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HDF5IOHandler.cpp
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/* Copyright 2017-2021 Fabian Koller
*
* This file is part of openPMD-api.
*
* openPMD-api 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.
*
* openPMD-api 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 openPMD-api.
* If not, see <http://www.gnu.org/licenses/>.
*/
#include "openPMD/IO/HDF5/HDF5IOHandler.hpp"
#include "openPMD/IO/AbstractIOHandler.hpp"
#include "openPMD/IO/AbstractIOHandlerImpl.hpp"
#include "openPMD/IO/FlushParametersInternal.hpp"
#include "openPMD/IO/HDF5/HDF5IOHandlerImpl.hpp"
#include "openPMD/auxiliary/Environment.hpp"
#include "openPMD/auxiliary/JSON_internal.hpp"
#include "openPMD/auxiliary/Variant.hpp"
#include <optional>
#include <sstream>
#include <stdexcept>
#if openPMD_HAVE_HDF5
#include "openPMD/Datatype.hpp"
#include "openPMD/Error.hpp"
#include "openPMD/IO/HDF5/HDF5Auxiliary.hpp"
#include "openPMD/IO/HDF5/HDF5FilePosition.hpp"
#include "openPMD/IO/IOTask.hpp"
#include "openPMD/auxiliary/Filesystem.hpp"
#include "openPMD/auxiliary/Mpi.hpp"
#include "openPMD/auxiliary/StringManip.hpp"
#include "openPMD/auxiliary/TypeTraits.hpp"
#include "openPMD/backend/Attribute.hpp"
#include <H5FDmpio.h>
#include <hdf5.h>
#endif
#include <complex>
#include <cstring>
#include <future>
#include <iostream>
#include <stack>
#include <string>
#include <typeinfo>
#include <unordered_map>
#include <utility>
#include <vector>
namespace openPMD
{
#if openPMD_HAVE_HDF5
#if openPMD_USE_VERIFY
#define VERIFY(CONDITION, TEXT) \
{ \
if (!(CONDITION)) \
throw std::runtime_error((TEXT)); \
}
#else
#define VERIFY(CONDITION, TEXT) \
do \
{ \
(void)sizeof(CONDITION); \
} while (0)
#endif
HDF5IOHandlerImpl::HDF5IOHandlerImpl(
AbstractIOHandler *handler,
json::TracingJSON config,
bool do_warn_unused_params)
: AbstractIOHandlerImpl(handler)
, m_datasetTransferProperty{H5P_DEFAULT}
, m_fileAccessProperty{H5P_DEFAULT}
, m_H5T_BOOL_ENUM{H5Tenum_create(H5T_NATIVE_INT8)}
, m_H5T_CFLOAT{H5Tcreate(H5T_COMPOUND, sizeof(float) * 2)}
, m_H5T_CDOUBLE{H5Tcreate(H5T_COMPOUND, sizeof(double) * 2)}
, m_H5T_CLONG_DOUBLE{H5Tcreate(H5T_COMPOUND, sizeof(long double) * 2)}
, m_H5T_LONG_DOUBLE_80_LE{H5Tcopy(H5T_IEEE_F64BE)}
, m_H5T_CLONG_DOUBLE_80_LE{H5Tcreate(H5T_COMPOUND, 16 * 2)}
{
// create a h5py compatible bool type
VERIFY(
m_H5T_BOOL_ENUM >= 0,
"[HDF5] Internal error: Failed to create bool enum");
std::string t{"TRUE"};
std::string f{"FALSE"};
int64_t tVal = 1;
int64_t fVal = 0;
herr_t status;
status = H5Tenum_insert(m_H5T_BOOL_ENUM, t.c_str(), &tVal);
VERIFY(
status == 0, "[HDF5] Internal error: Failed to insert into HDF5 enum");
status = H5Tenum_insert(m_H5T_BOOL_ENUM, f.c_str(), &fVal);
VERIFY(
status == 0, "[HDF5] Internal error: Failed to insert into HDF5 enum");
// create h5py compatible complex types
VERIFY(
m_H5T_CFLOAT >= 0,
"[HDF5] Internal error: Failed to create complex float");
VERIFY(
m_H5T_CDOUBLE >= 0,
"[HDF5] Internal error: Failed to create complex double");
VERIFY(
m_H5T_CLONG_DOUBLE >= 0,
"[HDF5] Internal error: Failed to create complex long double");
H5Tinsert(m_H5T_CFLOAT, "r", 0, H5T_NATIVE_FLOAT);
H5Tinsert(m_H5T_CFLOAT, "i", sizeof(float), H5T_NATIVE_FLOAT);
H5Tinsert(m_H5T_CDOUBLE, "r", 0, H5T_NATIVE_DOUBLE);
H5Tinsert(m_H5T_CDOUBLE, "i", sizeof(double), H5T_NATIVE_DOUBLE);
H5Tinsert(m_H5T_CLONG_DOUBLE, "r", 0, H5T_NATIVE_LDOUBLE);
H5Tinsert(m_H5T_CLONG_DOUBLE, "i", sizeof(long double), H5T_NATIVE_LDOUBLE);
// Create a type that understands 128bit floats with 80 bits of precision
// even on those platforms that do not have it (ARM64, PPC64).
// Otherwise, files created on e.g. AMD64 platforms might not be readable
// on such platforms.
H5Tset_size(m_H5T_LONG_DOUBLE_80_LE, 16);
H5Tset_order(m_H5T_LONG_DOUBLE_80_LE, H5T_ORDER_LE);
H5Tset_precision(m_H5T_LONG_DOUBLE_80_LE, 80);
H5Tset_fields(m_H5T_LONG_DOUBLE_80_LE, 79, 64, 15, 0, 64);
H5Tset_ebias(m_H5T_LONG_DOUBLE_80_LE, 16383);
H5Tset_norm(m_H5T_LONG_DOUBLE_80_LE, H5T_NORM_NONE);
VERIFY(
m_H5T_LONG_DOUBLE_80_LE >= 0,
"[HDF5] Internal error: Failed to create 128-bit long double");
H5Tinsert(m_H5T_CLONG_DOUBLE_80_LE, "r", 0, m_H5T_LONG_DOUBLE_80_LE);
H5Tinsert(m_H5T_CLONG_DOUBLE_80_LE, "i", 16, m_H5T_LONG_DOUBLE_80_LE);
VERIFY(
m_H5T_LONG_DOUBLE_80_LE >= 0,
"[HDF5] Internal error: Failed to create 128-bit complex long double");
// JSON option can overwrite env option:
if (config.json().contains("hdf5"))
{
m_config = config["hdf5"];
{
constexpr char const *const init_json_shadow_str = R"(
{
"dataset": {
"chunks": null
},
"independent_stores": null
})";
constexpr char const *const dataset_cfg_mask = R"(
{
"dataset": {
"chunks": null
}
})";
constexpr char const *const flush_cfg_mask = R"(
{
"independent_stores": null
})";
m_global_dataset_config = m_config.json();
json::filterByTemplate(
m_global_dataset_config,
nlohmann::json::parse(dataset_cfg_mask));
m_global_flush_config = m_config.json();
json::filterByTemplate(
m_global_flush_config, nlohmann::json::parse(flush_cfg_mask));
auto init_json_shadow = nlohmann::json::parse(init_json_shadow_str);
json::merge(m_config.getShadow(), init_json_shadow);
}
// unused params
if (do_warn_unused_params)
{
auto shadow = m_config.invertShadow();
if (shadow.size() > 0)
{
switch (m_config.originallySpecifiedAs)
{
case json::SupportedLanguages::JSON:
std::cerr
<< "Warning: parts of the backend configuration for "
"HDF5 remain unused:\n"
<< shadow << std::endl;
break;
case json::SupportedLanguages::TOML: {
auto asToml = json::jsonToToml(shadow);
std::cerr
<< "Warning: parts of the backend configuration for "
"HDF5 remain unused:\n"
<< json::format_toml(asToml) << std::endl;
break;
}
}
}
}
}
#if H5_VERSION_GE(1, 10, 0) && openPMD_HAVE_MPI
auto const hdf5_collective_metadata =
auxiliary::getEnvString("OPENPMD_HDF5_COLLECTIVE_METADATA", "ON");
if (hdf5_collective_metadata == "ON")
m_hdf5_collective_metadata = 1;
else
m_hdf5_collective_metadata = 0;
#endif
}
HDF5IOHandlerImpl::~HDF5IOHandlerImpl()
{
herr_t status;
status = H5Tclose(m_H5T_BOOL_ENUM);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close bool enum\n";
status = H5Tclose(m_H5T_CFLOAT);
if (status < 0)
std::cerr
<< "[HDF5] Internal error: Failed to close complex float type\n";
status = H5Tclose(m_H5T_CDOUBLE);
if (status < 0)
std::cerr
<< "[HDF5] Internal error: Failed to close complex double type\n";
status = H5Tclose(m_H5T_CLONG_DOUBLE);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close complex long "
"double type\n";
status = H5Tclose(m_H5T_LONG_DOUBLE_80_LE);
if (status < 0)
std::cerr
<< "[HDF5] Internal error: Failed to close long double type\n";
status = H5Tclose(m_H5T_CLONG_DOUBLE_80_LE);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close complex long "
"double type\n";
while (!m_openFileIDs.empty())
{
auto file = m_openFileIDs.begin();
status = H5Fclose(*file);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close HDF5 file "
"(serial)\n";
m_openFileIDs.erase(file);
}
if (m_datasetTransferProperty != H5P_DEFAULT)
{
status = H5Pclose(m_datasetTransferProperty);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close HDF5 dataset "
"transfer property\n";
}
if (m_fileAccessProperty != H5P_DEFAULT)
{
status = H5Pclose(m_fileAccessProperty);
if (status < 0)
std::cerr << "[HDF5] Internal error: Failed to close HDF5 file "
"access property\n";
}
}
void HDF5IOHandlerImpl::createFile(
Writable *writable, Parameter<Operation::CREATE_FILE> const ¶meters)
{
if (access::readOnly(m_handler->m_backendAccess))
throw std::runtime_error(
"[HDF5] Creating a file in read-only mode is not possible.");
if (!writable->written)
{
if (!auxiliary::directory_exists(m_handler->directory))
{
bool success = auxiliary::create_directories(m_handler->directory);
VERIFY(
success,
"[HDF5] Internal error: Failed to create directories during "
"HDF5 file creation");
}
std::string name = m_handler->directory + parameters.name;
if (!auxiliary::ends_with(name, ".h5"))
name += ".h5";
unsigned flags{};
switch (m_handler->m_backendAccess)
{
case Access::CREATE:
flags = H5F_ACC_TRUNC;
break;
case Access::APPEND:
if (auxiliary::file_exists(name))
{
flags = H5F_ACC_RDWR;
}
else
{
flags = H5F_ACC_TRUNC;
}
break;
case Access::READ_WRITE:
flags = H5F_ACC_EXCL;
break;
case Access::READ_ONLY:
case Access::READ_LINEAR:
// condition has been checked above
throw std::runtime_error(
"[HDF5] Control flow error in createFile backend access mode.");
}
hid_t id{};
if (flags == H5F_ACC_RDWR)
{
id = H5Fopen(name.c_str(), flags, m_fileAccessProperty);
}
else
{
id = H5Fcreate(
name.c_str(), flags, H5P_DEFAULT, m_fileAccessProperty);
}
VERIFY(id >= 0, "[HDF5] Internal error: Failed to create HDF5 file");
writable->written = true;
writable->abstractFilePosition =
std::make_shared<HDF5FilePosition>("/");
m_fileNames[writable] = name;
m_fileNamesWithID[std::move(name)] = id;
m_openFileIDs.insert(id);
}
}
void HDF5IOHandlerImpl::checkFile(
Writable *, Parameter<Operation::CHECK_FILE> ¶meters)
{
std::string name = m_handler->directory + parameters.name;
if (!auxiliary::ends_with(name, ".h5"))
{
name += ".h5";
}
bool fileExists =
auxiliary::file_exists(name) || auxiliary::directory_exists(name);
#if openPMD_HAVE_MPI
if (m_communicator.has_value())
{
bool fileExistsRes = false;
int status = MPI_Allreduce(
&fileExists,
&fileExistsRes,
1,
MPI_C_BOOL,
MPI_LOR, // logical or
m_communicator.value());
if (status != 0)
{
throw std::runtime_error("MPI Reduction failed!");
}
fileExists = fileExistsRes;
}
#endif
using FileExists = Parameter<Operation::CHECK_FILE>::FileExists;
*parameters.fileExists = fileExists ? FileExists::Yes : FileExists::No;
}
void HDF5IOHandlerImpl::createPath(
Writable *writable, Parameter<Operation::CREATE_PATH> const ¶meters)
{
if (access::readOnly(m_handler->m_backendAccess))
throw std::runtime_error(
"[HDF5] Creating a path in a file opened as read only is not "
"possible.");
hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1, 10, 0) && openPMD_HAVE_MPI
if (m_hdf5_collective_metadata)
{
H5Pset_all_coll_metadata_ops(gapl, true);
}
#endif
herr_t status;
if (!writable->written)
{
/* Sanitize path */
std::string path = parameters.path;
if (auxiliary::starts_with(path, '/'))
path = auxiliary::replace_first(path, "/", "");
if (!auxiliary::ends_with(path, '/'))
path += '/';
/* Open H5Object to write into */
Writable *position;
if (writable->parent)
position = writable->parent;
else
position = writable; /* root does not have a parent but might still
have to be written */
File file = getFile(position).value();
hid_t node_id =
H5Gopen(file.id, concrete_h5_file_position(position).c_str(), gapl);
VERIFY(
node_id >= 0,
"[HDF5] Internal error: Failed to open HDF5 group during path "
"creation");
/* Create the path in the file */
std::stack<hid_t> groups;
groups.push(node_id);
for (std::string const &folder : auxiliary::split(path, "/", false))
{
// avoid creation of paths that already exist
htri_t const found =
H5Lexists(groups.top(), folder.c_str(), H5P_DEFAULT);
if (found > 0)
continue;
hid_t group_id = H5Gcreate(
groups.top(),
folder.c_str(),
H5P_DEFAULT,
H5P_DEFAULT,
H5P_DEFAULT);
VERIFY(
group_id >= 0,
"[HDF5] Internal error: Failed to create HDF5 group during "
"path creation");
groups.push(group_id);
}
/* Close the groups */
while (!groups.empty())
{
status = H5Gclose(groups.top());
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 group during path "
"creation");
groups.pop();
}
writable->written = true;
writable->abstractFilePosition =
std::make_shared<HDF5FilePosition>(path);
m_fileNames[writable] = file.name;
}
status = H5Pclose(gapl);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 property during path "
"creation");
}
void HDF5IOHandlerImpl::createDataset(
Writable *writable, Parameter<Operation::CREATE_DATASET> const ¶meters)
{
if (access::readOnly(m_handler->m_backendAccess))
throw std::runtime_error(
"[HDF5] Creating a dataset in a file opened as read only is not "
"possible.");
if (parameters.joinedDimension.has_value())
{
error::throwOperationUnsupportedInBackend(
"HDF5", "Joined Arrays currently only supported in ADIOS2");
}
if (!writable->written)
{
/* Sanitize name */
std::string name = parameters.name;
if (auxiliary::starts_with(name, '/'))
name = auxiliary::replace_first(name, "/", "");
if (auxiliary::ends_with(name, '/'))
name = auxiliary::replace_last(name, "/", "");
std::vector<hsize_t> dims;
std::uint64_t num_elements = 1u;
for (auto const &val : parameters.extent)
{
dims.push_back(static_cast<hsize_t>(val));
num_elements *= val;
}
Datatype d = parameters.dtype;
if (d == Datatype::UNDEFINED)
{
// TODO handle unknown dtype
std::cerr << "[HDF5] Datatype::UNDEFINED caught during dataset "
"creation (serial HDF5)"
<< std::endl;
d = Datatype::BOOL;
}
json::TracingJSON config = [&]() {
auto parsed_config = json::parseOptions(
parameters.options, /* considerFiles = */ false);
if (auto hdf5_config_it = parsed_config.config.find("hdf5");
hdf5_config_it != parsed_config.config.end())
{
auto copy = m_global_dataset_config;
json::merge(copy, hdf5_config_it.value());
hdf5_config_it.value() = std::move(copy);
}
else
{
parsed_config.config["hdf5"] = m_global_dataset_config;
}
return parsed_config;
}();
// general
bool is_resizable_dataset = false;
if (config.json().contains("resizable"))
{
is_resizable_dataset = config["resizable"].json().get<bool>();
}
using chunking_t = std::vector<hsize_t>;
using compute_chunking_t =
std::variant<chunking_t, std::string /* either "none" or "auto"*/>;
bool chunking_config_from_json = false;
auto throw_chunking_error = [&chunking_config_from_json]() {
if (chunking_config_from_json)
{
throw error::BackendConfigSchema(
{"hdf5", "dataset", "chunks"},
R"(Must be "auto", "none", or a an array of integer.)");
}
else
{
throw error::WrongAPIUsage(
"Environment variable OPENPMD_HDF5_CHUNKS accepts values "
"'auto' and 'none'.");
}
};
compute_chunking_t compute_chunking =
auxiliary::getEnvString("OPENPMD_HDF5_CHUNKS", "auto");
// HDF5 specific
if (config.json().contains("hdf5") &&
config["hdf5"].json().contains("dataset"))
{
json::TracingJSON datasetConfig{config["hdf5"]["dataset"]};
if (datasetConfig.json().contains("chunks"))
{
chunking_config_from_json = true;
auto chunks_json = datasetConfig["chunks"];
if (chunks_json.json().is_string())
{
compute_chunking =
json::asLowerCaseStringDynamic(chunks_json.json())
.value();
}
else if (chunks_json.json().is_array())
{
try
{
compute_chunking =
chunks_json.json().get<std::vector<hsize_t>>();
}
catch (nlohmann::json::type_error const &)
{
throw_chunking_error();
}
}
else
{
throw_chunking_error();
}
}
}
std::optional<chunking_t> chunking = std::visit(
auxiliary::overloaded{
[&](chunking_t &&explicitly_specified)
-> std::optional<chunking_t> {
return std::move(explicitly_specified);
},
[&](std::string const &method_name)
-> std::optional<chunking_t> {
if (method_name == "auto")
{
return getOptimalChunkDims(dims, toBytes(d));
}
else if (method_name == "none")
{
return std::nullopt;
}
else
{
throw_chunking_error();
throw std::runtime_error("Unreachable!");
}
}},
std::move(compute_chunking));
parameters.warnUnusedParameters(
config,
"hdf5",
"Warning: parts of the backend configuration for HDF5 dataset '" +
name + "' remain unused:\n");
hid_t gapl = H5Pcreate(H5P_GROUP_ACCESS);
#if H5_VERSION_GE(1, 10, 0) && openPMD_HAVE_MPI
if (m_hdf5_collective_metadata)
{
H5Pset_all_coll_metadata_ops(gapl, true);
}
#endif
writable->abstractFilePosition.reset();
/* Open H5Object to write into */
File file{};
if (auto opt = getFile(writable->parent); opt.has_value())
{
file = opt.value();
}
else
{
throw error::Internal(
"[HDF5] CREATE_DATASET task must have a parent with an "
"associated file.");
}
hid_t node_id =
H5Gopen(file.id, concrete_h5_file_position(writable).c_str(), gapl);
VERIFY(
node_id >= 0,
"[HDF5] Internal error: Failed to open HDF5 group during dataset "
"creation");
if (m_handler->m_backendAccess == Access::APPEND)
{
// The dataset might already exist in the file from a previous run
// We delete it, otherwise we could not create it again with
// possibly different parameters.
if (htri_t link_id = H5Lexists(node_id, name.c_str(), H5P_DEFAULT);
link_id > 0)
{
// This only unlinks, but does not delete the dataset
// Deleting the actual dataset physically is now up to HDF5:
// > when removing an object with H5Ldelete, the HDF5 library
// > should be able to detect and recycle the file space when no
// > other reference to the deleted object exists
// https://github.com/openPMD/openPMD-api/pull/1007#discussion_r867223316
herr_t status = H5Ldelete(node_id, name.c_str(), H5P_DEFAULT);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to delete old dataset '" +
name + "' from group for overwriting.");
}
else if (link_id < 0)
{
throw std::runtime_error(
"[HDF5] Internal error: Failed to check for link existence "
"of '" +
name + "' inside group for overwriting.");
}
// else: link_id == 0: Link does not exist, nothing to do
}
std::vector<hsize_t> max_dims(dims.begin(), dims.end());
if (is_resizable_dataset)
max_dims.assign(dims.size(), H5F_UNLIMITED);
hid_t space = H5Screate_simple(
static_cast<int>(dims.size()), dims.data(), max_dims.data());
VERIFY(
space >= 0,
"[HDF5] Internal error: Failed to create dataspace during dataset "
"creation");
/* enable chunking on the created dataspace */
hid_t datasetCreationProperty = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_time(datasetCreationProperty, H5D_FILL_TIME_NEVER);
if (num_elements != 0u && chunking.has_value())
{
if (chunking->size() != parameters.extent.size())
{
std::string chunking_printed = [&]() {
if (chunking->empty())
{
return std::string("[]");
}
else
{
std::stringstream s;
auto it = chunking->begin();
auto end = chunking->end();
s << '[' << *it++;
for (; it != end; ++it)
{
s << ", " << *it;
}
s << ']';
return s.str();
}
}();
std::cerr << "[HDF5] Chunking for dataset '" << name
<< "' was specified as " << chunking_printed
<< ", but dataset has dimensionality "
<< parameters.extent.size() << ". Will ignore."
<< std::endl;
}
else
{
herr_t status = H5Pset_chunk(
datasetCreationProperty,
chunking->size(),
chunking->data());
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to set chunk size during "
"dataset creation");
}
}
std::string const &compression = ""; // @todo read from JSON
if (!compression.empty())
std::cerr
<< "[HDF5] Compression not yet implemented in HDF5 backend."
<< std::endl;
/*
{
std::vector< std::string > args = auxiliary::split(compression,
":"); std::string const& format = args[0]; if( (format == "zlib" ||
format == "gzip" || format == "deflate")
&& args.size() == 2 )
{
status = H5Pset_deflate(datasetCreationProperty,
std::stoi(args[1])); VERIFY(status == 0, "[HDF5] Internal error: Failed
to set deflate compression during dataset creation"); } else if( format
== "szip" || format == "nbit" || format == "scaleoffset" ) std::cerr <<
"[HDF5] Compression format " << format
<< " not yet implemented. Data will not be
compressed!"
<< std::endl;
else
std::cerr << "[HDF5] Compression format " << format
<< " unknown. Data will not be compressed!"
<< std::endl;
}
*/
GetH5DataType getH5DataType({
{typeid(bool).name(), m_H5T_BOOL_ENUM},
{typeid(std::complex<float>).name(), m_H5T_CFLOAT},
{typeid(std::complex<double>).name(), m_H5T_CDOUBLE},
{typeid(std::complex<long double>).name(), m_H5T_CLONG_DOUBLE},
});
Attribute a(0);
a.dtype = d;
hid_t datatype = getH5DataType(a);
VERIFY(
datatype >= 0,
"[HDF5] Internal error: Failed to get HDF5 datatype during dataset "
"creation");
hid_t group_id = H5Dcreate(
node_id,
name.c_str(),
datatype,
space,
H5P_DEFAULT,
datasetCreationProperty,
H5P_DEFAULT);
VERIFY(
group_id >= 0,
"[HDF5] Internal error: Failed to create HDF5 group during dataset "
"creation");
herr_t status;
status = H5Dclose(group_id);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset during "
"dataset creation");
status = H5Tclose(datatype);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 datatype during "
"dataset creation");
status = H5Pclose(datasetCreationProperty);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset creation "
"property during dataset creation");
status = H5Sclose(space);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset space during "
"dataset creation");
status = H5Gclose(node_id);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 group during dataset "
"creation");
status = H5Pclose(gapl);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 property during "
"dataset creation");
writable->written = true;
writable->abstractFilePosition =
std::make_shared<HDF5FilePosition>(name);
m_fileNames[writable] = file.name;
}
}
void HDF5IOHandlerImpl::extendDataset(
Writable *writable, Parameter<Operation::EXTEND_DATASET> const ¶meters)
{
if (access::readOnly(m_handler->m_backendAccess))
throw std::runtime_error(
"[HDF5] Extending a dataset in a file opened as read only is not "
"possible.");
if (!writable->written)
throw std::runtime_error(
"[HDF5] Extending an unwritten Dataset is not possible.");
auto res = getFile(writable);
if (!res)
res = getFile(writable->parent);
hid_t dataset_id = H5Dopen(
res.value().id,
concrete_h5_file_position(writable).c_str(),
H5P_DEFAULT);
VERIFY(
dataset_id >= 0,
"[HDF5] Internal error: Failed to open HDF5 dataset during dataset "
"extension");
// Datasets may only be extended if they have chunked layout, so let's see
// whether this one does
{
hid_t dataset_space = H5Dget_space(dataset_id);
int ndims = H5Sget_simple_extent_ndims(dataset_space);
VERIFY(
ndims >= 0,
"[HDF5]: Internal error: Failed to retrieve dimensionality of "
"dataset during dataset read.");
hid_t propertyList = H5Dget_create_plist(dataset_id);
std::vector<hsize_t> chunkExtent(ndims, 0);
int chunkDimensionality =
H5Pget_chunk(propertyList, ndims, chunkExtent.data());
if (chunkDimensionality < 0)
{
throw std::runtime_error(
"[HDF5] Cannot extend datasets unless written with chunked "
"layout.");
}
}
std::vector<hsize_t> size;
for (auto const &val : parameters.extent)
size.push_back(static_cast<hsize_t>(val));
herr_t status;
status = H5Dset_extent(dataset_id, size.data());
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to extend HDF5 dataset during dataset "
"extension");
status = H5Dclose(dataset_id);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset during dataset "
"extension");
}
void HDF5IOHandlerImpl::availableChunks(
Writable *writable, Parameter<Operation::AVAILABLE_CHUNKS> ¶meters)
{
auto fname = m_fileNames.find(writable);
VERIFY(
fname != m_fileNames.end(), "[HDF5] File name not found in writable");
auto fid = m_fileNamesWithID.find(fname->second);
VERIFY(
fid != m_fileNamesWithID.end(),
"[HDF5] File ID not found with file name");
hid_t dataset_id = H5Dopen(
fid->second, concrete_h5_file_position(writable).c_str(), H5P_DEFAULT);
VERIFY(
dataset_id >= 0,
"[HDF5] Internal error: Failed to open HDF5 dataset during dataset "
"read");
hid_t dataset_space = H5Dget_space(dataset_id);
int ndims = H5Sget_simple_extent_ndims(dataset_space);
VERIFY(
ndims >= 0,
"[HDF5]: Internal error: Failed to retrieve dimensionality of "
"dataset "
"during dataset read.");
// // now let's figure out whether this one has chunks
// hid_t propertyList = H5Dget_create_plist( dataset_id );
// std::vector< hsize_t > chunkExtent( ndims, 0 );
// int chunkDimensionality =
// H5Pget_chunk( propertyList, ndims, chunkExtent.data() );
// if( chunkDimensionality >= 0 )
// {
// /*
// * so, the dataset indeed has chunks
// * alas, this backend doesn't write chunks, so for now, reading them
// * is unimplemented
// *
// * https://hdf5.io/develop/group___h5_d.html#gaccff213d3e0765b86f66d08dd9959807
// * May or may not be helpful if implementing this properly one day.
// */
// }
std::vector<hsize_t> dims(ndims, 0);
// return value is equal to ndims
H5Sget_simple_extent_dims(dataset_space, dims.data(), nullptr);
Offset offset(ndims, 0);
Extent extent;
extent.reserve(ndims);
for (auto e : dims)
{
extent.push_back(e);
}
parameters.chunks->push_back(
WrittenChunkInfo(std::move(offset), std::move(extent)));
herr_t status;
status = H5Sclose(dataset_space);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset space during "
"availableChunks task");
status = H5Dclose(dataset_id);
VERIFY(
status == 0,
"[HDF5] Internal error: Failed to close HDF5 dataset during "
"availableChunks task");
}
void HDF5IOHandlerImpl::openFile(
Writable *writable, Parameter<Operation::OPEN_FILE> ¶meters)
{
if (!auxiliary::directory_exists(m_handler->directory))
throw error::ReadError(
error::AffectedObject::File,
error::Reason::Inaccessible,
"HDF5",
"Supplied directory is not valid: " + m_handler->directory);
std::string name = m_handler->directory + parameters.name;
if (!auxiliary::ends_with(name, ".h5"))
name += ".h5";
// this may (intentionally) overwrite
m_fileNames[writable] = name;
// check if file already open
auto search = m_fileNamesWithID.find(name);
if (search != m_fileNamesWithID.end())
{
return;
}
unsigned flags;
Access at = m_handler->m_backendAccess;
if (access::readOnly(at))
flags = H5F_ACC_RDONLY;
/*
* Within the HDF5 backend, APPEND and READ_WRITE mode are
* equivalent, but the openPMD frontend exposes no reading
* functionality in APPEND mode.
*/
else
flags = H5F_ACC_RDWR;
hid_t file_id;
file_id = H5Fopen(name.c_str(), flags, m_fileAccessProperty);
if (file_id < 0)
throw error::ReadError(