Skip to content

GitLab

Commit e9b15195 authored by David Rohr's avatar David Rohr
Browse files

Fix memory allocation for CC Probability

parent 62cf7c72
Hide whitespace changes
Inline Side-by-side
bioem.cpp
View file @ e9b15195
......@@ -270,7 +270,7 @@ int bioem::configure(int ac, char* av[])
printf("Time Precalculate %f\n", timer.GetCurrentElapsedTime());
timer.ResetStart();
}
pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, param.nTotCC, *this);
if (DebugOutput >= 2 && mpi_rank == 0)
{
......
bioem_cuda.cu
View file @ e9b15195
......@@ -397,8 +397,7 @@ int bioem_cuda::deviceInit()
gpumap->sum_RefMap = sum;
gpumap->sumsquare_RefMap = sumsquare;
checkCudaErrors(cudaMalloc(&pProb_memory, pProb_device.get_size(RefMap.ntotRefMap, param.nTotGridAngles, param.param_device.writeAngles)));
checkCudaErrors(cudaMalloc(&pProb_memory, pProb_device.get_sizeCC(RefMap.ntotRefMap, param.nTotCC, param.param_device.writeCC)));
checkCudaErrors(cudaMalloc(&pProb_memory, pProb_device.get_size(RefMap.ntotRefMap, param.nTotGridAngles, param.nTotCC, param.param_device.writeAngles, param.param_device.writeCC)));
for (int i = 0; i < 2; i++)
{
......@@ -484,15 +483,14 @@ int bioem_cuda::deviceStartRun()
{
maxRef = (size_t) RefMap.ntotRefMap * (size_t) GPUWorkload / 100;
pProb_host = new bioem_Probability;
pProb_host->init(maxRef, param.nTotGridAngles, *this);
pProb_host->initCC(maxRef, param.nTotCC, *this);
pProb_host->init(maxRef, param.nTotGridAngles, param.nTotCC, *this);
pProb_host->copyFrom(&pProb, *this);
}
pProb_device = *pProb_host;
pProb_device.ptr = pProb_memory;
pProb_device.set_pointers();
checkCudaErrors(cudaMemcpyAsync(pProb_device.ptr, pProb_host->ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.param_device.writeAngles), cudaMemcpyHostToDevice, cudaStream[0]));
checkCudaErrors(cudaMemcpyAsync(pProb_device.ptr, pProb_host->ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.nTotCC, param.param_device.writeAngles, param.param_device.writeCC), cudaMemcpyHostToDevice, cudaStream[0]));
if (FFTAlgo)
{
......@@ -527,7 +525,7 @@ int bioem_cuda::deviceStartRun()
int bioem_cuda::deviceFinishRun()
{
if (GPUAsync) cudaStreamSynchronize(cudaStream[0]);
checkCudaErrors(cudaMemcpyAsync(pProb_host->ptr, pProb_device.ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.param_device.writeAngles), cudaMemcpyDeviceToHost, cudaStream[0]));
checkCudaErrors(cudaMemcpyAsync(pProb_host->ptr, pProb_device.ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.nTotCC, param.param_device.writeAngles, param.param_device.writeCC), cudaMemcpyDeviceToHost, cudaStream[0]));
if (FFTAlgo)
{
......
include/map.h
View file @ e9b15195
......@@ -91,7 +91,7 @@ public:
{
public:
int max_prob_cent_x, max_prob_cent_y, max_prob_orient, max_prob_conv;
myfloat_t max_prob_norm,max_prob_mu;
myfloat_t max_prob_norm,max_prob_mu;
} max;
};
......@@ -105,7 +105,7 @@ public:
class bioem_Probability_cc
{
public:
myfloat_t forCC;
myfloat_t forCC;
};
class bioem_Probability
......@@ -113,39 +113,33 @@ class bioem_Probability
public:
int nMaps;
int nAngles;
int nCC;
int nCC;
__device__ __host__ bioem_Probability_map& getProbMap(int map) {return(ptr_map[map]);}
__device__ __host__ bioem_Probability_angle& getProbAngle(int map, int angle) {return(ptr_angle[angle * nMaps + map]);}
__device__ __host__ bioem_Probability_cc& getProbCC(int map, int cc) {return(ptr_cc[cc * nMaps + map]);}
__device__ __host__ bioem_Probability_cc& getProbCC(int map, int cc) {return(ptr_cc[cc * nMaps + map]);}
void* ptr;
bioem_Probability_map* ptr_map;
bioem_Probability_angle* ptr_angle;
bioem_Probability_cc* ptr_cc;
bioem_Probability_cc* ptr_cc;
static size_t get_size(size_t maps, size_t angles, bool writeAngles)
static size_t get_size(size_t maps, size_t angles, size_t cc, bool writeAngles, bool writeCC)
{
size_t size = sizeof(bioem_Probability_map);
if (writeAngles) size += angles * sizeof(bioem_Probability_angle);
if (writeCC) size += cc * sizeof(bioem_Probability_cc);
return(maps * size);
}
static size_t get_sizeCC(size_t maps, size_t cc, bool writeCC)
{
size_t size = sizeof(bioem_Probability_map);
if (writeCC) size += cc * sizeof(bioem_Probability_cc) ;
return(maps * size);
}
void init(size_t maps, size_t angles, bioem& bio);
void initCC(size_t maps, size_t cc, bioem& bio);
void init(size_t maps, size_t angles, size_t cc, bioem& bio);
void copyFrom(bioem_Probability* from, bioem& bio);
void set_pointers()
{
ptr_map = (bioem_Probability_map*) ptr;
ptr_angle = (bioem_Probability_angle*) (&ptr_map[nMaps]);
ptr_cc = (bioem_Probability_cc*) (&ptr_map[nMaps]);
ptr_cc = (bioem_Probability_cc*) (&ptr_angle[nMaps * nAngles]);
}
};
......
map.cpp
View file @ e9b15195
......@@ -280,23 +280,15 @@ int bioem_RefMap::precalculate(bioem_param& param, bioem& bio)
return(0);
}
void bioem_Probability::init(size_t maps, size_t angles, bioem& bio)
void bioem_Probability::init(size_t maps, size_t angles, size_t cc, bioem& bio)
{
nMaps = maps;
nAngles = angles;
ptr = bio.malloc_device_host(get_size(maps, angles, bio.param.param_device.writeAngles));
nCC = cc;
ptr = bio.malloc_device_host(get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC));
set_pointers();
}
void bioem_Probability::initCC(size_t maps, size_t cc, bioem& bio)
{
nMaps = maps;
nCC = cc;
ptr = bio.malloc_device_host(get_sizeCC(maps, cc, bio.param.param_device.writeCC));
set_pointers();
}
void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
{
bioem_Probability_map& pProbMap = getProbMap(0);
......@@ -305,13 +297,23 @@ void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
if (bio.param.param_device.writeAngles)
{
for (int iOrient = 0; iOrient < bio.param.nTotGridAngles; iOrient ++)
for (int iOrient = 0; iOrient < nAngles; iOrient ++)
{
bioem_Probability_angle& pProbAngle = getProbAngle(0, iOrient);
bioem_Probability_angle& pProbAngleFrom = from->getProbAngle(0, iOrient);
memcpy(&pProbAngle, &pProbAngleFrom, from->nMaps * sizeof(bioem_Probability_angle));
}
}
if (bio.param.param_device.writeCC)
{
for (int iCC = 0; iCC < nCC; iCC ++)
{
bioem_Probability_cc& pProbCC = getProbCC(0, iCC);
bioem_Probability_cc& pProbCCFrom = from->getProbCC(0, iCC);
memcpy(&pProbCC, &pProbCCFrom, from->nMaps * sizeof(bioem_Probability_cc));
}
}
}
int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment