1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Quincey Koziol <koziol@ncsa.uiuc.ed>
* Thursday, July 11, 2002
*
* Purpose: This is a "combination" MPI-2 and posix I/O driver.
* It uses MPI for coordinating the actions of several processes
* and posix I/O calls to do the actual I/O to the disk.
*
* This driver was derived from the H5FDmpio.c driver and may
* share bugs/quirks/etc.
*
* Limitations:
* There is no "collective" I/O mode with this driver.
*
* This will almost certainly _not_ work correctly for files
* accessed on distributed parallel systems with the file located
* on a non-parallel filesystem.
*
*/
/* Interface initialization */
#define H5_INTERFACE_INIT_FUNC H5FD_mpiposix_init_interface
#include "H5private.h" /* Generic Functions */
#include "H5ACprivate.h" /* Metadata cache */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5FDmpi.h" /* MPI-based file drivers */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */
/* Features:
* H5_HAVE_GPFS -- issue gpfs_fcntl() calls to hopefully improve
* performance when accessing files on a GPFS
* file system.
*
* REPORT_IO -- if set then report all POSIX file calls to stderr.
*
*/
/* #define REPORT_IO */
#ifdef H5_HAVE_GPFS
# include <gpfs_fcntl.h>
#endif
#ifdef H5_HAVE_PARALLEL
/*
* The driver identification number, initialized at runtime if H5_HAVE_PARALLEL
* is defined. This allows applications to still have the H5FD_MPIPOSIX
* "constants" in their source code (it also makes this file strictly ANSI
* compliant when H5_HAVE_PARALLEL isn't defined)
*/
static hid_t H5FD_MPIPOSIX_g = 0;
/* File operations */
#define OP_UNKNOWN 0
#define OP_READ 1
#define OP_WRITE 2
/*
* The description of a file belonging to this driver.
* The EOF value
* is only used just after the file is opened in order for the library to
* determine whether the file is empty, truncated, or okay. The MPIPOSIX driver
* doesn't bother to keep it updated since it's an expensive operation.
*/
typedef struct H5FD_mpiposix_t {
H5FD_t pub; /*public stuff, must be first */
int fd; /*the unix file handle */
MPI_Comm comm; /*communicator */
int mpi_rank; /* This process's rank */
int mpi_size; /* Total number of processes */
haddr_t eof; /*end-of-file marker */
haddr_t eoa; /*end-of-address marker */
haddr_t last_eoa; /* Last known end-of-address marker */
haddr_t pos; /* Current file I/O position */
int op; /* Last file I/O operation */
hsize_t naccess; /* Number of (write) accesses to file */
#ifdef H5_HAVE_GPFS
size_t blksize; /* Block size of file system */
#endif
hbool_t use_gpfs; /* Use GPFS to write things */
#ifndef _WIN32
/*
* On most systems the combination of device and i-node number uniquely
* identify a file.
*/
dev_t device; /*file device number */
ino_t inode; /*file i-node number */
#else
/*
* On _WIN32 the low-order word of a unique identifier associated with the
* file and the volume serial number uniquely identify a file. This number
* (which, both? -rpm) may change when the system is restarted or when the
* file is opened. After a process opens a file, the identifier is
* constant until the file is closed. An application can use this
* identifier and the volume serial number to determine whether two
* handles refer to the same file.
*/
int fileindexlo;
int fileindexhi;
#endif
/* Information from file open flags, for SWMR access */
hbool_t swmr_read; /* Whether the file is open for SWMR read access */
} H5FD_mpiposix_t;
/*
* This driver supports systems that have the lseek64() function by defining
* some macros here so we don't have to have conditional compilations later
* throughout the code.
*
* file_offset_t: The datatype for file offsets, the second argument of
* the lseek() or lseek64() call.
*
* file_seek: The function which adjusts the current file position,
* either lseek() or lseek64().
*/
/* adding for windows NT file system support. */
#ifdef H5_HAVE_LSEEK64
# define file_offset_t off64_t
# define file_seek lseek64
# define file_truncate ftruncate64
#elif defined (_WIN32) && !defined(__MWERKS__)
# /*MSVC*/
# define file_offset_t __int64
# define file_seek _lseeki64
# define file_truncate _ftruncatei64
#else
# define file_offset_t off_t
# define file_seek HDlseek
# define file_truncate HDftruncate
#endif
/*
* These macros check for overflow of various quantities. These macros
* assume that file_offset_t is signed and haddr_t and size_t are unsigned.
*
* ADDR_OVERFLOW: Checks whether a file address of type `haddr_t'
* is too large to be represented by the second argument
* of the file seek function.
*
* SIZE_OVERFLOW: Checks whether a buffer size of type `hsize_t' is too
* large to be represented by the `size_t' type.
*
* REGION_OVERFLOW: Checks whether an address and size pair describe data
* which can be addressed entirely by the second
* argument of the file seek function.
*/
#define MAXADDR (((haddr_t)1<<(8*sizeof(file_offset_t)-1))-1)
#define ADDR_OVERFLOW(A) (HADDR_UNDEF==(A) || \
((A) & ~(haddr_t)MAXADDR))
#define SIZE_OVERFLOW(Z) ((Z) & ~(hsize_t)MAXADDR)
#define REGION_OVERFLOW(A,Z) (ADDR_OVERFLOW(A) || SIZE_OVERFLOW(Z) || \
sizeof(file_offset_t)<sizeof(size_t) || \
HADDR_UNDEF==(A)+(Z) || \
(file_offset_t)((A)+(Z))<(file_offset_t)(A))
/* Callbacks */
static void *H5FD_mpiposix_fapl_get(H5FD_t *_file);
static void *H5FD_mpiposix_fapl_copy(const void *_old_fa);
static herr_t H5FD_mpiposix_fapl_free(void *_fa);
static H5FD_t *H5FD_mpiposix_open(const char *name, unsigned flags, hid_t fapl_id,
haddr_t maxaddr);
static herr_t H5FD_mpiposix_close(H5FD_t *_file);
static int H5FD_mpiposix_cmp(const H5FD_t *_f1, const H5FD_t *_f2);
static herr_t H5FD_mpiposix_query(const H5FD_t *_f1, unsigned long *flags);
static haddr_t H5FD_mpiposix_get_eoa(const H5FD_t *_file, H5FD_mem_t UNUSED type);
static herr_t H5FD_mpiposix_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr);
static haddr_t H5FD_mpiposix_get_eof(const H5FD_t *_file);
static herr_t H5FD_mpiposix_get_handle(H5FD_t *_file, hid_t fapl, void** file_handle);
static herr_t H5FD_mpiposix_read(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, haddr_t addr,
size_t size, void *buf);
static herr_t H5FD_mpiposix_write(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, haddr_t addr,
size_t size, const void *buf);
static herr_t H5FD_mpiposix_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing);
static int H5FD_mpiposix_mpi_rank(const H5FD_t *_file);
static int H5FD_mpiposix_mpi_size(const H5FD_t *_file);
static MPI_Comm H5FD_mpiposix_communicator(const H5FD_t *_file);
/* MPIPOSIX-specific file access properties */
typedef struct H5FD_mpiposix_fapl_t {
hbool_t use_gpfs; /*use GPFS hints */
MPI_Comm comm; /*communicator */
} H5FD_mpiposix_fapl_t;
/* The MPIPOSIX file driver information */
static const H5FD_class_mpi_t H5FD_mpiposix_g = {
{ /* Start of superclass information */
"mpiposix", /*name */
MAXADDR, /*maxaddr */
H5F_CLOSE_SEMI, /* fc_degree */
NULL, /*sb_size */
NULL, /*sb_encode */
NULL, /*sb_decode */
sizeof(H5FD_mpiposix_fapl_t), /*fapl_size */
H5FD_mpiposix_fapl_get, /*fapl_get */
H5FD_mpiposix_fapl_copy, /*fapl_copy */
H5FD_mpiposix_fapl_free, /*fapl_free */
0, /*dxpl_size */
NULL, /*dxpl_copy */
NULL, /*dxpl_free */
H5FD_mpiposix_open, /*open */
H5FD_mpiposix_close, /*close */
H5FD_mpiposix_cmp, /*cmp */
H5FD_mpiposix_query, /*query */
NULL, /*get_type_map */
NULL, /*alloc */
NULL, /*free */
H5FD_mpiposix_get_eoa, /*get_eoa */
H5FD_mpiposix_set_eoa, /*set_eoa */
H5FD_mpiposix_get_eof, /*get_eof */
H5FD_mpiposix_get_handle, /*get_handle */
H5FD_mpiposix_read, /*read */
H5FD_mpiposix_write, /*write */
NULL, /*flush */
H5FD_mpiposix_truncate, /*truncate */
NULL, /*lock */
NULL, /*unlock */
H5FD_FLMAP_SINGLE /*fl_map */
}, /* End of superclass information */
H5FD_mpiposix_mpi_rank, /*get_rank */
H5FD_mpiposix_mpi_size, /*get_size */
H5FD_mpiposix_communicator /*get_comm */
};
/*--------------------------------------------------------------------------
NAME
H5FD_mpiposix_init_interface -- Initialize interface-specific information
USAGE
herr_t H5FD_mpiposix_init_interface()
RETURNS
Non-negative on success/Negative on failure
DESCRIPTION
Initializes any interface-specific data or routines. (Just calls
H5FD_mpiposix_init currently).
--------------------------------------------------------------------------*/
static herr_t
H5FD_mpiposix_init_interface(void)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5FD_mpiposix_init_interface)
FUNC_LEAVE_NOAPI(H5FD_mpiposix_init())
} /* H5FD_mpiposix_init_interface() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_init
*
* Purpose: Initialize this driver by registering the driver with the
* library.
*
* Return: Success: The driver ID for the mpiposix driver.
*
* Failure: Negative.
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
H5FD_mpiposix_init(void)
{
hid_t ret_value=H5FD_MPIPOSIX_g; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_init, FAIL)
if (H5I_VFL!=H5Iget_type(H5FD_MPIPOSIX_g))
H5FD_MPIPOSIX_g = H5FD_register((const H5FD_class_t *)&H5FD_mpiposix_g,sizeof(H5FD_class_mpi_t),FALSE);
/* Set return value */
ret_value=H5FD_MPIPOSIX_g;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_init() */
/*---------------------------------------------------------------------------
* Function: H5FD_mpiposix_term
*
* Purpose: Shut down the VFD
*
* Return: <none>
*
* Programmer: Quincey Koziol
* Friday, Jan 30, 2004
*
* Modification:
*
*---------------------------------------------------------------------------
*/
void
H5FD_mpiposix_term(void)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5FD_mpiposix_term)
/* Reset VFL ID */
H5FD_MPIPOSIX_g=0;
FUNC_LEAVE_NOAPI_VOID
} /* end H5FD_mpiposix_term() */
/*-------------------------------------------------------------------------
* Function: H5Pset_fapl_mpiposix
*
* Purpose: Store the user supplied MPI communicator COMM in
* the file access property list FAPL_ID which can then be used
* to create and/or open the file. This function is available
* only in the parallel HDF5 library and is not collective.
*
* comm is the MPI communicator to be used for file open as
* defined in MPI_FILE_OPEN of MPI-2. This function makes a
* duplicate of comm. Any modification to comm after this function
* call returns has no effect on the access property list.
*
* If fapl_id has previously set comm value, it will be replaced
* and the old communicator is freed.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Albert Cheng, 2003-04-24
* Modified the description of the function that it now stores
* a duplicate of the communicator. Free the old duplicate if
* previously set. (Work is actually done by H5P_set_driver.)
*
* Bill Wendling, 2003-05-01
* Modified to take an extra flag indicating that we should
* use the GPFS hints (if available) for this file.
*
*-------------------------------------------------------------------------
*/
herr_t
H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm, hbool_t use_gpfs)
{
H5FD_mpiposix_fapl_t fa;
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value;
FUNC_ENTER_API(H5Pset_fapl_mpiposix, FAIL)
H5TRACE3("e", "iMcb", fapl_id, comm, use_gpfs);
/* Check arguments */
if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS)))
HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a file access list")
if (MPI_COMM_NULL == comm)
HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a valid communicator")
/* Initialize driver specific properties */
fa.comm = comm;
fa.use_gpfs = use_gpfs;
/* duplication is done during driver setting. */
ret_value= H5P_set_driver(plist, H5FD_MPIPOSIX, &fa);
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Pset_fapl_mpiposix() */
/*-------------------------------------------------------------------------
* Function: H5Pget_fapl_mpiposix
*
* Purpose: If the file access property list is set to the H5FD_MPIPOSIX
* driver then this function returns a duplicate of the MPI
* communicator through the comm pointer. It is the responsibility
* of the application to free the returned communicator.
*
* Return: Success: Non-negative with the communicator and
* information returned through the COMM
* argument if non-null. Since it is a duplicate
* of the stored object, future modifications to
* the access property list do not affect it and
* it is the responsibility of the application to
* free it.
*
* Failure: Negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Albert Cheng, 2003-04-24
* Return duplicate of the stored communicator.
*
* Bill Wendling, 2003-05-01
* Return the USE_GPFS flag.
*
*-------------------------------------------------------------------------
*/
herr_t
H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/, hbool_t *use_gpfs/*out*/)
{
H5FD_mpiposix_fapl_t *fa;
H5P_genplist_t *plist; /* Property list pointer */
int mpi_code; /* mpi return code */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Pget_fapl_mpiposix, FAIL)
H5TRACE3("e", "ixx", fapl_id, comm, use_gpfs);
if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS)))
HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a file access list")
if (H5FD_MPIPOSIX!=H5P_get_driver(plist))
HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "incorrect VFL driver")
if (NULL==(fa=H5P_get_driver_info(plist)))
HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info")
/* Get MPI Communicator */
if (comm){
if (MPI_SUCCESS != (mpi_code=MPI_Comm_dup(fa->comm, comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Comm_dup failed", mpi_code)
}
if (use_gpfs)
*use_gpfs = fa->use_gpfs;
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Pget_fapl_mpiposix() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_fapl_get
*
* Purpose: Returns a file access property list which could be used to
* create another file the same as this one.
*
* Return: Success: Ptr to new file access property list with all
* fields copied from the file pointer.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Albert Cheng, 2003-04-24
* Duplicate the communicator object so that the new
* property list is insulated from the old one.
*
*-------------------------------------------------------------------------
*/
static void *
H5FD_mpiposix_fapl_get(H5FD_t *_file)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
H5FD_mpiposix_fapl_t *fa = NULL;
int mpi_code; /* MPI return code */
void *ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_fapl_get, NULL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
if (NULL==(fa=H5MM_calloc(sizeof(H5FD_mpiposix_fapl_t))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Duplicate the communicator. */
if (MPI_SUCCESS != (mpi_code=MPI_Comm_dup(file->comm, &fa->comm)))
HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code)
fa->use_gpfs = file->use_gpfs;
/* Set return value */
ret_value=fa;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_fapl_get() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_fapl_copy
*
* Purpose: Copies the mpiposix-specific file access properties.
*
* Return: Success: Ptr to a new property list
*
* Failure: NULL
*
* Programmer: Albert Cheng
* Apr 24, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5FD_mpiposix_fapl_copy(const void *_old_fa)
{
void *ret_value = NULL;
const H5FD_mpiposix_fapl_t *old_fa = (const H5FD_mpiposix_fapl_t*)_old_fa;
H5FD_mpiposix_fapl_t *new_fa = NULL;
int mpi_code; /* MPI return code */
FUNC_ENTER_NOAPI(H5FD_mpiposix_fapl_copy, NULL)
if (NULL==(new_fa=H5MM_malloc(sizeof(H5FD_mpiposix_fapl_t))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Copy the general information */
HDmemcpy(new_fa, old_fa, sizeof(H5FD_mpiposix_fapl_t));
/* Duplicate communicator. */
if (MPI_SUCCESS != (mpi_code=MPI_Comm_dup(old_fa->comm, &new_fa->comm)))
HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code)
new_fa->use_gpfs = old_fa->use_gpfs;
ret_value = new_fa;
done:
if (NULL == ret_value){
/* cleanup */
if (new_fa)
H5MM_xfree(new_fa);
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_fapl_copy() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_fapl_free
*
* Purpose: Frees the mpiposix-specific file access properties.
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Albert Cheng
* Apr 24, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_fapl_free(void *_fa)
{
herr_t ret_value = SUCCEED;
H5FD_mpiposix_fapl_t *fa = (H5FD_mpiposix_fapl_t*)_fa;
FUNC_ENTER_NOAPI(H5FD_mpiposix_fapl_free, FAIL)
assert(fa);
/* Free the internal communicator */
assert(MPI_COMM_NULL!=fa->comm);
MPI_Comm_free(&fa->comm);
H5MM_xfree(fa);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_fapl_free() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_open
*
* Purpose: Opens a file with name NAME. The FLAGS are a bit field with
* purpose similar to the second argument of open(2) and which
* are defined in H5Fpublic.h. The file access property list
* FAPL_ID contains the properties driver properties and MAXADDR
* is the largest address which this file will be expected to
* access. This is collective.
*
* Return: Success: A new file pointer.
* Failure: NULL
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Albert Cheng, 2003-04-24
* Duplicate the communicator so that file is insulated from the
* old one.
*
*-------------------------------------------------------------------------
*/
static H5FD_t *
H5FD_mpiposix_open(const char *name, unsigned flags, hid_t fapl_id,
haddr_t maxaddr)
{
H5FD_mpiposix_t *file=NULL; /* New MPIPOSIX file struct */
int o_flags; /* Flags for file open call */
int fd=(-1); /* File handle for file opened */
int mpi_rank; /* MPI rank of this process */
int mpi_size; /* Total number of MPI processes */
int mpi_code; /* mpi return code */
const H5FD_mpiposix_fapl_t *fa=NULL; /* MPIPOSIX file access property list information */
H5FD_mpiposix_fapl_t _fa; /* Private copy of default file access property list information */
H5P_genplist_t *plist; /* Property list pointer */
h5_stat_t sb; /* Portable 'stat' struct */
#ifdef _WIN32
HFILE filehandle;
struct _BY_HANDLE_FILE_INFORMATION fileinfo;
int results;
#endif
H5FD_t *ret_value=NULL; /* Return value */
MPI_Comm comm_dup=MPI_COMM_NULL;
FUNC_ENTER_NOAPI(H5FD_mpiposix_open, NULL)
/* Check arguments */
if (!name || !*name)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "invalid file name")
if (0==maxaddr || HADDR_UNDEF==maxaddr)
HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, NULL, "bogus maxaddr")
if (ADDR_OVERFLOW(maxaddr))
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, NULL, "bogus maxaddr")
/* Obtain a pointer to mpiposix-specific file access properties */
if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list")
if (H5P_FILE_ACCESS_DEFAULT==fapl_id || H5FD_MPIPOSIX!=H5P_get_driver(plist)) {
_fa.comm = MPI_COMM_SELF; /*default*/
_fa.use_gpfs = FALSE;
fa = &_fa;
} /* end if */
else {
fa = H5P_get_driver_info(plist);
assert(fa);
} /* end else */
/* Duplicate the communicator for use by this file. */
if (MPI_SUCCESS != (mpi_code=MPI_Comm_dup(fa->comm, &comm_dup)))
HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code)
/* Get the MPI rank of this process and the total number of processes */
if (MPI_SUCCESS != (mpi_code=MPI_Comm_rank (comm_dup, &mpi_rank)))
HMPI_GOTO_ERROR(NULL, "MPI_Comm_rank failed", mpi_code)
if (MPI_SUCCESS != (mpi_code=MPI_Comm_size (comm_dup, &mpi_size)))
HMPI_GOTO_ERROR(NULL, "MPI_Comm_size failed", mpi_code)
/* Build the open flags */
o_flags = (H5F_ACC_RDWR & flags) ? O_RDWR : O_RDONLY;
/* Only set the creation flag(s) for process 0 */
if(mpi_rank==0) {
if (H5F_ACC_TRUNC & flags)
o_flags |= O_TRUNC;
if (H5F_ACC_CREAT & flags)
o_flags |= O_CREAT;
if (H5F_ACC_EXCL & flags)
o_flags |= O_EXCL;
} /* end if */
/* Process 0 opens (or creates) the file while the rest of the
* processes wait. Then process 0 signals the other processes and they
* open (never create) the file and all processes proceed.
*/
/* Process 0 opens (or creates) file and broadcasts result to other processes */
if(mpi_rank==0) {
/* Open the file */
fd=HDopen(name, o_flags, 0666);
} /* end if */
/* Broadcast the results of the open() from process 0 */
/* This is necessary because of the "tentative open" code in H5F_open()
* where the file is attempted to be opened with different flags from the
* user's, in order to check for the file's existence, etc. Here, process 0
* gets different flags from the other processes (since it is in charge of
* creating the file, if necessary) and can fail in situations where the
* other process's file opens would succeed, so allow the other processes
* to check for that situation and bail out now also. - QAK
*/
if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&fd, sizeof(int), MPI_BYTE, 0, comm_dup)))
HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code)
/* If the file open on process 0 failed, bail out on all processes now */
if(fd<0)
HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file")
/* Other processes (non 0) wait for broadcast result from process 0 and then open file */
if(mpi_rank!=0) {
/* Open the file */
if ((fd=HDopen(name, o_flags, 0666))<0)
HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file")
} /* end if */
/* Process 0 fstat()s the file and broadcasts the results to the other processes */
if(mpi_rank==0) {
/* Get the stat information */
if (HDfstat(fd, &sb)<0)
HGOTO_ERROR(H5E_FILE, H5E_BADFILE, NULL, "unable to fstat file")
} /* end if */
/* Broadcast the results of the fstat() from process 0 */
if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&sb, sizeof(h5_stat_t), MPI_BYTE, 0, comm_dup)))
HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code)
#ifdef H5_HAVE_GPFS
if (fa->use_gpfs) {
/*
* Free all byte range tokens. This is a good thing to do if raw data is aligned on 256kB boundaries (a GPFS page is
* 256kB). Care should be taken that there aren't too many sub-page writes, or the mmfsd may become overwhelmed. This
* should probably eventually be passed down here as a property. The gpfs_fcntl() will most likely fail if `fd' isn't
* on a GPFS file system. */
struct {
gpfsFcntlHeader_t hdr;
gpfsFreeRange_t fr;
} hint;
HDmemset(&hint, 0, sizeof hint);
hint.hdr.totalLength = sizeof hint;
hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
hint.fr.structLen = sizeof hint.fr;
hint.fr.structType = GPFS_FREE_RANGE;
hint.fr.start = 0;
hint.fr.length = 0;
if (gpfs_fcntl(fd, &hint)<0)
HGOTO_ERROR(H5E_FILE, H5E_FCNTL, NULL, "failed to send hints to GPFS")
}
#endif /* H5_HAVE_GPFS */
/* Build the file struct and initialize it */
if (NULL==(file=H5MM_calloc(sizeof(H5FD_mpiposix_t))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
#ifdef REPORT_IO
HDfprintf(stderr, "open: rank=%d name=%s file=0x%08lx\n", mpi_rank, name, (unsigned long)file);
#endif
/* Set the general file information */
file->fd = fd;
file->eof = sb.st_size;
/* for _WIN32 support. _WIN32 'stat' does not have st_blksize and st_blksize
is only used for the H5_HAVE_GPFS case */
#ifdef H5_HAVE_GPFS
file->blksize = sb.st_blksize;
#endif
/* Set this field in the H5FD_mpiposix_t struct for later use */
file->use_gpfs = fa->use_gpfs;
/* Set the MPI information */
file->comm = comm_dup;
file->mpi_rank = mpi_rank;
file->mpi_size = mpi_size;
/* Reset the last file I/O operation */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
/* Set the information for the file's device and inode */
#ifdef _WIN32
filehandle = _get_osfhandle(fd);
results = GetFileInformationByHandle((HANDLE)filehandle, &fileinfo);
file->fileindexhi = fileinfo.nFileIndexHigh;
file->fileindexlo = fileinfo.nFileIndexLow;
#else
file->device = sb.st_dev;
file->inode = sb.st_ino;
#endif
/* Check for SWMR reader access */
if(flags & H5F_ACC_SWMR_READ)
file->swmr_read = TRUE;
/* Indicate success */
ret_value=(H5FD_t *)file;
done:
/* Error cleanup */
if(ret_value==NULL) {
/* Close the file if it was left open */
if(fd!=(-1))
HDclose(fd);
if (MPI_COMM_NULL != comm_dup)
MPI_Comm_free(&comm_dup);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_open() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_close
*
* Purpose: Closes a file.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Albert Cheng, 2003-04-24
* Free the communicator stored.
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_close(H5FD_t *_file)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_close, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Close the unix file */
if (HDclose(file->fd)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTCLOSEFILE, FAIL, "unable to close file")
/* make sure all processes have closed the file before returning. */
MPI_Barrier(file->comm);
/* Clean up other stuff */
MPI_Comm_free(&file->comm);
H5MM_xfree(file);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_close() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_cmp
*
* Purpose: Compares two files belonging to this driver using an
* arbitrary (but consistent) ordering.
*
* Return: Success: A value like strcmp()
* Failure: never fails (arguments were checked by the
* caller).
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5FD_mpiposix_cmp(const H5FD_t *_f1, const H5FD_t *_f2)
{
const H5FD_mpiposix_t *f1 = (const H5FD_mpiposix_t*)_f1;
const H5FD_mpiposix_t *f2 = (const H5FD_mpiposix_t*)_f2;
int ret_value=0;
FUNC_ENTER_NOAPI(H5FD_mpiposix_cmp, H5FD_VFD_DEFAULT)
#ifdef _WIN32
if (f1->fileindexhi < f2->fileindexhi) HGOTO_DONE(-1)
if (f1->fileindexhi > f2->fileindexhi) HGOTO_DONE(1)
if (f1->fileindexlo < f2->fileindexlo) HGOTO_DONE(-1)
if (f1->fileindexlo > f2->fileindexlo) HGOTO_DONE(1)
#else
#ifdef H5_DEV_T_IS_SCALAR
if (f1->device < f2->device) HGOTO_DONE(-1)
if (f1->device > f2->device) HGOTO_DONE(1)
#else /* H5_DEV_T_IS_SCALAR */
/* If dev_t isn't a scalar value on this system, just use memcmp to
* determine if the values are the same or not. The actual return value
* shouldn't really matter...
*/
if(HDmemcmp(&(f1->device),&(f2->device),sizeof(dev_t))<0) HGOTO_DONE(-1)
if(HDmemcmp(&(f1->device),&(f2->device),sizeof(dev_t))>0) HGOTO_DONE(1)
#endif /* H5_DEV_T_IS_SCALAR */
if (f1->inode < f2->inode) HGOTO_DONE(-1)
if (f1->inode > f2->inode) HGOTO_DONE(1)
#endif
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_cmp() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_query
*
* Purpose: Set the flags that this VFL driver is capable of supporting.
* (listed in H5FDpublic.h)
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
* John Mainzer -- 9/21/05
* Modified code to turn off the
* H5FD_FEAT_ACCUMULATE_METADATA_WRITE flag.
* With the movement of all cache writes to process 0,
* this flag has become problematic in PHDF5.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_query(const H5FD_t UNUSED *_file, unsigned long *flags /* out */)
{
herr_t ret_value=SUCCEED;
FUNC_ENTER_NOAPI(H5FD_mpiposix_query, FAIL)
/* Set the VFL feature flags that this driver supports */
if(flags) {
*flags=0;
*flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */
*flags|=H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_query() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_get_eoa
*
* Purpose: Gets the end-of-address marker for the file. The EOA marker
* is the first address past the last byte allocated in the
* format address space.
*
* Return: Success: The end-of-address marker.
* Failure: HADDR_UNDEF
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Raymond Lu
* 21 Dec. 2006
* Added the parameter TYPE. It's only used for MULTI driver.
*
*-------------------------------------------------------------------------
*/
static haddr_t
H5FD_mpiposix_get_eoa(const H5FD_t *_file, H5FD_mem_t UNUSED type)
{
const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file;
haddr_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_get_eoa, HADDR_UNDEF)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Set return value */
ret_value=file->eoa;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_get_eoa() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_set_eoa
*
* Purpose: Set the end-of-address marker for the file. This function is
* called shortly after an existing HDF5 file is opened in order
* to tell the driver where the end of the HDF5 data is located.
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
* Raymond Lu
* 21 Dec. 2006
* Added the parameter TYPE. It's only used for MULTI driver.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_set_eoa(H5FD_t *_file, H5FD_mem_t UNUSED type, haddr_t addr)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_set_eoa, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
file->eoa = addr;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpi_posix_set_eoa() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_get_eof
*
* Purpose: Gets the end-of-file marker for the file. The EOF marker
* is the real size of the file.
*
* The MPIPOSIX driver doesn't bother keeping this field updated
* since that's a relatively expensive operation. Fortunately
* the library only needs the EOF just after the file is opened
* in order to determine whether the file is empty, truncated,
* or okay.
*
* Return: Success: The end-of-address marker.
* Failure: HADDR_UNDEF
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static haddr_t
H5FD_mpiposix_get_eof(const H5FD_t *_file)
{
const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file;
haddr_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_get_eof, HADDR_UNDEF)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Set return value */
ret_value=MAX(file->eof,file->eoa);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_get_eof() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_get_handle
*
* Purpose: Returns the file handle of MPI-POSIX file driver.
*
* Returns: Non-negative if succeed or negative if fails.
*
* Programmer: Raymond Lu
* Sept. 16, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_get_handle(H5FD_t *_file, hid_t UNUSED fapl, void** file_handle)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t *)_file;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5FD_mpiposix_get_handle, FAIL)
if(!file_handle)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file handle not valid")
*file_handle = &(file->fd);
done:
FUNC_LEAVE_NOAPI(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_read
*
* Purpose: Reads SIZE bytes of data from FILE beginning at address ADDR
* into buffer BUF according to data transfer properties in
* DXPL_ID using potentially complex file and buffer types to
* effect the transfer.
*
* Reading past the end of the file returns zeros instead of
* failing.
*
* Return: Success: Non-negative. Result is stored in caller-supplied
* buffer BUF.
* Failure: Negative, Contents of buffer BUF are undefined.
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, haddr_t addr, size_t size,
void *buf/*out*/)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
ssize_t nbytes; /* Number of bytes read each I/O call */
herr_t ret_value=SUCCEED;
FUNC_ENTER_NOAPI(H5FD_mpiposix_read, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
assert(buf);
/* Check for overflow conditions */
if (HADDR_UNDEF==addr)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined")
if (REGION_OVERFLOW(addr, size))
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
/* If the file is open for SWMR read access, allow access to data past
* the end of the allocated space (the 'eoa'). This is done because the
* eoa stored in the file's superblock might be out of sync with the
* objects being written within the file by the application performing
* SWMR write operations.
*/
if(!file->swmr_read && (addr + size) > file->eoa)
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
#ifdef REPORT_IO
{
int commrank;
MPI_Comm_rank(MPI_COMM_WORLD, &commrank);
HDfprintf(stderr, "read: rank=%d file=0x%08lx type=%d, addr=%a size=%Zu\n",
commrank, (unsigned long)file, (int)type, addr, size);
}
#endif
/* Seek to the correct location */
if ((addr!=file->pos || OP_READ!=file->op) &&
file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
/*
* Read data, being careful of interrupted system calls, partial results,
* and the end of the file.
*/
while (size>0) {
do {
nbytes = HDread(file->fd, buf, size);
} while (-1==nbytes && EINTR==errno);
if (-1==nbytes)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
if (0==nbytes) {
/* end of file but not end of format address space */
HDmemset(buf, 0, size);
break;
} /* end if */
assert(nbytes>=0);
assert((size_t)nbytes<=size);
size -= nbytes;
addr += (haddr_t)nbytes;
buf = (char*)buf + nbytes;
}
/* Update current position */
file->pos = addr;
file->op = OP_READ;
done:
/* Check for error */
if(ret_value<0) {
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_read() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_write
*
* Purpose: Writes SIZE bytes of data to FILE beginning at address ADDR
* from buffer BUF according to data transfer properties in
* DXPL_ID using potentially complex file and buffer types to
* effect the transfer.
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
* Quincey Koziol - 2002/07/18
* Added "block_before_meta_write" dataset transfer flag, which
* is set during writes from a metadata cache flush and indicates
* that all the processes must sync up before (one of them)
* writing metadata.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
size_t size, const void *buf)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
#if 0 /* JRM */
int mpi_code; /* MPI return code */
#endif /* JRM */
ssize_t nbytes; /* Number of bytes written each I/O call */
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_write, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
assert(H5I_GENPROP_LST==H5I_get_type(dxpl_id));
assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
assert(buf);
/* Check for overflow conditions */
if (HADDR_UNDEF==addr)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined")
if (REGION_OVERFLOW(addr, size))
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
if (addr+size>file->eoa)
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow")
/* Obtain the data transfer properties */
if(NULL == (plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list")
/* Metadata specific actions */
/* All metadata is now written from process 0 -- thus this function
* needs to be re-written to reflect this. For now I have simply
* commented out the code that attempts to synchronize metadata
* writes between processes, but we should really just flag an error
* whenever any process other than process 0 attempts to write
* metadata.
* -- JRM 9/1/05
*/
if(type!=H5FD_MEM_DRAW) {
unsigned block_before_meta_write=0; /* Whether to block before a metadata write */
/* Check if we need to syncronize all processes before attempting metadata write
* (Prevents race condition where the process writing the metadata goes ahead
* and writes the metadata to the file before all the processes have
* read the data, "transmitting" data from the "future" to the reading
* process. -QAK )
*
* The only time we don't want to block before a metadata write is when
* we are flushing out a bunch of metadata. Then, we block before the
* first write and don't block for further writes in the sequence.
*/
if(H5P_exist_plist(plist,H5AC_BLOCK_BEFORE_META_WRITE_NAME)>0)
if(H5P_get(plist,H5AC_BLOCK_BEFORE_META_WRITE_NAME,&block_before_meta_write)<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get H5AC property")
#if 0 /* JRM */
if(block_before_meta_write)
if (MPI_SUCCESS!= (mpi_code=MPI_Barrier(file->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
#endif /* JRM */
/* Only one process will do the actual write if all procs in comm write same metadata */
if (file->mpi_rank != H5_PAR_META_WRITE)
HGOTO_DONE(SUCCEED) /* skip the actual write */
} /* end if */
#ifdef REPORT_IO
{
int commrank;
MPI_Comm_rank(MPI_COMM_WORLD, &commrank);
HDfprintf(stderr, "write: rank=%d file=0x%08lx type=%d, addr=%a size=%Zu %s\n",
commrank, (unsigned long)file, (int)type, addr, size,
0==file->naccess?"(FIRST ACCESS)":"");
}
#endif
if (0==file->naccess++) {
/* First write access to this file */
#ifdef H5_HAVE_GPFS
if (file->use_gpfs) {
struct {
gpfsFcntlHeader_t hdr;
gpfsMultipleAccessRange_t mar;
} hint;
HDmemset(&hint, 0, sizeof hint);
hint.hdr.totalLength = sizeof hint;
hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
hint.mar.structLen = sizeof hint.mar;
hint.mar.structType = GPFS_MULTIPLE_ACCESS_RANGE;
hint.mar.accRangeCnt = 1;
hint.mar.accRangeArray[0].blockNumber = addr / file->blksize;
hint.mar.accRangeArray[0].start = addr % file->blksize;
hint.mar.accRangeArray[0].length = MIN(file->blksize-hint.mar.accRangeArray[0].start, size);
hint.mar.accRangeArray[0].isWrite = 1;
if (gpfs_fcntl(file->fd, &hint)<0)
HGOTO_ERROR(H5E_FILE, H5E_FCNTL, NULL, "failed to send hints to GPFS")
}
#endif /* H5_HAVE_GPFS */
}
/* Seek to the correct location */
if ((addr!=file->pos || OP_WRITE!=file->op) &&
file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
/*
* Write the data, being careful of interrupted system calls and partial
* results
*/
while (size>0) {
do {
nbytes = HDwrite(file->fd, buf, size);
} while (-1==nbytes && EINTR==errno);
if (-1==nbytes)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
assert(nbytes>0);
assert((size_t)nbytes<=size);
size -= nbytes;
addr += (haddr_t)nbytes;
buf = (const char*)buf + nbytes;
} /* end while */
/* Update current last file I/O information */
file->pos = addr;
file->op = OP_WRITE;
done:
/* Check for error */
if(ret_value<0) {
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
} /* end if */
#if 0 /* JRM */
/* Since metadata writes are now done by process 0 only, this broadcast
* is no longer needed. I leave it in and commented out to remind us
* that we need to re-work this function to reflect this reallity.
*
* -- JRM 9/1/05
*/
/* Guard against getting into metadata broadcast in failure cases */
else {
/* when only one process writes, need to broadcast the ret_value to other processes */
if (type!=H5FD_MEM_DRAW) {
if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&ret_value, sizeof(ret_value), MPI_BYTE, H5_PAR_META_WRITE, file->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code)
} /* end if */
} /* end else */
#endif /* JRM */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_write() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_truncate
*
* Purpose: Makes sure that the true file size is the same (or larger)
* than the end-of-address.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
H5FD_mpiposix_truncate(H5FD_t *_file, hid_t UNUSED dxpl_id, hbool_t UNUSED closing)
{
H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file;
#ifdef _WIN32
HFILE filehandle; /* Windows file handle */
LARGE_INTEGER li; /* 64-bit integer for SetFilePointer() call */
#endif /* _WIN32 */
int mpi_code; /* MPI return code */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(H5FD_mpiposix_truncate, FAIL)
HDassert(file);
HDassert(H5FD_MPIPOSIX == file->pub.driver_id);
/* Extend the file to make sure it's large enough */
if(file->eoa > file->last_eoa) {
/* Use the round-robin process to truncate (extend) the file */
if(file->mpi_rank == H5_PAR_META_WRITE) {
#ifdef _WIN32
/* Map the posix file handle to a Windows file handle */
filehandle = _get_osfhandle(file->fd);
/* Translate 64-bit integers into form Windows wants */
/* [This algorithm is from the Windows documentation for SetFilePointer()] */
li.QuadPart = file->eoa;
SetFilePointer((HANDLE)filehandle, li.LowPart, &li.HighPart, FILE_BEGIN);
if(SetEndOfFile((HANDLE)filehandle) == 0)
HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
#else /* _WIN32 */
if(-1==file_truncate(file->fd, (file_offset_t)file->eoa))
HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
#endif /* _WIN32 */
} /* end if */
/* Don't let any proc return until all have extended the file.
* (Prevents race condition where some processes go ahead and write
* more data to the file before all the processes have finished making
* it the shorter length, potentially truncating the file and dropping
* the new data written)
*/
if(MPI_SUCCESS != (mpi_code = MPI_Barrier(file->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
/* Update the 'last' eoa and eof values */
file->last_eoa = file->eoa;
file->eof = file->eoa;
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_truncate() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_mpi_rank
*
* Purpose: Returns the MPI rank for a process
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5FD_mpiposix_mpi_rank(const H5FD_t *_file)
{
const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file;
int ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_mpi_rank, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Set return value */
ret_value=file->mpi_rank;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_mpi_rank() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_mpi_size
*
* Purpose: Returns the number of MPI processes
*
* Return: Success: non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
H5FD_mpiposix_mpi_size(const H5FD_t *_file)
{
const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file;
int ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_mpi_size, FAIL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Set return value */
ret_value=file->mpi_size;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpiposix_mpi_size() */
/*-------------------------------------------------------------------------
* Function: H5FD_mpiposix_communicator
*
* Purpose: Returns the MPI communicator for the file.
*
* Return: Success: The communicator
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* Thursday, July 11, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static MPI_Comm
H5FD_mpiposix_communicator(const H5FD_t *_file)
{
const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file;
MPI_Comm ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5FD_mpiposix_communicator, MPI_COMM_NULL)
assert(file);
assert(H5FD_MPIPOSIX==file->pub.driver_id);
/* Set return value */
ret_value=file->comm;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_mpi_posix_communicator() */
#endif /*H5_HAVE_PARALLEL*/
|