ArrayDesc inferSchema(std::vector<ArrayDesc> schemas, boost::shared_ptr<Query> query)
{
Attributes atts;
atts.push_back(AttributeDesc(0, "attribute_name", TID_STRING, 0, 0));
atts.push_back(AttributeDesc(1, "min", TID_STRING, 0, 0));
atts.push_back(AttributeDesc(2, "max", TID_STRING, 0, 0));
atts.push_back(AttributeDesc(3, "distinct_count", TID_UINT64, 0, 0));
atts.push_back(AttributeDesc(4, "non_null_count", TID_UINT64, 0, 0));
const AttributeDesc *emptyIndicator = schemas[0].getEmptyBitmapAttribute();
set<string> a_s;
for (size_t i = 0; i < _parameters.size(); i++)
{
string attName = ((boost::shared_ptr<OperatorParamReference>&)_parameters[i])->getObjectName();
if (emptyIndicator && emptyIndicator->getName() == attName)
continue;
a_s.insert(attName);
}
size_t attsCount = (a_s.size() == 0 ? (emptyIndicator ? schemas[0].getAttributes().size() - 1 : schemas[0].getAttributes().size()) : a_s.size()) - 1;
Dimensions dims;
dims.push_back(DimensionDesc("attribute_number", 0, attsCount, ANALYZE_CHUNK_SIZE, 0));
return ArrayDesc(schemas[0].getName() + "_analyze", atts, dims);
}
void
Region::setDimensions(Dimensions& newDims)
{
// Can only set dimensions one time
if (dims_ == newDims)
return;
if (dims_.isUnspecified())
{
if (newDims.isDontcare())
{
NTA_THROW << "Invalid attempt to set region dimensions to dontcare value";
}
if (! newDims.isValid())
{
NTA_THROW << "Attempt to set region dimensions to invalid value:"
<< newDims.toString();
}
dims_ = newDims;
dimensionInfo_ = "Specified explicitly in setDimensions()";
} else {
NTA_THROW << "Attempt to set dimensions of region " << getName()
<< " to " << newDims.toString()
<< " but region already has dimensions " << dims_.toString();
}
// can only create the enabled node set after we know the number of dimensions
setupEnabledNodeSet();
}
void ConstRLEChunk::initialize(ArrayDesc const * desc, const Address &address, int compMethod)
{
_hasOverlap = false;
_compressionMethod = compMethod;
_arrayDesc = desc;
_firstPositionNoOlap = address.coords;
_addr = address;
Dimensions dim = desc->getDimensions();
_firstPosition.clear();
_lastPositionNoOlap.clear();
_lastPosition.clear();
_chunkIntervals.clear();
for (uint32_t i = 0; i < dim.size(); ++i)
{
if (dim[i].getChunkOverlap())
{
_hasOverlap = true;
}
_firstPosition.push_back( std::max<Coordinate>(_firstPositionNoOlap[i] - dim[i].getChunkOverlap(), dim[i].getStart()));
_lastPosition.push_back( std::min<Coordinate>(_firstPositionNoOlap[i] + dim[i].getChunkInterval() + 2 * dim[i].getChunkOverlap() - 1, dim[i].getEndMax()));
_lastPositionNoOlap.push_back( std::min<Coordinate>(_firstPositionNoOlap[i] + dim[i].getChunkInterval() - 1, dim[i].getEndMax()));
_chunkIntervals.push_back(_lastPosition[i] - _firstPosition[i] + 1);
}
}
//-*****************************************************************************
// Get the dimensions directly off of the dataspace on the dataset
// This isn't suitable for string and wstring
void
ReadDataSetDimensions( hid_t iParent,
const std::string &iName,
hsize_t iExtent,
Dimensions &oDims )
{
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
// Get the dimensions
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == 1, "H5Sget_simple_extent_ndims() must be 1." );
hsize_t hdim = 0;
rank = H5Sget_simple_extent_dims( dspaceId, &hdim, NULL );
oDims.setRank(1);
oDims[0] = hdim / iExtent;
}
else
{
oDims.setRank(1);
oDims[0] = 0;
}
}
unsigned Pulsar::Transposer::get_ndim (unsigned idim)
{
range_check (idim, "Pulsar::Transposer::get_ndim");
Dimensions dims (archive);
return dims.get_ndim( dim[idim] );
}
// Deserialize region
Region::Region(const std::string& name,
const std::string& nodeType,
const Dimensions& dimensions,
BundleIO& bundle,
Network * network) :
name_(name),
type_(nodeType),
initialized_(false),
enabledNodes_(NULL),
network_(network)
{
// Set region info before creating the RegionImpl so that the
// Impl has access to the region info in its constructor.
RegionImplFactory & factory = RegionImplFactory::getInstance();
spec_ = factory.getSpec(nodeType);
// Dimensions start off as unspecified, but if
// the RegionImpl only supports a single node, we
// can immediately set the dimensions.
if (spec_->singleNodeOnly)
if (!dimensions.isDontcare() && !dimensions.isUnspecified() &&
!dimensions.isOnes())
NTA_THROW << "Attempt to deserialize region of type " << nodeType
<< " with dimensions " << dimensions
<< " but region supports exactly one node.";
dims_ = dimensions;
impl_ = factory.deserializeRegionImpl(nodeType, bundle, this);
createInputsAndOutputs_();
}
void DCAttribute::writeAttribute(const char* name, const hid_t type, hid_t parent,
uint32_t ndims, const Dimensions dims, const void* src)
throw (DCException)
{
hid_t attr = -1;
if (H5Aexists(parent, name))
attr = H5Aopen(parent, name, H5P_DEFAULT);
else
{
hid_t dsp;
if( ndims == 1 && dims.getScalarSize() == 1 )
dsp = H5Screate(H5S_SCALAR);
else
dsp = H5Screate_simple( ndims, dims.getPointer(), dims.getPointer() );
attr = H5Acreate(parent, name, type, dsp, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dsp);
}
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened or created"));
if (H5Awrite(attr, type, src) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be written"));
}
H5Aclose(attr);
}
void SwapChain::Resize(const Dimensions& dimensions)
{
// Release outdated resources
backBuffer_.reset();
depthStencilTexture_.reset();
depthStencilView_.reset();
e_throw_com_ret_error(dxgiSwapChain_
->ResizeBuffers(dxgiSwapChainDesc_.BufferCount,
dimensions.GetWidth(), dimensions.GetHeight(),
dxgiSwapChainDesc_.BufferDesc.Format,
dxgiSwapChainDesc_.Flags), "IDXGISwapChain::ResizeBuffers");
// Temporarily grab the back buffer to get the view
boost::intrusive_ptr<ID3D11Texture2D> tempBackBuffer;
e_throw_com_ret_error(dxgiSwapChain_->GetBuffer(0,
__uuidof(ID3D11Texture2D),
ReceiveCOM(tempBackBuffer)), "IDXGISwapChain::GetBuffer");
// Now get the view
e_throw_com_ret_error(device_.GetD3DDevice()
.CreateRenderTargetView(tempBackBuffer.get(),
0,
ReceiveCOM(backBuffer_)), "ID3D11Device::CreateRenderTargetView");
// Create depth/stencil views
D3D11_TEXTURE2D_DESC depthTextureDesc = {0};
depthTextureDesc.Width = dimensions.GetWidth();
depthTextureDesc.Height = dimensions.GetHeight();
depthTextureDesc.MipLevels = 1;
depthTextureDesc.ArraySize = 1;
depthTextureDesc.Format = DXGI_FORMAT_D24_UNORM_S8_UINT;
depthTextureDesc.SampleDesc.Count = 1;
depthTextureDesc.SampleDesc.Quality = 0;
depthTextureDesc.Usage = D3D11_USAGE_DEFAULT;
depthTextureDesc.BindFlags = D3D11_BIND_DEPTH_STENCIL;
depthTextureDesc.CPUAccessFlags = 0;
depthTextureDesc.MiscFlags = 0;
e_throw_com_ret_error(device_.GetD3DDevice()
.CreateTexture2D(&depthTextureDesc,
NULL,
ReceiveCOM(depthStencilTexture_)), "ID3D11Device::CreateTexture2D");
D3D11_DEPTH_STENCIL_VIEW_DESC depthStencilViewDesc;
memset(&depthStencilViewDesc, 0, sizeof(depthStencilViewDesc));
depthStencilViewDesc.Format = depthTextureDesc.Format;
depthStencilViewDesc.ViewDimension = D3D11_DSV_DIMENSION_TEXTURE2D;
//depthStencilViewDesc.Texture2D.MipSlice = 0;
e_throw_com_ret_error(device_.GetD3DDevice()
.CreateDepthStencilView(depthStencilTexture_.get(),
&depthStencilViewDesc,
ReceiveCOM(depthStencilView_)), "ID3D11Device::CreateDepthStencilView");
e_throw_com_ret_error(dxgiSwapChain_
->SetFullscreenState(window_.GetWindowProperties().windowType == WindowType::FULLSCREEN ? TRUE : FALSE,
NULL), "IDXGISwapChain::SetFullscreenState");
}
const Dimensions<int> Renderer::getOutputSize() const
{
Dimensions<int> ret;
if(isLoaded())
if(SDL_GetRendererOutputSize(ren, ret.x().getPtr(), ret.y().getPtr()) < 0)
return Dimensions<int>(-1, -1);
return ret;
}
ArrayDesc inferSchema(std::vector< ArrayDesc> schemas, boost::shared_ptr< Query> query)
{
Attributes outputAttrs;
outputAttrs.push_back(AttributeDesc(0, "dummy", TID_DOUBLE, AttributeDesc::IS_NULLABLE, 0));
Dimensions outputDims;
outputDims.push_back(DimensionDesc("i",0,0,1,0));
return ArrayDesc("test_cache", outputAttrs, outputDims);
}
ArrayDesc inferSchema(std::vector< ArrayDesc> schemas, boost::shared_ptr< Query> query)
{
assert(schemas.size() == 2);
ArrayDesc const& patternDesc = schemas[0];
ArrayDesc const& catalogDesc = schemas[1];
Attributes const& catalogAttributes = catalogDesc.getAttributes(true);
Dimensions const& catalogDimensions = catalogDesc.getDimensions();
Attributes const& patternAttributes = patternDesc.getAttributes(true);
Dimensions resultDimensions = patternDesc.getDimensions();
size_t totalAttributes = catalogAttributes.size() + patternAttributes.size() + 1 + catalogDimensions.size();
Attributes matchAttributes(totalAttributes);
if (catalogDimensions.size() != resultDimensions.size())
{
stringstream left, right;
printDimNames(left, resultDimensions);
printDimNames(right, catalogDimensions);
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_DIMENSION_COUNT_MISMATCH)
<< "match" << left.str() << right.str();
}
for (size_t i = 0, n = catalogDimensions.size(); i < n; i++) {
if (!(catalogDimensions[i].getStartMin() == resultDimensions[i].getStartMin()
&& catalogDimensions[i].getChunkInterval() == resultDimensions[i].getChunkInterval()
&& catalogDimensions[i].getChunkOverlap() == resultDimensions[i].getChunkOverlap()))
{
// XXX To do: implement requiresRepart() method, remove interval/overlap checks
// above, use SCIDB_LE_START_INDEX_MISMATCH here.
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_ARRAYS_NOT_CONFORMANT);
}
}
size_t j = 0;
for (size_t i = 0, n = patternAttributes.size(); i < n; i++, j++) {
AttributeDesc const& attr = patternAttributes[i];
matchAttributes[j] = AttributeDesc(j, attr.getName(), attr.getType(), attr.getFlags(),
attr.getDefaultCompressionMethod(), attr.getAliases(), &attr.getDefaultValue(),
attr.getDefaultValueExpr());
}
for (size_t i = 0, n = catalogAttributes.size(); i < n; i++, j++) {
AttributeDesc const& attr = catalogAttributes[i];
matchAttributes[j] = AttributeDesc(j, "match_" + attr.getName(), attr.getType(), attr.getFlags(),
attr.getDefaultCompressionMethod(), attr.getAliases(), &attr.getDefaultValue(),
attr.getDefaultValueExpr());
}
for (size_t i = 0, n = catalogDimensions.size(); i < n; i++, j++) {
matchAttributes[j] = AttributeDesc(j, "match_" + catalogDimensions[i].getBaseName(), TID_INT64, 0, 0);
}
matchAttributes[j] = AttributeDesc(j, DEFAULT_EMPTY_TAG_ATTRIBUTE_NAME, TID_INDICATOR, AttributeDesc::IS_EMPTY_INDICATOR, 0);
int64_t maxCollisions = evaluate(((boost::shared_ptr<OperatorParamLogicalExpression>&)_parameters[1])->getExpression(),
query, TID_INT64).getInt64();
if (maxCollisions <= 0 || (int32_t)maxCollisions != maxCollisions) {
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_WRONG_OPERATOR_ARGUMENT2) << "positive";
}
resultDimensions.push_back(DimensionDesc("collision", 0, 0, maxCollisions-1, maxCollisions-1, (uint32_t)maxCollisions, 0));
return ArrayDesc("match", matchAttributes, resultDimensions);
}
virtual PhysicalBoundaries getOutputBoundaries(
std::vector<PhysicalBoundaries> const& inputBoundaries,
std::vector< ArrayDesc> const& inputSchemas) const
{
if (inputBoundaries[0].isEmpty()) {
return PhysicalBoundaries::createEmpty(_schema.getDimensions().size());
}
Coordinates newStart, newEnd;
Coordinates inStart = inputBoundaries[0].getStartCoords();
Coordinates inEnd = inputBoundaries[0].getEndCoords();
Dimensions dims = inputSchemas[0].getDimensions();
size_t nDims = dims.size();
size_t nParams = _parameters.size();
std::vector<std::string> sliceDimName(nParams/2);
for (size_t i = 0; i < nParams; i+=2) {
sliceDimName[i >> 1] = ((std::shared_ptr<OperatorParamReference>&)_parameters[i])->getObjectName();
}
for (size_t i = 0; i < nDims; i++) {
const std::string dimName = dims[i].getBaseName();
int k = safe_static_cast<int>(sliceDimName.size());
while (--k >= 0
&& sliceDimName[k] != dimName
&& !(sliceDimName[k][0] == '_' && (size_t)atoi(sliceDimName[k].c_str()+1) == i+1))
;
if (k < 0) {
//dimension i is present in output
newStart.push_back(inStart[i]);
newEnd.push_back(inEnd[i]);
} else {
//dimension i is not present in output; check value
Coordinate slice = ((std::shared_ptr<OperatorParamPhysicalExpression>&)_parameters[k*2+1])->getExpression()->evaluate().getInt64();
if (!inputBoundaries[0].isInsideBox(slice,i))
{
//the slice value is outside the box; guess what - the result is an empty array
return PhysicalBoundaries::createEmpty(_schema.getDimensions().size());
}
}
}
// This does nothing but calculate a few local values
// and then discard them.
//
// double resultCells = PhysicalBoundaries::getNumCells(newStart, newEnd);
// double origCells = inputBoundaries[0].getNumCells();
// double newDensity = 1.0;
// if (resultCells > 0.0)
// {
// newDensity = inputBoundaries[0].getDensity() * origCells / resultCells;
// newDensity = newDensity > 1.0 ? 1.0 : newDensity;
// }
return PhysicalBoundaries(newStart, newEnd);
}
void openH5File()
{
if (dataCollector == NULL)
{
DataSpace<simDim> mpi_pos;
DataSpace<simDim> mpi_size;
Dimensions splashMpiPos;
Dimensions splashMpiSize;
GridController<simDim> &gc = Environment<simDim>::get().GridController();
mpi_pos = gc.getPosition();
mpi_size = gc.getGpuNodes();
splashMpiPos.set(0, 0, 0);
splashMpiSize.set(1, 1, 1);
for (uint32_t i = 0; i < simDim; ++i)
{
splashMpiPos[i] = mpi_pos[i];
splashMpiSize[i] = mpi_size[i];
}
const uint32_t maxOpenFilesPerNode = 1;
dataCollector = new ParallelDomainCollector(
gc.getCommunicator().getMPIComm(),
gc.getCommunicator().getMPIInfo(),
splashMpiSize,
maxOpenFilesPerNode);
// set attributes for datacollector files
DataCollector::FileCreationAttr h5_attr;
h5_attr.enableCompression = false;
h5_attr.fileAccType = DataCollector::FAT_CREATE;
h5_attr.mpiPosition.set(splashMpiPos);
h5_attr.mpiSize.set(splashMpiSize);
}
// open datacollector
try
{
std::string filename = (foldername + std::string("/makroParticlePerSupercell"));
log<picLog::INPUT_OUTPUT > ("HDF5 open DataCollector with file: %1%") %
filename;
dataCollector->open(filename.c_str(), h5_attr);
}
catch (DCException e)
{
std::cerr << e.what() << std::endl;
throw std::runtime_error("Failed to open datacollector");
}
}
ArrayDesc inferSchema(std::vector< ArrayDesc> schemas, boost::shared_ptr< Query> query)
{
assert(schemas.size() >= 2);
assert(_parameters.size() == 0);
Attributes const& leftAttributes = schemas[0].getAttributes();
Dimensions const& leftDimensions = schemas[0].getDimensions();
Attributes const* newAttributes = &leftAttributes;
Dimensions newDims = leftDimensions;
size_t nDims = newDims.size();
for (size_t j = 1; j < schemas.size(); j++) {
Attributes const& rightAttributes = schemas[j].getAttributes();
Dimensions const& rightDimensions = schemas[j].getDimensions();
if (nDims != rightDimensions.size())
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_ARRAYS_NOT_CONFORMANT);
for (size_t i = 0; i < nDims; i++) {
if ( leftDimensions[i].getStart() != rightDimensions[i].getStart()
|| leftDimensions[i].getChunkInterval() != rightDimensions[i].getChunkInterval()
|| leftDimensions[i].getChunkOverlap() != rightDimensions[i].getChunkOverlap())
{
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_ARRAYS_NOT_CONFORMANT);
}
DimensionDesc& dim = newDims[i];
dim = DimensionDesc(dim.getBaseName(),
dim.getNamesAndAliases(),
min(dim.getStartMin(), rightDimensions[i].getStartMin()),
min(dim.getCurrStart(), rightDimensions[i].getCurrStart()),
max(dim.getCurrEnd(), rightDimensions[i].getCurrEnd()),
max(dim.getEndMax(), rightDimensions[i].getEndMax()),
dim.getChunkInterval(),
dim.getChunkOverlap());
}
if (leftAttributes.size() != rightAttributes.size()
&& (leftAttributes.size() != rightAttributes.size()+1
|| !leftAttributes[leftAttributes.size()-1].isEmptyIndicator())
&& (leftAttributes.size()+1 != rightAttributes.size()
|| !rightAttributes[rightAttributes.size()-1].isEmptyIndicator()))
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_ARRAYS_NOT_CONFORMANT);
size_t nAttrs = min(leftAttributes.size(), rightAttributes.size());
if (rightAttributes.size() > newAttributes->size()) {
newAttributes = &rightAttributes;
}
for (size_t i = 0; i < nAttrs; i++)
{
if (leftAttributes[i].getType() != rightAttributes[i].getType()
|| leftAttributes[i].getFlags() != rightAttributes[i].getFlags())
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_ARRAYS_NOT_CONFORMANT);
}
}
return ArrayDesc(schemas[0].getName(), *newAttributes, newDims);
}
ArrayDesc inferSchema(std::vector<ArrayDesc> schemas, boost::shared_ptr<Query> query)
{
ArrayDesc const& input = schemas[0];
assert(schemas.size() == 1);
string attName = _parameters.size() > 0 ? ((boost::shared_ptr<OperatorParamReference>&)_parameters[0])->getObjectName() :
input.getAttributes()[0].getName();
AttributeID inputAttributeID = 0;
bool found = false;
BOOST_FOREACH(const AttributeDesc& att, input.getAttributes())
{
if (att.getName() == attName)
{
found = true;
inputAttributeID = att.getId();
}
}
if (!found) {
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_DLA_ERROR14);
}
AttributeDesc rankedAttribute = input.getAttributes()[inputAttributeID];
if (rankedAttribute.isEmptyIndicator()) {
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_DLA_ERROR15);
}
Dimensions dims = input.getDimensions();
if (_parameters.size()>1)
{
vector<int> groupBy(_parameters.size()-1);
size_t i, j;
for (i = 0; i < _parameters.size() - 1; i++)
{
const string& dimName = ((boost::shared_ptr<OperatorParamReference>&)_parameters[i + 1])->getObjectName();
const string& dimAlias = ((boost::shared_ptr<OperatorParamReference>&)_parameters[i + 1])->getArrayName();
for (j = 0; j < dims.size(); j++)
{
if (dims[j].hasNameAndAlias(dimName, dimAlias))
{
break;
}
}
if (j >= dims.size())
throw USER_EXCEPTION(SCIDB_SE_INFER_SCHEMA, SCIDB_LE_DIMENSION_NOT_EXIST) << dimName;
}
}
return getRankingSchema(input, inputAttributeID);
}
inline void convertCoordinates(Coordinates const& srcPos, Dimensions const& srcDims, Coordinates& dstPos, Dimensions const& dstDims)
{
Coordinate offset = 0;
for (size_t i = 0, n = srcDims.size(); i < n; i++) {
offset *= srcDims[i].getLength();
offset += srcPos[i] - srcDims[i].getStart();
}
for (int i = dstDims.size(); --i >= 0;) {
dstPos[i] = dstDims[i].getStart() + (offset % dstDims[i].getLength());
offset /= dstDims[i].getLength();
}
}
TEST_F(DimensionsTest, DontCareDimensions) {
// dontcare dimensions [0]
Dimensions d;
d.push_back(0);
ASSERT_TRUE(!d.isUnspecified());
ASSERT_TRUE(d.isDontcare());
ASSERT_TRUE(d.isValid());
EXPECT_STREQ("[dontcare]", d.toString().c_str());
ASSERT_ANY_THROW(d.getIndex(zero));
ASSERT_ANY_THROW(d.getCount());
ASSERT_EQ((unsigned int)0, d.getDimension(0));
ASSERT_EQ((unsigned int)1, d.getDimensionCount());
}
inline Surface::self_ref
Surface::setSize(Dimensions<> dim)
{
this->dimensions_ = dim;
cairo_xcb_surface_set_size(
this->cairoSurface_.get(),
dim.width(),
dim.height()
);
return *this;
}
int detectFileMPISize(Options& options, Dimensions &fileMPISizeDim)
{
int result = RESULT_OK;
DataCollector *dc = NULL;
#if (SPLASH_SUPPORTED_PARALLEL==1)
if (options.parallelFile)
dc = new ParallelDataCollector(MPI_COMM_WORLD, MPI_INFO_NULL,
Dimensions(options.mpiSize, 1, 1), 1);
else
#endif
dc = new SerialDataCollector(1);
DataCollector::FileCreationAttr fileCAttr;
DataCollector::initFileCreationAttr(fileCAttr);
fileCAttr.fileAccType = DataCollector::FAT_READ;
try
{
dc->open(options.filename.c_str(), fileCAttr);
dc->getMPISize(fileMPISizeDim);
dc->close();
} catch (DCException e)
{
std::cerr << "[0] Detecting file MPI size failed!" << std::endl <<
e.what() << std::endl;
fileMPISizeDim.set(0, 0, 0);
result = RESULT_ERROR;
}
delete dc;
dc = NULL;
return result;
}
void PlayerData::GenerateVertices(Dimensions &dimensions)
{
float widthX = dimensions.getWidth()/2.0f;
float heightY = dimensions.getHeight()/2.0f;
float x= dimensions.getPosition().getX();
float y=dimensions.getPosition().getY();
vertices.clear();
vertices.push_back({glm::vec2(-widthX+x,-heightY+y)});
vertices.push_back({glm::vec2(widthX+x,-heightY+y)});
vertices.push_back({glm::vec2(widthX+x,heightY+y)});
vertices.push_back({glm::vec2(-widthX+x,heightY+y)});
vertices.push_back({glm::vec2(-widthX+x,-heightY+y)});
vertices.push_back({glm::vec2(widthX+x,heightY+y)});
}
void log4cxx_debug_dimensions(const std::string& prefix, const Dimensions& dims)
{
if(logger->isDebugEnabled()) {
for (size_t i=0; i<dims.size(); i++) {
LOG4CXX_DEBUG(logger, prefix << " dims["<<i<<"] from " << dims[i].getStartMin() << " to " << dims[i].getEndMax());
}
}
}
bool
Dimensions::operator==(const Dimensions& dims2) const
{
if ((std::vector<size_t>)(*this) == (std::vector<size_t>)dims2)
return true;
if (isOnes() && dims2.isOnes())
return true;
return false;
}
set<Type>
Library::getRealAtomTypes() const{
set<Type> s;
struct gl_list_t *l = DefinitionList();
if(!l){
throw runtime_error("No types found in library (perhaps no files have been loaded?)");
}
for(unsigned i = 1; i<=gl_length(l); ++i) {
Type t((const struct TypeDescription *)gl_fetch(l,i));
if(t.isRefinedReal()){
Dimensions d = t.getDimensions();
if(d.isWild() || d.isDimensionless())continue; // skip this one
// it's got some dimensions, add it to the list
s.insert(t);
}
}
gl_destroy(l);
return s;
}
void DCDataSet::create(const CollectionType& colType,
hid_t group, const Dimensions size, uint32_t ndims, bool compression)
throw (DCException)
{
log_msg(2, "DCDataSet::create (%s, size %s)", name.c_str(), size.toString().c_str());
if (opened)
throw DCException(getExceptionString("create: dataset is already open"));
// if the dataset already exists, remove/unlink it
// note that this won't free the memory occupied by this
// dataset, however, there currently is no function to delete
// a dataset
if (!checkExistence || (checkExistence && H5Lexists(group, name.c_str(), H5P_LINK_ACCESS_DEFAULT)))
H5Ldelete(group, name.c_str(), H5P_LINK_ACCESS_DEFAULT);
this->ndims = ndims;
this->compression = compression;
this->datatype = colType.getDataType();
getLogicalSize().set(size);
setChunking(colType.getSize());
setCompression();
if (getPhysicalSize().getScalarSize() != 0)
{
hsize_t *max_dims = new hsize_t[ndims];
for (size_t i = 0; i < ndims; ++i)
max_dims[i] = H5F_UNLIMITED;
dataspace = H5Screate_simple(ndims, getPhysicalSize().getPointer(), max_dims);
delete[] max_dims;
max_dims = NULL;
} else
dataspace = H5Screate(H5S_NULL);
if (dataspace < 0)
throw DCException(getExceptionString("create: Failed to create dataspace"));
// create the new dataset
dataset = H5Dcreate(group, this->name.c_str(), this->datatype, dataspace,
H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("create: Failed to create dataset"));
isReference = false;
opened = true;
}
//-*****************************************************************************
// Dimensions aren't a scalar, and thus must be read carefully.
void
ReadDimensions( hid_t iParent,
const std::string &iAttrName,
Dimensions &oDims )
{
// Assume a maximum rank of 128. This is totally reasonable.
uint32_t dimVals[128];
size_t readRank;
ReadSmallArray( iParent, iAttrName, H5T_STD_U32LE, H5T_NATIVE_UINT32,
128, readRank, ( void * )dimVals );
Dimensions retDims;
retDims.setRank( readRank );
for ( size_t r = 0; r < readRank; ++r )
{
retDims[r] = ( size_t )dimVals[r];
}
oDims = retDims;
}
static
void
fillGrid(Grid<GridT>& grid,
const Dimensions<DIM>& dimensions,
const std::array<int, DIM>& numberOfUnknownsPerDim)
{
for (uint i = 0; i < DIM; ++i) {
fillGrid(grid,
dimensions.dimension(i),
numberOfUnknownsPerDim[i]);
}
}
Pulsar::Dimensions Pulsar::Transposer::get_stride (const Dimensions& d) const
{
int increment = 1;
Dimensions stride;
stride.set_ndim (dim[0], increment);
increment *= d.get_ndim (dim[0]);
stride.set_ndim (dim[1], increment);
increment *= d.get_ndim (dim[1]);
stride.set_ndim (dim[2], increment);
increment *= d.get_ndim (dim[2]);
stride.set_if_zero (increment);
return stride;
}
void DCDataSet::createReference(hid_t refGroup,
hid_t srcGroup,
DCDataSet &srcDataSet,
Dimensions count,
Dimensions offset,
Dimensions stride)
throw (DCException)
{
if (opened)
throw DCException(getExceptionString("createReference: dataset is already open"));
if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
throw DCException(getExceptionString("createReference: this reference already exists"));
getLogicalSize().set(count);
this->ndims = srcDataSet.getNDims();
count.swapDims(this->ndims);
offset.swapDims(this->ndims);
stride.swapDims(this->ndims);
// select region hyperslab in source dataset
if (H5Sselect_hyperslab(srcDataSet.getDataSpace(), H5S_SELECT_SET,
offset.getPointer(), stride.getPointer(),
count.getPointer(), NULL) < 0 ||
H5Sselect_valid(srcDataSet.getDataSpace()) <= 0)
throw DCException(getExceptionString("createReference: failed to select hyperslap for reference"));
if (H5Rcreate(®ionRef, srcGroup, srcDataSet.getName().c_str(), H5R_DATASET_REGION,
srcDataSet.getDataSpace()) < 0)
throw DCException(getExceptionString("createReference: failed to create region reference"));
hsize_t ndims = 1;
dataspace = H5Screate_simple(1, &ndims, NULL);
if (dataspace < 0)
throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));
dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_DSETREG,
dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("createReference: failed to create dataset for reference"));
if (H5Dwrite(dataset, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
dsetWriteProperties, ®ionRef) < 0)
throw DCException(getExceptionString("createReference: failed to write reference"));
isReference = true;
opened = true;
}
END_TEST
START_TEST (test_Dimensions_createWithSize)
{
Dimensions* d = new(std::nothrow) Dimensions( 1.2 , 0.4 , 3.1415 );
fail_unless( d->getTypeCode () == SBML_LAYOUT_DIMENSIONS );
fail_unless( d->getMetaId () == "" );
// fail_unless( d->getNotes () == "" );
// fail_unless( d->getAnnotation () == "" );
fail_unless( d->getWidth () == 1.2 );
fail_unless( d->getHeight() == 0.4 );
fail_unless( d->getDepth () == 3.1415 );
delete d;
}
//-*****************************************************************************
// Dimensions aren't a scalar, and thus must be written carefully.
void
WriteDimensions( hid_t iParent,
const std::string &iAttrName,
const Dimensions &iDims )
{
size_t rank = iDims.rank();
// Create temporary storage to write
std::vector<uint32_t> dimStorage( rank );
// Copy into it.
for ( size_t r = 0; r < rank; ++r )
{
dimStorage[r] = ( uint32_t )iDims[r];
}
WriteSmallArray( iParent, iAttrName, H5T_STD_U32LE,
H5T_NATIVE_UINT32,
rank,
( const void * )&dimStorage.front() );
}