#32, removed all refs (unnecesary) to gpu

ofdock_taskpar_xl/host/inc/calcenergy.h

@@ -6,9 +6,9 @@
 #include "processligand.h"
 #include "getparameters.h"
 
-// This struct is passed to the GPU global functions (OpenCL kernels) as input.
-// Its members are parameters related to the ligand, the grid
-// and the genetic algorithm, or they are pointers of GPU (ADM FPGA) memory areas
+// Members of this struct are passed to the FPGA OpenCL kernels as inputs.
+// Struct members are parameters related to the ligand, the grid
+// and the genetic algorithm, or they are pointers of FPGA memory areas
 // used for storing different data such as the current
 // and the next population genotypes and energies, the grids,
 // the evaluation counters and the random number generator states.
@@ -70,7 +70,7 @@ typedef struct
 	cl_float4 	ref_orientation_quats_const  [MAX_NUM_OF_RUNS]      			__attribute__ ((aligned (XILINX_MEMALIGN)));
 } kernelconstant_static;
 
-int prepare_conststatic_fields_for_gpu(Liganddata* 	       myligand_reference,
+int prepare_conststatic_fields_for_fpga(Liganddata* 	       myligand_reference,
 				 	Dockpars*   	       mypars,
 				 	float*      	       cpu_ref_ori_angles,
 				 	kernelconstant_static* KerConstStatic);

ofdock_taskpar_xl/host/inc/performdocking.h

@@ -13,13 +13,13 @@ using std::vector;
 
 #define ELAPSEDSECS(stop,start) ((float) stop-start)/((float) CLOCKS_PER_SEC)
 
-int docking_with_gpu(const Gridinfo* 	mygrid,
-         	     /*const*/ float* 	cpu_floatgrids,
-		           Dockpars*	mypars,
-		     const Liganddata* 	myligand_init,
-		     const int* 	argc,
-		     char**		argv,
-		           clock_t 	clock_start_program);
+int docking_with_fpga(const     Gridinfo* 	mygrid,
+         	      /*const*/ float* 	        cpu_floatgrids,
+		                Dockpars*	mypars,
+		      const     Liganddata* 	myligand_init,
+		      const     int* 	        argc,
+		                char**		argv,
+		                clock_t 	clock_start_program);
 
 double check_progress(int* evals_of_runs,
 		      int generation_cnt,

ofdock_taskpar_xl/host/src/calcenergy.cpp

 #include "calcenergy.h"
 
 /*
-int prepare_const_fields_for_gpu(Liganddata*     myligand_reference,
-                                 Dockpars*       mypars,
-                                 float*          cpu_ref_ori_angles,
-                                 kernelconstant* KerConst)
-//The function fills the constant memory field of the GPU (ADM FPGA)
-//defined above (erased from here) and used during GPU docking,
+int prepare_const_fields_for_fpga(Liganddata*     myligand_reference,
+                                  Dockpars*       mypars,
+                                  float*          cpu_ref_ori_angles,
+                                  kernelconstant* KerConst)
+//The function fills the constant memory field of the FPGA and are
 //based on the parameters which describe the ligand,
 //the docking parameters and the reference orientation angles.
 //Short description of the field is as follows:
@@ -232,7 +231,7 @@ int prepare_const_fields_for_gpu(Liganddata*     myligand_reference,
 }
 */
 
-int prepare_conststatic_fields_for_gpu(Liganddata* 	       myligand_reference,
+int prepare_conststatic_fields_for_fpga(Liganddata* 	       myligand_reference,
 				 	Dockpars*   	       mypars,
 				 	float*      	       cpu_ref_ori_angles,
 				 	kernelconstant_static* KerConstStatic)
@@ -493,7 +492,7 @@ void make_reqrot_ordering(char number_of_req_rotations[MAX_NUM_OF_ATOMS],
 
 int gen_rotlist(Liganddata* myligand, int rotlist[MAX_NUM_OF_ROTATIONS])
 //The function generates the rotation list which will be stored in the constant memory field rotlist_const by
-//prepare_const_fields_for_gpu(). The structure of this array is described at that function.
+//prepare_const_fields_for_fpga(). The structure of this array is described at that function.
 {
 	int atom_id, rotb_id, parallel_rot_id, rotlist_id;
 	char number_of_req_rotations[MAX_NUM_OF_ATOMS];

ofdock_taskpar_xl/host/src/main.cpp

@@ -83,7 +83,7 @@ int main(int argc, char* argv[])
 	//------------------------------------------------------------
 	// Starting Docking
 	//------------------------------------------------------------
-	if (docking_with_gpu(&mygrid, floatgrids.data(), &mypars, &myligand_init, &argc, argv, clock_start_program) != 0)
+	if (docking_with_fpga(&mygrid, floatgrids.data(), &mypars, &myligand_init, &argc, argv, clock_start_program) != 0)
 		return 1;
 
 	/*

ofdock_taskpar_xl/host/src/performdocking.cpp

@@ -25,13 +25,13 @@ cl_mem mem_ref_orientation_quats_const;	// float [4*MAX_NUM_OF_RUNS];			// 4*100
 //// --------------------------------
 //// Docking
 //// --------------------------------
-int docking_with_gpu(const Gridinfo*   mygrid,
-	             /*const*/ float*  cpu_floatgrids,
-                           Dockpars*   mypars,
-		     const Liganddata* myligand_init,
-		     const int*        argc,
-		           char**      argv,
-		           clock_t     clock_start_program)
+int docking_with_fpga( const    Gridinfo*   mygrid,
+	              /*const*/ float*      cpu_floatgrids,
+                                Dockpars*   mypars,
+		      const     Liganddata* myligand_init,
+		      const     int*        argc,
+		                char**      argv,
+		                clock_t     clock_start_program)
 /* The function performs the docking algorithm and generates the corresponding result files.
 parameter mygrid:
 		describes the grid
@@ -241,7 +241,7 @@ filled with clock() */
 
 	Liganddata myligand_reference;
 
- 	//allocating GPU memory for floatgrids,
+ 	//allocating FPGA memory for floatgrids,
 	size_t size_floatgrids_nbytes = sizeof(float) * (mygrid->num_of_atypes+2) *
 					(mygrid->size_xyz[0]) * (mygrid->size_xyz[1]) * (mygrid->size_xyz[2]);
 
@@ -293,15 +293,10 @@ filled with clock() */
 	// allocating memory in CPU for generation counters
 	vector<int,aligned_allocator<int>> cpu_gens_of_runs (size_evals_of_runs_nelems, 0);
 
-	//preparing the constant data fields for the FPGA
-	// -----------------------------------------------------------------------------------------------------
-	// The original function does CUDA calls initializing const Kernel data.
-	// We create a struct to hold those constants
-	// and return them <here> (<here> = where prepare_const_fields_for_gpu() is called),
-	// so we can send them to Kernels from <here>, instead of from calcenergy.cpp as originally.
+	//preparing the constant data fields for the FPGA (calcenergy.cpp)
 	// -----------------------------------------------------------------------------------------------------
 	kernelconstant_static  KerConstStatic;
-	if (prepare_conststatic_fields_for_gpu(&myligand_reference, mypars, cpu_ref_ori_angles.data(), &KerConstStatic) == 1)
+	if (prepare_conststatic_fields_for_fpga(&myligand_reference, mypars, cpu_ref_ori_angles.data(), &KerConstStatic) == 1)
 		return 1;
 
 	//preparing parameter struct