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Commit 33298887 authored by Leonardo Solis's avatar Leonardo Solis
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#24, assigned DDR using c++ Xilinx style

parent 066c183b
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ofdock_taskpar_xl/host/src/performdocking.cpp
View file @ 33298887
...@@ -349,22 +349,8 @@ filled with clock() */ ...@@ -349,22 +349,8 @@ filled with clock() */
const unsigned int mul_tmp3 = (dockpars.num_of_atypes + 1) * dockpars.g3; const unsigned int mul_tmp3 = (dockpars.num_of_atypes + 1) * dockpars.g3;
// ----------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------
// Replaced by cl_mem extensions (custom connections to DDR banks)
#if 0 #if 0
// Hardware specific configuration (valid if 4 DDR banks are available, e.g.: AWS)
// Specifiying precisely which DDR memory bank is
// being pointed to by a kernel globgal memory pointer.
cl_mem_ext_ptr_t d_bank0_ext; // Ideally: DDR bank0 <-> Krnl_GA
cl_mem_ext_ptr_t d_bank1_ext; // Ideally: DDR bank1 <-> Krnl_Conform
cl_mem_ext_ptr_t d_bank2_ext; // Ideally: DDR bank2 <-> Krnl_InterE
cl_mem_ext_ptr_t d_bank3_ext; // Ideally: DDR bank3 <-> Krnl_IntraE
d_bank0_ext.flags = XCL_MEM_DDR_BANK0; d_bank0_ext.obj = NULL; d_bank0_ext.param = 0;
d_bank1_ext.flags = XCL_MEM_DDR_BANK1; d_bank1_ext.obj = NULL; d_bank1_ext.param = 0;
d_bank2_ext.flags = XCL_MEM_DDR_BANK2; d_bank2_ext.obj = NULL; d_bank2_ext.param = 0;
d_bank3_ext.flags = XCL_MEM_DDR_BANK3; d_bank3_ext.obj = NULL; d_bank3_ext.param = 0;
#endif
// -----------------------------------------------------------------------------------------------------
// These commands will allocate memory on the FPGA. The cl::Buffer objects can // These commands will allocate memory on the FPGA. The cl::Buffer objects can
// be used to reference the memory locations on the device. The cl::Buffer // be used to reference the memory locations on the device. The cl::Buffer
...@@ -446,6 +432,202 @@ filled with clock() */ ...@@ -446,6 +432,202 @@ filled with clock() */
cl::Buffer mem_dummy (context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data()); cl::Buffer mem_dummy (context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
#endif #endif
#endif
// -----------------------------------------------------------------------------------------------------
// For Allocating Buffer to specific Global Memory Bank,
// user has to use cl_mem_ext_ptr_t and provide the Banks
// Declaring two extensions for both buffers
// Krnl_GA cl_mem extensions
cl_mem_ext_ptr_t memExt_dockpars_conformations_current_Initial;
cl_mem_ext_ptr_t memExt_dockpars_conformations_current_Final;
cl_mem_ext_ptr_t memExt_dockpars_energies_current;
cl_mem_ext_ptr_t memExt_evals_performed;
cl_mem_ext_ptr_t memExt_gens_performed;
// Krnl_Conform cl_mem extensions
cl_mem_ext_ptr_t memExt_KerConstStatic_rotlist_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_ref_coords_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_rotbonds_moving_vectors_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_rotbonds_unit_vectors_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_ref_orientation_quats_const;
// Krnl_InterE cl_mem extensions
cl_mem_ext_ptr_t memExt_dockpars_fgrids;
cl_mem_ext_ptr_t memExt_KerConstStatic_InterE_atom_charges_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_InterE_atom_types_const;
// Krnl_IntraE cl_mem extensions
cl_mem_ext_ptr_t memExt_KerConstStatic_IntraE_atom_charges_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_IntraE_atom_types_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_intraE_contributors_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_reqm_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_reqm_hbond_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_atom1_types_reqm_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_atom2_types_reqm_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_VWpars_AC_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_VWpars_BD_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_dspars_S_const;
cl_mem_ext_ptr_t memExt_KerConstStatic_dspars_V_const;
// Specify Bank0 Memory for Krnl_GA & Krnl_Conform
memExt_dockpars_conformations_current_Initial.flags = XCL_MEM_DDR_BANK0;
memExt_dockpars_conformations_current_Final.flags = XCL_MEM_DDR_BANK0;
memExt_dockpars_energies_current.flags = XCL_MEM_DDR_BANK0;
memExt_evals_performed.flags = XCL_MEM_DDR_BANK0;
memExt_gens_performed.flags = XCL_MEM_DDR_BANK0;
memExt_KerConstStatic_rotlist_const.flags = XCL_MEM_DDR_BANK0;
memExt_KerConstStatic_ref_coords_const.flags = XCL_MEM_DDR_BANK0;
memExt_KerConstStatic_rotbonds_moving_vectors_const.flags = XCL_MEM_DDR_BANK0;
memExt_KerConstStatic_rotbonds_unit_vectors_const.flags = XCL_MEM_DDR_BANK0;
memExt_KerConstStatic_ref_orientation_quats_const.flags = XCL_MEM_DDR_BANK0;
// Specify Bank1 Memory for Krnl_InterE & Krnl_IntraE
memExt_dockpars_fgrids.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_InterE_atom_charges_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_InterE_atom_types_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_IntraE_atom_charges_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_IntraE_atom_types_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_intraE_contributors_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_reqm_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_reqm_hbond_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_atom1_types_reqm_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_atom2_types_reqm_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_VWpars_AC_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_VWpars_BD_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_dspars_S_const.flags = XCL_MEM_DDR_BANK1;
memExt_KerConstStatic_dspars_V_const.flags = XCL_MEM_DDR_BANK1;
// Specifying the mapping from host arrays to Krnl_GA & Krnl_Conform
memExt_dockpars_conformations_current_Initial.obj = cpu_init_populations.data();
memExt_dockpars_conformations_current_Final.obj = cpu_final_populations.data();
memExt_dockpars_energies_current.obj = cpu_energies.data();
memExt_evals_performed.obj = cpu_evals_of_runs.data();
memExt_gens_performed.obj = cpu_gens_of_runs.data();
memExt_KerConstStatic_rotlist_const.obj = &KerConstStatic.rotlist_const[0];
memExt_KerConstStatic_ref_coords_const.obj = &KerConstStatic.ref_coords_const[0];
memExt_KerConstStatic_rotbonds_moving_vectors_const.obj = &KerConstStatic.rotbonds_moving_vectors_const[0];
memExt_KerConstStatic_rotbonds_unit_vectors_const.obj = &KerConstStatic.rotbonds_unit_vectors_const[0];
memExt_KerConstStatic_ref_orientation_quats_const.obj = &KerConstStatic.ref_orientation_quats_const[0];
// Specifying the mapping from host arrays to Krnl_InterE & Krnl_IntraE
memExt_dockpars_fgrids.obj = cpu_floatgrids;
memExt_KerConstStatic_InterE_atom_charges_const.obj = &KerConstStatic.atom_charges_const[0];
memExt_KerConstStatic_InterE_atom_types_const.obj = &KerConstStatic.atom_types_const[0];
memExt_KerConstStatic_IntraE_atom_charges_const.obj = &KerConstStatic.atom_charges_const[0];
memExt_KerConstStatic_IntraE_atom_types_const.obj = &KerConstStatic.atom_types_const[0];
memExt_KerConstStatic_intraE_contributors_const.obj = &KerConstStatic.intraE_contributors_const[0];
memExt_KerConstStatic_reqm_const.obj = &KerConstStatic.reqm_const;
memExt_KerConstStatic_reqm_hbond_const.obj = &KerConstStatic.reqm_hbond_const;
memExt_KerConstStatic_atom1_types_reqm_const.obj = &KerConstStatic.atom1_types_reqm_const;
memExt_KerConstStatic_atom2_types_reqm_const.obj = &KerConstStatic.atom2_types_reqm_const;
memExt_KerConstStatic_VWpars_AC_const.obj = &KerConstStatic.VWpars_AC_const[0];
memExt_KerConstStatic_VWpars_BD_const.obj = &KerConstStatic.VWpars_BD_const[0];
memExt_KerConstStatic_dspars_S_const.obj = &KerConstStatic.dspars_S_const[0];
memExt_KerConstStatic_dspars_V_const.obj = &KerConstStatic.dspars_V_const[0];
// Setting param to zero
memExt_dockpars_conformations_current_Initial.param = 0;
memExt_dockpars_conformations_current_Final.param = 0;
memExt_dockpars_energies_current.param = 0;
memExt_evals_performed.param = 0;
memExt_gens_performed.param = 0;
memExt_KerConstStatic_rotlist_const.param = 0;
memExt_KerConstStatic_ref_coords_const.param = 0;
memExt_KerConstStatic_rotbonds_moving_vectors_const.param = 0;
memExt_KerConstStatic_rotbonds_unit_vectors_const.param = 0;
memExt_KerConstStatic_ref_orientation_quats_const.param = 0;
memExt_dockpars_fgrids.param = 0;
memExt_KerConstStatic_InterE_atom_charges_const.param = 0;
memExt_KerConstStatic_InterE_atom_types_const.param = 0;
memExt_KerConstStatic_IntraE_atom_charges_const.param = 0;
memExt_KerConstStatic_IntraE_atom_types_const.param = 0;
memExt_KerConstStatic_intraE_contributors_const.param = 0;
memExt_KerConstStatic_reqm_const.param = 0;
memExt_KerConstStatic_reqm_hbond_const.param = 0;
memExt_KerConstStatic_atom1_types_reqm_const.param = 0;
memExt_KerConstStatic_atom2_types_reqm_const.param = 0;
memExt_KerConstStatic_VWpars_AC_const.param = 0;
memExt_KerConstStatic_VWpars_BD_const.param = 0;
memExt_KerConstStatic_dspars_S_const.param = 0;
memExt_KerConstStatic_dspars_V_const.param = 0;
// -----------------------------------------------------------------------------------------------------
// Krnl_GA buffers
cl::Buffer mem_dockpars_conformations_current_Initial
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_populations_nbytes, &memExt_dockpars_conformations_current_Initial);
cl::Buffer mem_dockpars_conformations_current_Final
(context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_populations_nbytes, &memExt_dockpars_conformations_current_Final);
cl::Buffer mem_dockpars_energies_current (context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_energies_nbytes, &memExt_dockpars_energies_current);
cl::Buffer mem_evals_performed (context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_evals_of_runs_nbytes, &memExt_evals_performed);
cl::Buffer mem_gens_performed (context, CL_MEM_WRITE_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_evals_of_runs_nbytes, &memExt_gens_performed);
// Krnl_Conform buffers
cl::Buffer mem_KerConstStatic_rotlist_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ROTATIONS*sizeof(int), &memExt_KerConstStatic_rotlist_const);
cl::Buffer mem_KerConstStatic_ref_coords_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATOMS*sizeof(cl_float3), &memExt_KerConstStatic_ref_coords_const);
cl::Buffer mem_KerConstStatic_rotbonds_moving_vectors_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), &memExt_KerConstStatic_rotbonds_moving_vectors_const);
cl::Buffer mem_KerConstStatic_rotbonds_unit_vectors_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ROTBONDS*sizeof(cl_float3), &memExt_KerConstStatic_rotbonds_unit_vectors_const);
cl::Buffer mem_KerConstStatic_ref_orientation_quats_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_RUNS*sizeof(cl_float4), &memExt_KerConstStatic_ref_orientation_quats_const);
// Krnl_InterE buffers
cl::Buffer mem_dockpars_fgrids (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
size_floatgrids_nbytes, &memExt_dockpars_fgrids);
cl::Buffer mem_KerConstStatic_InterE_atom_charges_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATOMS*sizeof(float), &memExt_KerConstStatic_InterE_atom_charges_const);
cl::Buffer mem_KerConstStatic_InterE_atom_types_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATOMS*sizeof(char), &memExt_KerConstStatic_InterE_atom_types_const);
// Krnl_IntraE buffers
cl::Buffer mem_KerConstStatic_IntraE_atom_charges_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATOMS*sizeof(float), &memExt_KerConstStatic_IntraE_atom_charges_const);
cl::Buffer mem_KerConstStatic_IntraE_atom_types_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATOMS*sizeof(char), &memExt_KerConstStatic_IntraE_atom_types_const);
cl::Buffer mem_KerConstStatic_intraE_contributors_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3), &memExt_KerConstStatic_intraE_contributors_const);
cl::Buffer mem_KerConstStatic_reqm_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
ATYPE_NUM*sizeof(float), &memExt_KerConstStatic_reqm_const);
cl::Buffer mem_KerConstStatic_reqm_hbond_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
ATYPE_NUM*sizeof(float), &memExt_KerConstStatic_reqm_hbond_const);
cl::Buffer mem_KerConstStatic_atom1_types_reqm_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
ATYPE_NUM*sizeof(unsigned int), &memExt_KerConstStatic_atom1_types_reqm_const);
cl::Buffer mem_KerConstStatic_atom2_types_reqm_const
(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
ATYPE_NUM*sizeof(unsigned int), &memExt_KerConstStatic_atom2_types_reqm_const);
cl::Buffer mem_KerConstStatic_VWpars_AC_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &memExt_KerConstStatic_VWpars_AC_const);
cl::Buffer mem_KerConstStatic_VWpars_BD_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &memExt_KerConstStatic_VWpars_BD_const);
cl::Buffer mem_KerConstStatic_dspars_S_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATYPES*sizeof(float), &memExt_KerConstStatic_dspars_S_const);
cl::Buffer mem_KerConstStatic_dspars_V_const (context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR | CL_MEM_EXT_PTR_XILINX,
MAX_NUM_OF_ATYPES*sizeof(float), &memExt_KerConstStatic_dspars_V_const);
#if !defined(SW_EMU)
//allocating CPU memory for dummy data (one integer)
vector<int,aligned_allocator<int>> cpu_dummy (1);
// IMPORTANT: enable this dummy global argument only for "hw" build.
// https://forums.xilinx.com/t5/SDAccel/ERROR-KernelCheck-83-114-in-sdx-2017-4/td-p/818135
cl::Buffer mem_dummy (context, CL_MEM_USE_HOST_PTR | CL_MEM_READ_ONLY, sizeof(int), cpu_dummy.data());
#endif
// ----------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------
//Separate Read/write Buffer vector is needed to migrate data between host/device //Separate Read/write Buffer vector is needed to migrate data between host/device
std::vector<cl::Memory> inBufVec, outBufVec; std::vector<cl::Memory> inBufVec, outBufVec;
......
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