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
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
2108
2109
2110
2111
2112
2113
2114
2115
2116
2117
2118
2119
2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
2140
2141
2142
2143
2144
2145
2146
2147
2148
2149
2150
2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
2161
2162
2163
2164
2165
2166
2167
2168
2169
2170
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
2188
2189
2190
2191
2192
2193
2194
2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
2239
2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
2252
2253
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282
2283
2284
2285
2286
2287
2288
2289
2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
2304
2305
2306
2307
2308
2309
2310
2311
2312
2313
2314
2315
2316
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2340
2341
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
2354
2355
2356
2357
2358
2359
2360
2361
2362
2363
2364
2365
2366
2367
2368
2369
2370
2371
2372
2373
2374
2375
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
2386
2387
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
2399
2400
2401
2402
2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
2450
2451
2452
2453
2454
2455
2456
2457
2458
2459
2460
2461
2462
2463
2464
2465
2466
2467
2468
2469
2470
2471
2472
2473
2474
2475
2476
2477
2478
2479
2480
2481
2482
2483
2484
2485
2486
2487
2488
2489
2490
2491
2492
2493
2494
2495
2496
2497
2498
2499
2500
2501
2502
2503
2504
2505
2506
2507
2508
2509
2510
2511
2512
2513
2514
2515
2516
2517
2518
2519
2520
2521
2522
2523
2524
2525
2526
2527
2528
2529
2530
2531
2532
2533
2534
2535
2536
2537
2538
2539
2540
2541
2542
2543
2544
2545
2546
2547
2548
2549
2550
2551
2552
2553
2554
2555
2556
2557
2558
2559
2560
2561
2562
2563
2564
2565
2566
2567
2568
2569
2570
2571
2572
2573
2574
2575
2576
2577
2578
2579
2580
2581
2582
2583
2584
2585
2586
2587
2588
2589
2590
2591
2592
2593
2594
2595
2596
2597
2598
2599
2600
2601
2602
2603
2604
2605
2606
2607
2608
2609
2610
2611
2612
2613
2614
2615
2616
2617
2618
2619
2620
2621
2622
2623
2624
2625
2626
2627
2628
2629
2630
2631
2632
2633
2634
2635
2636
2637
2638
2639
2640
2641
2642
2643
2644
2645
2646
2647
2648
2649
2650
2651
2652
2653
2654
2655
2656
2657
2658
2659
2660
2661
2662
2663
2664
2665
2666
2667
2668
2669
2670
2671
2672
2673
2674
2675
2676
2677
2678
2679
2680
2681
2682
2683
2684
2685
2686
2687
2688
2689
2690
2691
2692
2693
2694
2695
2696
2697
2698
2699
2700
2701
2702
2703
2704
2705
2706
2707
2708
2709
2710
2711
2712
2713
2714
2715
2716
2717
2718
2719
2720
2721
2722
2723
2724
2725
2726
2727
2728
2729
2730
2731
2732
2733
2734
2735
2736
2737
2738
2739
2740
2741
2742
2743
2744
2745
2746
2747
2748
2749
2750
2751
2752
2753
2754
2755
2756
2757
2758
2759
2760
2761
2762
2763
2764
2765
2766
2767
2768
2769
2770
2771
2772
2773
2774
2775
2776
2777
2778
2779
2780
2781
2782
2783
2784
2785
2786
2787
2788
2789
2790
2791
2792
2793
2794
2795
2796
2797
2798
2799
2800
2801
2802
2803
2804
2805
2806
2807
2808
2809
2810
2811
2812
2813
2814
2815
2816
2817
2818
2819
2820
2821
2822
2823
2824
2825
2826
2827
2828
2829
2830
2831
2832
2833
2834
2835
2836
2837
2838
2839
2840
2841
2842
2843
2844
2845
2846
2847
2848
2849
2850
2851
2852
2853
2854
2855
2856
2857
2858
2859
2860
2861
2862
2863
2864
2865
2866
2867
2868
2869
2870
2871
2872
2873
2874
2875
2876
2877
2878
2879
2880
2881
2882
2883
2884
2885
2886
2887
2888
2889
2890
2891
2892
2893
2894
2895
2896
2897
2898
2899
2900
2901
2902
2903
2904
2905
2906
2907
2908
2909
2910
2911
2912
2913
2914
2915
2916
2917
2918
2919
2920
2921
2922
2923
2924
2925
2926
2927
2928
2929
2930
2931
2932
2933
2934
2935
2936
2937
2938
2939
2940
2941
2942
2943
2944
2945
2946
2947
2948
2949
2950
2951
2952
2953
2954
2955
2956
2957
2958
2959
2960
2961
2962
2963
2964
2965
2966
2967
2968
2969
2970
2971
2972
2973
2974
2975
2976
2977
2978
2979
2980
2981
2982
2983
2984
2985
2986
2987
2988
2989
2990
2991
2992
2993
2994
2995
2996
2997
2998
2999
3000
3001
3002
3003
3004
3005
3006
3007
3008
3009
3010
3011
3012
3013
3014
3015
3016
3017
3018
3019
3020
3021
3022
3023
3024
3025
3026
3027
3028
3029
3030
3031
3032
3033
3034
3035
3036
3037
3038
3039
3040
3041
3042
3043
3044
3045
3046
3047
3048
3049
3050
3051
3052
3053
3054
3055
3056
3057
3058
3059
3060
3061
3062
3063
3064
3065
3066
3067
3068
3069
3070
3071
3072
3073
3074
3075
3076
3077
3078
3079
3080
3081
3082
3083
3084
3085
3086
3087
3088
3089
3090
3091
3092
3093
3094
3095
3096
3097
3098
3099
3100
3101
3102
3103
3104
3105
3106
3107
3108
3109
3110
3111
3112
3113
3114
3115
3116
3117
3118
3119
3120
3121
3122
3123
3124
3125
3126
3127
3128
3129
3130
3131
3132
3133
3134
3135
3136
3137
3138
3139
3140
3141
3142
3143
3144
3145
3146
3147
3148
3149
3150
3151
3152
3153
3154
3155
3156
3157
3158
3159
3160
3161
3162
3163
3164
3165
3166
3167
3168
3169
3170
3171
3172
3173
3174
3175
3176
3177
3178
3179
3180
3181
3182
3183
3184
3185
3186
3187
3188
3189
3190
3191
3192
3193
3194
3195
3196
3197
3198
3199
3200
3201
3202
3203
3204
3205
3206
3207
3208
3209
3210
3211
3212
3213
3214
3215
3216
3217
3218
3219
3220
3221
3222
3223
3224
3225
3226
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/* Pablo information */
/* (Put before include files to avoid problems with inline functions) */
#define PABLO_MASK H5Dio_mask
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Sprivate.h" /* Dataspace functions */
#include "H5TBprivate.h" /* Threaded, balanced, binary trees (TBBTs) */
#include "H5Vprivate.h" /* Vector and array functions */
/*#define H5D_DEBUG*/
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
# include "H5Rpublic.h"
#endif /*H5_HAVE_PARALLEL*/
/* Local typedefs */
/* Information for mapping between file space and memory space */
/* Structure holding information about a chunk's selection for mapping */
typedef struct H5D_chunk_info_t {
hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */
H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
} H5D_chunk_info_t;
/* Main structure holding the mapping between file chunks and memory */
typedef struct fm_map {
H5TB_TREE *fsel; /* TBBT containing file dataspaces for all chunks */
hsize_t last_index; /* Index of last chunk operated on */
H5S_t *file_space; /* Pointer to the file dataspace */
H5S_t *mem_space; /* Pointer to the memory dataspace */
hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */
H5S_t *last_chunk; /* Pointer to last memory chunk's dataspace */
H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */
unsigned f_ndims; /* Number of dimensions for file dataspace */
H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */
unsigned m_ndims; /* Number of dimensions for memory dataspace */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
H5O_layout_t *layout; /* Dataset layout information*/
H5S_sel_type msel_type; /* Selection type in memory */
} fm_map;
/* Interface initialization */
static int interface_initialize_g = 0;
#define INTERFACE_INIT NULL
/* Local functions */
static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
hid_t dset_xfer_plist, void *buf/*out*/);
static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
hid_t dset_xfer_plist, const void *buf);
static herr_t
H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/);
static herr_t
H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf);
static herr_t
H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/);
static herr_t
H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf);
#ifdef H5_HAVE_PARALLEL
static herr_t
H5D_io_assist_mpio(hid_t dxpl_id, H5D_dxpl_cache_t *dxpl_cache,
hbool_t *xfer_mode_changed);
static herr_t
H5D_io_restore_mpio(hid_t dxpl_id);
#endif /*H5_HAVE_PARALLEL*/
static herr_t H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm);
static herr_t H5D_destroy_chunk_map(const fm_map *fm);
static void H5D_free_chunk_info(void *chunk_info);
static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims,
const hsize_t chunks[], hsize_t chunk_idx);
static herr_t H5D_create_chunk_file_map_hyper(const fm_map *fm);
static herr_t H5D_create_chunk_mem_map_hyper(const fm_map *fm);
static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, hsize_t ndims,
hssize_t *coords, void *fm);
static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, hsize_t ndims,
hssize_t *coords, void *fm);
static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf,
const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id);
/* Declare a free list to manage blocks of single datatype element data */
H5FL_BLK_DEFINE(type_elem);
/* Declare a free list to manage blocks of type conversion data */
H5FL_BLK_DEFINE(type_conv);
/* Declare a free list to manage the H5D_chunk_info_t struct */
H5FL_DEFINE_STATIC(H5D_chunk_info_t);
/*--------------------------------------------------------------------------
NAME
H5Dfill
PURPOSE
Fill a selection in memory with a value
USAGE
herr_t H5Dfill(fill, fill_type, space, buf, buf_type)
const void *fill; IN: Pointer to fill value to use
hid_t fill_type_id; IN: Datatype of the fill value
void *buf; IN/OUT: Memory buffer to fill selection within
hid_t buf_type_id; IN: Datatype of the elements in buffer
hid_t space_id; IN: Dataspace describing memory buffer &
containing selection to use.
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Use the selection in the dataspace to fill elements in a memory buffer.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
If "fill" parameter is NULL, use all zeros as fill value
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id)
{
H5S_t *space; /* Dataspace */
H5T_t *fill_type; /* Fill-value datatype */
H5T_t *buf_type; /* Buffer datatype */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dfill, FAIL)
H5TRACE5("e","xixii",fill,fill_type_id,buf,buf_type_id,space_id);
/* Check args */
if (buf==NULL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer")
if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace")
if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
if(H5S_NULL == H5S_get_simple_extent_type(space))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "null dataspace isn't valid")
/* Fill the selection in the memory buffer */
if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dfill() */
/*--------------------------------------------------------------------------
NAME
H5D_fill
PURPOSE
Fill a selection in memory with a value (internal version)
USAGE
herr_t H5D_fill(fill, fill_type, buf, buf_type, space)
const void *fill; IN: Pointer to fill value to use
H5T_t *fill_type; IN: Datatype of the fill value
void *buf; IN/OUT: Memory buffer to fill selection within
H5T_t *buf_type; IN: Datatype of the elements in buffer
H5S_t *space; IN: Dataspace describing memory buffer &
containing selection to use.
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Use the selection in the dataspace to fill elements in a memory buffer.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
If "fill" parameter is NULL, use all zeros as fill value. If "fill_type"
parameter is NULL, use "buf_type" for the fill value datatype.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id)
{
H5T_path_t *tpath = NULL; /* Conversion information*/
uint8_t *tconv_buf = NULL; /* Data type conv buffer */
uint8_t *bkg_buf = NULL; /* Temp conversion buffer */
hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */
size_t src_type_size; /* Size of source type */
size_t dst_type_size; /* Size of destination type*/
size_t buf_size; /* Desired buffer size */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_fill)
/* Check args */
assert(fill_type);
assert(buf);
assert(buf_type);
assert(space);
/* Get the memory and file datatype sizes */
src_type_size = H5T_get_size(fill_type);
dst_type_size = H5T_get_size(buf_type);
/* Get the maximum buffer size needed and allocate it */
buf_size=MAX(src_type_size,dst_type_size);
if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Check for actual fill value to replicate */
if(fill==NULL)
/* If there's no fill value, just use zeros */
HDmemset(tconv_buf,0,dst_type_size);
else {
/* Copy the user's data into the buffer for conversion */
HDmemcpy(tconv_buf,fill,src_type_size);
/* Set up type conversion function */
if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
/* Convert memory buffer into disk buffer */
if (!H5T_path_noop(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
/* Perform data type conversion */
if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
} /* end if */
} /* end if */
/* Fill the selection in the memory buffer */
if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
done:
if (tconv_buf)
H5FL_BLK_FREE(type_elem,tconv_buf);
if (bkg_buf)
H5FL_BLK_FREE(type_elem,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_fill() */
/*--------------------------------------------------------------------------
NAME
H5D_get_dxpl_cache
PURPOSE
Get all the values for the DXPL cache.
USAGE
herr_t H5D_get_dxpl_cache(dxpl_id, cache)
hid_t dxpl_id; IN: DXPL to query
H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DXPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5D_get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t *cache)
{
H5P_genplist_t *dx_plist; /* Data transfer property list */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_get_dxpl_cache,FAIL)
/* Check args */
assert(cache);
/* Get the dataset transfer property list */
if (NULL == (dx_plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
/* Get maximum temporary buffer size */
if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size")
/* Get temporary buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_TCONV_BUF_NAME, &cache->tconv_buf)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve temporary buffer pointer")
/* Get background buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_NAME, &cache->bkgr_buf)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer pointer")
/* Get background buffer type */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &cache->bkgr_buf_type)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
/* Get B-tree split ratios */
if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
/* Get B-tree split ratios */
if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
/* Get I/O vector size */
if(H5P_get(dx_plist, H5D_XFER_HYPER_VECTOR_SIZE_NAME, &cache->vec_size)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O vector size")
#ifdef H5_HAVE_PARALLEL
/* Collect Parallel I/O information for possible later use */
if(H5P_get(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &cache->xfer_mode)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method")
#endif /*H5_HAVE_PARALLEL*/
/* Get error detection properties */
if(H5P_get(dx_plist, H5D_XFER_EDC_NAME, &cache->err_detect)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve error detection info")
/* Get filter callback function */
if(H5P_get(dx_plist, H5D_XFER_FILTER_CB_NAME, &cache->filter_cb)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve filter callback function")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_get_dxpl_cache() */
/*--------------------------------------------------------------------------
NAME
H5D_get_dcpl_cache
PURPOSE
Get all the values for the DCPL cache.
USAGE
herr_t H5D_get_dcpl_cache(dcpl_id, cache)
hid_t dcpl_id; IN: DCPL to query
H5D_dcpl_cache_t *cache;IN/OUT: DCPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DCPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D_get_dcpl_cache(hid_t dcpl_id, H5D_dcpl_cache_t *cache)
{
H5P_genplist_t *dc_plist; /* Data transfer property list */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_get_dcpl_cache)
/* Check args */
assert(cache);
/* Get the dataset transfer property list */
if (NULL == (dc_plist = H5I_object(dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Get I/O pipeline info */
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &cache->pline)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O pipeline info")
/* Get fill value info */
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &cache->fill)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve fill value info")
/* Get fill time info */
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &cache->fill_time)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve fill time")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_get_dcpl_cache() */
/*-------------------------------------------------------------------------
* Function: H5Dread
*
* Purpose: Reads (part of) a DSET from the file into application
* memory BUF. The part of the dataset to read is defined with
* MEM_SPACE_ID and FILE_SPACE_ID. The data points are
* converted from their file type to the MEM_TYPE_ID specified.
* Additional miscellaneous data transfer properties can be
* passed to this function with the PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
* ARGS BADTYPE Not a data space.
* ARGS BADTYPE Not a data type.
* ARGS BADTYPE Not a dataset.
* ARGS BADTYPE Not xfer parms.
* ARGS BADVALUE No output buffer.
* DATASET READERROR Can't read data.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dread, FAIL)
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == dset->ent.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type")
if (H5S_ALL != mem_space_id) {
if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if(H5S_select_valid(mem_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
if (H5S_ALL != file_space_id) {
if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if(H5S_select_valid(file_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == plist_id)
plist_id= H5P_DATASET_XFER_DEFAULT;
else
if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* read raw data */
if (H5D_read(dset, mem_type, mem_space, file_space, plist_id, buf/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
done:
FUNC_LEAVE_API(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5Dwrite
*
* Purpose: Writes (part of) a DSET from application memory BUF to the
* file. The part of the dataset to write is defined with the
* MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
* are converted from their current type (MEM_TYPE_ID) to their
* file data type. Additional miscellaneous data transfer
* properties can be passed to this function with the
* PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, const void *buf)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_API(H5Dwrite, FAIL)
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == dset->ent.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type")
if (H5S_ALL != mem_space_id) {
if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if (H5S_select_valid(mem_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
if (H5S_ALL != file_space_id) {
if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
/* Check for valid selection */
if (H5S_select_valid(file_space)!=TRUE)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
}
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == plist_id)
plist_id= H5P_DATASET_XFER_DEFAULT;
else
if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer")
/* write raw data */
if (H5D_write(dset, mem_type, mem_space, file_space, plist_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
done:
FUNC_LEAVE_API(ret_value)
}
/*-------------------------------------------------------------------------
* Function: H5D_read
*
* Purpose: Reads (part of) a DATASET into application memory BUF. See
* H5Dread() for complete details.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 1998-06-09
* The data space is no longer cached in the dataset struct.
*
* Robb Matzke, 1998-08-11
* Added timing calls around all the data space I/O functions.
*
* rky, 1998-09-18
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 1999-07-02
* Changed xfer_parms parameter to xfer plist parameter, so it
* could be passed to H5T_convert.
*
* Albert Cheng, 2000-11-21
* Added the code that when it detects it is not safe to process a
* COLLECTIVE read request without hanging, it changes it to
* INDEPENDENT calls.
*
* Albert Cheng, 2000-11-27
* Changed to use the optimized MPIO transfer for Collective calls only.
*
* Raymond Lu, 2001-10-2
* Changed the way to retrieve property for generic property list.
*
* Raymond Lu, 2002-2-26
* For the new fill value design, data space can either be allocated
* or not allocated at this stage. Fill value or data from space is
* returned to outgoing buffer.
*
* QAK - 2002/04/02
* Removed the must_convert parameter and move preconditions to
* H5S_<foo>_opt_possible() routine
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/)
{
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */
#ifdef H5_HAVE_PARALLEL
hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */
#endif /*H5_HAVE_PARALLEL*/
H5D_dxpl_cache_t dxpl_cache; /* Data transfer property cache */
H5D_dcpl_cache_t dcpl_cache; /* Dataset creation property cache */
unsigned sconv_flags=0; /* Flags for the space conversion */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_read)
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
if (!file_space)
file_space = dataset->space;
if (!mem_space)
mem_space = file_space;
if(H5S_NULL == H5S_get_simple_extent_type(mem_space) ||
H5S_NULL == H5S_get_simple_extent_type(file_space))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "null dataspace isn't supported")
if((snelmts = H5S_get_select_npoints(mem_space))<0)
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t);
/* Fill the DCPL cache values for later use */
if (H5D_get_dcpl_cache(dataset->dcpl_id,&dcpl_cache)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dcpl cache")
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
#ifdef H5_HAVE_PARALLEL
/* Collective access is not permissible without a MPI based VFD */
if (dxpl_cache.xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only")
/* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */
/* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */
if (H5S_mpi_opt_types_g && dxpl_cache.xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file))
sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE;
#endif /*H5_HAVE_PARALLEL*/
/* Make certain that the number of elements in each selection is the same */
if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space))
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes")
/* Retrieve dataset properties */
/* <none needed in the general case> */
/* If space hasn't been allocated and not using external storage,
* return fill value to buffer if fill time is upon allocation, or
* do nothing if fill time is never. If the dataset is compact and
* fill time is NEVER, there is no way to tell whether part of data
* has been overwritten. So just proceed in reading.
*/
if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT
&& dataset->layout.addr==HADDR_UNDEF) {
H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */
/* Retrieve dataset's fill-value properties */
if(H5P_is_fill_value_defined(&dcpl_cache.fill, &fill_status)<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* Should be impossible, but check anyway... */
if(fill_status == H5D_FILL_VALUE_UNDEFINED &&
(dcpl_cache.fill_time == H5D_FILL_TIME_ALLOC || dcpl_cache.fill_time == H5D_FILL_TIME_IFSET))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read")
/* If we're never going to fill this dataset, just leave the junk in the user's buffer */
if(dcpl_cache.fill_time == H5D_FILL_TIME_NEVER)
HGOTO_DONE(SUCCEED)
/* Go fill the user's selection with the dataset's fill value */
if(H5D_fill(dcpl_cache.fill.buf,dataset->type,buf,mem_type,mem_space,dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed")
else
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
} else if (!H5T_path_noop(tpath)) {
if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 ||
(dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
} /* end if */
/* Set the storage flags for the space conversion check */
switch(dataset->layout.type) {
case H5D_COMPACT:
sconv_flags |= H5S_CONV_STORAGE_COMPACT;
break;
case H5D_CONTIGUOUS:
sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS;
break;
case H5D_CHUNKED:
sconv_flags |= H5S_CONV_STORAGE_CHUNKED;
break;
default:
assert(0 && "Unhandled layout type!");
} /* end switch */
/* Get dataspace functions */
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space")
#ifdef H5_HAVE_PARALLEL
/* Don't reset the transfer mode if we can't or won't use it */
if(!use_par_opt_io || !H5T_path_noop(tpath))
H5D_io_assist_mpio(dxpl_id, &dxpl_cache, &xfer_mode_changed);
#endif /*H5_HAVE_PARALLEL*/
/* Determine correct I/O routine to invoke */
if(dataset->layout.type!=H5D_CHUNKED) {
if(H5D_contig_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, &dcpl_cache,
&dxpl_cache, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
} /* end if */
else {
if(H5D_chunk_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, &dcpl_cache,
&dxpl_cache, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
} /* end else */
done:
#ifdef H5_HAVE_PARALLEL
/* Restore xfer_mode due to the kludge */
if (xfer_mode_changed)
H5D_io_restore_mpio(dxpl_id);
#endif /*H5_HAVE_PARALLEL*/
if (src_id >= 0) {
if(H5I_dec_ref(src_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if (dst_id >= 0) {
if(H5I_dec_ref(dst_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_read() */
/*-------------------------------------------------------------------------
* Function: H5D_write
*
* Purpose: Writes (part of) a DATASET to a file from application memory
* BUF. See H5Dwrite() for complete details.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is no longer cached in the dataset struct.
*
* rky 980918
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 2 July 1999
* Changed xfer_parms parameter to xfer plist parameter, so it could
* be passed to H5T_convert
*
* Albert Cheng, 2000-11-21
* Added the code that when it detects it is not safe to process a
* COLLECTIVE write request without hanging, it changes it to
* INDEPENDENT calls.
*
* Albert Cheng, 2000-11-27
* Changed to use the optimized MPIO transfer for Collective calls only.
*
* Raymond Lu, 2001-10-2
* Changed the way to retrieve property for generic property list.
*
* Raymond Lu, 2002-2-26
* For the new fill value design, space may not be allocated until
* this function is called. Allocate and initialize space if it
* hasn't been.
*
* QAK - 2002/04/02
* Removed the must_convert parameter and move preconditions to
* H5S_<foo>_opt_possible() routine
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, const void *buf)
{
hssize_t snelmts; /*total number of elmts (signed) */
hsize_t nelmts; /*total number of elmts */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */
#ifdef H5_HAVE_PARALLEL
hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */
#endif /*H5_HAVE_PARALLEL*/
H5D_dxpl_cache_t dxpl_cache; /* Data transfer property cache */
H5D_dcpl_cache_t dcpl_cache; /* Dataset creation property cache */
unsigned sconv_flags=0; /* Flags for the space conversion */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_write)
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
/* If MPI based VFD is used, no VL datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
if (IS_H5FD_MPI(dataset->ent.file) && H5T_detect_class(mem_type, H5T_VLEN)>0)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet")
/* If MPI based VFD is used, no VL datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
/* We should really use H5T_detect_class() here, but it will be difficult
* to detect the type of the reference if it is nested... -QAK
*/
if (IS_H5FD_MPI(dataset->ent.file) &&
H5T_get_class(mem_type)==H5T_REFERENCE &&
H5T_get_ref_type(mem_type)==H5R_DATASET_REGION)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet")
/* Check if we are allowed to write to this file */
if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
/* Fill the DCPL cache values for later use */
if (H5D_get_dcpl_cache(dataset->dcpl_id,&dcpl_cache)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dcpl cache")
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
if (!file_space)
file_space = dataset->space;
if (!mem_space)
mem_space = file_space;
if(H5S_NULL == H5S_get_simple_extent_type(mem_space) ||
H5S_NULL == H5S_get_simple_extent_type(file_space))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "null dataspace isn't supported")
if((snelmts = H5S_get_select_npoints(mem_space))<0)
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t);
#ifdef H5_HAVE_PARALLEL
/* Collective access is not permissible without a MPI based VFD */
if (dxpl_cache.xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only")
/* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */
/* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */
if (H5S_mpi_opt_types_g && dxpl_cache.xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file))
sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE;
#endif /*H5_HAVE_PARALLEL*/
/* Make certain that the number of elements in each selection is the same */
if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space))
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes")
/* Retrieve dataset properties */
/* <none needed currently> */
/* Allocate data space and initialize it if it hasn't been. */
if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT
&& dataset->layout.addr==HADDR_UNDEF) {
hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */
hbool_t full_overwrite; /* Whether we are over-writing all the elements */
/* Get the number of elements in file dataset's dataspace */
if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0)
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset")
/* Always allow fill values to be written if the dataset has a VL datatype */
if(H5T_detect_class(dataset->type, H5T_VLEN))
full_overwrite=FALSE;
else
full_overwrite=(hsize_t)file_nelmts==nelmts ? TRUE : FALSE;
/* Allocate storage */
if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, full_overwrite)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
} /* end if */
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type atoms. Data type
* conversion is necessary if the user has set the `need_bkg' to a high
* enough value in xfer_parms since turning off data type conversion also
* turns off background preservation.
*/
if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types")
} else if (!H5T_path_noop(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion")
} /* end if */
/* Set the storage flags for the space conversion check */
switch(dataset->layout.type) {
case H5D_COMPACT:
sconv_flags |= H5S_CONV_STORAGE_COMPACT;
break;
case H5D_CONTIGUOUS:
sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS;
break;
case H5D_CHUNKED:
sconv_flags |= H5S_CONV_STORAGE_CHUNKED;
break;
default:
assert(0 && "Unhandled layout type!");
} /* end switch */
/* Get dataspace functions */
if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space")
#ifdef H5_HAVE_PARALLEL
/* Don't reset the transfer mode if we can't or won't use it */
if(!use_par_opt_io || !H5T_path_noop(tpath)) {
H5D_io_assist_mpio(dxpl_id, &dxpl_cache, &xfer_mode_changed);
} /* end if */
#endif /*H5_HAVE_PARALLEL*/
/* Determine correct I/O routine to invoke */
if(dataset->layout.type!=H5D_CHUNKED) {
if(H5D_contig_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, &dcpl_cache,
&dxpl_cache, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end if */
else {
if(H5D_chunk_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, &dcpl_cache,
&dxpl_cache, dxpl_id, src_id, dst_id, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end else */
#ifdef OLD_WAY
/*
* This was taken out because it can be called in a parallel program with
* independent access, causing the metadata cache to get corrupted. Its been
* disabled for all types of access (serial as well as parallel) to make the
* modification time consistent for all programs. -QAK
*/
/*
* Update modification time. We have to do this explicitly because
* writing to a dataset doesn't necessarily change the object header.
*/
if (H5O_touch(&(dataset->ent), FALSE, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time")
#endif /* OLD_WAY */
done:
#ifdef H5_HAVE_PARALLEL
/* Restore xfer_mode due to the kludge */
if (xfer_mode_changed)
H5D_io_restore_mpio(dxpl_id);
#endif /*H5_HAVE_PARALLEL*/
if (src_id >= 0) {
if(H5I_dec_ref(src_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if (dst_id >= 0) {
if(H5I_dec_ref(dst_id)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_write() */
/*-------------------------------------------------------------------------
* Function: H5D_contig_read
*
* Purpose: Read from a contiguous dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath,
H5S_conv_t *sconv, const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/)
{
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
/*
* If there is no type conversion then read directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
dcpl_cache, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type),
file_space, mem_space, dxpl_cache, dxpl_id, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].read_timer), &timer);
sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type);
sconv->stats[1].read_ncalls++;
#endif
/* Check return value from optimized read */
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
} else
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = dxpl_cache->max_temp_buf;
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX(src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/* Figure out the strip mine size. */
if (H5S_select_iter_init(&file_iter, file_space, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&mem_iter, mem_space, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&bkg_iter, mem_space, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
need_bkg=dxpl_cache->bkgr_buf_type;
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX(path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=dxpl_cache->bkgr_buf)) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dcpl_cache, (H5D_storage_t *)&(dataset->efl), src_type_size, file_space,
&file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter,
smine_nelmts, dxpl_cache, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space,
&mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
} /* end for */
done:
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if (tconv_buf && NULL==dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_contig_read() */
/*-------------------------------------------------------------------------
* Function: H5D_contig_write
*
* Purpose: Write to a contiguous dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf)
{
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
/*
* If there is no type conversion then write directly from the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
dcpl_cache, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type),
file_space, mem_space, dxpl_cache, dxpl_id, buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].write_timer), &timer);
sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
sconv->stats[0].write_ncalls++;
#endif
/* Check return value from optimized write */
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
} else
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case.
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = dxpl_cache->max_temp_buf;
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/* Figure out the strip mine size. */
if (H5S_select_iter_init(&file_iter, file_space, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&mem_iter, mem_space, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&bkg_iter, file_space, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if(H5T_detect_class(dataset->type, H5T_VLEN)) {
/* Old data is retrieved into background buffer for VL datatype. The
* data is used later for freeing heap objects. */
need_bkg = H5T_BKG_YES;
} else if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
need_bkg=dxpl_cache->bkgr_buf_type;
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX (path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=dxpl_cache->bkgr_buf)) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Start strip mining... */
for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (nelmts-smine_start));
/*
* Gather data from application buffer into the data type conversion
* buffer. Also gather data from the file into the background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter,
smine_nelmts, dxpl_cache, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].gath_timer), &timer);
sconv->stats[0].gath_nbytes += n * src_type_size;
sconv->stats[0].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dcpl_cache, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space,
&bkg_iter, smine_nelmts, dxpl_cache, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_fscat(dataset->ent.file, &(dataset->layout),
dcpl_cache, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, &file_iter,
smine_nelmts, dxpl_cache, dxpl_id, tconv_buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed")
} /* end for */
done:
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if (tconv_buf && NULL==dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv,bkg_buf);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_contig_write() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_read
*
* Purpose: Read from a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_read(hsize_t
#ifdef NDEBUG
UNUSED
#endif /* NDEBUG */
nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, void *buf/*out*/)
{
fm_map fm; /* File<->memory mapping */
H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
hssize_t schunk_nelmts; /* Number of elements selected in current chunk */
hsize_t chunk_nelmts; /* Number of elements selected in current chunk */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5D_storage_t store; /*union of EFL and chunk pointer in file space */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
/*
* If there is no type conversion then read directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree node */
chunk_info=chunk_node->data;
#ifdef H5S_DEBUG
/* Get the number of elements selected in this chunk */
if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
#endif /* H5S_DEBUG */
/* Pass in chunk's coordinates in a union. */
store.chunk_coords = chunk_info->coords;
/* Perform the actual read operation */
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
dcpl_cache, &store, H5T_get_size(dataset->type),
chunk_info->fspace, chunk_info->mspace, dxpl_cache, dxpl_id, buf);
/* Check return value from optimized read */
if (status<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed")
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].read_timer), &timer);
sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type);
sconv->stats[1].read_ncalls++;
#endif
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = dxpl_cache->max_temp_buf;
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
need_bkg=dxpl_cache->bkgr_buf_type;
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX(path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=dxpl_cache->bkgr_buf)) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Loop over all the chunks, performing I/O on each */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree nodes */
chunk_info=chunk_node->data;
/* Get the number of elements selected in this chunk */
if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
/* initialize selection iterator */
if (H5S_select_iter_init(&file_iter, chunk_info->fspace, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&mem_iter, chunk_info->mspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&bkg_iter, chunk_info->mspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/* Pass in chunk's coordinates in a union*/
store.chunk_coords = chunk_info->coords;
for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 ||
dataset->layout.type==H5D_COMPACT);
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dcpl_cache, &store, src_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, dst_type_size, chunk_info->mspace, &bkg_iter,
smine_nelmts, dxpl_cache, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0,
tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_mscat(tconv_buf, dst_type_size, chunk_info->mspace,
&mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
} /* end for */
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
file_iter_init=0;
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
mem_iter_init=0;
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
bkg_iter_init=0;
} /* end if */
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
if (tconv_buf && NULL==dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv,bkg_buf);
/* Release selection iterators, if necessary */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
/* Release chunk mapping information */
if(H5D_destroy_chunk_map(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_read() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_write
*
* Purpose: Writes to a chunked dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_write(hsize_t
#ifdef NDEBUG
UNUSED
#endif /* NDEBUG */
nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv,
const H5D_dcpl_cache_t *dcpl_cache,
const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
hid_t src_id, hid_t dst_id, const void *buf)
{
fm_map fm; /* File<->memory mapping */
H5TB_NODE *chunk_node; /* Current node in chunk TBBT */
herr_t status; /*function return status*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
hsize_t request_nelmts; /*requested strip mine */
hssize_t schunk_nelmts; /* Number of elements selected in current chunk */
hsize_t chunk_nelmts; /* Number of elements selected in current chunk */
hsize_t smine_start; /*strip mine start loc */
hsize_t n, smine_nelmts; /*elements per strip */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5D_storage_t store; /*union of EFL and chunk pointer in file space */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Map elements between file and memory for each chunk*/
if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping")
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - After creating chunk map, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/*
* If there is no type conversion then write directly from the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Performing optimized I/O, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree node */
chunk_info=chunk_node->data;
#ifdef H5S_DEBUG
/* Get the number of elements selected in this chunk */
if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
#endif /* H5S_DEBUG */
/* Pass in chunk's coordinates in a union. */
store.chunk_coords = chunk_info->coords;
/* Perform the actual write operation */
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
dcpl_cache, &store, H5T_get_size(dataset->type),
chunk_info->fspace, chunk_info->mspace, dxpl_cache, dxpl_id, buf);
/* Check return value from optimized write */
if (status<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed")
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Done performing optimized I/O, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].write_timer), &timer);
sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
sconv->stats[0].write_ncalls++;
#endif
/* direct xfer accomplished successfully */
HGOTO_DONE(SUCCEED)
} /* end if */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
HDfprintf(stderr,"%s: rank=%d - Performing NON-optimized I/O\n",FUNC,mpi_rank);
}
#endif /* QAK */
/*
* This is the general case(type conversion).
*/
/* Compute element sizes and other parameters */
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = dxpl_cache->max_temp_buf;
/* XXX: This could cause a problem if the user sets their buffer size
* to the same size as the default, and then the dataset elements are
* too large for the buffer... - QAK
*/
if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF &&
target_size<MAX(src_type_size, dst_type_size))
target_size = MAX(src_type_size, dst_type_size);
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Sanity check elements in temporary buffer */
if (request_nelmts==0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
/*
* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
* buffer which is the exact size, we allocate the target size. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if(H5T_detect_class(dataset->type, H5T_VLEN)) {
/* Old data is retrieved into background buffer for VL datatype. The
* data is used later for freeing heap objects. */
need_bkg = H5T_BKG_YES;
} else if (H5T_path_bkg(tpath)) {
H5T_bkg_t path_bkg; /* Type conversion's background info */
/* Retrieve the bkgr buffer property */
need_bkg=dxpl_cache->bkgr_buf_type;
path_bkg = H5T_path_bkg(tpath);
need_bkg = MAX (path_bkg, need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
} /* end if */
if (need_bkg && NULL==(bkg_buf=dxpl_cache->bkgr_buf)) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion")
} /* end if */
/* Loop over all the chunks, performing I/O on each */
/* Get first node in chunk tree */
chunk_node=H5TB_first(fm.fsel->root);
/* Iterate through chunks to be operated on */
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the tree node */
chunk_info=chunk_node->data;
/* Get the number of elements selected in this chunk */
if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection")
H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t);
assert(chunk_nelmts<=nelmts);
/* initialize selection iterator */
if (H5S_select_iter_init(&file_iter, chunk_info->fspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&mem_iter, chunk_info->mspace, src_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&bkg_iter, chunk_info->fspace, dst_type_size)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
/*pass in chunk's coordinates in a union*/
store.chunk_coords = chunk_info->coords;
for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start));
smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start));
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_mgath(buf, src_type_size, chunk_info->mspace, &mem_iter,
smine_nelmts, dxpl_cache, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5S_select_fgath(dataset->ent.file, &(dataset->layout),
dcpl_cache, &store, dst_type_size, chunk_info->fspace,
&bkg_iter, smine_nelmts, dxpl_cache, dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
} /* end if */
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0,
tconv_buf, bkg_buf, dxpl_id)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5S_select_fscat(dataset->ent.file, &(dataset->layout),
dcpl_cache, &store, dst_type_size, chunk_info->fspace,
&file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += n * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0)
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed")
} /* end for */
/* Release selection iterators */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
file_iter_init=0;
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
mem_iter_init=0;
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
bkg_iter_init=0;
} /* end if */
/* Get the next chunk node in the tree */
chunk_node=H5TB_next(chunk_node);
} /* end while */
done:
if (tconv_buf && NULL==dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv,bkg_buf);
/* Release selection iterators, if necessary */
if(file_iter_init) {
if(H5S_select_iter_release(&file_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(mem_iter_init) {
if(H5S_select_iter_release(&mem_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if(bkg_iter_init) {
if(H5S_select_iter_release(&bkg_iter)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
/* Release chunk mapping information */
if(H5D_destroy_chunk_map(&fm) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_write() */
#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5D_io_assist_mpio
*
* Purpose: Common logic for determining if the MPI transfer mode should
* be changed.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_io_assist_mpio(hid_t dxpl_id, H5D_dxpl_cache_t *dxpl_cache,
hbool_t *xfer_mode_changed)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_io_assist_mpio)
/* The following may not handle a collective call correctly
* since it does not ensure all processes can handle the write
* request according to the MPI collective specification.
* Do the collective request via independent mode.
*/
if (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE) {
H5P_genplist_t *dx_plist; /* Data transer property list */
/* Get the dataset transfer property list */
if (NULL == (dx_plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Kludge: change the xfer_mode to independent, handle the request,
* then xfer_mode before return.
* Better way is to get a temporary data_xfer property with
* INDEPENDENT xfer_mode and pass it downwards.
*/
dxpl_cache->xfer_mode = H5FD_MPIO_INDEPENDENT;
if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &dxpl_cache->xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
*xfer_mode_changed=TRUE; /* restore it before return */
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_io_assist_mpio() */
/*-------------------------------------------------------------------------
* Function: H5D_io_restore_mpio
*
* Purpose: Common logic for restoring MPI transfer mode
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Friday, February 6, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_io_restore_mpio(hid_t dxpl_id)
{
H5P_genplist_t *dx_plist; /* Data transer property list */
H5FD_mpio_xfer_t xfer_mode; /*xfer_mode for this request */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_io_restore_mpio)
/* Get the dataset transfer property list */
if (NULL == (dx_plist = H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Kludge: change the xfer_mode to independent, handle the request,
* then xfer_mode before return.
* Better way is to get a temporary data_xfer property with
* INDEPENDENT xfer_mode and pass it downwards.
*/
xfer_mode = H5FD_MPIO_COLLECTIVE;
if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_io_restore_mpio() */
#endif /*H5_HAVE_PARALLEL*/
/*-------------------------------------------------------------------------
* Function: H5D_chunk_coords_assist
*
* Purpose: Compute the coords for a particular chunk (in CHUNK_IDX),
* based on the size of the dataset's dataspace (given in
* NDIMS and CHUNKS), putting the resulting chunk's coordinate
* offsets in the COORDS array.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, const hsize_t chunks[], hsize_t chunk_idx)
{
hsize_t tmp; /* Size of "down elements" in each dimension */
size_t i, j; /* Local index variables */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_coords_assist)
for(i=0; i<ndims; i++) {
tmp=1;
for(j=i+1; j<ndims; j++)
tmp *= chunks[j];
coords[i] = (hssize_t)(chunk_idx / tmp);
chunk_idx = chunk_idx % tmp;
}
coords[ndims] = 0;
FUNC_LEAVE_NOAPI(SUCCEED)
}
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_map
*
* Purpose: Creates the mapping between elements selected in each chunk
* and the elements in the memory selection.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space,
const H5S_t *mem_space, fm_map *fm)
{
H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */
H5S_t *equiv_mspace=NULL; /* Equivalent memory dataspace */
hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */
hbool_t iter_init=0; /* Selection iteration info has been initialized */
unsigned f_ndims; /* The number of dimensions of the file's dataspace */
int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
hsize_t nchunks, last_nchunks; /* Number of chunks in dataset */
H5TB_NODE *curr_node; /* Current node in TBBT */
H5S_sel_type fsel_type; /* Selection type on disk */
char bogus; /* "bogus" buffer to pass to selection iterator */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map)
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Initialize fm_map structure */
HDmemset(fm, 0, sizeof(fm_map));
/* Get layout for dataset */
fm->layout = &(dataset->layout);
/* Check if the memory space is scalar & make equivalent memory space */
if((sm_ndims = H5S_get_simple_extent_ndims(mem_space))<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
if(sm_ndims==0) {
hsize_t dims[H5O_LAYOUT_NDIMS]; /* Temporary dimension information */
/* Set up "equivalent" n-dimensional dataspace with size '1' in each dimension */
for(u=0; u<dataset->layout.ndims-1; u++)
dims[u]=1;
if((equiv_mspace = H5S_create_simple(dataset->layout.ndims-1,dims,NULL))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space")
} /* end else */
else {
if((equiv_mspace = H5S_copy(mem_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
} /* end else */
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(equiv_mspace))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims=f_ndims=dataset->layout.ndims-1;
if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
H5_ASSIGN_OVERFLOW(fm->m_ndims,sm_ndims,int,unsigned);
/* De-select the mem space copy */
if(H5S_select_none(tmp_mspace)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space")
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
/* Decide the number of chunks in each dimension*/
last_nchunks=0;
nchunks=1;
for(u=0; u<f_ndims; u++) {
/* Round up to the next integer # of chunks, to accomodate partial chunks */
fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u];
/* Track total number of chunks in dataset */
nchunks *= fm->chunks[u];
/* Check if the chunk indices will overflow */
if(nchunks<last_nchunks)
HGOTO_ERROR (H5E_DATASET, H5E_OVERFLOW, FAIL, "too many chunks")
last_nchunks=nchunks;
} /* end for */
/* Compute the "down" size of 'chunks' information */
if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks)<0)
HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* Initialize TBBT for chunk selections */
if((fm->fsel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL)
HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for chunk selections")
/* Save chunk template information */
fm->mchunk_tmpl=tmp_mspace;
/* Initialize "last chunk" information */
fm->last_index=(hsize_t)-1;
fm->last_chunk=NULL;
/* Copy the dataspaces */
if((fm->file_space = H5S_copy(file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file dataspace")
if((fm->mem_space = H5S_copy(equiv_mspace))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory dataspace")
/* Get type of selection on disk & in memory */
if((fsel_type=H5S_get_select_type(file_space))<0)
HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
if((fm->msel_type=H5S_get_select_type(equiv_mspace))<0)
HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
/* Check if file selection is a point selection */
if(fsel_type==H5S_SEL_POINTS) {
/* Create temporary datatypes for selection iteration */
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Reset "last chunk" info */
fm->last_index=(hsize_t)-1;
fm->last_chunk=NULL;
} /* end if */
else {
/* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
if(H5S_hyper_convert(fm->file_space)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
/* Normalize the hyperslab selections by adjusting them by the offset */
if(H5S_hyper_normalize_offset(fm->file_space)<0)
HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Before creating chunk selections, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
/* Build the file selection for each chunk */
if(H5D_create_chunk_file_map_hyper(fm)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - After creating file chunk selections, time=%f\n",FUNC,mpi_rank,time);
HDfprintf(stderr,"%s: rank=%d - H5S_select_shape_same=%d\n",FUNC,mpi_rank,H5S_select_shape_same(file_space,equiv_mspace));
}
#endif /* QAK */
/* Clean file chunks' hyperslab span "scratch" information */
curr_node=H5TB_first(fm->fsel->root);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info=curr_node->data;
assert(chunk_info);
/* Clean hyperslab span's "scratch" information */
if(H5S_hyper_reset_scratch(chunk_info->fspace)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
/* Get the next chunk node in the TBBT */
curr_node=H5TB_next(curr_node);
} /* end while */
} /* end else */
/* Build the memory selection for each chunk */
if(fsel_type!=H5S_SEL_POINTS && H5S_select_shape_same(file_space,equiv_mspace)==TRUE) {
if(H5S_hyper_convert(fm->mem_space)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
/* Normalize the hyperslab selections by adjusting them by the offset */
if(H5S_hyper_normalize_offset(fm->mem_space)<0)
HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
/* If the selections are the same shape, use the file chunk information
* to generate the memory chunk information quickly.
*/
if(H5D_create_chunk_mem_map_hyper(fm)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
} /* end if */
else {
size_t elmt_size; /* Memory datatype size */
/* Create temporary datatypes for selection iteration */
if(f_tid<0) {
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0)
HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
} /* end if */
/* Create selection iterator for memory selection */
if((elmt_size=H5T_get_size(mem_type))==0)
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if (H5S_select_iter_init(&(fm->mem_iter), equiv_mspace, elmt_size)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init=1; /* Selection iteration info has been initialized */
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
/* Clean up hyperslab stuff, if necessary */
if(fm->msel_type!=H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
curr_node=H5TB_first(fm->fsel->root);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info=curr_node->data;
assert(chunk_info);
/* Clean hyperslab span's "scratch" information */
if(H5S_hyper_reset_scratch(chunk_info->mspace)<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
/* Get the next chunk node in the TBBT */
curr_node=H5TB_next(curr_node);
} /* end while */
} /* end if */
} /* end else */
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - After creating chunk selections, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
done:
/* Release the [potentially partially built] chunk mapping information if an error occurs */
if(ret_value<0) {
if(tmp_mspace && !fm->mchunk_tmpl) {
if(H5S_close(tmp_mspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if (H5D_destroy_chunk_map(fm)<0)
HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
if(equiv_mspace) {
if(H5S_close(equiv_mspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if(iter_init) {
if (H5S_select_iter_release(&(fm->mem_iter))<0)
HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
}
if(f_tid!=(-1)) {
if(H5I_dec_ref(f_tid)<0)
HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
#ifdef QAK
{
int mpi_rank;
double time;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
time = MPI_Wtime();
HDfprintf(stderr,"%s: rank=%d - Leaving, time=%f\n",FUNC,mpi_rank,time);
}
#endif /* QAK */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_map() */
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
PURPOSE
Internal routine to destroy a chunk info node (Wrapper for compatibility
with H5TB_dfree)
USAGE
void H5D_free_chunk_info(chunk_info)
void *chunk_info; IN: Pointer to chunk info to destroy
RETURNS
No return value
DESCRIPTION
Releases all the memory for a chunk info node.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static void
H5D_free_chunk_info(void *_chunk_info)
{
H5D_chunk_info_t *chunk_info=(H5D_chunk_info_t *)_chunk_info;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info)
assert(chunk_info);
/* Close the chunk's file dataspace */
(void)H5S_close(chunk_info->fspace);
/* Close the chunk's memory dataspace */
(void)H5S_close(chunk_info->mspace);
/* Free the actual chunk info */
H5FL_FREE(H5D_chunk_info_t,chunk_info);
FUNC_LEAVE_NOAPI_VOID
} /* H5D_free_chunk_info() */
/*-------------------------------------------------------------------------
* Function: H5D_destroy_chunk_map
*
* Purpose: Destroy chunk mapping information.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Saturday, May 17, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_destroy_chunk_map(const fm_map *fm)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_destroy_chunk_map)
/* Free the chunk info tree */
if(fm->fsel)
H5TB_dfree(fm->fsel,H5D_free_chunk_info,NULL);
/* Free the file dataspace */
if(fm->file_space)
if(H5S_close(fm->file_space)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace")
/* Free the memory dataspace */
if(fm->mem_space)
if(H5S_close(fm->mem_space)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory dataspace")
/* Free the memory chunk dataspace template */
if(fm->mchunk_tmpl)
if(H5S_close(fm->mchunk_tmpl)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_destroy_chunk_map() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_file_map_hyper
*
* Purpose: Create all chunk selections in file.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_file_map_hyper(const fm_map *fm)
{
H5S_t *tmp_fspace=NULL; /* Temporary file dataspace */
hssize_t sel_points; /* Number of elements in file selection */
hssize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hssize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hssize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hssize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */
hsize_t chunk_index; /* Index of chunk */
int curr_dim; /* Current dimension to increment */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_file_map_hyper)
/* Sanity check */
assert(fm->f_ndims>0);
/* Make a copy of file dataspace */
if((tmp_fspace = H5S_copy(fm->file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Get number of elements selected in file */
if((sel_points=H5S_get_select_npoints(tmp_fspace))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
/* Get offset of first block in file selection */
if(H5S_get_select_bounds(tmp_fspace, sel_start, sel_end)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Set initial chunk location & hyperslab size */
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t);
start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u];
coords[u]=start_coords[u];
count[u]=fm->layout->dim[u];
} /* end for */
/* Select initial chunk as hyperslab */
if(H5S_select_hyperslab(tmp_fspace,H5S_SELECT_SET,coords,NULL,count,NULL)<0) /*lint !e772 The coords and count arrays should always be initialized */
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create hyperslab selection")
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Iterate through each chunk in the dataset */
while(sel_points) {
/* Check for intersection of temporary chunk and file selection */
if(H5S_hyper_intersect(tmp_fspace,fm->file_space)==TRUE) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */
hssize_t chunk_points; /* Number of elements in chunk selection */
/* Create "temporary" chunk for selection operations (copy file space) */
if((tmp_fchunk = H5S_copy(fm->file_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* "AND" temporary chunk and current chunk */
if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,NULL)<0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection")
} /* end if */
/* Resize chunk's dataspace dimensions to size of chunk */
if(H5S_set_extent_real(tmp_fchunk,count)<0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
} /* end if */
/* Move selection back to have correct offset in chunk */
if(H5S_hyper_adjust(tmp_fchunk,coords)<0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
} /* end if */
/* Add temporary chunk to the list of chunks */
/* Allocate the file & memory chunk information */
if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
/* Initialize the chunk information */
/* Set the chunk index */
new_chunk_info->index=chunk_index;
/* Set the file chunk dataspace */
new_chunk_info->fspace=tmp_fchunk;
/* Set the memory chunk dataspace */
new_chunk_info->mspace=NULL;
/* Compute the chunk's coordinates */
if(H5D_chunk_coords_assist(new_chunk_info->coords, fm->f_ndims, fm->chunks, chunk_index)<0) {
H5D_free_chunk_info(new_chunk_info);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTCOUNT,FAIL,"can't compute chunk info")
} /* end if */
/* Insert the new chunk into the TBBT tree */
if(H5TB_dins(fm->fsel,new_chunk_info,new_chunk_info)==NULL) {
H5D_free_chunk_info(new_chunk_info);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into TBBT")
} /* end if */
/* Get number of elements selected in chunk */
if((chunk_points=H5S_get_select_npoints(tmp_fchunk))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
/* Decrement # of points left in file selection */
sel_points-=chunk_points;
/* Leave if we are done */
if(sel_points==0)
HGOTO_DONE(SUCCEED)
assert(sel_points>0);
} /* end if */
/* Increment chunk index */
chunk_index++;
/* Set current increment dimension */
curr_dim=(int)fm->f_ndims-1;
/* Increment chunk location in fastest changing dimension */
H5_CHECK_OVERFLOW(count[curr_dim],hsize_t,hssize_t);
coords[curr_dim]+=(hssize_t)count[curr_dim];
/* Bring chunk location back into bounds, if necessary */
if(coords[curr_dim]>sel_end[curr_dim]) {
do {
/* Reset current dimension's location to 0 */
coords[curr_dim]=start_coords[curr_dim]; /*lint !e771 The start_coords will always be initialized */
/* Decrement current dimension */
curr_dim--;
/* Increment chunk location in current dimension */
coords[curr_dim]+=(hssize_t)count[curr_dim];
} while(coords[curr_dim]>sel_end[curr_dim]);
/* Re-Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
/* Move template chunk's offset to current location of chunk */
if(H5S_hyper_move(tmp_fspace,coords)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't move chunk selection")
} /* end while */
done:
if(tmp_fspace)
if(H5S_close(tmp_fspace)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace copy")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_file_map_hyper() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_mem_map_hyper
*
* Purpose: Create all chunk selections in memory by copying the file
* chunk selections and adjusting their offsets to be correct
* for the memory.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 29, 2003
*
* Assumptions: That the file and memory selections are the same shape.
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_mem_map_hyper(const fm_map *fm)
{
H5TB_NODE *curr_node; /* Current node in TBBT */
hsize_t file_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in file selection */
hsize_t mem_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in memory selection */
hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */
hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_mem_map_hyper)
#ifdef QAK
{
hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */
if(H5S_get_simple_extent_dims(fm->mem_space, mem_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
HDfprintf(stderr,"%s: mem_dims={",FUNC);
for(u=0; u<fm->m_ndims; u++)
HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n"));
}
#endif /* QAK */
/* Sanity check */
assert(fm->f_ndims>0);
/* Get offset of first block in file selection */
if(H5S_get_select_hyper_blocklist(fm->file_space, 1, (hsize_t)0, (hsize_t)1, file_off)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info")
/* Get offset of first block in memory selection */
if(H5S_get_select_hyper_blocklist(fm->mem_space, 1, (hsize_t)0, (hsize_t)1, mem_off)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info")
/* Calculate the adjustment for memory selection from file selection */
assert(fm->m_ndims==fm->f_ndims);
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(file_off[u],hsize_t,hssize_t);
H5_CHECK_OVERFLOW(mem_off[u],hsize_t,hssize_t);
adjust[u]=(hssize_t)file_off[u]-(hssize_t)mem_off[u];
} /* end for */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1) {
HDfprintf(stderr,"%s: rank=%d - adjust={",FUNC,mpi_rank);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
} /* end if */
}
#endif /* QAK */
#ifdef QAK
HDfprintf(stderr,"%s: adjust={",FUNC);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
#endif /* QAK */
/* Iterate over each chunk in the chunk list */
curr_node=H5TB_first(fm->fsel->root);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get pointer to chunk's information */
chunk_info=curr_node->data;
assert(chunk_info);
/* Copy the information */
/* Copy the memory dataspace */
if((chunk_info->mspace = H5S_copy(fm->mem_space))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Release the current selection */
if(H5S_select_release(chunk_info->mspace)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
/* Copy the file chunk's selection */
if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection")
/* Compensate for the chunk offset */
for(u=0; u<fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t);
chunk_adjust[u]=adjust[u]-(chunk_info->coords[u]*(hssize_t)fm->layout->dim[u]); /*lint !e771 The adjust array will always be initialized */
} /* end for */
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1) {
HDfprintf(stderr,"%s: rank=%d - Before adjusting memory selection\n",FUNC,mpi_rank);
HDfprintf(stderr,"%s: rank=%d - chunk_adjust={",FUNC,mpi_rank);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
} /* end if */
}
#endif /* QAK */
#ifdef QAK
HDfprintf(stderr,"%s: Before adjusting memory selection\n",FUNC);
HDfprintf(stderr,"%s: chunk_adjust={",FUNC);
for(u=0; u<fm->f_ndims; u++)
HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n"));
#endif /* QAK */
/* Adjust the selection */
if(H5S_hyper_adjust(chunk_info->mspace,chunk_adjust)<0) /*lint !e772 The chunk_adjust array will always be initialized */
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef QAK
{
int mpi_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
if(mpi_rank==1)
HDfprintf(stderr,"%s: rank=%d - After adjusting memory selection\n",FUNC,mpi_rank);
}
#endif /* QAK */
#ifdef QAK
HDfprintf(stderr,"%s: After adjusting memory selection\n",FUNC);
{
hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */
if(H5S_get_simple_extent_dims(chunk_info->mspace, mem_dims, NULL)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
HDfprintf(stderr,"%s: mem_dims={",FUNC);
for(u=0; u<fm->m_ndims; u++)
HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n"));
}
#endif /* QAK */
/* Get the next chunk node in the TBBT */
curr_node=H5TB_next(curr_node);
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_mem_map_hyper() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_file_cb
*
* Purpose: Callback routine for file selection iterator. Used when
* creating selections in file for each point selected.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Wednesday, July 23, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm)
{
fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */
H5S_t *fspace; /* Memory chunk's dataspace */
hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */
hsize_t chunk_index; /* Chunk index */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb)
/* Calculate the index of this chunk */
if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory TBBTs */
if(chunk_index==fm->last_index) {
/* If the chunk index is the same as the last chunk index we used,
* get the cached spaces to operate on.
*/
fspace=fm->last_chunk;
} /* end if */
else {
H5TB_NODE *chunk_node; /* TBBT node holding chunk information */
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the tree.
*/
/* Get the chunk node from the TBBT */
if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL) {
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */
/* Allocate the file & memory chunk information */
if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
/* Initialize the chunk information */
/* Set the chunk index */
new_chunk_info->index=chunk_index;
/* Create a dataspace for the chunk */
if((fspace = H5S_create_simple(fm->f_ndims,fm->layout->dim,NULL))==NULL) {
H5FL_FREE(H5D_chunk_info_t,new_chunk_info);
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk")
} /* end if */
/* De-select the chunk space */
if(H5S_select_none(fspace)<0) {
(void)H5S_close(fspace);
H5FL_FREE(H5D_chunk_info_t,new_chunk_info);
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace")
} /* end if */
/* Set the file chunk dataspace */
new_chunk_info->fspace=fspace;
/* Set the memory chunk dataspace */
new_chunk_info->mspace=NULL;
/* Compute the chunk's coordinates */
if(H5D_chunk_coords_assist(new_chunk_info->coords, fm->f_ndims, fm->chunks, chunk_index)<0) {
H5D_free_chunk_info(new_chunk_info);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTCOUNT,FAIL,"can't compute chunk info")
} /* end if */
/* Insert the new chunk into the TBBT tree */
if(H5TB_dins(fm->fsel,new_chunk_info,new_chunk_info)==NULL) {
H5D_free_chunk_info(new_chunk_info);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into TBBT")
} /* end if */
} /* end if */
else
/* Get the memory space information from the node */
fspace=((H5D_chunk_info_t *)(chunk_node->data))->fspace;
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
fm->last_chunk=fspace;
} /* end else */
/* Get the coordinates of the element in the chunk */
for(u=0; u<fm->f_ndims; u++)
coords_in_chunk[u]=coords[u]%fm->layout->dim[u];
/* Add point to file selection for chunk */
if(H5S_select_elements(fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_file_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_mem_cb
*
* Purpose: Callback routine for file selection iterator. Used when
* creating selections in memory for each chunk.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* Thursday, April 10, 2003
*
* Modifications:
* QAK - 2003/04/17
* Hacked on it a lot. :-)
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm)
{
fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */
H5S_t *mspace; /* Memory chunk's dataspace */
hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */
hsize_t chunk_index; /* Chunk index */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb)
/* Calculate the index of this chunk */
if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory TBBTs */
if(chunk_index==fm->last_index) {
/* If the chunk index is the same as the last chunk index we used,
* get the cached spaces to operate on.
*/
mspace=fm->last_chunk;
} /* end if */
else {
H5TB_NODE *chunk_node; /* TBBT node holding chunk information */
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the tree.
*/
/* Get the chunk node from the TBBT */
if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL)
HGOTO_ERROR(H5E_DATASPACE,H5E_NOTFOUND,FAIL,"can't locate chunk in TBBT")
/* Get the memory space information from the node */
mspace=((H5D_chunk_info_t *)(chunk_node->data))->mspace;
/* Check if the chunk already has a memory space */
if(mspace==NULL) {
/* Copy the template memory chunk dataspace */
if((mspace = H5S_copy(fm->mchunk_tmpl))==NULL)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
/* Set the chunk's memory dataspace for later use */
((H5D_chunk_info_t *)(chunk_node->data))->mspace=mspace;
} /* end else */
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
fm->last_chunk=mspace;
} /* end else */
/* Get coordinates of selection iterator for memory */
if(H5S_select_iter_coords(&fm->mem_iter,coords_in_mem)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates")
/* Add point to memory selection for chunk */
if(fm->msel_type==H5S_SEL_POINTS) {
if(H5S_select_elements(mspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_mem)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
} /* end if */
else {
if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
} /* end else */
/* Move memory selection iterator to next element in selection */
if(H5S_select_iter_next(&fm->mem_iter,1)<0)
HGOTO_ERROR (H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_mem_cb() */
|