openPMD-api
HDF5IOHandlerImpl.hpp
1 /* Copyright 2017-2021 Fabian Koller
2  *
3  * This file is part of openPMD-api.
4  *
5  * openPMD-api is free software: you can redistribute it and/or modify
6  * it under the terms of of either the GNU General Public License or
7  * the GNU Lesser General Public License as published by
8  * the Free Software Foundation, either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * openPMD-api is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14  * GNU General Public License and the GNU Lesser General Public License
15  * for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * and the GNU Lesser General Public License along with openPMD-api.
19  * If not, see <http://www.gnu.org/licenses/>.
20  */
21 #pragma once
22 
23 #include "openPMD/config.hpp"
24 #if openPMD_HAVE_HDF5
25 #include "openPMD/IO/AbstractIOHandlerImpl.hpp"
26 
27 #include "openPMD/auxiliary/JSON.hpp"
28 #include "openPMD/auxiliary/Option.hpp"
29 
30 #include <hdf5.h>
31 #include <unordered_map>
32 #include <unordered_set>
33 #endif
34 
35 namespace openPMD
36 {
37 #if openPMD_HAVE_HDF5
39 {
40 public:
41  HDF5IOHandlerImpl(AbstractIOHandler *, nlohmann::json config);
42  ~HDF5IOHandlerImpl() override;
43 
44  void
46  void
48  void createDataset(
50  void extendDataset(
52  void availableChunks(
54  void openFile(Writable *, Parameter<Operation::OPEN_FILE> const &) override;
55  void
57  void openPath(Writable *, Parameter<Operation::OPEN_PATH> const &) override;
59  void
61  void
63  void deleteDataset(
65  void deleteAttribute(
66  Writable *, Parameter<Operation::DELETE_ATT> const &) override;
67  void writeDataset(
68  Writable *, Parameter<Operation::WRITE_DATASET> const &) override;
69  void writeAttribute(
70  Writable *, Parameter<Operation::WRITE_ATT> const &) override;
74  void
77 
78  std::unordered_map<Writable *, std::string> m_fileNames;
79  std::unordered_map<std::string, hid_t> m_fileNamesWithID;
80 
81  std::unordered_set<hid_t> m_openFileIDs;
82 
83  hid_t m_datasetTransferProperty;
84  hid_t m_fileAccessProperty;
85  hid_t m_fileCreateProperty;
86 
87  hbool_t m_hdf5_collective_metadata = 1;
88 
89  // h5py compatible types for bool and complex
90  hid_t m_H5T_BOOL_ENUM;
91  hid_t m_H5T_CFLOAT;
92  hid_t m_H5T_CDOUBLE;
93  hid_t m_H5T_CLONG_DOUBLE;
94 
95 private:
96  auxiliary::TracingJSON m_config;
97  std::string m_chunks = "auto";
98  struct File
99  {
100  std::string name;
101  hid_t id;
102  };
104 }; // HDF5IOHandlerImpl
105 #else
106 class HDF5IOHandlerImpl
107 {}; // HDF5IOHandlerImpl
108 #endif
109 
110 } // namespace openPMD
void writeAttribute(Writable *, Parameter< Operation::WRITE_ATT > const &) override
Create a single attribute and fill the value, possibly overwriting an existing attribute.
Definition: HDF5IOHandler.cpp:1213
void readDataset(Writable *, Parameter< Operation::READ_DATASET > &) override
Read a chunk of data from an existing dataset.
Definition: HDF5IOHandler.cpp:1513
void extendDataset(Writable *, Parameter< Operation::EXTEND_DATASET > const &) override
Increase the extent of an existing dataset.
Definition: HDF5IOHandler.cpp:545
void createFile(Writable *, Parameter< Operation::CREATE_FILE > const &) override
Create a new file in physical storage, possibly overriding an existing file.
Definition: HDF5IOHandler.cpp:195
void deleteDataset(Writable *, Parameter< Operation::DELETE_DATASET > const &) override
Delete an existing dataset.
Definition: HDF5IOHandler.cpp:1003
void readAttribute(Writable *, Parameter< Operation::READ_ATT > &) override
Read the value of an existing attribute.
Definition: HDF5IOHandler.cpp:1624
void openDataset(Writable *, Parameter< Operation::OPEN_DATASET > &) override
Open an existing dataset and determine its datatype and extent.
Definition: HDF5IOHandler.cpp:785
Interface for communicating between logical and physically persistent data.
Definition: AbstractIOHandler.hpp:122
Simple Option type based on variantSrc::variant.
Definition: Option.hpp:45
void listPaths(Writable *, Parameter< Operation::LIST_PATHS > &) override
List all paths/sub-groups inside a group, non-recursively.
Definition: HDF5IOHandler.cpp:2069
void listDatasets(Writable *, Parameter< Operation::LIST_DATASETS > &) override
List all datasets inside a group, non-recursively.
Definition: HDF5IOHandler.cpp:2125
Public definitions of openPMD-api.
Definition: Date.cpp:28
Layer to mirror structure of logical data and persistent data in file.
Definition: Writable.hpp:63
void openPath(Writable *, Parameter< Operation::OPEN_PATH > const &) override
Open all contained groups in a path, possibly recursively.
Definition: HDF5IOHandler.cpp:724
void deleteAttribute(Writable *, Parameter< Operation::DELETE_ATT > const &) override
Delete an existing attribute.
Definition: HDF5IOHandler.cpp:1055
void createPath(Writable *, Parameter< Operation::CREATE_PATH > const &) override
Create all necessary groups for a path, possibly recursively.
Definition: HDF5IOHandler.cpp:235
void closeFile(Writable *, Parameter< Operation::CLOSE_FILE > const &) override
Close the file corresponding with the writable and release file handles.
Definition: HDF5IOHandler.cpp:706
Extend nlohmann::json with tracing of which keys have been accessed by operator[]().
Definition: JSON.hpp:52
void createDataset(Writable *, Parameter< Operation::CREATE_DATASET > const &) override
Create a new dataset of given type, extent and storage properties.
Definition: HDF5IOHandler.cpp:326
void availableChunks(Writable *, Parameter< Operation::AVAILABLE_CHUNKS > &) override
Report chunks that are available for loading from the dataset represented by this writable...
Definition: HDF5IOHandler.cpp:606
void deletePath(Writable *, Parameter< Operation::DELETE_PATH > const &) override
Delete all objects within an existing path.
Definition: HDF5IOHandler.cpp:951
void deleteFile(Writable *, Parameter< Operation::DELETE_FILE > const &) override
Delete an existing file from physical storage.
Definition: HDF5IOHandler.cpp:917
void writeDataset(Writable *, Parameter< Operation::WRITE_DATASET > const &) override
Write a chunk of data into an existing dataset.
Definition: HDF5IOHandler.cpp:1090
Definition: HDF5IOHandlerImpl.hpp:38
Definition: AbstractIOHandlerImpl.hpp:35
void openFile(Writable *, Parameter< Operation::OPEN_FILE > const &) override
Open an existing file assuming it conforms to openPMD.
Definition: HDF5IOHandler.cpp:664
void listAttributes(Writable *, Parameter< Operation::LIST_ATTS > &) override
List all attributes associated with an object.
Definition: HDF5IOHandler.cpp:2182