all TARGETS=sw_emu DEVICES=$(BOARD)
-	cp ./xclbin/$(XCLBINS).sw_emu.*.xclbin .
-	mv ./$(XCLBINS).sw_emu.*.xclbin ./$(XCLBINS).xclbin
+	#cp ./xclbin/$(XCLBINS).sw_emu.*.xclbin .
+	#mv ./$(XCLBINS).sw_emu.*.xclbin ./$(XCLBINS).xclbin
 	@echo $(newline)
 	@echo "==============================================================================="
 	@echo "INFO: sw emulation file created under: \"./xclbin/$(XCLBINS).sw_emu.*.xclbin\" "

--- a/ofdock_taskpar_xl/host/inc/performdocking.h
+++ b/ofdock_taskpar_xl/host/inc/performdocking.h
@@ -24,7 +24,11 @@
 #include "Kernels.h"
 //#include "ImportBinary.h"
 //#include "ImportSource.h"
-#include "BufferObjects.h"
+#include "BufferObjects.h"
+
+#include "xcl2.hpp"
+#include <vector>
+using std::vector;

 #define ELAPSEDSECS(stop,start) ((float) stop-start)/((float) CLOCKS_PER_SEC)


--- a/ofdock_taskpar_xl/host/inc/processgrid.h
+++ b/ofdock_taskpar_xl/host/inc/processgrid.h
@@ -16,6 +16,10 @@

 #include "miscellaneous.h"

+// Added for allocating fgrids
+#include <vector>
+using std::vector;
+
 #define getvalue_4Darr(mempoi, grinf, t, z, y, x)                  *(mempoi + (grinf).size_xyz[0] * (y + (grinf).size_xyz[1] * (z + (grinf).size_xyz[2]*t)) + x)
 #define getvalue_4Darr_withsize(mempoi, gridsize_xyz, t, z, y, x)  *(mempoi + gridsize_xyz[0]*(y + gridsize_xyz[1] * (z + gridsize_xyz[2]*t)) + x)
 //The macro helps to access the grid point values
@@ -41,6 +45,6 @@ typedef struct
 int get_gridinfo(const char*, Gridinfo*);

 int get_gridvalues_f(const Gridinfo* mygrid,
-		     float** fgrids);
+		     float* fgrids);

 #endif /* PROCESSGRID_H_ */
--- a/ofdock_taskpar_xl/host/src/main.cpp
+++ b/ofdock_taskpar_xl/host/src/main.cpp
@@ -26,8 +26,6 @@ int main(int argc, char* argv[])
 	Liganddata myligand_init;
 	Dockpars mypars;

-	float* floatgrids;
-
 	clock_t clock_start_program, clock_stop_program;


@@ -57,6 +55,11 @@ int main(int argc, char* argv[])
 	if (get_gridinfo(mypars.fldfile, &mygrid) != 0)
 		return 1;

+	//allocating CPU memory for floatgrids
+	size_t size_fgrid_nelems = (mygrid.num_of_atypes+2) * mygrid.size_xyz[0] * mygrid.size_xyz[1] * mygrid.size_xyz[2];
+	vector<float,aligned_allocator<float>> floatgrids(size_fgrid_nelems);
+
+
 	// Filling the atom types filed of myligand according to the grid types
 	if (init_liganddata(mypars.ligandfile, &myligand_init, &mygrid) != 0)
 		return 1;
@@ -66,7 +69,7 @@ int main(int argc, char* argv[])
 		return 1;

 	//Reading the grid files and storing values in the memory region pointed by floatgrids
-	if (get_gridvalues_f(&mygrid, &floatgrids) != 0)
+	if (get_gridvalues_f(&mygrid, floatgrids.data()) != 0)
 		return 1;

 	//------------------------------------------------------------
@@ -85,7 +88,7 @@ int main(int argc, char* argv[])
 		print_ref_lig_energies_f(myligand_init,
 					 mypars.smooth,
 					 mygrid,
-					 floatgrids,
+					 floatgrids.data(),
 					 mypars.coeffs.scaled_AD4_coeff_elec,
 					 mypars.coeffs.AD4_coeff_desolv,
 					 mypars.qasp);
@@ -94,11 +97,9 @@ int main(int argc, char* argv[])
 	//------------------------------------------------------------
 	// Starting Docking
 	//------------------------------------------------------------
-	if (docking_with_gpu(&mygrid, floatgrids, &mypars, &myligand_init, &argc, argv, clock_start_program) != 0)
+	if (docking_with_gpu(&mygrid, floatgrids.data(), &mypars, &myligand_init, &argc, argv, clock_start_program) != 0)
 		return 1;

-	if(floatgrids) {free(floatgrids);}
-
 /*
 	clock_stop_program = clock();
 	printf("Program run time: %.3f sec\n", ELAPSEDSECS(clock_stop_program, clock_start_program));

--- a/ofdock_taskpar_xl/host/src/performdocking.cpp
+++ b/ofdock_taskpar_xl/host/src/performdocking.cpp
--- a/ofdock_taskpar_xl/host/src/processgrid.cpp
+++ b/ofdock_taskpar_xl/host/src/processgrid.cpp
 #include "processgrid.h"
-#include "AOCLUtils/aocl_utils.h"
-
-using namespace aocl_utils;

 int get_gridinfo(const char* fldfilename, Gridinfo* mygrid)
 {
@@ -99,7 +96,7 @@ int get_gridinfo(const char* fldfilename, Gridinfo* mygrid)
 	return 0;
 }

-int get_gridvalues_f(const Gridinfo* mygrid, float** fgrids)
+int get_gridvalues_f(const Gridinfo* mygrid, float* fgrids)
 //The function reads the grid point values from the .map files
 //that correspond to the receptor given by the first parameter.
 //It allocates the proper amount of memory and stores the data there,
@@ -112,23 +109,13 @@ int get_gridvalues_f(const Gridinfo* mygrid, float** fgrids)
 	char tempstr [128];
 	float* mypoi;

-/*
-	*fgrids = (float*) malloc((sizeof(float))*(mygrid->num_of_atypes+2)*
-						  (mygrid->size_xyz[0])*
-					          (mygrid->size_xyz[1])*
-						  (mygrid->size_xyz[2]));
-*/
-	*fgrids = (float*) alignedMalloc((sizeof(float))*(mygrid->num_of_atypes+2)*
-						  (mygrid->size_xyz[0])*
-					          (mygrid->size_xyz[1])*
-						  (mygrid->size_xyz[2]));
-	if (*fgrids == NULL)
+	if (fgrids == NULL)
 	{
 		printf("Error: not enough memory!\n");
 		return 1;
 	}

-	mypoi = *fgrids;
+	mypoi = fgrids;

 	for (t=0; t < mygrid->num_of_atypes+2; t++)
 	{