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SerialDataCollector.cpp
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SerialDataCollector.cpp
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/**
* Copyright 2013-2015 Felix Schmitt, Axel Huebl
*
* This file is part of libSplash.
*
* libSplash is free software: you can redistribute it and/or modify
* it under the terms of of either the GNU General Public License or
* the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* libSplash is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License and the GNU Lesser General Public License
* for more details.
*
* You should have received a copy of the GNU General Public License
* and the GNU Lesser General Public License along with libSplash.
* If not, see <http://www.gnu.org/licenses/>.
*/
#include <cstring>
#include <time.h>
#include <stdlib.h>
#include <cassert>
#include <sys/stat.h>
#include "splash/SerialDataCollector.hpp"
#include "splash/basetypes/basetypes.hpp"
#include "splash/core/DCAttribute.hpp"
#include "splash/core/DCDataSet.hpp"
#include "splash/core/DCGroup.hpp"
#include "splash/core/DCHelper.hpp"
#include "splash/core/SDCHelper.hpp"
#include "splash/core/logging.hpp"
#include "splash/basetypes/basetypes.hpp"
namespace splash
{
/*******************************************************************************
* PRIVATE FUNCTIONS
*******************************************************************************/
void SerialDataCollector::setFileAccessParams(hid_t& fileAccProperties)
{
fileAccProperties = H5P_FILE_ACCESS_DEFAULT;
int metaCacheElements = 0;
size_t rawCacheElements = 0;
size_t rawCacheSize = 0;
double policy = 0.0;
// set new cache size
H5Pget_cache(fileAccProperties, &metaCacheElements, &rawCacheElements, &rawCacheSize, &policy);
rawCacheSize = 256 * 1024 * 1024;
H5Pset_cache(fileAccProperties, metaCacheElements, rawCacheElements, rawCacheSize, policy);
log_msg(3, "Raw Data Cache (File) = %llu KiB", (long long unsigned) (rawCacheSize / 1024));
}
bool SerialDataCollector::fileExists(std::string filename)
{
struct stat fileInfo;
return (stat(filename.c_str(), &fileInfo) == 0);
}
std::string SerialDataCollector::getFullFilename(const Dimensions mpiPos, std::string baseFilename) const
{
std::stringstream serial_filename;
serial_filename << baseFilename << "_" << mpiPos[0] << "_" << mpiPos[1] <<
"_" << mpiPos[2] << ".h5";
return serial_filename.str();
}
std::string SerialDataCollector::getExceptionString(std::string func, std::string msg,
const char *info)
{
std::stringstream full_msg;
full_msg << "Exception for SerialDataCollector::" << func <<
": " << msg;
if (info != NULL)
full_msg << " (" << info << ")";
return full_msg.str();
}
/*******************************************************************************
* PUBLIC FUNCTIONS
*******************************************************************************/
SerialDataCollector::SerialDataCollector(uint32_t maxFileHandles) :
handles(maxFileHandles, HandleMgr::FNS_MPI),
fileStatus(FST_CLOSED),
maxID(-1),
mpiTopology(1, 1, 1)
{
#ifdef COL_TYPE_CPP
throw DCException("Check your defines !");
#endif
parseEnvVars();
if (H5open() < 0)
throw DCException(getExceptionString("SerialDataCollector",
"failed to initialize/open HDF5 library"));
#ifndef SPLASH_VERBOSE_HDF5
// surpress automatic output of HDF5 exception messages
if (H5Eset_auto2(H5E_DEFAULT, NULL, NULL) < 0)
throw DCException(getExceptionString("SerialDataCollector",
"failed to disable error printing"));
#endif
// set some default file access parameters
setFileAccessParams(fileAccProperties);
}
SerialDataCollector::~SerialDataCollector()
{
}
void SerialDataCollector::open(const char* filename, FileCreationAttr &attr)
throw (DCException)
{
log_msg(1, "opening serial data collector");
if (filename == NULL)
throw DCException(getExceptionString("open", "filename must not be null"));
if (fileStatus != FST_CLOSED)
throw DCException(getExceptionString("open", "this access is not permitted"));
switch (attr.fileAccType)
{
case FAT_READ:
openRead(filename, attr);
break;
case FAT_WRITE:
openWrite(filename, attr);
break;
case FAT_CREATE:
openCreate(filename, attr);
break;
case FAT_READ_MERGED:
openMerge(filename);
break;
}
}
void SerialDataCollector::close()
{
log_msg(1, "closing serial data collector");
if (fileStatus == FST_CREATING || fileStatus == FST_WRITING)
{
DCGroup group;
group.open(handles.get(0), SDC_GROUP_HEADER);
// write number of iterations
try
{
ColTypeInt32 ctInt32;
DCAttribute::writeAttribute(SDC_ATTR_MAX_ID, ctInt32.getDataType(),
group.getHandle(), &maxID);
} catch (const DCException& e)
{
log_msg(0, "Exception: %s", e.what());
log_msg(1, "continuing...");
}
}
maxID = -1;
mpiTopology.set(1, 1, 1);
// close opened hdf5 file handles
handles.close();
fileStatus = FST_CLOSED;
}
void SerialDataCollector::readGlobalAttribute(
const char* name,
void* data,
Dimensions *mpiPosition)
throw (DCException)
{
// mpiPosition is allowed to be NULL here
if (name == NULL || data == NULL)
throw DCException(getExceptionString("readGlobalAttribute", "a parameter was null"));
if (fileStatus == FST_CLOSED || fileStatus == FST_CREATING)
throw DCException(getExceptionString("readGlobalAttribute", "this access is not permitted"));
std::stringstream group_custom_name;
if (mpiPosition == NULL || fileStatus == FST_MERGING)
group_custom_name << SDC_GROUP_CUSTOM;
else
group_custom_name << SDC_GROUP_CUSTOM << "_" <<
(*mpiPosition)[0] << "_" << (*mpiPosition)[1] << "_" << (*mpiPosition)[2];
const std::string custom_string = group_custom_name.str();
uint32_t mpi_rank = 0;
if (fileStatus == FST_MERGING)
{
Dimensions mpi_pos(0, 0, 0);
if (mpiPosition != NULL)
mpi_pos = *mpiPosition;
mpi_rank = mpi_pos[2] * mpiTopology[0] * mpiTopology[1] + mpi_pos[1] * mpiTopology[0] + mpi_pos[0];
}
DCGroup group_custom;
group_custom.open(handles.get(mpi_rank), custom_string.c_str());
try
{
DCAttribute::readAttribute(name, group_custom.getHandle(), data);
} catch (const DCException&)
{
throw DCException(getExceptionString("readGlobalAttribute", "failed to open attribute", name));
}
}
void SerialDataCollector::writeGlobalAttribute(const CollectionType& type,
const char* name,
const void* data)
throw (DCException)
{
const Dimensions dims(1, 1, 1);
writeGlobalAttribute(type, name, 1u, dims, data);
}
void SerialDataCollector::writeGlobalAttribute(const CollectionType& type,
const char* name,
uint32_t ndims,
const Dimensions dims,
const void* data)
throw (DCException)
{
if (name == NULL || data == NULL)
throw DCException(getExceptionString("writeGlobalAttribute", "a parameter was null"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("writeGlobalAttribute", "this access is not permitted"));
if (ndims < 1u || ndims > DSP_DIM_MAX)
throw DCException(getExceptionString("writeGlobalAttribute", "maximum dimension `ndims` is invalid"));
DCGroup group_custom;
group_custom.open(handles.get(0), SDC_GROUP_CUSTOM);
try
{
DCAttribute::writeAttribute(name, type.getDataType(), group_custom.getHandle(), ndims, dims, data);
} catch (const DCException& e)
{
std::cerr << e.what() << std::endl;
throw DCException(getExceptionString("writeGlobalAttribute", "failed to write attribute", name));
}
}
void SerialDataCollector::readAttribute(int32_t id,
const char *dataName,
const char *attrName,
void* data,
Dimensions *mpiPosition)
throw (DCException)
{
// mpiPosition is allowed to be NULL here
if (attrName == NULL || data == NULL)
throw DCException(getExceptionString("readAttribute", "a parameter was null"));
// dataName may be NULL, attribute is read to iteration group in that case
if (dataName && strlen(dataName) == 0)
throw DCException(getExceptionString("readAttribute", "empty dataset name"));
if (strlen(attrName) == 0)
throw DCException(getExceptionString("readAttribute", "empty attribute name"));
if (fileStatus == FST_CLOSED || fileStatus == FST_CREATING)
throw DCException(getExceptionString("readAttribute", "this access is not permitted"));
std::string group_path, obj_name;
std::string dataNameInternal = "";
if (dataName)
dataNameInternal.assign(dataName);
DCDataSet::getFullDataPath(dataNameInternal, SDC_GROUP_DATA, id, group_path, obj_name);
Dimensions mpi_pos(0, 0, 0);
if ((fileStatus == FST_MERGING) && (mpiPosition != NULL))
{
mpi_pos.set(*mpiPosition);
}
DCGroup group;
group.open(handles.get(mpi_pos), group_path);
if (dataName)
{
// read attribute from the dataset or group
hid_t obj_id = -1;
if (H5Lexists(group.getHandle(), obj_name.c_str(), H5P_LINK_ACCESS_DEFAULT))
{
obj_id = H5Oopen(group.getHandle(), obj_name.c_str(), H5P_DEFAULT);
try
{
DCAttribute::readAttribute(attrName, obj_id, data);
} catch (const DCException&)
{
H5Oclose(obj_id);
throw;
}
H5Oclose(obj_id);
} else
{
throw DCException(getExceptionString("readAttribute",
"dataset not found", obj_name.c_str()));
}
} else
{
// read attribute from the iteration group
DCAttribute::readAttribute(attrName, group.getHandle(), data);
}
}
void SerialDataCollector::writeAttribute(int32_t id,
const CollectionType& type,
const char *dataName,
const char *attrName,
const void* data)
throw (DCException)
{
const Dimensions dims(1, 1, 1);
SerialDataCollector::writeAttribute( id, type, dataName, attrName,
1u, dims, data);
}
void SerialDataCollector::writeAttribute(int32_t id,
const CollectionType& type,
const char *dataName,
const char *attrName,
uint32_t ndims,
const Dimensions dims,
const void* data)
throw (DCException)
{
if (attrName == NULL || data == NULL)
throw DCException(getExceptionString("writeAttribute", "a parameter was null"));
// dataName may be NULL, attribute is attached to iteration group in that case
if (dataName && strlen(dataName) == 0)
throw DCException(getExceptionString("writeAttribute", "empty dataset name"));
if (strlen(attrName) == 0)
throw DCException(getExceptionString("writeAttribute", "empty attribute name"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("writeAttribute", "this access is not permitted"));
if (ndims < 1u || ndims > DSP_DIM_MAX)
throw DCException(getExceptionString("writeAttribute", "maximum dimension `ndims` is invalid"));
std::string group_path, obj_name;
std::string dataNameInternal = "";
if (dataName)
dataNameInternal.assign(dataName);
DCDataSet::getFullDataPath(dataNameInternal, SDC_GROUP_DATA, id, group_path, obj_name);
DCGroup group;
if (dataName)
{
// attach attribute to the dataset or group
group.open(handles.get(0), group_path);
hid_t obj_id = H5Oopen(group.getHandle(), obj_name.c_str(), H5P_DEFAULT);
if (obj_id < 0)
{
throw DCException(getExceptionString("writeAttribute",
"object not found", obj_name.c_str()));
}
try
{
DCAttribute::writeAttribute(attrName, type.getDataType(), obj_id, ndims, dims, data);
} catch (const DCException&)
{
H5Oclose(obj_id);
throw;
}
H5Oclose(obj_id);
} else
{
// attach attribute to the iteration group
group.openCreate(handles.get(0), group_path);
DCAttribute::writeAttribute(attrName, type.getDataType(), group.getHandle(), ndims, dims, data);
}
}
void SerialDataCollector::read(int32_t id,
const char* name,
Dimensions &sizeRead,
void* data)
throw (DCException)
{
this->read(id, name, Dimensions(0, 0, 0), Dimensions(0, 0, 0), sizeRead, data);
}
void SerialDataCollector::read(int32_t id,
const char* name,
const Dimensions dstBuffer,
const Dimensions dstOffset,
Dimensions &sizeRead,
void* data)
throw (DCException)
{
if (fileStatus != FST_READING && fileStatus != FST_WRITING && fileStatus != FST_MERGING)
throw DCException(getExceptionString("read", "this access is not permitted"));
uint32_t ndims = 0;
readCompleteDataSet(handles.get(0), id, name, dstBuffer, dstOffset,
Dimensions(0, 0, 0), sizeRead, ndims, data);
}
CollectionType* SerialDataCollector::readMeta(int32_t id,
const char* name,
const Dimensions dstBuffer,
const Dimensions dstOffset,
Dimensions &sizeRead)
throw (DCException)
{
if (fileStatus != FST_READING && fileStatus != FST_WRITING && fileStatus != FST_MERGING)
throw DCException(getExceptionString("readMeta", "this access is not permitted"));
uint32_t ndims = 0;
return readDataSetMeta(handles.get(id), id, name, dstBuffer, dstOffset,
Dimensions(0, 0, 0), sizeRead, ndims);
}
void SerialDataCollector::write(int32_t id, const CollectionType& type, uint32_t ndims,
const Selection select, const char* name, const void* data)
throw (DCException)
{
if (name == NULL)
throw DCException(getExceptionString("write", "parameter name is NULL"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("write", "this access is not permitted"));
if (ndims < 1 || ndims > DSP_DIM_MAX)
throw DCException(getExceptionString("write", "maximum dimension is invalid"));
if (id > this->maxID)
this->maxID = id;
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.openCreate(handles.get(0), group_path);
// write data to the group
try
{
writeDataSet(group.getHandle(), type, ndims, select, dset_name.c_str(), data);
} catch (const DCException&)
{
throw;
}
}
void SerialDataCollector::append(int32_t id, const CollectionType& type,
size_t count, const char* name, const void* data)
throw (DCException)
{
append(id, type, count, 0, 1, name, data);
}
void SerialDataCollector::append(int32_t id, const CollectionType& type,
size_t count, size_t offset, size_t stride, const char* name, const void* data)
throw (DCException)
{
if (name == NULL)
throw DCException(getExceptionString("append", "parameter name is NULL"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("append", "this access is not permitted"));
if (id > this->maxID)
this->maxID = id;
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.openCreate(handles.get(0), group_path);
// write data to the group
try
{
appendDataSet(group.getHandle(), type, count, offset,
stride, dset_name.c_str(), data);
} catch (const DCException&)
{
throw;
}
}
void SerialDataCollector::remove(int32_t id)
throw (DCException)
{
log_msg(1, "removing group %d", id);
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("remove", "this access is not permitted"));
std::stringstream group_id_name;
group_id_name << SDC_GROUP_DATA << "/" << id;
DCGroup::remove(handles.get(0), group_id_name.str());
// update maxID to new highest group
maxID = 0;
size_t num_groups = 0;
getEntryIDs(NULL, &num_groups);
int32_t *groups = new int32_t[num_groups];
getEntryIDs(groups, NULL);
for (size_t i = 0; i < num_groups; ++i)
if (groups[i] > maxID)
maxID = groups[i];
delete[] groups;
groups = NULL;
}
void SerialDataCollector::remove(int32_t id, const char* name)
throw (DCException)
{
log_msg(1, "removing dataset %s from group %d", name, id);
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("remove", "this access is not permitted"));
if (name == NULL)
throw DCException(getExceptionString("remove", "parameter name is NULL"));
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.open(handles.get(0), group_path);
if (H5Ldelete(group.getHandle(), dset_name.c_str(), H5P_LINK_ACCESS_DEFAULT) < 0)
{
throw DCException(getExceptionString("remove",
"failed to remove dataset", dset_name.c_str()));
}
}
void SerialDataCollector::createReference(int32_t srcID,
const char *srcName,
int32_t dstID,
const char *dstName)
throw (DCException)
{
if (srcName == NULL || dstName == NULL)
throw DCException(getExceptionString("createReference", "a parameter was NULL"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("createReference", "this access is not permitted"));
if (srcID == dstID && srcName == dstName)
throw DCException(getExceptionString("createReference",
"a reference must not be identical to the referenced data", srcName));
// open source group
std::string src_group_path, src_dset_name;
DCDataSet::getFullDataPath(srcName, SDC_GROUP_DATA, srcID, src_group_path, src_dset_name);
DCGroup src_group, dst_group;
src_group.open(handles.get(0), src_group_path);
// open destination group
std::string dst_group_path, dst_dset_name;
DCDataSet::getFullDataPath(dstName, SDC_GROUP_DATA, dstID, dst_group_path, dst_dset_name);
// if destination group does not exist, it is created
dst_group.openCreate(handles.get(0), dst_group_path);
// open source dataset
try
{
DCDataSet src_dataset(src_dset_name.c_str());
src_dataset.open(src_group.getHandle());
DCDataSet dst_dataset(dst_dset_name.c_str());
// create the actual reference as a new dataset
dst_dataset.createReference(dst_group.getHandle(),
src_group.getHandle(), src_dataset);
dst_dataset.close();
src_dataset.close();
} catch (const DCException& e)
{
throw e;
}
}
void SerialDataCollector::createReference(int32_t srcID,
const char *srcName,
int32_t dstID,
const char *dstName,
Dimensions count,
Dimensions offset,
Dimensions stride)
throw (DCException)
{
if (srcName == NULL || dstName == NULL)
throw DCException(getExceptionString("createReference", "a parameter was NULL"));
if (fileStatus == FST_CLOSED || fileStatus == FST_READING || fileStatus == FST_MERGING)
throw DCException(getExceptionString("createReference", "this access is not permitted"));
if (srcID == dstID && srcName == dstName)
throw DCException(getExceptionString("createReference",
"a reference must not be identical to the referenced data", srcName));
// open source group
std::string src_group_path, src_dset_name;
DCDataSet::getFullDataPath(srcName, SDC_GROUP_DATA, srcID, src_group_path, src_dset_name);
DCGroup src_group, dst_group;
src_group.open(handles.get(0), src_group_path);
// open destination group
std::string dst_group_path, dst_dset_name;
DCDataSet::getFullDataPath(dstName, SDC_GROUP_DATA, dstID, dst_group_path, dst_dset_name);
// if destination group does not exist, it is created
dst_group.openCreate(handles.get(0), dst_group_path);
// open source dataset
try
{
DCDataSet src_dataset(src_dset_name.c_str());
src_dataset.open(src_group.getHandle());
DCDataSet dst_dataset(dst_dset_name.c_str());
// create the actual reference as a new dataset
dst_dataset.createReference(dst_group.getHandle(), src_group.getHandle(),
src_dataset, count, offset, stride);
dst_dataset.close();
src_dataset.close();
} catch (const DCException& e)
{
throw e;
}
}
int32_t SerialDataCollector::getMaxID()
{
return maxID;
}
void SerialDataCollector::getMPISize(Dimensions& mpiSize)
{
mpiSize.set(this->mpiTopology);
}
void SerialDataCollector::getEntryIDs(int32_t* ids, size_t* count)
throw (DCException)
{
DCGroup group;
group.open(handles.get(0), SDC_GROUP_DATA);
hsize_t data_entries = 0;
if (H5Gget_num_objs(group.getHandle(), &data_entries) < 0)
{
throw DCException(getExceptionString("getEntryIDs",
"Failed to get entries in data group", SDC_GROUP_DATA));
}
if (count != NULL)
*count = data_entries;
if (ids != NULL)
{
for (size_t i = 0; i < data_entries; i++)
{
char *group_id_name = NULL;
ssize_t group_id_name_len = H5Gget_objname_by_idx(group.getHandle(), i, NULL, 0);
if (group_id_name_len < 0)
{
throw DCException(getExceptionString("getEntryIDs",
"Failed to get object name in group", group_id_name));
}
group_id_name = new char[group_id_name_len + 1];
H5Gget_objname_by_idx(group.getHandle(), i, group_id_name, group_id_name_len + 1);
ids[i] = atoi(group_id_name);
delete[] group_id_name;
}
}
}
void SerialDataCollector::getEntriesForID(int32_t id, DCEntry *entries, size_t *count)
throw (DCException)
{
std::stringstream group_id_name;
group_id_name << SDC_GROUP_DATA << "/" << id;
// open data group for id
DCGroup group;
group.open(handles.get(0), group_id_name.str());
DCGroup::VisitObjCBType param;
param.count = 0;
param.entries = entries;
DCGroup::getEntriesInternal(group.getHandle(), group_id_name.str(), "", ¶m);
if (count)
*count = param.count;
}
/*******************************************************************************
* PROTECTED FUNCTIONS
*******************************************************************************/
void SerialDataCollector::openCreate(const char *filename,
FileCreationAttr& attr)
throw (DCException)
{
this->fileStatus = FST_CREATING;
// appends the mpiPosition to the filename (e.g. myfile_0_1_0.h5)
std::string full_filename = getFullFilename(attr.mpiPosition, filename);
DCHelper::testFilename(full_filename);
this->enableCompression = attr.enableCompression;
log_msg(1, "compression = %d", attr.enableCompression);
// open file
handles.open(full_filename, fileAccProperties, H5F_ACC_TRUNC);
this->maxID = 0;
this->mpiTopology.set(attr.mpiSize);
// write datatypes and header information to the file
SDCHelper::writeHeader(handles.get(0), attr.mpiPosition, &(this->maxID),
&(this->enableCompression), &(this->mpiTopology), false);
// the custom group hold user-specified attributes
DCGroup group;
group.create(handles.get(0), SDC_GROUP_CUSTOM);
group.close();
// the data group holds the actual simulation data
group.create(handles.get(0), SDC_GROUP_DATA);
group.close();
}
void SerialDataCollector::openWrite(const char* filename, FileCreationAttr& attr)
throw (DCException)
{
fileStatus = FST_WRITING;
std::string full_filename = filename;
if (full_filename.find(".h5") == std::string::npos)
full_filename = getFullFilename(attr.mpiPosition, filename);
DCHelper::testFilename(full_filename);
this->enableCompression = attr.enableCompression;
if (fileExists(full_filename))
{
// read reference data from target file
SDCHelper::getReferenceData(full_filename.c_str(), &(this->maxID), &(this->mpiTopology));
handles.open(full_filename, fileAccProperties, H5F_ACC_RDWR);
} else
{
openCreate(filename, attr);
}
}
void SerialDataCollector::openMerge(const char* filename)
throw (DCException)
{
this->fileStatus = FST_MERGING;
// open reference file to get mpi information
std::string full_filename = getFullFilename(Dimensions(0, 0, 0), filename);
DCHelper::testFilename(full_filename);
if (!fileExists(full_filename))
{
this->fileStatus = FST_CLOSED;
throw DCException(getExceptionString("openMerge", "File not found.", full_filename.c_str()));
}
// read reference data from target file
SDCHelper::getReferenceData(full_filename.c_str(), &(this->maxID), &(this->mpiTopology));
// no compression for in-memory datasets
this->enableCompression = false;
handles.open(mpiTopology, filename, fileAccProperties, H5F_ACC_RDONLY);
}
void SerialDataCollector::openRead(const char* filename, FileCreationAttr& attr)
throw (DCException)
{
this->fileStatus = FST_READING;
std::string full_filename = filename;
if (full_filename.find(".h5") == std::string::npos)
full_filename = getFullFilename(attr.mpiPosition, filename);
DCHelper::testFilename(full_filename);
if (!fileExists(full_filename))
{
this->fileStatus = FST_CLOSED;
throw DCException(getExceptionString("openRead", "File not found", full_filename.c_str()));
}
// read reference data from target file
SDCHelper::getReferenceData(full_filename.c_str(), &(this->maxID), &(this->mpiTopology));
handles.open(full_filename, fileAccProperties, H5F_ACC_RDONLY);
}
void SerialDataCollector::writeDataSet(hid_t group,
const CollectionType& datatype,
uint32_t ndims,
const Selection select,
const char* name,
const void* data) throw (DCException)
{
log_msg(2, "writeDataSet");
DCDataSet dataset(name);
// always create dataset but write data only if all dimensions > 0 and data available
// not extensible
dataset.create(datatype, group, select.count, ndims,
this->enableCompression, false);
if (data && (select.count.getScalarSize() > 0))
dataset.write(select, Dimensions(0, 0, 0), data);
dataset.close();
}
void SerialDataCollector::appendDataSet(hid_t group, const CollectionType& datatype,
size_t count, size_t offset, size_t stride, const char* name, const void* data)
throw (DCException)
{
log_msg(2, "appendDataSet");
DCDataSet dataset(name);
if (!dataset.open(group))
{
Dimensions data_size(count, 1, 1);
// create dataset extensible
dataset.create(datatype, group, data_size, 1, this->enableCompression, true);
if (count > 0)
dataset.write(Selection(data_size,
Dimensions(offset + count * stride, 1, 1),
Dimensions(offset, 0, 0),
Dimensions(stride, 1, 1)),
Dimensions(0, 0, 0),
data);
} else
if (count > 0)
dataset.append(count, offset, stride, data);
dataset.close();
}
size_t SerialDataCollector::getNDims(H5Handle h5File,
int32_t id,
const char* name)
{
if (h5File < 0 || name == NULL)
throw DCException(getExceptionString("getNDims", "invalid parameters"));
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.open(h5File, group_path);
size_t ndims = 0;
try
{
DCDataSet dataset(dset_name.c_str());
dataset.open(group.getHandle());
ndims = dataset.getNDims();
dataset.close();
} catch (const DCException& e)
{
throw e;
}
return ndims;
}
void SerialDataCollector::readCompleteDataSet(H5Handle h5File,
int32_t id,
const char* name,
const Dimensions dstBuffer,
const Dimensions dstOffset,
const Dimensions srcOffset,
Dimensions &sizeRead,
uint32_t& srcDims,
void* dst)
throw (DCException)
{
log_msg(2, "readCompleteDataSet");
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.open(h5File, group_path);
DCDataSet dataset(dset_name.c_str());
dataset.open(group.getHandle());
Dimensions src_size(dataset.getSize() - srcOffset);
dataset.read(dstBuffer, dstOffset, src_size, srcOffset, sizeRead, srcDims, dst);
dataset.close();
}
void SerialDataCollector::readDataSet(H5Handle h5File,
int32_t id,
const char* name,
const Dimensions dstBuffer,
const Dimensions dstOffset,
const Dimensions srcSize,
const Dimensions srcOffset,
Dimensions &sizeRead,
uint32_t& srcDims,
void* dst)
throw (DCException)
{
log_msg(2, "readDataSet");
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.open(h5File, group_path);
DCDataSet dataset(dset_name.c_str());
dataset.open(group.getHandle());
dataset.read(dstBuffer, dstOffset, srcSize, srcOffset, sizeRead, srcDims, dst);
dataset.close();
}
CollectionType* SerialDataCollector::readDataSetMeta(H5Handle h5File,
int32_t id,
const char* name,
const Dimensions dstBuffer,
const Dimensions dstOffset,
const Dimensions srcOffset,
Dimensions &sizeRead,
uint32_t& srcDims)
throw (DCException)
{
log_msg(2, "readDataSetMeta");
std::string group_path, dset_name;
DCDataSet::getFullDataPath(name, SDC_GROUP_DATA, id, group_path, dset_name);
DCGroup group;
group.open(h5File, group_path);
DCDataSet dataset(dset_name.c_str());
dataset.open(group.getHandle());