Arcane  v3.14.10.0
Documentation utilisateur
Chargement...
Recherche...
Aucune correspondance
Hdf5ReaderWriter.cc
1// -*- tab-width: 2; indent-tabs-mode: nil; coding: utf-8-with-signature -*-
2//-----------------------------------------------------------------------------
3// Copyright 2000-2023 CEA (www.cea.fr) IFPEN (www.ifpenergiesnouvelles.com)
4// See the top-level COPYRIGHT file for details.
5// SPDX-License-Identifier: Apache-2.0
6//-----------------------------------------------------------------------------
7/*---------------------------------------------------------------------------*/
8/* Hdf5ReaderWriter.cc (C) 2000-2023 */
9/* */
10/* Lecture/Ecriture au format HDF5. */
11/*---------------------------------------------------------------------------*/
12/*---------------------------------------------------------------------------*/
13
14#include "arcane/utils/String.h"
15#include "arcane/utils/StringBuilder.h"
16#include "arcane/utils/OStringStream.h"
17#include "arcane/utils/ScopedPtr.h"
18#include "arcane/utils/List.h"
19#include "arcane/utils/ArcanePrecomp.h"
20#include "arcane/utils/ITraceMng.h"
21#include "arcane/utils/PlatformUtils.h"
22#include "arcane/utils/CheckedConvert.h"
23#include "arcane/utils/ArrayShape.h"
24
25#include "arcane/Item.h"
26#include "arcane/ISubDomain.h"
27#include "arcane/StdNum.h"
28#include "arcane/IVariable.h"
29#include "arcane/CheckpointService.h"
30#include "arcane/Directory.h"
31#include "arcane/IParallelMng.h"
32#include "arcane/IParallelReplication.h"
33#include "arcane/Service.h"
34#include "arcane/ArcaneException.h"
35#include "arcane/ItemGroup.h"
36#include "arcane/ItemEnumerator.h"
37#include "arcane/VerifierService.h"
38#include "arcane/IVariableMng.h"
39#include "arcane/FactoryService.h"
40#include "arcane/IData.h"
41#include "arcane/Timer.h"
42#include "arcane/ISerializedData.h"
43#include "arcane/IIOMng.h"
44#include "arcane/IXmlDocumentHolder.h"
45
46#include "arcane/datatype/DataTypeTraits.h"
47
48#include "arcane/SerializeBuffer.h"
49#include "arcane/ISerializeMessageList.h"
50#include "arcane/SerializeMessage.h"
51
52#include "arcane/hdf5/Hdf5ReaderWriter.h"
53
54#include "arcane/hdf5/Hdf5ReaderWriter_axl.h"
55
56#include <array>
57//#define ARCANE_TEST_HDF5MPI
58
59/*---------------------------------------------------------------------------*/
60/*---------------------------------------------------------------------------*/
61
62namespace Arcane
63{
64
65/*---------------------------------------------------------------------------*/
66/*---------------------------------------------------------------------------*/
67
68using namespace Hdf5Utils;
69
70static herr_t _Hdf5ReaderWriterIterateMe(hid_t,const char*,void*);
71
72/*---------------------------------------------------------------------------*/
73/*---------------------------------------------------------------------------*/
74
75namespace
76{
77constexpr Int32 VARIABLE_INFO_SIZE = 10 + ArrayShape::MAX_NB_DIMENSION;
78}
79
80/*---------------------------------------------------------------------------*/
81/*---------------------------------------------------------------------------*/
82
83Hdf5ReaderWriter::
84Hdf5ReaderWriter(ISubDomain* sd,const String& filename,
85 const String& sub_group_name,
86 Integer fileset_size, Integer currentIndex, Integer index_modulo,
87 eOpenMode open_mode,[[maybe_unused]] bool do_verif)
88: TraceAccessor(sd->traceMng())
89, m_parallel_mng(sd->parallelMng())
90, m_open_mode(open_mode)
91, m_filename(filename)
92, m_sub_group_name(sub_group_name)
93, m_is_initialized(false)
94, m_io_timer(sd,"Hdf5Timer",Timer::TimerReal)
95, m_is_parallel(false)
96, m_my_rank(m_parallel_mng->commRank())
97, m_send_rank(m_my_rank)
98, m_last_recv_rank(m_my_rank)
99, m_fileset_size(fileset_size)
100, m_index_write(currentIndex)
101, m_index_modulo(index_modulo)
102{
103
104 if (m_fileset_size!=1 && m_parallel_mng->isParallel()){
105 m_is_parallel = true;
106 Integer nb_rank = m_parallel_mng->commSize();
107 if (m_fileset_size==0){
108 m_send_rank = 0;
109 m_last_recv_rank = nb_rank;
110 }
111 else{
112 m_send_rank = (m_my_rank / m_fileset_size) * m_fileset_size;
113 m_last_recv_rank = m_send_rank + m_fileset_size;
114 if (m_last_recv_rank>nb_rank)
115 m_last_recv_rank = nb_rank;
116 --m_last_recv_rank;
117 }
118 }
119 sd->traceMng()->info() << " INFOS PARALLEL: my_rank=" << m_my_rank
120 << " send_rank=" << m_send_rank
121 << " last_recv_rank=" << m_last_recv_rank
122 << " filename=" << filename;
123}
124
125
126/*---------------------------------------------------------------------------*/
127/*---------------------------------------------------------------------------*/
128void Hdf5ReaderWriter::
129initialize()
130{
131 if (m_is_initialized)
132 return;
133 m_is_initialized = true;
134 HInit();
135 info() << "INIT HDF5 READER/WRITER";
136 {
137 unsigned vmajor = 0;
138 unsigned vminor = 0;
139 unsigned vrel = 0;
140 ::H5get_libversion(&vmajor,&vminor,&vrel);
141 info() << "HDF5 version = " << vmajor << '.' << vminor << '.' << vrel;
142 }
143 info() << "SubGroup is '" << m_sub_group_name <<"'";
144 if (m_open_mode==OpenModeRead){
145 m_file_id.openRead(m_filename);
146 m_sub_group_id.recursiveOpen(m_file_id,m_sub_group_name);
147 }
148 else{
149 // Si ce n'est pas moi qui écrit, n'ouvre pas le fichier
150 if (m_send_rank!=m_my_rank)
151 return;
152 if (m_open_mode==OpenModeTruncate){
153 hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
154#ifdef ARCANE_TEST_HDF5MPI
155 void* arcane_comm = subDomain()->parallelMng()->getMPICommunicator();
156 if (!arcane_comm)
157 ARCANE_FATAL("No MPI environment available");
158 MPI_Comm mpi_comm = *((MPI_Comm*)arcane_comm);
159 MPI_Info mpi_info = MPI_INFO_NULL;
160 //H5Pset_fapl_mpiposix(plist_id, mpi_comm, MPI_INFO_NULL); //mpi_info);
161 H5Pset_fapl_mpio(plist_id, mpi_comm, MPI_INFO_NULL); //mpi_info);
162 H5Pset_fclose_degree(plist_id,H5F_CLOSE_STRONG);
163#endif
164 int mdc_nelmts;
165 size_t rdcc_nelmts;
166 size_t rdcc_nbytes;
167 double rdcc_w0;
168 herr_t r = H5Pget_cache(plist_id,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
169 info() << " CACHE SIZE r=" << r << " mdc=" << mdc_nelmts
170 << " rdcc=" << rdcc_nelmts << " rdcc_bytes=" << rdcc_nbytes << " w0=" << rdcc_w0;
171 mdc_nelmts *= 10;
172 rdcc_nelmts *= 10;
173 rdcc_nbytes = 10000000;
174 r = H5Pset_cache(plist_id,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
175 info() << " SET CACHE SIZE R1=" << r;
176 //r = H5Pset_fapl_stdio(plist_id);
177 //info() << " R2=" << r;
178 hsize_t sieve_buf = (1024 << 12);
179 r = H5Pset_sieve_buf_size(plist_id,sieve_buf);
180 info() << " SIEVE_BUF=" << sieve_buf << " r=" << r;
181 hsize_t small_block_size = 0;
182 r = H5Pget_small_data_block_size(plist_id,&small_block_size);
183 info() << " SMALL BLOCK SIZE=" << small_block_size;
184 small_block_size <<= 10;
185 r = H5Pset_small_data_block_size(plist_id,small_block_size);
186 info() << " SET SMALL BLOCK SIZE s=" << small_block_size << " r=" << r;
187
188 m_file_id.openTruncate(m_filename,plist_id);
189 }
190 else if (m_open_mode==OpenModeAppend){
191 m_file_id.openAppend(m_filename);
192 }
193 if (m_sub_group_name!="/"){
194 m_sub_group_id.checkDelete(m_file_id,m_sub_group_name);
195 m_sub_group_id.recursiveCreate(m_file_id,m_sub_group_name);
196 }
197 else
198 m_sub_group_id.open(m_file_id,m_sub_group_name);
199 }
200 if (m_file_id.isBad())
201 ARCANE_THROW(ReaderWriterException,"Unable to open file '{0}'",m_filename);
202
203 if (m_sub_group_id.isBad())
204 ARCANE_THROW(ReaderWriterException,"HDF5 group '{0}' not found",m_sub_group_name);
205
206 if (m_open_mode==OpenModeRead){
207 int index = 0;
208 //H5Giterate(m_sub_group_id.id(),"Variables",&index,_Hdf5ReaderWriterIterateMe,this);
209 H5Giterate(m_file_id.id(),m_sub_group_name.localstr(),&index,_Hdf5ReaderWriterIterateMe,this);
210 }
211}
212
213
214/*---------------------------------------------------------------------------*/
215/*---------------------------------------------------------------------------*/
216
217Hdf5ReaderWriter::
218~Hdf5ReaderWriter()
219{
220}
221
222/*---------------------------------------------------------------------------*/
223/*---------------------------------------------------------------------------*/
224
225void Hdf5ReaderWriter::
226_checkValid()
227{
228 if (m_is_initialized)
229 return;
230 fatal() << "Use of a Hdf5ReaderWriter instance not initialized";
231}
232
233/*---------------------------------------------------------------------------*/
234/*---------------------------------------------------------------------------*/
235
236String Hdf5ReaderWriter::
237_variableGroupName(IVariable* var)
238{
239 return var->fullName();
240}
241
242/*---------------------------------------------------------------------------*/
243/*---------------------------------------------------------------------------*/
244/*!
245 * \brief Ecriture en parallèle.
246 *
247 * \warning En cours de test, pas utilisable.
248 */
249void Hdf5ReaderWriter::
250_writeValParallel(IVariable* v,const ISerializedData* sdata)
251{
252 SerializeBuffer sb;
253 sb.setMode(ISerializer::ModeReserve);
254 sb.reserve(DT_Int32,1); // Pour indiquer la fin des envois
255 sb.reserve(v->fullName());
256 sb.reserve(m_sub_group_name); //!< Nom du groupe.
257 sb.reserve(DT_Int32,1); // Pour indiquer le rand duquel le message provient
258 sdata->serialize(&sb);
259 sb.allocateBuffer();
260 sb.setMode(ISerializer::ModePut);
261 sb.putInt32(1); // Indique qu'il s'agit d'un message non vide
262 sb.put(v->fullName());
263 sb.put(m_sub_group_name); //!< Nom du groupe.
264 sb.put(m_my_rank);
265 sdata->serialize(&sb);
266 m_parallel_mng->sendSerializer(&sb,m_send_rank);
267}
268
269/*---------------------------------------------------------------------------*/
270/*---------------------------------------------------------------------------*/
271
272void Hdf5ReaderWriter::
273_directReadVal(IVariable* v,IData* data)
274{
275 _checkValid();
276 info(4) << "DIRECT READ VAL v=" << v->name();
277 _readVal(v,data);
278}
279
280/*---------------------------------------------------------------------------*/
281/*---------------------------------------------------------------------------*/
282
283void Hdf5ReaderWriter::
284_directWriteVal(IVariable* v,IData* data)
285{
286 _checkValid();
287 Ref<ISerializedData> sdata(data->createSerializedDataRef(false));
288 if (m_is_parallel && m_send_rank!=m_my_rank){
289 _writeValParallel(v,sdata.get());
290 }
291 else{
292 _writeVal(v->fullName(),m_sub_group_name,sdata.get());
293 }
294}
295
296/*---------------------------------------------------------------------------*/
297/*---------------------------------------------------------------------------*/
298
299static herr_t
300_Hdf5ReaderWriterIterateMe(hid_t g,const char* mn,void* ptr)
301{
302 Hdf5ReaderWriter* rw = reinterpret_cast<Hdf5ReaderWriter*>(ptr);
303 return rw->iterateMe(g,mn);
304}
305
306/*---------------------------------------------------------------------------*/
307/*---------------------------------------------------------------------------*/
308
309herr_t Hdf5ReaderWriter::
310iterateMe(hid_t group_id,const char* member_name)
311{
312 ARCANE_UNUSED(group_id);
313 m_variables_name.add(StringView(member_name));
314 return 0;
315}
316
317/*---------------------------------------------------------------------------*/
318/*---------------------------------------------------------------------------*/
319
320void Hdf5ReaderWriter::
321_writeVal(const String& var_group_name,
322 const String& sub_group_name,
323 const ISerializedData* sdata,
324 const Int32 from_rank)
325{
326 const bool hits_modulo=(m_index_modulo!=0) && (m_index_write!=0) && ((m_index_write%m_index_modulo)==0);
327 Timer::Sentry ts(&m_io_timer);
328
329 info(4) << " SDATA name=" << var_group_name << " nb_element=" << sdata->nbElement()
330 << " dim=" << sdata->nbDimension() << " datatype=" << sdata->baseDataType()
331 << " nb_basic_element=" << sdata->nbBaseElement()
332 << " is_multi=" << sdata->isMultiSize()
333 << " dimensions_size=" << sdata->extents().size()
334 << " memory_size=" << sdata->memorySize()
335 << " bytes_size=" << sdata->constBytes().size()
336 << " shape=" << sdata->shape().dimensions();
337
338 Integer nb_dimension = sdata->nbDimension();
339 Int64ConstArrayView dimensions = sdata->extents();
340
341 hid_t save_typeid = m_types.saveType(sdata->baseDataType());
342 hid_t trueid = m_types.nativeType(sdata->baseDataType());
343 const void* ptr = sdata->constBytes().data();
344 Int64 nb_base_element = sdata->nbBaseElement();
345
346 HGroup var_base_group;
347 var_base_group.recursiveCreate(m_file_id,sub_group_name);
348
349 // Création du groupe contenant les informations de la variable
350 HGroup group_id;
351 group_id.recursiveCreate(var_base_group,var_group_name);
352 if (group_id.isBad())
353 ARCANE_THROW(ReaderWriterException,"HDF5 group '{0}' not found",var_group_name);
354
355 Int64 nb_element = sdata->nbElement();
356 bool is_multi_size = sdata->isMultiSize();
357 Int64 dim2_size = 0;
358 Int64 dim1_size = 0;
359 if (nb_dimension==2 && !is_multi_size){
360 dim1_size = dimensions[0];
361 dim2_size = dimensions[1];
362 }
363 Integer dimension_array_size = dimensions.size();
364
365 // Sauve les informations concernant les tailles et dimensions de la variable
366 {
367 hsize_t att_dims[1];
368 att_dims[0] = VARIABLE_INFO_SIZE;
369 HSpace space_id;
370 space_id.createSimple(1,att_dims);
371 std::array<Int64,VARIABLE_INFO_SIZE> dim_val_buf;
372 SmallSpan<Int64> dim_val(dim_val_buf);
373 dim_val.fill(0);
374
375 dim_val[0] = nb_dimension;
376 dim_val[1] = dim1_size;
377 dim_val[2] = dim2_size;
378 dim_val[3] = nb_element;
379 dim_val[4] = nb_base_element;
380 dim_val[5] = dimension_array_size;
381 dim_val[6] = is_multi_size ? 1 : 0;
382 dim_val[7] = sdata->baseDataType();
383 dim_val[8] = sdata->memorySize();
384 {
385 ArrayShape shape = sdata->shape();
386 Int32 shape_nb_dim = shape.nbDimension();
387 auto shape_dims = shape.dimensions();
388 dim_val[9] = shape_nb_dim;
389 for (Integer i=0; i<shape_nb_dim; ++i )
390 dim_val[10+i] = shape_dims[i];
391 }
392 HAttribute att_id;
393 if (m_is_parallel && hits_modulo && (from_rank!=0))
394 att_id.remove(group_id,"Dims");
395 att_id.create(group_id,"Dims",m_types.saveType(dim1_size),space_id);
396 herr_t herr = att_id.write(m_types.nativeType(dim2_size),dim_val.data());
397 if (herr<0)
398 ARCANE_THROW(ReaderWriterException,"Wrong dimensions written for variable '{0}'",var_group_name);
399 }
400
401 // Si la variable est de type tableau à deux dimensions, sauve les
402 // tailles de la deuxième dimension par élément.
403 if (dimension_array_size!=0){
404 hsize_t att_dims[1];
405 att_dims[0] = dimension_array_size;
406 HSpace space_id;
407 HDataset array_id;
408 space_id.createSimple(1,att_dims);
409 array_id.recursiveCreate(group_id,"Dim2",m_types.saveType(dim1_size),space_id,H5P_DEFAULT);
410 herr_t herr = array_id.write(m_types.nativeType(dim1_size),dimensions.data());
411 if (herr<0)
412 ARCANE_THROW(ReaderWriterException,"Wrong dimensions written for variable '{0}'",var_group_name);
413 }
414
415 // Maintenant, sauve les valeurs si necessaire
416 if (nb_base_element!=0 && ptr!=nullptr){
417 debug(Trace::High) << "Variable " << var_group_name << " begin dumped (nb_base_element=" << nb_base_element << ").";
418 hsize_t dims[1];
419 dims[0] = nb_base_element;
420 HSpace space_id;
421 space_id.createSimple(1,dims);
422 if (space_id.isBad())
423 ARCANE_THROW(ReaderWriterException,"Wrong dataspace for variable '{0}'",var_group_name);
424
425 HDataset dataset_id;
426 hid_t plist_id = H5P_DEFAULT;
427
428#if 0
429 if (nb_element>=10000){
430 plist_id = H5Pcreate(H5P_DATASET_CREATE);
431 hsize_t chunk_dim[1];
432 chunk_dim[0] = (4096 << 1);
433 herr_t r = H5Pset_chunk(plist_id,1,chunk_dim);
434 info() << " SET CHUNK FOR " << var_group_name << " s=" << nb_element;
435 }
436#endif
437 dataset_id.recursiveCreate(group_id,"Values",save_typeid,space_id,plist_id);
438 if (dataset_id.isBad())
439 ARCANE_THROW(ReaderWriterException,"Wrong dataset for variable '{0}'",var_group_name);
440
441 herr_t herr = dataset_id.write(trueid,ptr);
442 if (herr<0)
443 ARCANE_THROW(ReaderWriterException,"Wrong dataset written for variable '{0}'",var_group_name);
444 }
445}
446
447/*---------------------------------------------------------------------------*/
448/*---------------------------------------------------------------------------*/
449
450Ref<ISerializedData> Hdf5ReaderWriter::
451_readDim2(IVariable* var)
452{
453 const int max_dim = 256; // Nombre maxi de dimensions des tableaux HDF
454 String vname = _variableGroupName(var);
455 info(4) << " READ DIM name=" << vname;
456 Int64 dimension_array_size = 0;
457 Int64 nb_element = 0;
458 Integer nb_dimension = -1;
459 // Regarde si le nom correspondant est dans la liste des variables.
460 // S'il n'y est pas, cela signifie que le tableau n'a pas été sauvé et
461 // donc que ses dimensions sont nulles.
462 {
463 bool is_found = false;
464 for( StringList::Enumerator i(m_variables_name); ++i; )
465 if (*i==vname){
466 is_found = true;
467 break;
468 }
469 if (!is_found)
470 ARCANE_THROW(ReaderWriterException,"No HDF5 group named '{0} exists",vname);
471 }
472
473 // Récupère le groupe contenant les informations de la variable
474 HGroup group_id;
475 //group_id.open(m_variable_group_id,vname);
476 group_id.open(m_sub_group_id,vname);
477 if (group_id.isBad())
478 ARCANE_THROW(ReaderWriterException,"HDF5 group '{0}' not found",vname);
479
480 bool is_multi_size = false;
481 eDataType data_type = DT_Unknown;
482 Int64 memory_size = 0;
483 Int64 nb_base_element = 0;
484 Int64 dim1_size = 0;
485 Int64 dim2_size = 0;
486 UniqueArray<Int64> dims;
487 ArrayShape data_shape;
488
489 // Récupère les informations concernant les tailles et dimensions de la variable
490 {
491 HAttribute att_id;
492 att_id.open(group_id,"Dims");
493 HSpace space_id = att_id.getSpace();
494
495 // On attend une seule dimension, et le nombre d'eléments de
496 // l'attribut (hdf_dims[0]) doit être égal à 1 ou 2.
497 hsize_t hdf_dims[max_dim];
498 hsize_t max_dims[max_dim];
499 H5Sget_simple_extent_dims(space_id.id(),hdf_dims,max_dims);
500
501 if (hdf_dims[0]!=VARIABLE_INFO_SIZE)
502 ARCANE_THROW(ReaderWriterException,"Wrong dimensions for variable '{0}' (found={1} expected={2})",
503 vname, hdf_dims[0], VARIABLE_INFO_SIZE);
504
505 std::array<Int64,VARIABLE_INFO_SIZE> dim_val_buf;
506 att_id.read(m_types.nativeType(Int64()),dim_val_buf.data());
507
508 SmallSpan<const Int64> dim_val(dim_val_buf);
509
510 nb_dimension = CheckedConvert::toInteger(dim_val[0]);
511 dim1_size = dim_val[1];
512 dim2_size = dim_val[2];
513 nb_element = dim_val[3];
514 nb_base_element = dim_val[4];
515 dimension_array_size = dim_val[5];
516 is_multi_size = dim_val[6]!=0;
517 data_type = (eDataType)dim_val[7];
518 memory_size = dim_val[8];
519 Int32 shape_nb_dim = CheckedConvert::toInt32(dim_val[9]);
520 data_shape.setNbDimension(shape_nb_dim);
521 for (Integer i=0; i<shape_nb_dim; ++i )
522 data_shape.setDimension(i,CheckedConvert::toInt32(dim_val[10+i]));
523 }
524
525 info(4) << " READ DIM name=" << vname
526 << " nb_dim=" << nb_dimension << " dim1_size=" << dim1_size
527 << " dim2_size=" << dim2_size << " nb_element=" << nb_element
528 << " dimension_size=" << dimension_array_size
529 << " is_multi_size=" << is_multi_size
530 << " data_type" << data_type
531 << " shape=" << data_shape.dimensions();
532
533 if (dimension_array_size>0){
534 HDataset array_id;
535 array_id.open(group_id,"Dim2");
536 if (array_id.isBad())
537 ARCANE_THROW(ReaderWriterException,"Wrong dataset for variable '{0}'",vname);
538
539 HSpace space_id = array_id.getSpace();
540 if (space_id.isBad())
541 ARCANE_THROW(ReaderWriterException,"Wrong dataspace for variable '{0}'",vname);
542
543 hsize_t hdf_dims[max_dim];
544 hsize_t max_dims[max_dim];
545 H5Sget_simple_extent_dims(space_id.id(),hdf_dims,max_dims);
546 // Vérifie que le nombre d'éléments du dataset est bien égal à celui
547 // attendu.
548 if ((Int64)hdf_dims[0]!=dimension_array_size){
549 ARCANE_THROW(ReaderWriterException,"Wrong number of elements in 'Dim2' for variable '{0}' (found={1} expected={2})",
550 vname, hdf_dims[0], dimension_array_size);
551
552 }
553 dim2_size = 0;
554 dims.resize(dimension_array_size);
555 herr_t herr = array_id.read(m_types.nativeType(Int64()),dims.data());
556 if (herr<0)
557 ARCANE_THROW(ReaderWriterException,"Wrong dataset read for variable '{0}'",vname);
558 }
559 Ref<ISerializedData> sdata = arcaneCreateSerializedDataRef(data_type,memory_size,nb_dimension,nb_element,
560 nb_base_element,is_multi_size,dims,data_shape);
561 return sdata;
562}
563
564/*---------------------------------------------------------------------------*/
565/*---------------------------------------------------------------------------*/
566
567/*---------------------------------------------------------------------------*/
568/*---------------------------------------------------------------------------*/
569
570void Hdf5ReaderWriter::
571write(IVariable* v,IData* data)
572{
573 _directWriteVal(v,data);
574}
575
576/*---------------------------------------------------------------------------*/
577/*---------------------------------------------------------------------------*/
578
579void Hdf5ReaderWriter::
580_readVal(IVariable* v,IData* data)
581{
582 String var_group_name = _variableGroupName(v);
583 info(4) << " TRY TO READ var_group=" << var_group_name;
584 Ref<ISerializedData> sd(_readDim2(v));
585 Int64 storage_size = sd->memorySize();
586 info(4) << " READ DATA n=" << storage_size;
587 data->allocateBufferForSerializedData(sd.get());
588 if (storage_size!=0){
589 // Récupère le groupe contenant les informations de la variable
590 HGroup group_id;
591 //group_id.open(m_variable_group_id,var_group_name);
592 group_id.open(m_sub_group_id,var_group_name);
593 if (group_id.isBad())
594 ARCANE_THROW(ReaderWriterException,"No HDF5 group with name '{0}' exists",var_group_name);
595 HDataset dataset_id;
596 dataset_id.open(group_id,"Values");
597 if (dataset_id.isBad())
598 ARCANE_THROW(ReaderWriterException,"Wrong dataset for variable '{0}'",var_group_name);
599 void* ptr = sd->writableBytes().data();
600 info() << "READ Variable " << var_group_name << " ptr=" << ptr;;
601 hid_t trueid = m_types.nativeType(sd->baseDataType());
602 dataset_id.read(trueid,ptr);
603 }
604 data->assignSerializedData(sd.get());
605}
606
607
608/*---------------------------------------------------------------------------*/
609/*---------------------------------------------------------------------------*/
610
611void Hdf5ReaderWriter::
612read(IVariable* var,IData* data)
613{
614 _directReadVal(var,data);
615}
616
617/*---------------------------------------------------------------------------*/
618/*---------------------------------------------------------------------------*/
619
620void Hdf5ReaderWriter::
621setMetaData(const String& meta_data)
622{
623 if (m_is_parallel){
624 IParallelMng* pm = m_parallel_mng;
625 //Integer nb_rank = pm->commSize();
626 if (m_send_rank!=m_my_rank){
627 // Envoie le groupe et les meta donnees
628 SerializeBuffer sb;
629 sb.setMode(ISerializer::ModeReserve);
630 sb.reserve(m_sub_group_name);
631 sb.reserve(meta_data);
632 sb.allocateBuffer();
633 sb.setMode(ISerializer::ModePut);
634 sb.put(m_sub_group_name);
635 sb.put(meta_data);
636 m_parallel_mng->sendSerializer(&sb,m_send_rank);
637 }
638 else{
639 _setMetaData(meta_data,m_sub_group_name);
640 for( Integer i=m_send_rank+1; i<=m_last_recv_rank; ++i ){
641 SerializeBuffer sb;
642 pm->recvSerializer(&sb,i);
643 sb.setMode(ISerializer::ModeGet);
644 String remote_group_name;
645 String remote_meta_data;
646 sb.get(remote_group_name);
647 sb.get(remote_meta_data);
648 _setMetaData(remote_meta_data,remote_group_name);
649 }
650 }
651 }
652 else
653 _setMetaData(meta_data,m_sub_group_name);
654}
655
656/*---------------------------------------------------------------------------*/
657/*---------------------------------------------------------------------------*/
658
659void Hdf5ReaderWriter::
660_setMetaData(const String& meta_data,const String& sub_group_name)
661{
662 const bool hits_modulo=(m_index_modulo!=0) && (m_index_write!=0) && ((m_index_write%m_index_modulo)==0);
663 HGroup base_group;
664 if (hits_modulo)
665 base_group.recursiveOpen(m_file_id,sub_group_name);
666 else
667 base_group.recursiveCreate(m_file_id,sub_group_name);
668
669 ByteConstArrayView meta_data_utf8 = meta_data.utf8();
670 const Byte* _meta_data = meta_data_utf8.data();
671 hsize_t dims[1];
672 dims[0] = meta_data_utf8.size() + 1;
673
674 HSpace space_id;
675 space_id.createSimple(1,dims);
676 if (space_id.isBad())
677 throw ReaderWriterException(A_FUNCINFO,"Wrong space for meta-data ('MetaData')");
678
679 HDataset dataset_id;
680 if (hits_modulo)
681 dataset_id.recursiveCreate(base_group,"MetaData", m_types.nativeType(Byte()), space_id, H5P_DEFAULT);
682 else
683 dataset_id.create(base_group,"MetaData", m_types.nativeType(Byte()), space_id, H5P_DEFAULT);
684 if (dataset_id.isBad())
685 throw ReaderWriterException(A_FUNCINFO,"Wrong dataset for meta-data ('MetaData')");
686
687 herr_t herr = dataset_id.write(m_types.nativeType(Byte()),_meta_data);
688 if (herr<0)
689 throw ReaderWriterException(A_FUNCINFO,"Unable to write meta-data ('MetaData')");
690}
691
692/*---------------------------------------------------------------------------*/
693/*---------------------------------------------------------------------------*/
694
695String Hdf5ReaderWriter::
696metaData()
697{
698 HDataset dataset_id;
699 dataset_id.open(m_sub_group_id,"MetaData");
700 if (dataset_id.isBad()){
701 throw ReaderWriterException(A_FUNCINFO,"Wrong dataset for meta-data ('MetaData')");
702 }
703 HSpace space_id = dataset_id.getSpace();
704 if (space_id.isBad()){
705 throw ReaderWriterException(A_FUNCINFO,"Wrong space for meta-data ('MetaData')");
706 }
707 const int max_dim = 256;
708 hsize_t hdf_dims[max_dim];
709 hsize_t max_dims[max_dim];
710 H5Sget_simple_extent_dims(space_id.id(),hdf_dims,max_dims);
711 if (hdf_dims[0]<=0)
712 throw ReaderWriterException(A_FUNCINFO,"Wrong number of elements for meta-data ('MetaData')");
713 Integer nb_byte = static_cast<Integer>(hdf_dims[0]);
714 ByteUniqueArray uchars(nb_byte);
715 dataset_id.read(m_types.nativeType(Byte()),uchars.data());
716 String s(uchars);
717 return s;
718}
719
720/*---------------------------------------------------------------------------*/
721/*---------------------------------------------------------------------------*/
722
723void Hdf5ReaderWriter::
724endWrite()
725{
726 if (m_is_parallel){
727 if (m_my_rank==m_send_rank){
728 _receiveRemoteVariables();
729 }
730 else{
731 // Envoie un message de fin
732 SerializeBuffer sb;
733 sb.setMode(ISerializer::ModeReserve);
734 sb.reserve(DT_Int32,1); // Pour indiquer la fin des envoies
735 sb.allocateBuffer();
736 sb.setMode(ISerializer::ModePut);
737 sb.putInt32(0); // Indique qu'il s'agit d'un message de fin
738 m_parallel_mng->sendSerializer(&sb,m_send_rank);
739 }
740 }
741 {
742 info() << " Hdf5Timer: nb_activated=" << m_io_timer.nbActivated()
743 << " time=" << m_io_timer.totalTime();
744 }
745}
746
747/*---------------------------------------------------------------------------*/
748/*---------------------------------------------------------------------------*/
749
750void Hdf5ReaderWriter::
751_receiveRemoteVariables()
752{
753 IParallelMng* pm = m_parallel_mng;
754 Integer nb_remaining = m_last_recv_rank - m_send_rank;
755 info() << "NB REMAINING = " << nb_remaining;
756 Ref<ISerializeMessageList> m_messages(pm->createSerializeMessageListRef());
757 while(nb_remaining>0){
758 ScopedPtrT<ISerializeMessage> sm(new SerializeMessage(m_my_rank,NULL_SUB_DOMAIN_ID,ISerializeMessage::MT_Recv));
759 m_messages->addMessage(sm.get());
760 m_messages->processPendingMessages();
761 m_messages->waitMessages(Parallel::WaitAll);
762 ISerializer* sb = sm->serializer();
763 sb->setMode(ISerializer::ModeGet);
764 Int32 id = sb->getInt32();
765 if (id==0)
766 --nb_remaining;
767 else
768 _writeRemoteVariable(sb);
769 }
770}
771
772/*---------------------------------------------------------------------------*/
773/*---------------------------------------------------------------------------*/
774
775void Hdf5ReaderWriter::
776_writeRemoteVariable(ISerializer* sb)
777{
778 String var_name;
779 sb->get(var_name);
780 String group_name;
781 sb->get(group_name);
782 Int32 rank = sb->getInt32();
783 //warning()<<"[\33[46;30m_writeRemoteVariable\33[m] rank="<<rank;
784 Ref<ISerializedData> sdata = arcaneCreateEmptySerializedDataRef();
785 sb->setReadMode(ISerializer::ReadReplace);
786 sdata->serialize(sb);
787 _writeVal(var_name,group_name,sdata.get(),rank);
788}
789
790/*---------------------------------------------------------------------------*/
791/*---------------------------------------------------------------------------*/
792
793/*---------------------------------------------------------------------------*/
794/*---------------------------------------------------------------------------*/
795/*!
796 * \brief Protection/reprise au format ArcaneHdf5.
797 */
798class ArcaneHdf5CheckpointService2
799: public ArcaneHdf5ReaderWriterObject
800{
801 public:
802 ArcaneHdf5CheckpointService2(const ServiceBuildInfo& sbi)
803 : ArcaneHdf5ReaderWriterObject(sbi),
804 m_write_index(0),
805 m_writer(nullptr),
806 m_reader(nullptr),
807 m_fileset_size(1),
808 m_index_modulo(0){}
809
810 virtual IDataWriter* dataWriter() { return m_writer; }
811 virtual IDataReader* dataReader() { return m_reader; }
812
813 virtual void notifyBeginWrite();
814 virtual void notifyEndWrite();
815 virtual void notifyBeginRead();
816 virtual void notifyEndRead();
817 virtual void close() {}
818 virtual String readerServiceName() const { return "ArcaneHdf5CheckpointReader2"; }
819
820 private:
821
822 Integer m_write_index;
823 Hdf5ReaderWriter* m_writer;
824 Hdf5ReaderWriter* m_reader;
825 Integer m_fileset_size;
826 Integer m_index_modulo;
827
828 private:
829
830 String _defaultFileName()
831 {
832 info() << "USE DEFAULT FILE NAME";
833 IParallelMng* pm = subDomain()->parallelMng();
834 Integer rank = pm->commRank();
835 StringBuilder buf;
836
837 // Ajoute si besoin le numero du processeur
838 if (pm->isParallel()){
839 Integer file_id = rank;
840 if (m_fileset_size!=0)
841 file_id = (rank / m_fileset_size) * m_fileset_size;
842 buf = "arcanedump.";
843 buf += file_id;
844 }
845 else{
846 buf = "arcanedump";
847 }
848
849 // Ajoute si besoin le numero du replica
850 IParallelReplication* pr = subDomain()->parallelMng()->replication();
851 if (pr->hasReplication()){
852 buf += "_r";
853 buf += pr->replicationRank();
854 }
855
856 buf += ".h5";
857 return buf.toString();
858 }
859
860 Directory _defaultDirectory(){
861 return Directory(baseDirectoryName());
862 }
863 void _parseMetaData(String meta_data);
864};
865
866/*---------------------------------------------------------------------------*/
867/*---------------------------------------------------------------------------*/
868
869void ArcaneHdf5CheckpointService2::
870_parseMetaData(String meta_data)
871{
872 IIOMng* io_mng = subDomain()->ioMng();
873 ScopedPtrT<IXmlDocumentHolder> xml_doc(io_mng->parseXmlBuffer(meta_data.utf8(),"MetaData"));
874 XmlNode root = xml_doc->documentNode().documentElement();
875 Integer version = root.attr("version").valueAsInteger();
876 if (version!=1){
877 throw ReaderWriterException(A_FUNCINFO,"Bad version (expected 1)");
878 }
879 {
880 Integer fileset_size = root.child("fileset-size").valueAsInteger();
881 if (fileset_size<0) fileset_size = 0;
882 m_fileset_size = fileset_size;
883 }
884 {
885 Integer index_modulo = root.child("index-modulo").valueAsInteger();
886 if (index_modulo<0) index_modulo = 0;
887 m_index_modulo=index_modulo;
888 }
889 info() << " FileSet size=" << m_fileset_size;
890 info() << " Index modulo=" << m_index_modulo;
891}
892
893/*---------------------------------------------------------------------------*/
894/*---------------------------------------------------------------------------*/
895
896void ArcaneHdf5CheckpointService2::
897notifyBeginRead()
898{
899 String meta_data = readerMetaData();
900 _parseMetaData(meta_data);
901
902 info() << " GET META DATA READER " << readerMetaData()
903 << " filename=" << fileName();
904
905 if (fileName().null()){
906 Directory dump_dir(_defaultDirectory());
907 setFileName(dump_dir.file(_defaultFileName()));
908 }
909 info() << " READ CHECKPOINT FILENAME = " << fileName();
910 StringBuilder sub_group;
911 sub_group = "SubDomain";
912 sub_group += subDomain()->subDomainId();
913 sub_group += "/Index";
914
915 Integer index = currentIndex();
916 if (m_index_modulo!=0)
917 index %= m_index_modulo;
918 sub_group += index;
919
920 m_reader = new Hdf5ReaderWriter(subDomain(),
921 fileName(),
922 sub_group.toString(),
923 0,
924 currentIndex(),
925 m_index_modulo,
926 Hdf5ReaderWriter::OpenModeRead);
927 m_reader->initialize();
928}
929
930/*---------------------------------------------------------------------------*/
931/*---------------------------------------------------------------------------*/
932
933void ArcaneHdf5CheckpointService2::
934notifyEndRead()
935{
936 delete m_reader;
937 m_reader = 0;
938}
939
940/*---------------------------------------------------------------------------*/
941/*---------------------------------------------------------------------------*/
942
943void ArcaneHdf5CheckpointService2::
944notifyBeginWrite()
945{
946 if (options()){
947 // Récupération du nombre de fichiers par groupe
948 m_fileset_size = options()->filesetSize();
949 // Récupération du nombre d'indexes au maximum par fichiers
950 m_index_modulo = options()->indexModulo();
951 }
952
953 if (fileName().null()){
954 Directory dump_dir(_defaultDirectory());
955 setFileName(dump_dir.file(_defaultFileName()));
956 }
957 Hdf5ReaderWriter::eOpenMode open_mode = Hdf5ReaderWriter::OpenModeAppend;
958 Integer write_index = checkpointTimes().size();
959 --write_index;
960
961 if (write_index==0)
962 open_mode = Hdf5ReaderWriter::OpenModeTruncate;
963
964 // Test de l'option m_index_modulo pour savoir la profondeur du modulo
965 if (m_index_modulo!=0)
966 write_index%=m_index_modulo;
967
968 StringBuilder sub_group;
969 sub_group = "SubDomain";
970 sub_group += subDomain()->parallelMng()->commRank();
971 sub_group += "/Index";
972 sub_group += write_index;
973
974 m_writer = new Hdf5ReaderWriter(subDomain(),
975 fileName(),
976 sub_group,
977 m_fileset_size,
978 checkpointTimes().size()-1,
979 m_index_modulo,
980 open_mode);
981 m_writer->initialize();
982}
983
984
985/*---------------------------------------------------------------------------*/
986/*---------------------------------------------------------------------------*/
987
988void ArcaneHdf5CheckpointService2::
989notifyEndWrite()
990{
991 OStringStream ostr;
992 ostr() << "<infos version='1'>\n";
993 ostr() << " <fileset-size>" << m_fileset_size << "</fileset-size>\n";
994 ostr() << " <index-modulo>" << m_index_modulo << "</index-modulo>\n";
995 ostr() << "</infos>\n";
996 setReaderMetaData(ostr.str());
997 ++m_write_index;
998 delete m_writer;
999 m_writer = 0;
1000}
1001
1002/*---------------------------------------------------------------------------*/
1003/*---------------------------------------------------------------------------*/
1004
1005ARCANE_REGISTER_SERVICE(ArcaneHdf5CheckpointService2,
1006 ServiceProperty("ArcaneHdf5CheckpointReader2",ST_SubDomain),
1007 ARCANE_SERVICE_INTERFACE(ICheckpointReader));
1008
1009ARCANE_REGISTER_SERVICE(ArcaneHdf5CheckpointService2,
1010 ServiceProperty("ArcaneHdf5CheckpointWriter2",ST_SubDomain),
1011 ARCANE_SERVICE_INTERFACE(ICheckpointWriter));
1012
1013ARCANE_REGISTER_SERVICE_HDF5READERWRITER(ArcaneHdf5Checkpoint2,
1014 ArcaneHdf5CheckpointService2);
1015
1016/*---------------------------------------------------------------------------*/
1017/*---------------------------------------------------------------------------*/
1018
1019} // End namespace Arcane
1020
1021/*---------------------------------------------------------------------------*/
1022/*---------------------------------------------------------------------------*/
ARCANE_THROW
#define ARCANE_THROW(exception_class,...)
Macro pour envoyer une exception avec formattage.
Definition ArcaneGlobal.h:798
ARCANE_FATAL
#define ARCANE_FATAL(...)
Macro envoyant une exception FatalErrorException.
Definition ArcaneGlobal.h:809
ARCANE_SERVICE_INTERFACE
#define ARCANE_SERVICE_INTERFACE(ainterface)
Macro pour déclarer une interface lors de l'enregistrement d'un service.
Definition ServiceFactory.h:475
Arcane::ArcaneHdf5CheckpointService2
Protection/reprise au format ArcaneHdf5.
Definition Hdf5ReaderWriter.cc:800
Arcane::Directory
Classe gérant un répertoire.
Definition Directory.h:33
Arcane::Hdf5ReaderWriter
Lecture/Ecriture au format HDF5.
Definition Hdf5ReaderWriter.h:79
Arcane::Hdf5Utils::HDataset
Encapsule un hid_t pour un dataset.
Definition Hdf5Utils.h:382
Arcane::Hdf5Utils::HGroup
Encapsule un hid_t pour un groupe.
Definition Hdf5Utils.h:281
Arcane::Hdf5Utils::HSpace
Encapsule un hid_t pour un dataspace.
Definition Hdf5Utils.h:335
Arcane::IDataReader
Interface de lecture des données d'une variable.
Definition IDataReader.h:41
Arcane::IDataWriter
Interface d'écriture des données d'une variable.
Definition IDataWriter.h:49
Arcane::IData
Interface d'une donnée.
Definition IData.h:33
Arcane::IData::allocateBufferForSerializedData
virtual void allocateBufferForSerializedData(ISerializedData *sdata)=0
Alloue la mémoire pour lire les valeurs sérialisées sdata.
Arcane::IData::assignSerializedData
virtual void assignSerializedData(const ISerializedData *sdata)=0
Assigne à la donnée les valeurs sérialisées sdata.
Arcane::IIOMng
Interface du gestionnaire des entrées sorties.
Definition IIOMng.h:42
Arcane::IIOMng::parseXmlBuffer
virtual IXmlDocumentHolder * parseXmlBuffer(Span< const Byte > buffer, const String &name)=0
Lit et analyse le fichier XML contenu dans le buffer buffer.
Arcane::IParallelMng
Interface du gestionnaire de parallélisme pour un sous-domaine.
Definition IParallelMng.h:52
Arcane::IParallelMng::commRank
virtual Int32 commRank() const =0
Rang de cette instance dans le communicateur.
Arcane::IParallelMng::isParallel
virtual bool isParallel() const =0
Retourne true si l'exécution est parallèle.
Arcane::IParallelReplication
Informations sur la réplication des sous-domaines en parallèle.
Definition IParallelReplication.h:36
Arcane::IParallelReplication::hasReplication
virtual bool hasReplication() const =0
Indique si la réplication est active.
Arcane::IParallelReplication::replicationRank
virtual Int32 replicationRank() const =0
Rang dans la réplication (de 0 à nbReplication()-1)
Arcane::ScopedPtrT
Encapsulation d'un pointeur qui se détruit automatiquement.
Definition ScopedPtr.h:44
Arcane::ServiceBuildInfo
Structure contenant les informations pour créer un service.
Definition ServiceBuildInfo.h:198
Arcane::XmlNode
Noeud d'un arbre DOM.
Definition XmlNode.h:51
Arcane::XmlNode::attr
XmlNode attr(const String &name, bool throw_exception=false) const
Retourne l'attribut de nom name.
Definition XmlNode.cc:248
Arcane::XmlNode::documentElement
XmlNode documentElement() const
Retourne le noeud élément du document.
Definition XmlNode.cc:556
Arcane::XmlNode::child
XmlNode child(const String &name) const
Noeud fils de celui-ci de nom name.
Definition XmlNode.cc:64
Arcane::XmlNode::valueAsInteger
Integer valueAsInteger(bool throw_exception=false) const
Valeur du noeud convertie en entier.
Definition XmlNode.cc:432
Arccore::Array::data
const T * data() const
Accès à la racine du tableau hors toute protection.
Definition arccore/src/collections/arccore/collections/Array.h:1385
Arccore::BasicSerializer::allocateBuffer
void allocateBuffer() override
Alloue la mémoire du sérialiseur.
Definition BasicSerializer.cc:1186
Arccore::BasicSerializer::reserve
void reserve(eDataType dt, Int64 n) override
Réserve de la mémoire pour n objets de type dt.
Definition BasicSerializer.cc:744
Arccore::BasicSerializer::put
void put(Span< const Real > values) override
Ajoute le tableau values.
Definition BasicSerializer.cc:829
Arccore::BasicSerializer::setMode
void setMode(eMode new_mode) override
Positionne le fonctionnement actuel.
Definition BasicSerializer.cc:1204
Arccore::BasicSerializer::get
void get(RealArrayView values) override
Récupère le tableau values.
Definition BasicSerializer.h:250
Arccore::ConstArrayView
Vue constante d'un tableau de type T.
Definition arccore/src/base/arccore/base/ArrayView.h:533
Arccore::ConstArrayView::size
constexpr Integer size() const noexcept
Nombre d'éléments du tableau.
Definition arccore/src/base/arccore/base/ArrayView.h:713
Arccore::ConstArrayView::data
constexpr const_pointer data() const noexcept
Pointeur sur la mémoire allouée.
Definition arccore/src/base/arccore/base/ArrayView.h:759
Arccore::StringBuilder
Constructeur de chaîne de caractère unicode.
Definition arccore/src/base/arccore/base/StringBuilder.h:47
Arccore::StringBuilder::toString
String toString() const
Retourne la chaîne de caractères construite.
Definition StringBuilder.cc:215
Arccore::String
Chaîne de caractères unicode.
Definition arccore/src/base/arccore/base/String.h:70
Arccore::String::utf8
ByteConstArrayView utf8() const
Retourne la conversion de l'instance dans l'encodage UTF-8.
Definition String.cc:275
Arccore::UniqueArray
Vecteur 1D de données avec sémantique par valeur (style STL).
Definition arccore/src/collections/arccore/collections/Array.h:1807
ARCANE_REGISTER_SERVICE
#define ARCANE_REGISTER_SERVICE(aclass, a_service_property,...)
Macro pour enregistrer un service.
Definition ServiceFactory.h:516
Arcane
-*- tab-width: 2; indent-tabs-mode: nil; coding: utf-8-with-signature -*-
Definition AbstractCaseDocumentVisitor.cc:20
Arcane::arcaneCreateSerializedDataRef
Ref< ISerializedData > arcaneCreateSerializedDataRef(eDataType data_type, Int64 memory_size, Integer nb_dim, Int64 nb_element, Int64 nb_base_element, bool is_multi_size, Int64ConstArrayView dimensions)
Créé des données sérialisées.
Definition SerializedData.cc:413
Arcane::arcaneCreateEmptySerializedDataRef
Ref< ISerializedData > arcaneCreateEmptySerializedDataRef()
Créé des données sérialisées.
Definition SerializedData.cc:426
Arcane::Byte
unsigned char Byte
Type d'un octet.
Definition UtilsTypes.h:142
Arcane::eDataType
eDataType
Type d'une donnée.
Definition DataTypes.h:39
Arcane::DT_Unknown
@ DT_Unknown
Donnée de type inconnue ou non initialisée.
Definition DataTypes.h:54
Arcane::Int64ConstArrayView
ConstArrayView< Int64 > Int64ConstArrayView
Equivalent C d'un tableau à une dimension d'entiers 64 bits.
Definition UtilsTypes.h:638
Arccore::Integer
Int32 Integer
Type représentant un entier.
Definition ArccoreGlobal.h:240