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allocating page-aligned memory #210

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Oct 31, 2019
Merged

allocating page-aligned memory #210

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29 changes: 15 additions & 14 deletions src/xmipp/libraries/reconstruction/reconstruct_fourier_buffer_data.h
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
#define XMIPP_LIBRARIES_DATA_RECONSTRUCT_FOURIER_BUFFER_DATA_H_

#include "reconstruct_fourier_projection_traverse_space.h"
#include "core/utils/memory_utils.h"

/**
* Struct holding data for calculating Fourier Reconstruction
Expand All @@ -51,31 +52,31 @@ struct RecFourierBufferData
hasFFTs(hasFFTs), hasCTFs(hasCTFs),
fftSizeX(fftSizeX), fftSizeY(fftSizeY), paddedImgSize(paddedImgSize),
maxNoOfImages(maxNoOfImages),noOfSymmetries(noOfSymmetries), noOfImages(0) {
spaces = new RecFourierProjectionTraverseSpace[maxNoOfImages * noOfSymmetries];
spaces = memoryUtils::page_aligned_alloc<RecFourierProjectionTraverseSpace>(maxNoOfImages * noOfSymmetries, false);
if (hasFFTs) {
paddedImages = NULL;
FFTs = new float[fftSizeX * fftSizeY * maxNoOfImages * 2](); // *2 since it's complex
paddedImages = nullptr;
FFTs = memoryUtils::page_aligned_alloc<float>(fftSizeX * fftSizeY * maxNoOfImages * 2, true); // *2 since it's complex
} else {
FFTs = NULL;
paddedImages = new float[paddedImgSize * paddedImgSize * maxNoOfImages]();
FFTs = nullptr;
paddedImages = memoryUtils::page_aligned_alloc<float>(paddedImgSize * paddedImgSize * maxNoOfImages, true);
}

if (hasCTFs) {
CTFs = new float[fftSizeX * fftSizeY * maxNoOfImages]();
modulators = new float[fftSizeX * fftSizeY * maxNoOfImages]();
CTFs = memoryUtils::page_aligned_alloc<float>(fftSizeX * fftSizeY * maxNoOfImages, true);
modulators = memoryUtils::page_aligned_alloc<float>(fftSizeX * fftSizeY * maxNoOfImages, true);
} else {
CTFs = modulators = NULL;
CTFs = modulators = nullptr;
}
};

~RecFourierBufferData() {
delete[] FFTs;
delete[] CTFs;
delete[] paddedImages;
delete[] modulators;
FFTs = CTFs = paddedImages = modulators = NULL;
free(FFTs);
free(CTFs);
free(paddedImages);
free(modulators);
FFTs = CTFs = paddedImages = modulators = nullptr;

delete[] spaces;
free(spaces);
spaces = NULL;
}

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7 changes: 5 additions & 2 deletions src/xmipp/libraries/reconstruction_adapt_cuda/reconstruct_fourier_gpu.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -422,7 +422,8 @@ void* ProgRecFourierGPU::threadRoutine(void* threadArgs) {
GPU::setDevice(parent->device);

// allocate buffer
threadParams->buffer = new RecFourierBufferData( ! parent->fftOnGPU, hasCTF,
void *rawMem = memoryUtils::page_aligned_alloc<RecFourierBufferData>(1, false);
threadParams->buffer = new(rawMem) RecFourierBufferData( ! parent->fftOnGPU, hasCTF, // placement of the object to specific location
parent->maxVolumeIndexX / 2, parent->maxVolumeIndexYZ, parent->paddedImgSize,
parent->bufferSize, (int)parent->R_repository.size());
pinMemory(threadParams->buffer);
Expand Down Expand Up @@ -455,8 +456,10 @@ void* ProgRecFourierGPU::threadRoutine(void* threadArgs) {

// clean after itself
releaseWrapper(threadParams->gpuStream);
threadParams->buffer->~RecFourierBufferData(); // <- explicit destructor call
free(rawMem);
unpinMemory(threadParams->buffer);
delete threadParams->buffer;
free(threadParams->buffer);
threadParams->buffer = NULL;
threadParams->selFile = NULL;
barrier_wait( &parent->barrier );// notify that thread finished
Expand Down