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Commit d28d761d authored by Andrew J. Burns (Cont's avatar Andrew J. Burns (Cont
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fixed some issues with adding to previously created files

parent 73ceb409
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Showing with 139 additions and 80 deletions
core/XdmfHDF5Writer.cpp
View file @ d28d761d
......@@ -370,6 +370,7 @@ XdmfHDF5Writer::write(XdmfArray & array,
std::list<std::vector<unsigned int> > stridesWritten;
std::list<std::vector<unsigned int> > dimensionsWritten;
std::list<std::vector<unsigned int> > dataSizesWritten;
std::list<unsigned int> arrayOffsetsWritten;
// Open a hdf5 dataset and write to it on disk.
hsize_t size = array.getSize();
......@@ -392,7 +393,16 @@ XdmfHDF5Writer::write(XdmfArray & array,
shared_ptr<XdmfHeavyDataController> heavyDataController =
previousControllers[i];
//stats for the data currently stored in the array
const std::vector<unsigned int> & dimensions = heavyDataController->getDimensions();
std::vector<unsigned int> dimensions;
if (mMode != Hyperslab)
{
dimensions = array.getDimensions();
}
else
{
dimensions = heavyDataController->getDimensions();
}
std::vector<unsigned int> dataspaceDimensions = dimensions;
std::vector<unsigned int> start(dimensions.size(), 0);
std::vector<unsigned int> stride(dimensions.size(), 1);
......@@ -438,6 +448,7 @@ XdmfHDF5Writer::write(XdmfArray & array,
//check if slab already exists
int numData = mImpl->openFile(hdf5FilePath,
fapl);
printf("number of data items in the hyperslab = %d\n", numData);
if (numData > 0) {//if it already exists the file does not need to be split.
splittingPossible = false;
}
......@@ -880,6 +891,7 @@ else
//if the array hasn't been split
if (amountAlreadyWritten == 0)
{
printf("fits and isn't split\n");
//just pass all data to the partial vectors
for (int j = 0; j < dimensions.size(); j++)//done using a loop so that data is copied, not referenced
{
......@@ -891,6 +903,7 @@ else
}
else//if the array has been split
{
printf("fits and is split\n");
int dimensionIndex = previousDimensions.size() - 1;
//loop previous dimensions in
......@@ -978,15 +991,24 @@ else
else//otherwise, take remaining size and start removing dimensions until the dimension block is less, then take a fraction of the dimension
{
//calculate the number of values of the data type you're using will fit
printf("file size limit = %d\npreviousDataSize = %d\nfileSize = %d\nbyte size = %d\n", mImpl->mHDF5FileSizeLimit*(1024*1024), previousDataSize, fileSize,
(mImpl->mHDF5FileSizeLimit*(1024*1024) - (previousDataSize + fileSize)));
unsigned int usableSpace = (mImpl->mHDF5FileSizeLimit*(1024*1024) - (previousDataSize + fileSize)) / dataItemSize;
if (mImpl->mHDF5FileSizeLimit*(1024*1024) < (previousDataSize + fileSize))
{
usableSpace = 0;
}
//if the array hasn't been split
if (amountAlreadyWritten == 0)
{
printf("doesn't fit and isn't split\n");
//see if it will fit in the next file
//if it will just go to the next file
//otherwise split it.
printf("usableSpace before check = %d\n", usableSpace);
if ((remainingValues * dataItemSize) + 800 > mImpl->mHDF5FileSizeLimit*(1024*1024) && usableSpace > 0)
{
//figure out the size of the largest block that will fit.
unsigned int blockSizeSubtotal = 1;
int dimensionIndex = 0;
......@@ -1002,6 +1024,7 @@ else
//determine how many of those blocks will fit
unsigned int numBlocks = usableSpace / blockSizeSubtotal;//this should be less than the current value for the dimension
printf("numBlocks = %d\nusableSpace = %d\nblockSizeSubtotal = %d\n", numBlocks, usableSpace, blockSizeSubtotal);
//add dimensions as required.
int j = 0;
......@@ -1024,6 +1047,10 @@ else
{//for hyperslab in general
//determine how many values from the array will fit into the blocks being used with the dimensions specified
unsigned int displacement = (numBlocks - start[j]) / stride[j];
if (numBlocks - (displacement * stride[j]) - start[j] > 0)
{
displacement++;
}
if (dimensions[j] <= displacement)//if there are less values than there are space for, just write all of them.
{
partialDimensions.push_back(dimensions[j]);
......@@ -1037,6 +1064,7 @@ else
}
else//if the array has been split
{//This case should not come up often as it requires truly gigantic data sets
printf("doesn't fit and is split\n");
//see if it will fit in the next file
//if it will just go to the next file
//otherwise split it.
......@@ -1086,7 +1114,10 @@ else
//determine how many values from the array will fit into the blocks being used
//with the dimensions specified
unsigned int displacement = (numBlocks - newStart) / stride[j];
if (numBlocks - (displacement * stride[j]) - newStart > 0)
{
displacement++;
}
if ((dimensions[j] - previousDimensions[j]) <= displacement)
{//if there are less values than there are space for, just write all of them.
partialDimensions.push_back(dimensions[j] - previousDimensions[j]);
......@@ -1124,44 +1155,65 @@ else
}
}
if (partialDimensions.size() > 0)
{//building the array to be written
int containedInDimensions = 1;//count moved
unsigned int startTotal = 0;
for (int j = 0 ; j < partialDimensions.size(); j++)
{
if (mMode == Hyperslab)
{
startTotal += partialStarts[j] * containedInDimensions;
}
containedInDimensions *= partialDimensions[j];
printf("contained in dimensions = %d\n", containedInDimensions);
}
int containedInPriorDimensions = controllerIndexOffset;//starting index
printf("controller index offset for pulling array data %d\n", controllerIndexOffset);
int startOffset = 1;
for (int j = 0; j < previousDimensions.size(); j++)
for (int j = 0; j < previousDataSizes.size(); j++)
{
startOffset *= previousDimensions[j];
startOffset *= previousDataSizes[j];
}
if (previousDimensions.size() == 0)
if (previousDataSizes.size() == 0)
{
startOffset = 0;
}
containedInPriorDimensions += startOffset;
printf("total index offset for pulling array data %d\n", containedInPriorDimensions);
int dimensionTotal = 1;
for (int j = 0; j < dimensions.size(); j++)
{
printf("dimension[%d] = %d\n", j, dimensions[j]);
dimensionTotal *= dimensions[j];
}
if (containedInDimensions + containedInPriorDimensions == dimensionTotal)
//start = partialStarts multiplied together + amount already written
//stride = strides multiplied together
unsigned int totalStride = 1;
if (mMode == Hyperslab)
{
for (int j = 0; j < partialStrides.size(); j++)
{
totalStride*=partialStrides[j];
}
}
if (containedInDimensions*totalStride + containedInPriorDimensions == dimensionTotal)
{
controllerIndexOffset += dimensionTotal;
}
shared_ptr<XdmfArray> partialArray = XdmfArray::New();
if (datatype == H5T_NATIVE_CHAR){
partialArray->initialize(XdmfArrayType::Int8(), 0);
char movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1169,7 +1221,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::Int16(), 0);
short movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1177,7 +1229,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::Int32(), 0);
int movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1185,7 +1237,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::Int64(), 0);
long movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1193,7 +1245,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::Float32(), 0);
float movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
......@@ -1202,7 +1254,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::Float64(), 0);
double movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1210,7 +1262,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::UInt8(), 0);
unsigned char movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1218,7 +1270,7 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::UInt16(), 0);
unsigned short movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
......@@ -1226,12 +1278,12 @@ if (partialDimensions.size() > 0)
partialArray->initialize(XdmfArrayType::UInt32(), 0);
unsigned int movedData [containedInDimensions];
array.getValues(containedInPriorDimensions, movedData, containedInDimensions);
array.getValues(containedInPriorDimensions + startTotal, movedData, containedInDimensions, totalStride);
partialArray->insert(0, movedData, containedInDimensions);
}
else if (closeDatatype) {//closeDatatype is only true if strings are being used
partialArray->initialize(XdmfArrayType::String(), 0);
for (int j = containedInPriorDimensions; j < containedInPriorDimensions + containedInDimensions; j++){
for (int j = containedInPriorDimensions + startTotal; j < containedInPriorDimensions + containedInDimensions*totalStride; j+=totalStride){
partialArray->pushBack(array.getValue<std::string>(j));
}
}
......@@ -1243,7 +1295,7 @@ if (partialDimensions.size() > 0)
stridesWritten.push_back(partialStrides);
dimensionsWritten.push_back(partialDimensions);
dataSizesWritten.push_back(partialDataSizes);
arrayOffsetsWritten.push_back(containedInPriorDimensions);
//for hyperslab the space is controlled by the dataspace dimensions
//so use that since the dimensions should be equal to the dataspace dimensions in all other variations
......@@ -1357,12 +1409,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize() ; j++){
partialArray->pushBack(array.getValue<char>(j));
}
*/
}
else if (datatype == H5T_NATIVE_SHORT){
partialArray->initialize(XdmfArrayType::Int16(), 0);
......@@ -1377,12 +1423,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<short>(j));
}
*/
}
else if (datatype == H5T_NATIVE_INT){
partialArray->initialize(XdmfArrayType::Int32(), 0);
......@@ -1397,12 +1437,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<int>(j));
}
*/
}
else if (datatype == H5T_NATIVE_LONG){
partialArray->initialize(XdmfArrayType::Int64(), 0);
......@@ -1417,12 +1451,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<long>(j));
}
*/
}
else if (datatype == H5T_NATIVE_FLOAT){
partialArray->initialize(XdmfArrayType::Float32(), 0);
......@@ -1437,12 +1465,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<float>(j));
}
*/
}
else if (datatype == H5T_NATIVE_DOUBLE){
partialArray->initialize(XdmfArrayType::Float64(), 0);
......@@ -1457,12 +1479,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<double>(j));
}
*/
}
else if (datatype == H5T_NATIVE_UCHAR){
partialArray->initialize(XdmfArrayType::UInt8(), 0);
......@@ -1477,12 +1493,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<unsigned char>(j));
}
*/
}
else if (datatype == H5T_NATIVE_USHORT){
partialArray->initialize(XdmfArrayType::UInt16(), 0);
......@@ -1497,12 +1507,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<unsigned short>(j));
}
*/
}
else if (datatype == H5T_NATIVE_UINT) {
partialArray->initialize(XdmfArrayType::UInt32(), 0);
......@@ -1517,12 +1521,6 @@ if (mMode == Append) {
array.getValues(controllerIndexOffset, movedData, movedSize);
partialArray->insert(0, movedData, movedSize);
j+=movedSize;
/*
for (j = controllerIndexOffset; j < controllerIndexOffset + heavyDataController->getSize() && j < array.getSize(); j++){
partialArray->pushBack(array.getValue<unsigned int>(j));
}
*/
}
else if (closeDatatype) {//closeDatatype is only true if strings are being used
partialArray->initialize(XdmfArrayType::String(), 0);
......@@ -1532,11 +1530,11 @@ if (mMode == Append) {
}
}
controllerIndexOffset = j;//set the offset to the point after the end of the current subset
if (partialArray->getSize()==0) {
break;
}
arrayOffsetsWritten.push_back(controllerIndexOffset);
controllerIndexOffset = j;//set the offset to the point after the end of the current subset
arraysWritten.push_back(partialArray);
filesWritten.push_back(hdf5FilePath);
......@@ -1562,6 +1560,7 @@ if (mMode == Append) {
std::list<std::vector<unsigned int> >::iterator strideWalker = stridesWritten.begin();
std::list<std::vector<unsigned int> >::iterator dimensionWalker = dimensionsWritten.begin();
std::list<std::vector<unsigned int> >::iterator dataSizeWalker = dataSizesWritten.begin();
std::list<unsigned int>::iterator arrayOffsetWalker = arrayOffsetsWritten.begin();
//loop based on the amount of blocks split from the array.
......@@ -1573,7 +1572,19 @@ if (mMode == Append) {
std::vector<unsigned int> curStride = *strideWalker;
std::vector<unsigned int> curDimensions = *dimensionWalker;
std::vector<unsigned int> curDataSize = *dataSizeWalker;
unsigned int curArrayOffset = *arrayOffsetWalker;
printf("filename = %s\n", curFileName);
for (int j = 0; j < curStart.size(); j++)
{
printf("start[%d] = %d\n", j, curStart[j]);
}
for (int j = 0; j < curStride.size(); j++)
{
printf("stride[%d] = %d\n", j, curStride[j]);
}
printf("array start offset = %d\n", curArrayOffset);
printf("array contains:\n%s\n", curArray->getValuesString());
bool closeFile = false;
......@@ -1836,6 +1847,8 @@ if (mMode == Append) {
curDataSize);
}
newDataController->setArrayOffset(curArrayOffset);
array.insert(newDataController);
fileNameWalker++;
......@@ -1844,6 +1857,7 @@ if (mMode == Append) {
strideWalker++;
dimensionWalker++;
dataSizeWalker++;
arrayOffsetWalker++;
}
......
core/XdmfHeavyDataController.cpp
View file @ d28d761d
......@@ -40,7 +40,8 @@ XdmfHeavyDataController::XdmfHeavyDataController(const std::string & filePath,
mFilePath(filePath),
mStart(start),
mStride(stride),
mType(type)
mType(type),
mArrayStartOffset(0)
{
if(!(mStart.size() == mStride.size() &&
mStride.size() == mDimensions.size()))
......@@ -85,6 +86,18 @@ XdmfHeavyDataController::getSize() const
std::multiplies<unsigned int>());
}
void
XdmfHeavyDataController::setArrayOffset(unsigned int newOffset)
{
mArrayStartOffset = newOffset;
}
unsigned int
XdmfHeavyDataController::getArrayOffset() const
{
return mArrayStartOffset;
}
std::vector<unsigned int>
XdmfHeavyDataController::getStart() const
{
......
core/XdmfHeavyDataController.hpp
View file @ d28d761d
......@@ -184,6 +184,38 @@ public:
*/
unsigned int getSize() const;
/**
* For use in conjunction with heavy data controllers set to arrays, the offset within the array from which the controller will be inserted
* Is also set when created by a writer.
*
* C++
*
* @dontinclude ExampleXdmfHeavyDataController.cpp
*
* Python
*
* @dontinclude XdmfExampleHeavyDataController.py
*
* @param newOffset the new index at which the controller will be written
*/
void setArrayOffset(unsigned int newOffset);
/**
* Gets the index at which the controller will offset when an array reads it from its associated controllers.
* Set when created by a Writer or set manually.
*
* C++
*
* @dontinclude ExampleXdmfHeavyDataController.cpp
*
* Python
*
* @dontinclude XdmfExampleHeavyDataController.py
*
* @return the offset that the array will read from
*/
unsigned int getArrayOffset() const;
/**
* Get the start index of the heavy data set owned by this controller.
*
......@@ -266,6 +298,7 @@ protected:
const std::string mFilePath;
const std::vector<unsigned int> mStart;
const std::vector<unsigned int> mStride;
unsigned int mArrayStartOffset;
const shared_ptr<const XdmfArrayType> mType;
private:
......
tests/Cxx/HugeWriteArray.cpp
View file @ d28d761d
......@@ -14,7 +14,7 @@ int main(int, char **)
{
writtenArray->pushBack(i);
}
std::vector<unsigned int> starts;
/* std::vector<unsigned int> starts;
std::vector<unsigned int> strides;
std::vector<unsigned int> dimensions;
std::vector<unsigned int> dataspaces;
......@@ -38,15 +38,14 @@ int main(int, char **)
writtenArray->insert(arrayController);
starts[0] = 5;
arrayController = XdmfHDF5Controller::New("arraydata.h5", "Data", XdmfArrayType::Int32(), starts, strides, dimensions, dataspaces);
writtenArray->insert(arrayController);
writtenArray->insert(arrayController);*/
shared_ptr<XdmfHDF5Writer> arrayHeavyWriter = XdmfHDF5Writer::New("arraydata.h5");
arrayHeavyWriter->setFileSizeLimit(1);
arrayHeavyWriter->setMode(XdmfHDF5Writer::Hyperslab);
// arrayHeavyWriter->setMode(XdmfHDF5Writer::Hyperslab);
shared_ptr<XdmfWriter> arrayWriter = XdmfWriter::New("arraydata.xmf", arrayHeavyWriter);
arrayWriter->setLightDataLimit(5);
writtenArray->accept(arrayWriter);
printf("%s\n\n", writtenArray->getValuesString());
writtenArray->release();
printf("after release\narray contains: %s\n", writtenArray->getValuesString());
writtenArray->read();
......
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