#define CL_HPP_CL_1_2_DEFAULT_BUILD #define CL_HPP_TARGET_OPENCL_VERSION 120 #define CL_HPP_MINIMUM_OPENCL_VERSION 120 #define CL_HPP_ENABLE_PROGRAM_CONSTRUCTION_FROM_ARRAY_COMPATIBILITY 1 #define CL_USE_DEPRECATED_OPENCL_1_2_APIS #include #include #include #include #include #include #include #include #include "../fmindex.h" #include "../util.h" std::vector get_xilinx_devices(); char *read_binary_file(const std::string &xclbin_file_name, unsigned &nb); int main(int argc, char **argv) { if (argc < 6) { fprintf( stderr, "Usage: %s \n", argv[0]); return 1; } int use_ndrange = atoi(argv[4]); int local_size = atoi(argv[5]); // Load FM-index. fm_index *index = FMIndexReadFromFile(argv[1], 1); if (!index) { fprintf(stderr, "Could not read FM-index from file.\n"); return 1; } // Load test file. unsigned pattern_count, pattern_sz, max_match_count; char *patterns; if (!(LoadTestData(argv[3], &patterns, &pattern_count, &pattern_sz, &max_match_count, 1))) { fprintf(stderr, "Could not read test data file.\n"); return 1; } // Initialize OpenCL. cl_int err; unsigned fileBufSize; std::vector devices = get_xilinx_devices(); devices.resize(1); cl::Device device = devices[0]; cl::Context context(device, NULL, NULL, NULL, &err); char *fileBuf = read_binary_file(argv[2], fileBufSize); cl::Program::Binaries bins{{fileBuf, fileBufSize}}; cl::Program program(context, devices, bins, NULL, &err); cl::CommandQueue q(context, device, CL_QUEUE_PROFILING_ENABLE, &err); cl::Kernel kernel(program, "fmindex", &err); // Create OpenCL buffers for host data. cl::Buffer bwt_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(char) * index->bwt_sz, index->bwt, &err); cl::Buffer alphabet_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(char) * index->alphabet_sz, index->alphabet, &err); cl::Buffer ranks_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(ranks_t) * index->bwt_sz * index->alphabet_sz, index->ranks, &err); cl::Buffer sa_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(sa_t) * index->bwt_sz, index->sa, &err); cl::Buffer ranges_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(ranges_t) * 2 * index->alphabet_sz, index->ranges, &err); cl::Buffer patterns_buf(context, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(char) * pattern_count * pattern_sz, patterns, &err); cl::Buffer out_buf(context, CL_MEM_WRITE_ONLY, sizeof(unsigned long) * (pattern_count * (max_match_count + 1)), NULL, &err); // Map OpenCL buffers to kernel arguments. kernel.setArg(0, bwt_buf); kernel.setArg(1, alphabet_buf); kernel.setArg(2, ranks_buf); kernel.setArg(3, sa_buf); kernel.setArg(4, ranges_buf); kernel.setArg(5, patterns_buf); kernel.setArg(6, out_buf); // Map OpenCL buffers to kernel arguments including scalars. kernel.setArg(0, bwt_buf); kernel.setArg(1, alphabet_buf); kernel.setArg(2, ranks_buf); kernel.setArg(3, sa_buf); kernel.setArg(4, ranges_buf); kernel.setArg(5, patterns_buf); kernel.setArg(6, out_buf); kernel.setArg(7, index->bwt_sz); kernel.setArg(8, index->alphabet_sz); kernel.setArg(9, pattern_count); kernel.setArg(10, pattern_sz); kernel.setArg(11, max_match_count + 1); // Schedule transfer of inputs and output. q.enqueueMigrateMemObjects( {bwt_buf, alphabet_buf, ranks_buf, sa_buf, ranges_buf, patterns_buf}, 0); if (use_ndrange) q.enqueueNDRangeKernel(kernel, 0, pattern_count, local_size); else q.enqueueTask(kernel); q.enqueueMigrateMemObjects({out_buf}, CL_MIGRATE_MEM_OBJECT_HOST); q.finish(); // Release resources. delete[] fileBuf; FMIndexFree(index); return EXIT_SUCCESS; } // ------------------------------------------------------------------------------------ // Utility functions // ------------------------------------------------------------------------------------ std::vector get_xilinx_devices() { size_t i; cl_int err; std::vector platforms; err = cl::Platform::get(&platforms); cl::Platform platform; for (i = 0; i < platforms.size(); i++) { platform = platforms[i]; std::string platformName = platform.getInfo(&err); if (platformName == "Xilinx") { std::cerr << "INFO: Found Xilinx Platform" << std::endl; break; } } if (i == platforms.size()) { std::cerr << "ERROR: Failed to find Xilinx platform" << std::endl; exit(EXIT_FAILURE); } // Getting ACCELERATOR Devices and selecting 1st such device std::vector devices; err = platform.getDevices(CL_DEVICE_TYPE_ACCELERATOR, &devices); return devices; } char *read_binary_file(const std::string &xclbin_file_name, unsigned &nb) { if (access(xclbin_file_name.c_str(), R_OK) != 0) { printf("ERROR: %s xclbin not available please build\n", xclbin_file_name.c_str()); exit(EXIT_FAILURE); } // Loading XCL Bin into char buffer std::cerr << "INFO: Loading '" << xclbin_file_name << "'\n"; std::ifstream bin_file(xclbin_file_name.c_str(), std::ifstream::binary); bin_file.seekg(0, bin_file.end); nb = bin_file.tellg(); bin_file.seekg(0, bin_file.beg); char *buf = new char[nb]; bin_file.read(buf, nb); return buf; }