Skip to content

GitLab

Commit c9754f9e authored by qon's avatar qon
Browse files

Change all line endings in files to unix style

parent 27a1ff28
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 1373 additions and 1373 deletions
bioem.cpp
View file @ c9754f9e
This diff is collapsed.
bioem_cuda.cu
View file @ c9754f9e
#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"));
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);
if (GPUAsync)
{
checkCudaErrors(cudaEventSynchronize(cudaEvent[iConv & 1]));
}
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)
{
checkCudaErrors(cudaEventRecord(cudaEvent[iConv & 1], cudaStream));
}
else
{
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;
}
#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"));
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);
if (GPUAsync)
{
checkCudaErrors(cudaEventSynchronize(cudaEvent[iConv & 1]));
}
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)
{
checkCudaErrors(cudaEventRecord(cudaEvent[iConv & 1], cudaStream));
}
else
{
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.h
View file @ c9754f9e
#ifndef BIOEM_H
#define BIOEM_H
#include <fstream>
#include <iostream>
#include <complex>
#include "defs.h"
#include "bioem.h"
#include "model.h"
#include "map.h"
#include "param.h"
class bioem
{
public:
bioem();
virtual ~bioem();
int configure(int ac, char* av[]);
int precalculate(); // Is it better to pass directly the input File names?
int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
int run();
int doProjections(int iMap);
int createConvolutedProjectionMap(int iOreint,int iMap, mycomplex_t* lproj,bioem_map& Mapconv);
virtual int compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map);
int createProjection(int iMap, mycomplex_t* map);
int calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare);
bioem_Probability* pProb;
protected:
virtual int deviceInit();
virtual int deviceStartRun();
virtual int deviceFinishRun();
bioem_param param;
bioem_model Model;
bioem_RefMap RefMap;
int nReferenceMaps; //Maps in memory at a time
int nReferenceMapsTotal; //Maps in total
int nProjectionMaps; //Maps in memory at a time
int nProjectionMapsTotal; //Maps in total
};
#endif
#ifndef BIOEM_H
#define BIOEM_H
#include <fstream>
#include <iostream>
#include <complex>
#include "defs.h"
#include "bioem.h"
#include "model.h"
#include "map.h"
#include "param.h"
class bioem
{
public:
bioem();
virtual ~bioem();
int configure(int ac, char* av[]);
int precalculate(); // Is it better to pass directly the input File names?
int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
int run();
int doProjections(int iMap);
int createConvolutedProjectionMap(int iOreint,int iMap, mycomplex_t* lproj,bioem_map& Mapconv);
virtual int compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map);
int createProjection(int iMap, mycomplex_t* map);
int calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare);
bioem_Probability* pProb;
protected:
virtual int deviceInit();
virtual int deviceStartRun();
virtual int deviceFinishRun();
bioem_param param;
bioem_model Model;
bioem_RefMap RefMap;
int nReferenceMaps; //Maps in memory at a time
int nReferenceMapsTotal; //Maps in total
int nProjectionMaps; //Maps in memory at a time
int nProjectionMapsTotal; //Maps in total
};
#endif
include/defs.h
View file @ c9754f9e
#ifndef BIOEM_DEFS_H
#define BIOEM_DEFS_H
typedef float myfloat_t;
typedef double mycomplex_t[2];
#define BIOEM_FLOAT_3_PHYSICAL_SIZE 3 //Possible set to 4 for GPU
#define BIOEM_MAP_SIZE_X 224
#define BIOEM_MAP_SIZE_Y 224
#define BIOEM_MODEL_SIZE 120000
#define BIOEM_MAX_MAPS 12000
#define MAX_REF_CTF 200
#define MAX_ORIENT 20000
struct myfloat3_t
{
myfloat_t pos[BIOEM_FLOAT_3_PHYSICAL_SIZE];
};
#ifdef BIOEM_GPUCODE
#define myThreadIdxX threadIdx.x
#define myThreadIdxY threadIdx.y
#define myBlockDimX blockDim.x
#define myBlockDimY blockDim.y
#define myBlockIdxX blockIdx.x
#define myBlockIdxY blockIdx.y
#else
#define __device__
#define __host__
#define myThreadIdxX 0
#define myThreadIdxY 0
#define myBlockDimX 1
#define myBlockDimY 1
#define myBlockIdxX 0
#define myBlockIdxY 0
#endif
#define CUDA_THREAD_COUNT 256
#define CUDA_BLOCK_COUNT 1024 * 16
#define CUDA_MAX_SHIFT_REDUCE 1024
#endif
#ifndef BIOEM_DEFS_H
#define BIOEM_DEFS_H
typedef float myfloat_t;
typedef double mycomplex_t[2];
#define BIOEM_FLOAT_3_PHYSICAL_SIZE 3 //Possible set to 4 for GPU
#define BIOEM_MAP_SIZE_X 224
#define BIOEM_MAP_SIZE_Y 224
#define BIOEM_MODEL_SIZE 120000
#define BIOEM_MAX_MAPS 12000
#define MAX_REF_CTF 200
#define MAX_ORIENT 20000
struct myfloat3_t
{
myfloat_t pos[BIOEM_FLOAT_3_PHYSICAL_SIZE];
};
#ifdef BIOEM_GPUCODE
#define myThreadIdxX threadIdx.x
#define myThreadIdxY threadIdx.y
#define myBlockDimX blockDim.x
#define myBlockDimY blockDim.y
#define myBlockIdxX blockIdx.x
#define myBlockIdxY blockIdx.y
#else
#define __device__
#define __host__
#define myThreadIdxX 0
#define myThreadIdxY 0
#define myBlockDimX 1
#define myBlockDimY 1
#define myBlockIdxX 0
#define myBlockIdxY 0
#endif
#define CUDA_THREAD_COUNT 256
#define CUDA_BLOCK_COUNT 1024 * 16
#define CUDA_MAX_SHIFT_REDUCE 1024
#endif
include/map.h
View file @ c9754f9e
#ifndef BIOEM_MAP_H
#define BIOEM_MAP_H