SEXP R_cuCtxSetCacheConfig(SEXP r_config)
{
SEXP r_ans = R_NilValue;
enum CUfunc_cache_enum config = (enum CUfunc_cache_enum) INTEGER(r_config)[0];
CUresult ans;
ans = cuCtxSetCacheConfig(config);
r_ans = Renum_convert_CUresult(ans) ;
return(r_ans);
}
void RTC_VIT(unsigned int number, const char* GPU_kernel, HMMER_PROFILE *hmm,
unsigned int *seq_1D, unsigned int *offset, unsigned int *seq_len,
unsigned int *iLen, unsigned int sum, double *pVal,
int warp, int maxreg, dim3 GRID, dim3 BLOCK)
{
/*********************************/
/* 0. Prepare for cuda drive API */
/*********************************/
CUdevice cuDevice;
CUcontext context;
CUmodule module;
CUfunction kernel;
checkCudaErrors(cuInit(0));
checkCudaErrors(cuDeviceGet(&cuDevice, 0));
checkCudaErrors(cuCtxCreate(&context, 0, cuDevice));
/*********************************************/
/* 1. Device Property: fixed based on Device */
/*********************************************/
/****************************************/
/* 2. Device Memory Allocation and copy */
/****************************************/
StopWatchInterface *timer;
sdkCreateTimer(&timer);
sdkStartTimer(&timer);
/* Driver API pointers */
CUdeviceptr d_seq, d_offset, d_len, d_len_6r, mat_v, trans, score;
/* Allocation */
checkCudaErrors(cuMemAlloc(&d_seq, sum * sizeof(unsigned int))); /* copy 1D database */
checkCudaErrors(cuMemAlloc(&d_offset, number * sizeof(unsigned int))); /* copy offset of each seq*/
checkCudaErrors(cuMemAlloc(&d_len, number * sizeof(unsigned int))); /* copy raw length of each seq */
checkCudaErrors(cuMemAlloc(&d_len_6r, number * sizeof(unsigned int))); /* copy padding length of each seq */
checkCudaErrors(cuMemAlloc(&mat_v, hmm->vitQ * PROTEIN_TYPE * sizeof(__32int__))); /* striped EMISSION score */
checkCudaErrors(cuMemAlloc(&trans, hmm->vitQ * TRANS_TYPE * sizeof(__32int__))); /* striped transition score */
checkCudaErrors(cuMemAlloc(&score, number * sizeof(double))); /* P-Value as output */
/* H to D copy */
checkCudaErrors(cuMemcpyHtoD(d_seq, seq_1D, sum * sizeof(unsigned int)));
checkCudaErrors(cuMemcpyHtoD(d_offset, offset, number * sizeof(unsigned int)));
checkCudaErrors(cuMemcpyHtoD(d_len, seq_len, number * sizeof(unsigned int)));
checkCudaErrors(cuMemcpyHtoD(d_len_6r, iLen, number * sizeof(unsigned int)));
checkCudaErrors(cuMemcpyHtoD(mat_v, hmm->vit_vec, hmm->vitQ * PROTEIN_TYPE * sizeof(__32int__)));
checkCudaErrors(cuMemcpyHtoD(trans, hmm->trans_vec, hmm->vitQ * TRANS_TYPE * sizeof(__32int__)));
sdkStopTimer(&timer);
printf("Alloc & H to D Copy time: %f (ms)\n", sdkGetTimerValue(&timer));
sdkDeleteTimer(&timer);
/********************************************************/
/* 3. Runtime compilation, Generate PTX and Load module */
/********************************************************/
sdkCreateTimer(&timer);
sdkStartTimer(&timer);
/* NVRTC create handle */
nvrtcProgram prog;
NVRTC_SAFE_CALL("nvrtcCreateProgram", nvrtcCreateProgram(&prog, // prog
GPU_kernel, // buffer
NULL, // name: CUDA program name. name can be NULL; “default_program” is used when it is NULL.
0, // numHeaders (I put header file path with -I later)
NULL, // headers' content
NULL)); // include full name of headers
/* 1. eliminate const through pointer */
char *a = NULL;
const char *b = a;
const char **opts = &b;
/* 2. elminate const through reference */
//char a_value = 'c';
//char* aa = &a_value;
//const char *&bb = aa; // no way with const
//const char**&ref = aa; // no way
/* Dynamic Options */
char **test_char = new char*[8];
test_char[0] = new char[__INCLUDE__.length() + strlen("simd_def.h") + 1]; // #include simd_def.h
strcpy(test_char[0], get_option(__INCLUDE__, "simd_def.h").c_str());
test_char[1] = new char[__INCLUDE__.length() + strlen("simd_functions.h") + 1]; // #include simd_functions.h
strcpy(test_char[1], get_option(__INCLUDE__, "simd_functions.h").c_str());
test_char[2] = new char[__RDC__.length() + __F__.length() + 1]; // -rdc=false
strcpy(test_char[2], get_option(__RDC__, __F__).c_str());
test_char[3] = new char[__ARCH__.length() + __CC35__.length() + 1]; // -arch=compute_35
strcpy(test_char[3], get_option(__ARCH__, __CC35__).c_str());
test_char[4] = new char[__MAXREG__.length() + int2str(maxreg).length() + 1]; // -maxrregcount = <?>
strcpy(test_char[4], get_option(__MAXREG__, int2str(maxreg)).c_str());
test_char[5] = new char[__RIB__.length() + int2str(warp).length() + 1]; // #define RIB <?> : warps per block
strcpy(test_char[5], get_option(__RIB__, int2str(warp)).c_str());
test_char[6] = new char[__SIZE__.length() + int2str((int)force_local_size).length() + 1]; // #define SIZE 40
strcpy(test_char[6], get_option(__SIZE__, int2str((int)force_local_size)).c_str());
test_char[7] = new char[__Q__.length() + int2str(hmm->vitQ).length() + 1]; // #define Q <?>
strcpy(test_char[7], get_option(__Q__, int2str(hmm->vitQ)).c_str());
/* 1. change const char** through pointer */
//char* **test = const_cast<char** *>(&opts);
//*test = test_char;
/* 2. change const char** through reference */
char** &test_ref = const_cast<char** &>(opts);
test_ref = test_char;
/* NVRTC compile */
NVRTC_SAFE_CALL("nvrtcCompileProgram", nvrtcCompileProgram(prog, // prog
8, // numOptions
opts)); // options
sdkStopTimer(&timer);
printf("nvrtc Creat and Compile: %f (ms)\n", sdkGetTimerValue(&timer));
sdkDeleteTimer(&timer);
//======================================================================================//
// /* dump log */ //
// size_t logSize; //
// NVRTC_SAFE_CALL("nvrtcGetProgramLogSize", nvrtcGetProgramLogSize(prog, &logSize)); //
// char *log = (char *) malloc(sizeof(char) * logSize + 1); //
// NVRTC_SAFE_CALL("nvrtcGetProgramLog", nvrtcGetProgramLog(prog, log)); //
// log[logSize] = '\x0'; //
// std::cerr << "\n compilation log ---\n"; //
// std::cerr << log; //
// std::cerr << "\n end log ---\n"; //
// free(log); //
//======================================================================================//
/* NVRTC fetch PTX */
sdkCreateTimer(&timer);
sdkStartTimer(&timer);
size_t ptxsize;
NVRTC_SAFE_CALL("nvrtcGetPTXSize", nvrtcGetPTXSize(prog, &ptxsize));
char *ptx = new char[ptxsize];
NVRTC_SAFE_CALL("nvrtcGetPTX", nvrtcGetPTX(prog, ptx));
NVRTC_SAFE_CALL("nvrtcDestroyProgram", nvrtcDestroyProgram(&prog)); // destroy program instance
/* Launch PTX by driver API */
checkCudaErrors(cuModuleLoadDataEx(&module, ptx, 0, 0, 0));
checkCudaErrors(cuModuleGetFunction(&kernel, module, "KERNEL")); // return the handle of function, name is the same as real kernel function
sdkStopTimer(&timer);
printf("Compile & Load time: %f (ms)\n", sdkGetTimerValue(&timer));
sdkDeleteTimer(&timer);
/**************************************/
/* 4. GPU kernel launch by driver API */
/**************************************/
sdkCreateTimer(&timer);
sdkStartTimer(&timer);
cuCtxSetCacheConfig(CU_FUNC_CACHE_PREFER_L1);
/* parameters for kernel funciton */
void *arr[] = { &d_seq, &number, &d_offset,
&score, &d_len, &d_len_6r, &mat_v, &trans,
&(hmm->base_vs), &(hmm->E_lm), &(hmm->ddbound_vs),
&(hmm->scale_w), &(hmm->vitQ), &(hmm->MU[1]), &(hmm->LAMBDA[1])};
/* launch kernel */
checkCudaErrors(cuLaunchKernel( kernel,
GRID.x, GRID.y, GRID.z, /* grid dim */
BLOCK.x, BLOCK.y, BLOCK.z, /* block dim */
0,0, /* SMEM, stream */
&arr[0], /* kernel params */
0)); /* extra opts */
/* wait for kernel finish */
checkCudaErrors(cuCtxSynchronize()); /* block for a context's task to complete */
sdkStopTimer(&timer);
printf("Kernel time: %f (ms)\n", sdkGetTimerValue(&timer));
sdkDeleteTimer(&timer);
/*****************************************/
/* 5. P-value return and post-processing */
/*****************************************/
sdkCreateTimer(&timer);
sdkStartTimer(&timer);
checkCudaErrors(cuMemcpyDtoH(pVal, score, number * sizeof(double)));
sdkStopTimer(&timer);
printf("D to H copy time: %f (ms)\n", sdkGetTimerValue(&timer));
sdkDeleteTimer(&timer);
/* count the number of seqs pass */
unsigned long pass_vit = 0; /* # of seqs pass vit */
for (int i = 0; i < number; i++)
{
if (pVal[i] <= F2)
pass_vit++;
}
printf("| PASS VIT \n");
printf("| ALL | FWD |\n");
printf("| %d | %d |\n", pass_vit, pass_vit);
/************************/
/* 6. clean the context */
/************************/
checkCudaErrors(cuDevicePrimaryCtxReset(cuDevice)); /* reset */
checkCudaErrors(cuCtxSynchronize()); /* block for a context's task to complete */
}
