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FieldIOHdf5.h
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1 ///////////////////////////////////////////////////////////////////////////////
2 //
3 // File: FieldIOHdf5.h
4 //
5 // For more information, please see: http://www.nektar.info
6 //
7 // The MIT License
8 //
9 // Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10 // Department of Aeronautics, Imperial College London (UK), and Scientific
11 // Computing and Imaging Institute, University of Utah (USA).
12 //
13 // Permission is hereby granted, free of charge, to any person obtaining a
14 // copy of this software and associated documentation files (the "Software"),
15 // to deal in the Software without restriction, including without limitation
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17 // and/or sell copies of the Software, and to permit persons to whom the
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19 //
20 // The above copyright notice and this permission notice shall be included
21 // in all copies or substantial portions of the Software.
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23 // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
24 // OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
25 // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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29 // DEALINGS IN THE SOFTWARE.
30 //
31 // Description: Field IO to/from HDF5
32 //
33 ///////////////////////////////////////////////////////////////////////////////
34 
35 #ifndef NEKTAR_LIB_UTILITIES_BASIC_UTILS_FIELDIOHDF5_H
36 #define NEKTAR_LIB_UTILITIES_BASIC_UTILS_FIELDIOHDF5_H
37 
41 
42 namespace Nektar
43 {
44 namespace LibUtilities
45 {
46 
47 namespace H5
48 {
49 class Group;
50 typedef std::shared_ptr<Group> GroupSharedPtr;
51 } // namespace H5
52 
53 /**
54  * @class Class encapsulating simple HDF5 data source using H5 reader utilities.
55  */
56 class H5DataSource : public DataSource
57 {
58 public:
59  /// Constructor based on filename.
60  H5DataSource(const std::string &fn, H5::PListSharedPtr parallelProps)
61  : doc(H5::File::Open(fn, H5F_ACC_RDONLY, parallelProps))
62  {
63  }
64 
65  /// Get H5::FileSharedPtr reference to file.
67  {
68  return doc;
69  }
70 
71  /// Get H5::FileSharedPtr reference to file.
72  const H5::FileSharedPtr Get() const
73  {
74  return doc;
75  }
76 
77  /// Static constructor for this data source.
78  static DataSourceSharedPtr create(const std::string &fn,
79  H5::PListSharedPtr parallelProps)
80  {
81  return DataSourceSharedPtr(new H5DataSource(fn, parallelProps));
82  }
83 
84 private:
85  /// HDF5 document.
87 };
88 typedef std::shared_ptr<H5DataSource> H5DataSourceSharedPtr;
89 
90 /**
91  * @class Simple class for writing hierarchical data using HDF5.
92  */
93 class H5TagWriter : public TagWriter
94 {
95 public:
96  /// Default constructor.
98  {
99  }
100 
101 protected:
102  /// Add a child node.
103  TagWriterSharedPtr v_AddChild(const std::string &name)
104  {
105  H5::GroupSharedPtr child = m_Group->CreateGroup(name);
106  return TagWriterSharedPtr(new H5TagWriter(child));
107  }
108 
109  /// Set an attribute key/value pair on this tag.
110  void v_SetAttr(const std::string &key, const std::string &val)
111  {
112  m_Group->SetAttribute(key, val);
113  }
114 
115 private:
116  /// HDF5 group for this tag.
118 };
119 typedef std::shared_ptr<H5TagWriter> H5TagWriterSharedPtr;
120 
121 /**
122  * @class Class for operating on HDF5-based FLD files.
123  *
124  * This class implements a HDF5 reader/writer based on MPI/O that is designed to
125  * operate on a single file across all processors of a simulation. The
126  * definition follows vaguely similar lines to XML output but is stored somewhat
127  * differently to accommodate parallel reading and writing. At a basic level
128  * metadata is organised as follows:
129  *
130  * - Nektar++ data lies in the root `/NEKTAR` group.
131  * - The contents of a FieldDefinitions object is hashed to construct a unique
132  * identifier for each object, which becomes the name of a group within the
133  * root group. We then use the H5TagWriter to assign the field definitions
134  * to each group.
135  * - In a similar fashion, we create a `Metadata` group to contain field
136  * metadata that is written.
137  *
138  * We then define five data sets to contain field data:
139  *
140  * - The `DATA` dataset contains the double-precision modal coefficient data.
141  * - The `IDS` dataset contains the element IDs of the elements that are
142  * written out.
143  * - The `POLYORDERS` dataset is written if the field data contains variable
144  * polynomial order, and contains the (possibly hetergeneous) mode orders in
145  * each direction for each of the elements.
146  * - The `HOMOGENEOUSZIDS` dataset contains the IDs of z-planes for
147  * homogeneous simulations, if the data are homogeneous.
148  * - The `HOMOGENEOUSYIDS` dataset contains the IDs of y-planes for
149  * homogeneous simulations, if the data are homogeneous.
150  * - The `HOMOGENEOUSSIDS` dataset contains the strip IDs for
151  * homogeneous simulations, if the data are homogeneous and use strips.
152  *
153  * The ordering is defined according to the `DECOMPOSITION` dataset. A
154  * `decomposition' in this class is essentially a single field definition with
155  * its accompanying data. Data are written into each dataset by the order of
156  * each decomposition. Each decomposition contains the following seven integers
157  * that define it per field definition per processor:
158  *
159  * - Number of elements in this field definition (index #ELEM_DCMP_IDX).
160  * - Number of entries in the `DATA` array for this field definition
161  * (index #VAL_DCMP_IDX)
162  * - Number of entries in the `POLYORDERS` array for this field definition
163  * (index #ORDER_DCMP_IDX)
164  * - Number of entries in the `HOMOGENEOUSZIDS` array (index #HOMZ_DCMP_IDX).
165  * - Number of entries in the `HOMOGENEOUSYIDS` array (index #HOMY_DCMP_IDX).
166  * - Number of entries in the `HOMOGENEOUSSIDS` array (index #HOMS_DCMP_IDX).
167  * - Hash of the field definition, represented as a 32-bit integer, which
168  * describes the name of the attribute that contains the rest of the field
169  * definition information (e.g. field names, basis type, etc).
170  *
171  * The number of decompositions is therefore calculated as the field size
172  * divided by #MAX_DCMPS which allows us to calculate the offsets of the data
173  * for each field definition within the arrays.
174  */
175 class FieldIOHdf5 : public FieldIO
176 {
177 public:
178  static const unsigned int FORMAT_VERSION;
179 
180  static const unsigned int ELEM_DCMP_IDX;
181  static const unsigned int VAL_DCMP_IDX;
182  static const unsigned int ORDER_DCMP_IDX;
183  static const unsigned int HOMY_DCMP_IDX;
184  static const unsigned int HOMZ_DCMP_IDX;
185  static const unsigned int HOMS_DCMP_IDX;
186  static const unsigned int HASH_DCMP_IDX;
187  static const unsigned int MAX_DCMPS;
188 
189  static const unsigned int ELEM_CNT_IDX;
190  static const unsigned int VAL_CNT_IDX;
191  static const unsigned int ORDER_CNT_IDX;
192  static const unsigned int HOMY_CNT_IDX;
193  static const unsigned int HOMZ_CNT_IDX;
194  static const unsigned int HOMS_CNT_IDX;
195  static const unsigned int MAX_CNTS;
196 
197  static const unsigned int IDS_IDX_IDX;
198  static const unsigned int DATA_IDX_IDX;
199  static const unsigned int ORDER_IDX_IDX;
200  static const unsigned int HOMY_IDX_IDX;
201  static const unsigned int HOMZ_IDX_IDX;
202  static const unsigned int HOMS_IDX_IDX;
203  static const unsigned int MAX_IDXS;
204 
205  /// Creates an instance of this class
207  LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
208  {
210  sharedFilesystem);
211  }
212 
213  /// Name of class
214  LIB_UTILITIES_EXPORT static std::string className;
215 
217  bool sharedFilesystem);
218 
220  {
221  }
222 
223 protected:
224  LIB_UTILITIES_EXPORT virtual void v_Write(
225  const std::string &outFile,
226  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
227  std::vector<std::vector<NekDouble>> &fielddata,
228  const FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap,
229  const bool backup = false) override;
230 
231  LIB_UTILITIES_EXPORT virtual void v_Import(
232  const std::string &infilename,
233  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
234  std::vector<std::vector<NekDouble>> &fielddata =
236  FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap,
237  const Array<OneD, int> &ElementIDs = NullInt1DArray) override;
238 
240  const std::string &filename,
241  FieldMetaDataMap &fieldmetadatamap) override;
242 
243  virtual const std::string &v_GetClassName() const override;
244 
245 private:
247  {
248  OffsetHelper() : data(0), order(0), homy(0), homz(0), homs(0)
249  {
250  }
252  : data(in.data), order(in.order), homy(in.homy), homz(in.homz),
253  homs(in.homs)
254  {
255  }
256  OffsetHelper &operator=(const OffsetHelper &in) = default;
257 
258  uint64_t data, order, homy, homz, homs;
259  };
260 
262  DataSourceSharedPtr dataSource, FieldMetaDataMap &fieldmetadatamap);
263 
266  std::vector<uint64_t> &decomps, uint64_t decomp, OffsetHelper offset,
267  std::string group, FieldDefinitionsSharedPtr def);
268 
270  H5::PListSharedPtr readPL, H5::DataSetSharedPtr data_dset,
271  H5::DataSpaceSharedPtr data_fspace, uint64_t data_i,
272  std::vector<uint64_t> &decomps, uint64_t decomp,
273  const FieldDefinitionsSharedPtr fielddef,
274  std::vector<NekDouble> &fielddata);
275 };
276 } // namespace LibUtilities
277 } // namespace Nektar
278 #endif
#define LIB_UTILITIES_EXPORT
void ImportFieldData(H5::PListSharedPtr readPL, H5::DataSetSharedPtr data_dset, H5::DataSpaceSharedPtr data_fspace, uint64_t data_i, std::vector< uint64_t > &decomps, uint64_t decomp, const FieldDefinitionsSharedPtr fielddef, std::vector< NekDouble > &fielddata)
Import the field data from the HDF5 document.
static const unsigned int ELEM_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of elements in the cnt array.
Definition: FieldIOHdf5.h:189
static FieldIOSharedPtr create(LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
Creates an instance of this class.
Definition: FieldIOHdf5.h:206
static const unsigned int MAX_CNTS
A helper for FieldIOHdf5::v_Write. Describes the maximum number of items in the cnt array per field d...
Definition: FieldIOHdf5.h:195
virtual DataSourceSharedPtr v_ImportFieldMetaData(const std::string &filename, FieldMetaDataMap &fieldmetadatamap) override
Import field metadata from filename and return the data source which wraps filename.
virtual const std::string & v_GetClassName() const override
Get class name.
virtual void v_Write(const std::string &outFile, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble >> &fielddata, const FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const bool backup=false) override
Write a HDF5 file to outFile given the field definitions fielddefs, field data fielddata and metadata...
static const unsigned int HOMY_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of homogeneous y-planes in th...
Definition: FieldIOHdf5.h:192
static std::string className
Name of class.
Definition: FieldIOHdf5.h:214
virtual void v_Import(const std::string &infilename, std::vector< FieldDefinitionsSharedPtr > &fielddefs, std::vector< std::vector< NekDouble >> &fielddata=NullVectorNekDoubleVector, FieldMetaDataMap &fieldinfomap=NullFieldMetaDataMap, const Array< OneD, int > &ElementIDs=NullInt1DArray) override
Import a HDF5 format file.
static const unsigned int ORDER_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:182
static const unsigned int HOMZ_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of homogeneous z-planes in th...
Definition: FieldIOHdf5.h:193
static const unsigned int FORMAT_VERSION
Version of the Nektar++ HDF5 format, which is embedded into the main NEKTAR group as an attribute.
Definition: FieldIOHdf5.h:178
static const unsigned int HASH_DCMP_IDX
The hash of the field definition information, which defines the name of the attribute containing the ...
Definition: FieldIOHdf5.h:186
static const unsigned int HOMS_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of homogeneous strips in the ...
Definition: FieldIOHdf5.h:194
static const unsigned int VAL_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of data points in the cnt arr...
Definition: FieldIOHdf5.h:190
static const unsigned int IDS_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the element IDs within the indexing set.
Definition: FieldIOHdf5.h:197
static const unsigned int HOMS_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:185
static const unsigned int ELEM_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:180
static const unsigned int ORDER_CNT_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of order points in the cnt ar...
Definition: FieldIOHdf5.h:191
void ImportFieldDef(H5::PListSharedPtr readPL, H5::GroupSharedPtr root, std::vector< uint64_t > &decomps, uint64_t decomp, OffsetHelper offset, std::string group, FieldDefinitionsSharedPtr def)
Import field definitions from a HDF5 document.
static const unsigned int ORDER_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the element order within the indexing se...
Definition: FieldIOHdf5.h:199
static const unsigned int HOMZ_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:184
static const unsigned int MAX_DCMPS
A helper for FieldIOHdf5::v_Write. Describes the maximum number of items in the decomposition per fie...
Definition: FieldIOHdf5.h:187
FieldIOHdf5(LibUtilities::CommSharedPtr pComm, bool sharedFilesystem)
Construct the FieldIO object for HDF5 output.
static const unsigned int MAX_IDXS
A helper for FieldIOHdf5::v_Write. Describes the maximum number of items in the indexing set.
Definition: FieldIOHdf5.h:203
static const unsigned int VAL_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:181
static const unsigned int DATA_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the data size within the indexing set.
Definition: FieldIOHdf5.h:198
void ImportHDF5FieldMetaData(DataSourceSharedPtr dataSource, FieldMetaDataMap &fieldmetadatamap)
Import field metadata from dataSource.
static const unsigned int HOMS_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of homogeneous strips within ...
Definition: FieldIOHdf5.h:202
static const unsigned int HOMY_DCMP_IDX
A helper for FieldIOHdf5::v_Write and FieldIOHdf5::v_Import. Describes the position of the number of ...
Definition: FieldIOHdf5.h:183
static const unsigned int HOMZ_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of z-planes within the indexi...
Definition: FieldIOHdf5.h:201
static const unsigned int HOMY_IDX_IDX
A helper for FieldIOHdf5::v_Write. Describes the position of the number of y-planes within the indexi...
Definition: FieldIOHdf5.h:200
Class for operating on Nektar++ input/output files.
Definition: FieldIO.h:229
H5DataSource(const std::string &fn, H5::PListSharedPtr parallelProps)
Constructor based on filename.
Definition: FieldIOHdf5.h:60
const H5::FileSharedPtr Get() const
Get H5::FileSharedPtr reference to file.
Definition: FieldIOHdf5.h:72
H5::FileSharedPtr Get()
Get H5::FileSharedPtr reference to file.
Definition: FieldIOHdf5.h:66
H5::FileSharedPtr doc
HDF5 document.
Definition: FieldIOHdf5.h:86
static DataSourceSharedPtr create(const std::string &fn, H5::PListSharedPtr parallelProps)
Static constructor for this data source.
Definition: FieldIOHdf5.h:78
void v_SetAttr(const std::string &key, const std::string &val)
Set an attribute key/value pair on this tag.
Definition: FieldIOHdf5.h:110
H5::GroupSharedPtr m_Group
HDF5 group for this tag.
Definition: FieldIOHdf5.h:117
TagWriterSharedPtr v_AddChild(const std::string &name)
Add a child node.
Definition: FieldIOHdf5.h:103
H5TagWriter(H5::GroupSharedPtr grp)
Default constructor.
Definition: FieldIOHdf5.h:97
Base class for writing hierarchical data (XML or HDF5).
Definition: FieldIO.h:59
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
std::shared_ptr< DataSpace > DataSpaceSharedPtr
Definition: H5.h:83
std::shared_ptr< PList > PListSharedPtr
Definition: H5.h:97
std::shared_ptr< File > FileSharedPtr
Definition: H5.h:93
std::shared_ptr< Group > GroupSharedPtr
Definition: FieldIOHdf5.h:49
std::shared_ptr< DataSet > DataSetSharedPtr
Definition: H5.h:95
std::shared_ptr< H5TagWriter > H5TagWriterSharedPtr
Definition: FieldIOHdf5.h:119
std::shared_ptr< TagWriter > TagWriterSharedPtr
Definition: FieldIO.h:80
std::shared_ptr< H5DataSource > H5DataSourceSharedPtr
Definition: FieldIOHdf5.h:88
std::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:327
std::shared_ptr< DataSource > DataSourceSharedPtr
Definition: FieldIO.h:90
std::map< std::string, std::string > FieldMetaDataMap
Definition: FieldIO.h:52
static FieldMetaDataMap NullFieldMetaDataMap
Definition: FieldIO.h:53
static std::vector< std::vector< NekDouble > > NullVectorNekDoubleVector
std::shared_ptr< FieldDefinitions > FieldDefinitionsSharedPtr
Definition: FieldIO.h:186
std::shared_ptr< Comm > CommSharedPtr
Pointer to a Communicator object.
Definition: Comm.h:54
The above copyright notice and this permission notice shall be included.
Definition: CoupledSolver.h:2
static Array< OneD, int > NullInt1DArray
OffsetHelper & operator=(const OffsetHelper &in)=default