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Commit 6532f7f3 authored by qon's avatar qon
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Add Option for asnychronous GPU processing, add test implementation with... 

Add Option for asnychronous GPU processing, add test implementation with explicit SSE for CPU (currently disabled)
parent 92d5b2ba
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Showing with 254 additions and 187 deletions
bioem.cpp
View file @ 6532f7f3
......@@ -266,8 +266,15 @@ int bioem::run()
/*** Comparing each calculated convoluted map with all experimental maps ***/
timer.ResetStart();
compareRefMaps(iProjectionOut, iConv, conv_map);
printf("Time Comparison %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());
const double compTime = timer.GetCurrentElapsedTime();
const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;
printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iProjectionOut, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
}
}
......
bioem_algorithm.h
View file @ 6532f7f3
#ifndef BIOEM_ALGORITHM_H
#define BIOEM_ALGORITHM_H
//#include <boost/iterator/iterator_concepts.hpp>
#ifndef BIOEM_GPUCODE
//#define SSECODE //Explicit SSE code, not correct yet since loop counter is assumed multiple of 4, anyway not faster than autovectorized code.
#endif
#ifdef SSECODE
#include <emmintrin.h>
#include <smmintrin.h>
#endif
template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMap(const int iRefMap, const int iOrient, const int iConv, const bioem_map& Mapconv, bioem_Probability* pProb, const bioem_param_device& param, const RefT& RefMap,
......@@ -12,10 +22,14 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
// Taking into account the center displacement
/*** Inizialzing crosscorrelations of calculated projected convolutions ***/
myfloat_t sum=0.0;
#ifdef SSECODE
myfloat_t sum, sumsquare, crossproMapConv;
__m128 sum_v = _mm_setzero_ps(), sumsquare_v = _mm_setzero_ps(), cross_v = _mm_setzero_ps(), d1, d2;
#else
myfloat_t sum=0.0;
myfloat_t sumsquare=0.0;
myfloat_t crossproMapConv=0.0;
#endif
/****** Loop over Pixels to calculate dot product and cross-correlations of displaced Ref Conv. Map***/
if (GPUAlgo != 2 || iRefMap < RefMap.ntotRefMap)
{
......@@ -43,9 +57,25 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
for (int i = iStart; i < iEnd; i += 1)
{
#ifdef SSECODE
const float* ptr1 = &Mapconv.points[i + cent_x][jStart + cent_y];
const float* ptr2 = RefMap.getp(iRefMap, i, jStart);
int j;
const int count = jEnd - jStart;
for (j = 0;j <= count - 4;j += 4)
{
d1 = _mm_loadu_ps(ptr1);
d2 = _mm_loadu_ps(ptr2);
sum_v = _mm_add_ps(sum_v, d1);
sumsquare_v = _mm_add_ps(sumsquare_v, _mm_mul_ps(d1, d1));
cross_v = _mm_add_ps(cross_v, _mm_mul_ps(d1, d2));
ptr1 += 4;
ptr2 += 4;
}
#else
for (int j = jStart; j < jEnd; j += 1)
{
const myfloat_t pointMap = Mapconv.points[i+cent_x][j+cent_y];
const myfloat_t pointMap = Mapconv.points[i + cent_x][j + cent_y];
const myfloat_t pointRefMap = RefMap.get(iRefMap, i, j);
crossproMapConv += pointMap * pointRefMap;
// Crosscorrelation of calculated displaced map
......@@ -53,7 +83,19 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
// Calculate Sum of pixels squared
sumsquare += pointMap*pointMap;
}
#endif
}
#ifdef SSECODE
sum_v = _mm_hadd_ps(sum_v, sum_v);
sumsquare_v = _mm_hadd_ps(sumsquare_v, sumsquare_v);
cross_v = _mm_hadd_ps(cross_v, cross_v);
sum_v = _mm_hadd_ps(sum_v, sum_v);
sumsquare_v = _mm_hadd_ps(sumsquare_v, sumsquare_v);
cross_v = _mm_hadd_ps(cross_v, cross_v);
sum = _mm_cvtss_f32(sum_v);
sumsquare = _mm_cvtss_f32(sumsquare_v);
crossproMapConv = _mm_cvtss_f32(cross_v);
#endif
}
/********** Calculating elements in BioEM Probability formula ********/
......
bioem_cuda.cu
View file @ 6532f7f3
#define BIOEM_GPUCODE
#define BIOEM_GPUCODE
#if defined(_WIN32)
#include <windows.h>
#endif
#include <iostream>
using namespace std;
#include "bioem_cuda_internal.h"
#include "bioem_algorithm.h"
//__constant__ bioem_map gConvMap;
static inline void checkCudaErrors(cudaError_t error)
{
if (error != cudaSuccess)
{
printf("CUDA Error %d / %s\n", error, cudaGetErrorString(error));
exit(1);
}
}
bioem_cuda::bioem_cuda()
{
deviceInitialized = 0;
GPUAlgo = getenv("GPUALGO") == NULL ? 2 : atoi(getenv("GPUALGO"));
}
bioem_cuda::~bioem_cuda()
{
deviceExit();
}
__global__ void compareRefMap_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap_Mod* RefMap, const int cent_x, const int cent_y)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < RefMap->ntotRefMap)
{
compareRefMap<0>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y);
}
}
__global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap_Mod* RefMap)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < RefMap->ntotRefMap)
{
compareRefMapShifted<1>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap);
}
}
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap* RefMap, const int blockoffset, const int nShifts, const int nShiftBits)
{
const size_t myid = (myBlockIdxX + blockoffset) * myBlockDimX + myThreadIdxX;
const int iRefMap = myid >> (nShiftBits << 1);
const int myRef = myThreadIdxX >> (nShiftBits << 1);
const int myShiftIdx = (myid >> nShiftBits) & (nShifts - 1);
const int myShiftIdy = myid & (nShifts - 1);
const int myShift = myid & (nShifts * nShifts - 1);
const int cent_x = myShiftIdx * param.GridSpaceCenter - param.maxDisplaceCenter;
const int cent_y = myShiftIdy * param.GridSpaceCenter - param.maxDisplaceCenter;
compareRefMap<2>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef);
}
template <class T> static inline T divup(T num, T divider) {return((num + divider - 1) / divider);}
static inline bool IsPowerOf2(int x) {return ((x > 0) && ((x & (x - 1)) == 0));}
#endif
#include <iostream>
using namespace std;
#include "bioem_cuda_internal.h"
#include "bioem_algorithm.h"
//__constant__ bioem_map gConvMap;
static inline void checkCudaErrors(cudaError_t error)
{
if (error != cudaSuccess)
{
printf("CUDA Error %d / %s\n", error, cudaGetErrorString(error));
exit(1);
}
}
bioem_cuda::bioem_cuda()
{
deviceInitialized = 0;
GPUAlgo = getenv("GPUALGO") == NULL ? 2 : atoi(getenv("GPUALGO"));
GPUAsync = getenv("GPUASYNC") == NULL ? 0 : atoi(getenv("GPUASYNC"));
}
bioem_cuda::~bioem_cuda()
{
deviceExit();
}
__global__ void compareRefMap_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap_Mod* RefMap, const int cent_x, const int cent_y)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < RefMap->ntotRefMap)
{
compareRefMap<0>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y);
}
}
__global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap_Mod* RefMap)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < RefMap->ntotRefMap)
{
compareRefMapShifted<1>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap);
}
}
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap* RefMap, const int blockoffset, const int nShifts, const int nShiftBits)
{
const size_t myid = (myBlockIdxX + blockoffset) * myBlockDimX + myThreadIdxX;
const int iRefMap = myid >> (nShiftBits << 1);
const int myRef = myThreadIdxX >> (nShiftBits << 1);
const int myShiftIdx = (myid >> nShiftBits) & (nShifts - 1);
const int myShiftIdy = myid & (nShifts - 1);
const int myShift = myid & (nShifts * nShifts - 1);
const int cent_x = myShiftIdx * param.GridSpaceCenter - param.maxDisplaceCenter;
const int cent_y = myShiftIdy * param.GridSpaceCenter - param.maxDisplaceCenter;
compareRefMap<2>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef);
}
template <class T> static inline T divup(T num, T divider) {return((num + divider - 1) / divider);}
static inline bool IsPowerOf2(int x) {return ((x > 0) && ((x & (x - 1)) == 0));}
#if defined(_WIN32)
static inline int ilog2 (int value)
{
DWORD index;
_BitScanReverse (&index, value);
return(value);
}
#else
static inline int ilog2(int value) {return 31 - __builtin_clz(value);}
#endif
int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map)
{
//cudaMemcpyToSymbolAsync(&gConvMap, &conv_map, sizeof(bioem_map), 0, cudaMemcpyHostToDevice, cudaStream);
checkCudaErrors(cudaMemcpyAsync(pConvMap_device, &conv_map, sizeof(bioem_map), cudaMemcpyHostToDevice, cudaStream));
if (GPUAlgo == 2) //Loop over shifts
{
const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
if (!IsPowerOf2(nShifts))
{
cout << "Invalid number of displacements, no power of two\n";
exit(1);
}
if (CUDA_THREAD_COUNT % (nShifts * nShifts))
{
cout << "CUDA Thread count is no multiple of number of shifts\n";
exit(1);
}
if (nShifts > CUDA_MAX_SHIFT_REDUCE)
{
cout << "Too many displacements for CUDA reduction\n";
exit(1);
}
const int nShiftBits = ilog2(nShifts);
size_t totalBlocks = divup((size_t) RefMap.ntotRefMap * (size_t) nShifts * (size_t) nShifts, (size_t) CUDA_THREAD_COUNT);
size_t nBlocks = CUDA_BLOCK_COUNT;
for (size_t i = 0;i < totalBlocks;i += nBlocks)
{
compareRefMapLoopShifts_kernel <<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream>>> (iProjectionOut, iConv, pConvMap_device, pProb_device, param.param_device, pRefMap_device, i, nShifts, nShiftBits);
}
}
else if (GPUAlgo == 1) //Split shifts in multiple kernels
{
for (int cent_x = -param.param_device.maxDisplaceCenter; cent_x <= param.param_device.maxDisplaceCenter; cent_x=cent_x+param.param_device.GridSpaceCenter)
{
for (int cent_y = -param.param_device.maxDisplaceCenter; cent_y <= param.param_device.maxDisplaceCenter; cent_y=cent_y+param.param_device.GridSpaceCenter)
{
compareRefMap_kernel <<<divup(RefMap.ntotRefMap, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device, pProb_device, param.param_device, pRefMap_device_Mod, cent_x, cent_y);
}
}
}
else if (GPUAlgo == 0) //All shifts in one kernel
{
compareRefMapShifted_kernel <<<divup(RefMap.ntotRefMap, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device, pProb_device, param.param_device, pRefMap_device_Mod);
}
else
{
cout << "Invalid GPU Algorithm selected\n";
exit(1);
}
checkCudaErrors(cudaStreamSynchronize(cudaStream));
return(0);
}
int bioem_cuda::deviceInit()
{
deviceExit();
checkCudaErrors(cudaStreamCreate(&cudaStream));
checkCudaErrors(cudaMalloc(&pRefMap_device, sizeof(bioem_RefMap)));
checkCudaErrors(cudaMalloc(&pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap));
checkCudaErrors(cudaMalloc(&pConvMap_device, sizeof(bioem_map)));
pRefMap_device_Mod = (bioem_RefMap_Mod*) pRefMap_device;
if (GPUAlgo == 0 || GPUAlgo == 1)
{
bioem_RefMap_Mod* RefMapGPU = new bioem_RefMap_Mod(RefMap);
cudaMemcpy(pRefMap_device_Mod, RefMapGPU, sizeof(bioem_RefMap), cudaMemcpyHostToDevice);
delete RefMapGPU;
}
else
{
cudaMemcpy(pRefMap_device, &RefMap, sizeof(bioem_RefMap), cudaMemcpyHostToDevice);
}
deviceInitialized = 1;
return(0);
}
int bioem_cuda::deviceExit()
{
if (deviceInitialized == 0) return(0);
cudaStreamDestroy(cudaStream);
cudaFree(pRefMap_device);
cudaFree(pProb_device);
cudaFree(pConvMap_device);
cudaThreadExit();
deviceInitialized = 0;
return(0);
}
int bioem_cuda::deviceStartRun()
{
cudaMemcpy(pProb_device, pProb, sizeof(bioem_Probability) * RefMap.ntotRefMap, cudaMemcpyHostToDevice);
return(0);
}
int bioem_cuda::deviceFinishRun()
{
cudaMemcpy(pProb, pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap, cudaMemcpyDeviceToHost);
return(0);
}
bioem* bioem_cuda_create()
{
return new bioem_cuda;
}
}
#else
static inline int ilog2(int value) {return 31 - __builtin_clz(value);}
#endif
int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map)
{
//cudaMemcpyToSymbolAsync(&gConvMap, &conv_map, sizeof(bioem_map), 0, cudaMemcpyHostToDevice, cudaStream);
if (GPUAsync)
{
checkCudaErrors(cudaEventSynchronize(cudaEvent[iConv & 1]));
checkCudaErrors(cudaEventRecord(cudaEvent[iConv & 1], cudaStream));
}
checkCudaErrors(cudaMemcpyAsync(pConvMap_device[iConv & 1], &conv_map, sizeof(bioem_map), cudaMemcpyHostToDevice, cudaStream));
if (GPUAlgo == 2) //Loop over shifts
{
const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
if (!IsPowerOf2(nShifts))
{
cout << "Invalid number of displacements, no power of two\n";
exit(1);
}
if (CUDA_THREAD_COUNT % (nShifts * nShifts))
{
cout << "CUDA Thread count (" << CUDA_THREAD_COUNT << ") is no multiple of number of shifts (" << (nShifts * nShifts) << ")\n";
exit(1);
}
if (nShifts > CUDA_MAX_SHIFT_REDUCE)
{
cout << "Too many displacements for CUDA reduction\n";
exit(1);
}
const int nShiftBits = ilog2(nShifts);
size_t totalBlocks = divup((size_t) RefMap.ntotRefMap * (size_t) nShifts * (size_t) nShifts, (size_t) CUDA_THREAD_COUNT);
size_t nBlocks = CUDA_BLOCK_COUNT;
for (size_t i = 0;i < totalBlocks;i += nBlocks)
{
compareRefMapLoopShifts_kernel <<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device, i, nShifts, nShiftBits);
}
}
else if (GPUAlgo == 1) //Split shifts in multiple kernels
{
for (int cent_x = -param.param_device.maxDisplaceCenter; cent_x <= param.param_device.maxDisplaceCenter; cent_x=cent_x+param.param_device.GridSpaceCenter)
{
for (int cent_y = -param.param_device.maxDisplaceCenter; cent_y <= param.param_device.maxDisplaceCenter; cent_y=cent_y+param.param_device.GridSpaceCenter)
{
compareRefMap_kernel <<<divup(RefMap.ntotRefMap, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod, cent_x, cent_y);
}
}
}
else if (GPUAlgo == 0) //All shifts in one kernel
{
compareRefMapShifted_kernel <<<divup(RefMap.ntotRefMap, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod);
}
else
{
cout << "Invalid GPU Algorithm selected\n";
exit(1);
}
if (GPUAsync == 0) checkCudaErrors(cudaStreamSynchronize(cudaStream));
return(0);
}
int bioem_cuda::deviceInit()
{
deviceExit();
checkCudaErrors(cudaStreamCreate(&cudaStream));
checkCudaErrors(cudaMalloc(&pRefMap_device, sizeof(bioem_RefMap)));
checkCudaErrors(cudaMalloc(&pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap));
for (int i = 0;i < 2;i++)
{
checkCudaErrors(cudaEventCreate(&cudaEvent[i]));
checkCudaErrors(cudaMalloc(&pConvMap_device[i], sizeof(bioem_map)));
}
pRefMap_device_Mod = (bioem_RefMap_Mod*) pRefMap_device;
if (GPUAlgo == 0 || GPUAlgo == 1)
{
bioem_RefMap_Mod* RefMapGPU = new bioem_RefMap_Mod(RefMap);
cudaMemcpy(pRefMap_device_Mod, RefMapGPU, sizeof(bioem_RefMap), cudaMemcpyHostToDevice);
delete RefMapGPU;
}
else
{
cudaMemcpy(pRefMap_device, &RefMap, sizeof(bioem_RefMap), cudaMemcpyHostToDevice);
}
deviceInitialized = 1;
return(0);
}
int bioem_cuda::deviceExit()
{
if (deviceInitialized == 0) return(0);
cudaStreamDestroy(cudaStream);
cudaFree(pRefMap_device);
cudaFree(pProb_device);
for (int i = 0;i < 2;i++)
{
cudaEventDestroy(cudaEvent[i]);
cudaFree(pConvMap_device);
}
cudaThreadExit();
deviceInitialized = 0;
return(0);
}
int bioem_cuda::deviceStartRun()
{
cudaMemcpy(pProb_device, pProb, sizeof(bioem_Probability) * RefMap.ntotRefMap, cudaMemcpyHostToDevice);
return(0);
}
int bioem_cuda::deviceFinishRun()
{
if (GPUAsync) cudaStreamSynchronize(cudaStream);
cudaMemcpy(pProb, pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap, cudaMemcpyDeviceToHost);
return(0);
}
bioem* bioem_cuda_create()
{
return new bioem_cuda;
}
include/bioem_cuda_internal.h
View file @ 6532f7f3
......@@ -22,12 +22,14 @@ protected:
int deviceInitialized;
cudaStream_t cudaStream;
cudaEvent_t cudaEvent[2];
bioem_RefMap_Mod* pRefMap_device_Mod;
bioem_RefMap* pRefMap_device;
bioem_Probability* pProb_device;
bioem_map* pConvMap_device;
bioem_map* pConvMap_device[2];
int GPUAlgo;
int GPUAsync;
};
#endif
include/map.h
View file @ 6532f7f3
......@@ -35,6 +35,7 @@ public:
bool dumpMap, loadMap;
__host__ __device__ inline myfloat_t get(int map, int x, int y) const {return(Ref[map].points[x][y]);}
__host__ __device__ inline const myfloat_t* getp(int map, int x, int y) const {return(&Ref[map].points[x][y]);}
};
......
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