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
3227
3228
3229
3230
3231
3232
3233
3234
3235
3236
3237
3238
3239
3240
3241
3242
3243
3244
3245
3246
3247
3248
3249
3250
3251
3252
3253
3254
3255
3256
3257
3258
3259
3260
3261
3262
3263
3264
3265
3266
3267
3268
3269
3270
3271
3272
3273
3274
3275
3276
3277
3278
3279
3280
3281
3282
3283
3284
3285
3286
3287
3288
3289
3290
3291
3292
3293
3294
3295
3296
3297
3298
3299
3300
3301
3302
3303
3304
3305
3306
3307
3308
3309
3310
3311
3312
3313
3314
3315
3316
3317
3318
3319
3320
3321
3322
3323
3324
3325
3326
3327
3328
3329
3330
3331
3332
3333
3334
3335
3336
3337
3338
3339
3340
3341
3342
3343
3344
3345
3346
3347
3348
3349
3350
3351
3352
3353
3354
3355
3356
3357
3358
3359
3360
3361
3362
3363
3364
3365
3366
3367
3368
3369
3370
3371
3372
3373
3374
3375
3376
3377
3378
3379
3380
3381
3382
3383
3384
3385
3386
3387
3388
3389
3390
3391
3392
3393
3394
3395
3396
3397
3398
3399
3400
3401
3402
3403
3404
3405
3406
3407
3408
3409
3410
3411
3412
3413
3414
3415
3416
3417
3418
3419
3420
3421
3422
3423
3424
3425
3426
3427
3428
3429
3430
3431
3432
3433
3434
3435
3436
3437
3438
3439
3440
3441
3442
3443
3444
3445
3446
3447
3448
3449
3450
3451
3452
3453
3454
3455
3456
3457
3458
3459
3460
3461
3462
3463
3464
3465
3466
3467
3468
3469
3470
3471
3472
3473
3474
3475
3476
3477
3478
3479
3480
3481
3482
3483
3484
3485
3486
3487
3488
3489
3490
3491
3492
3493
3494
3495
3496
3497
3498
3499
3500
3501
3502
3503
3504
3505
3506
3507
3508
3509
3510
3511
3512
3513
3514
3515
3516
3517
3518
3519
3520
3521
3522
3523
3524
3525
3526
3527
3528
3529
3530
3531
3532
3533
3534
3535
3536
3537
3538
3539
3540
3541
3542
3543
3544
3545
3546
3547
3548
3549
3550
3551
3552
3553
3554
3555
3556
3557
3558
3559
3560
3561
3562
3563
3564
3565
3566
3567
3568
3569
3570
3571
3572
3573
3574
3575
3576
3577
3578
3579
3580
3581
3582
3583
3584
3585
3586
3587
3588
3589
3590
3591
3592
3593
3594
3595
3596
3597
3598
3599
3600
3601
3602
3603
3604
3605
3606
3607
3608
3609
3610
3611
3612
3613
3614
3615
3616
3617
3618
3619
3620
3621
3622
3623
3624
3625
3626
3627
3628
3629
3630
3631
3632
3633
3634
3635
3636
3637
3638
3639
3640
3641
3642
3643
3644
3645
3646
3647
3648
3649
3650
3651
3652
3653
3654
3655
3656
3657
3658
3659
3660
3661
3662
3663
3664
3665
3666
3667
3668
3669
3670
3671
3672
3673
3674
3675
3676
3677
3678
3679
3680
3681
3682
3683
3684
3685
3686
3687
3688
3689
3690
3691
3692
3693
3694
3695
3696
3697
3698
3699
3700
3701
3702
3703
3704
3705
3706
3707
3708
3709
3710
3711
3712
3713
3714
3715
3716
3717
3718
3719
3720
3721
3722
3723
3724
3725
3726
3727
3728
3729
3730
3731
3732
3733
3734
3735
3736
3737
3738
3739
3740
3741
3742
3743
3744
3745
3746
3747
3748
3749
3750
3751
3752
3753
3754
3755
3756
3757
3758
3759
3760
3761
3762
3763
3764
3765
3766
3767
3768
3769
3770
3771
3772
3773
3774
3775
3776
3777
3778
3779
3780
3781
3782
3783
3784
3785
3786
3787
3788
3789
3790
3791
3792
3793
3794
3795
3796
3797
3798
3799
3800
3801
3802
3803
3804
3805
3806
3807
3808
3809
3810
3811
3812
3813
3814
3815
3816
3817
3818
3819
3820
3821
3822
3823
3824
3825
3826
3827
3828
3829
3830
3831
3832
3833
3834
3835
3836
3837
3838
3839
3840
3841
3842
3843
3844
3845
3846
3847
3848
3849
3850
3851
3852
3853
3854
3855
3856
3857
3858
3859
3860
3861
3862
3863
3864
3865
3866
3867
3868
3869
3870
3871
3872
3873
3874
3875
3876
3877
3878
3879
3880
3881
3882
3883
3884
3885
3886
3887
3888
3889
3890
3891
3892
3893
3894
3895
3896
3897
3898
3899
3900
3901
3902
3903
3904
3905
3906
3907
3908
3909
3910
3911
3912
3913
3914
3915
3916
3917
3918
3919
3920
3921
3922
3923
3924
3925
3926
3927
3928
3929
3930
3931
3932
3933
3934
3935
3936
3937
3938
3939
3940
3941
3942
3943
3944
3945
3946
3947
3948
3949
3950
3951
3952
3953
3954
3955
3956
3957
3958
3959
3960
3961
3962
3963
3964
3965
3966
3967
3968
3969
3970
3971
3972
3973
3974
3975
3976
3977
3978
3979
3980
3981
3982
3983
3984
3985
3986
3987
3988
3989
3990
3991
3992
3993
3994
3995
3996
3997
3998
3999
4000
4001
4002
4003
4004
4005
4006
4007
4008
4009
4010
4011
4012
4013
4014
4015
4016
4017
4018
4019
4020
4021
4022
4023
4024
4025
4026
4027
4028
4029
4030
4031
4032
4033
4034
4035
4036
4037
4038
4039
4040
4041
4042
4043
4044
4045
4046
4047
4048
4049
4050
4051
4052
4053
4054
4055
4056
4057
4058
4059
4060
4061
4062
4063
4064
4065
4066
4067
4068
4069
4070
4071
4072
4073
4074
4075
4076
4077
4078
4079
4080
4081
4082
4083
4084
4085
4086
4087
4088
4089
4090
4091
4092
4093
4094
4095
4096
4097
4098
4099
4100
4101
4102
4103
4104
4105
4106
4107
4108
4109
4110
4111
4112
4113
4114
4115
4116
4117
4118
4119
4120
4121
4122
4123
4124
4125
4126
4127
4128
4129
4130
4131
4132
4133
4134
4135
4136
4137
4138
4139
4140
4141
4142
4143
4144
4145
4146
4147
4148
4149
4150
4151
4152
4153
4154
4155
4156
4157
4158
4159
4160
4161
4162
4163
4164
4165
4166
4167
4168
4169
4170
4171
4172
4173
4174
4175
4176
4177
4178
4179
4180
4181
4182
4183
4184
4185
4186
4187
4188
4189
4190
4191
4192
4193
4194
4195
4196
4197
4198
4199
4200
4201
4202
4203
4204
4205
4206
4207
4208
4209
4210
4211
4212
4213
4214
4215
4216
4217
4218
4219
4220
4221
4222
4223
4224
4225
4226
4227
4228
4229
4230
4231
4232
4233
4234
4235
4236
4237
4238
4239
4240
4241
4242
4243
4244
4245
4246
4247
4248
4249
4250
4251
4252
4253
4254
4255
4256
4257
4258
4259
4260
4261
4262
4263
4264
4265
4266
4267
4268
4269
4270
4271
4272
4273
4274
4275
4276
4277
4278
4279
4280
4281
4282
4283
4284
4285
4286
4287
4288
4289
4290
4291
4292
4293
4294
4295
4296
4297
4298
4299
4300
4301
4302
4303
4304
4305
4306
4307
4308
4309
4310
4311
4312
4313
4314
4315
4316
4317
4318
4319
4320
4321
4322
4323
4324
4325
4326
4327
4328
4329
4330
4331
4332
4333
4334
4335
4336
4337
4338
4339
4340
4341
4342
4343
4344
4345
4346
4347
4348
4349
4350
4351
4352
4353
4354
4355
4356
4357
4358
4359
4360
4361
4362
4363
4364
4365
4366
4367
4368
4369
4370
4371
4372
4373
4374
4375
4376
4377
4378
4379
4380
4381
4382
4383
4384
4385
4386
4387
4388
4389
4390
4391
4392
4393
4394
4395
4396
4397
4398
4399
4400
4401
4402
4403
4404
4405
4406
4407
4408
4409
4410
4411
4412
4413
4414
4415
4416
4417
4418
4419
4420
4421
4422
4423
4424
4425
4426
4427
4428
4429
4430
4431
4432
4433
4434
4435
4436
4437
4438
4439
4440
4441
4442
4443
4444
4445
4446
4447
4448
4449
4450
4451
4452
4453
4454
4455
4456
4457
4458
4459
4460
4461
4462
4463
4464
4465
4466
4467
4468
4469
4470
4471
4472
4473
4474
4475
4476
4477
4478
4479
4480
4481
4482
4483
4484
4485
4486
4487
4488
4489
4490
4491
4492
4493
4494
4495
4496
4497
4498
4499
4500
4501
4502
4503
4504
4505
4506
4507
4508
4509
4510
4511
4512
4513
4514
4515
4516
4517
4518
4519
4520
4521
4522
4523
4524
4525
4526
4527
4528
4529
4530
4531
4532
4533
4534
4535
4536
4537
4538
4539
4540
4541
4542
4543
4544
4545
4546
4547
4548
4549
4550
4551
4552
4553
4554
4555
4556
4557
4558
4559
4560
4561
4562
4563
4564
4565
4566
4567
4568
4569
4570
4571
4572
4573
4574
4575
4576
4577
4578
4579
4580
4581
4582
4583
4584
4585
4586
4587
4588
4589
4590
4591
4592
4593
4594
4595
4596
4597
4598
4599
4600
4601
4602
4603
4604
4605
4606
4607
4608
4609
4610
4611
4612
4613
4614
4615
4616
4617
4618
4619
4620
4621
4622
4623
4624
4625
4626
4627
4628
4629
4630
4631
4632
4633
4634
4635
4636
4637
4638
4639
4640
4641
4642
4643
4644
4645
4646
4647
4648
4649
4650
4651
4652
4653
4654
4655
4656
4657
4658
4659
4660
4661
4662
4663
4664
4665
4666
4667
4668
4669
4670
4671
4672
4673
4674
4675
4676
4677
4678
4679
4680
4681
4682
4683
4684
4685
4686
4687
4688
4689
4690
4691
4692
4693
4694
4695
4696
4697
4698
4699
4700
4701
4702
4703
4704
4705
4706
4707
4708
4709
4710
4711
4712
4713
4714
4715
4716
4717
4718
4719
4720
4721
4722
4723
4724
4725
4726
4727
4728
4729
4730
4731
4732
4733
4734
4735
4736
4737
4738
4739
4740
4741
4742
4743
4744
4745
4746
4747
4748
4749
4750
4751
4752
4753
4754
4755
4756
4757
4758
4759
4760
4761
4762
4763
4764
4765
4766
4767
4768
4769
4770
4771
4772
4773
4774
4775
4776
4777
4778
4779
4780
4781
4782
4783
4784
4785
4786
4787
4788
4789
4790
4791
4792
4793
4794
4795
4796
4797
4798
4799
4800
4801
4802
4803
4804
4805
4806
4807
4808
4809
4810
4811
4812
4813
4814
4815
4816
4817
4818
4819
4820
4821
4822
4823
4824
4825
4826
4827
4828
4829
4830
4831
4832
4833
4834
4835
4836
4837
4838
4839
4840
4841
4842
4843
4844
4845
4846
4847
4848
4849
4850
4851
4852
4853
4854
4855
4856
4857
4858
4859
4860
4861
4862
4863
4864
4865
4866
4867
4868
4869
4870
4871
4872
4873
4874
4875
4876
4877
4878
4879
4880
4881
4882
4883
4884
4885
4886
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/* Programmer: Quincey Koziol <koziol@hdfgroup.org>
* Thursday, April 24, 2008
*
* Purpose: Abstract indexed (chunked) I/O functions. The logical
* multi-dimensional data space is regularly partitioned into
* same-sized "chunks", the first of which is aligned with the
* logical origin. The chunks are indexed by different methods,
* that map a chunk index to disk address. Each chunk can be
* compressed independently and the chunks may move around in the
* file as their storage requirements change.
*
* Cache: Disk I/O is performed in units of chunks and H5MF_alloc()
* contains code to optionally align chunks on disk block
* boundaries for performance.
*
* The chunk cache is an extendible hash indexed by a function
* of storage B-tree address and chunk N-dimensional offset
* within the dataset. Collisions are not resolved -- one of
* the two chunks competing for the hash slot must be preempted
* from the cache. All entries in the hash also participate in
* a doubly-linked list and entries are penalized by moving them
* toward the front of the list. When a new chunk is about to
* be added to the cache the heap is pruned by preempting
* entries near the front of the list to make room for the new
* entry which is added to the end of the list.
*/
/****************/
/* Module Setup */
/****************/
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
/***********/
/* Headers */
/***********/
#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 "H5Vprivate.h" /* Vector and array functions */
/****************/
/* Local Macros */
/****************/
/* Macros for iterating over chunks to operate on */
#define H5D_CHUNK_GET_FIRST_NODE(map) (map->use_single ? (H5SL_node_t *)(1) : H5SL_first(map->sel_chunks))
#define H5D_CHUNK_GET_NODE_INFO(map, node) (map->use_single ? map->single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node))
#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map->use_single ? (H5SL_node_t *)NULL : H5SL_next(node))
/*
* Feature: If this constant is defined then every cache preemption and load
* causes a character to be printed on the standard error stream:
*
* `.': Entry was preempted because it has been completely read or
* completely written but not partially read and not partially
* written. This is often a good reason for preemption because such
* a chunk will be unlikely to be referenced in the near future.
*
* `:': Entry was preempted because it hasn't been used recently.
*
* `#': Entry was preempted because another chunk collided with it. This
* is usually a relatively bad thing. If there are too many of
* these then the number of entries in the cache can be increased.
*
* c: Entry was preempted because the file is closing.
*
* w: A chunk read operation was eliminated because the library is
* about to write new values to the entire chunk. This is a good
* thing, especially on files where the chunk size is the same as
* the disk block size, chunks are aligned on disk block boundaries,
* and the operating system can also eliminate a read operation.
*/
/*#define H5D_CHUNK_DEBUG */
/******************/
/* Local Typedefs */
/******************/
/* Stack of chunks to remove during a "prune" iteration */
typedef struct H5D_chunk_prune_stack_t {
H5D_chunk_rec_t rec; /* Chunk record */
struct H5D_chunk_prune_stack_t *next; /* Next chunk in stack */
} H5D_chunk_prune_stack_t;
/* Callback info for iteration to prune chunks */
typedef struct H5D_chunk_it_ud1_t {
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
const H5D_chk_idx_info_t *idx_info; /* Chunked index info */
const H5D_io_info_t *io_info; /* I/O info for dataset operation */
const hsize_t *dims; /* New dataset dimensions */
const hbool_t *shrunk_dims; /* Dimensions which have been shrunk */
const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */
H5D_chunk_prune_stack_t *rm_stack; /* Stack of chunks outside the new dimensions */
H5S_t *chunk_space; /* Dataspace for a chunk */
uint32_t elmts_per_chunk;/* Elements in chunk */
hsize_t *hyper_start; /* Starting location of hyperslab */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init; /* Whether the fill value buffer has been initialized */
} H5D_chunk_it_ud1_t;
/* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */
typedef struct H5D_chunk_id_ud2_t {
/* down */
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
const hsize_t *down_chunks; /* "down chunk" element counts for chunks */
/* up */
haddr_t *chunk_addr; /* Array of chunk addresses to fill in */
} H5D_chunk_it_ud2_t;
/* Callback info for iteration to copy data */
typedef struct H5D_chunk_it_ud3_t {
H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */
H5F_t *file_src; /* Source file for copy */
H5D_chk_idx_info_t *idx_info_dst; /* Dest. chunk index info object */
void *buf; /* Buffer to hold chunk data for read/write */
void *bkg; /* Buffer for background information during type conversion */
size_t buf_size; /* Buffer size */
hbool_t do_convert; /* Whether to perform type conversions */
/* needed for converting variable-length data */
hid_t tid_src; /* Datatype ID for source datatype */
hid_t tid_dst; /* Datatype ID for destination datatype */
hid_t tid_mem; /* Datatype ID for memory datatype */
H5T_t *dt_src; /* Source datatype */
H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */
H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */
void *reclaim_buf; /* Buffer for reclaiming data */
size_t reclaim_buf_size; /* Reclaim buffer size */
uint32_t nelmts; /* Number of elements in buffer */
H5S_t *buf_space; /* Dataspace describing buffer */
/* needed for compressed variable-length data */
H5O_pline_t *pline; /* Filter pipeline */
/* needed for copy object pointed by refs */
H5O_copy_t *cpy_info; /* Copy options */
} H5D_chunk_it_ud3_t;
/* Callback info for iteration to dump index */
typedef struct H5D_chunk_it_ud4_t {
FILE *stream; /* Output stream */
hbool_t header_displayed; /* Node's header is displayed? */
unsigned ndims; /* Number of dimensions for chunk/dataset */
} H5D_chunk_it_ud4_t;
/********************/
/* Local Prototypes */
/********************/
/* Chunked layout operation callbacks */
static herr_t H5D_chunk_construct(H5F_t *f, H5D_t *dset);
static herr_t H5D_chunk_io_init(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space,
const H5S_t *mem_space, H5D_chunk_map_t *fm);
static herr_t H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
static herr_t H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
static herr_t H5D_chunk_io_term(const H5D_chunk_map_t *fm);
/* "Nonexistent" layout operation callback */
static ssize_t
H5D_nonexistent_readvv(const H5D_io_info_t *io_info,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
/* Helper routines */
static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline);
static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline);
static herr_t H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last,
const H5D_chunk_ud_t *udata);
static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
static herr_t H5D_create_chunk_map_single(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims,
const hsize_t *coords, void *fm);
static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
const hsize_t *coords, void *fm);
/*********************/
/* Package Variables */
/*********************/
/* Chunked storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{
H5D_chunk_construct,
H5D_chunk_init,
H5D_chunk_is_space_alloc,
H5D_chunk_io_init,
H5D_chunk_read,
H5D_chunk_write,
#ifdef H5_HAVE_PARALLEL
H5D_chunk_collective_read,
H5D_chunk_collective_write,
#endif /* H5_HAVE_PARALLEL */
NULL,
NULL,
H5D_chunk_io_term
}};
/*******************/
/* Local Variables */
/*******************/
/* "nonexistent" storage layout I/O ops */
const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{
NULL,
NULL,
NULL,
NULL,
NULL,
NULL,
#ifdef H5_HAVE_PARALLEL
NULL,
NULL,
#endif /* H5_HAVE_PARALLEL */
H5D_nonexistent_readvv,
NULL,
NULL
}};
/* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */
H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t);
/* Declare a free list to manage H5D_rdcc_ent_t objects */
H5FL_DEFINE_STATIC(H5D_rdcc_ent_t);
/* Declare a free list to manage the H5D_chunk_info_t struct */
H5FL_DEFINE(H5D_chunk_info_t);
/* Declare a free list to manage the chunk sequence information */
H5FL_BLK_DEFINE_STATIC(chunk);
/* Declare a free list to manage H5D_chunk_sl_ck_t objects */
H5FL_DEFINE_STATIC(H5D_chunk_prune_stack_t);
/*-------------------------------------------------------------------------
* Function: H5D_chunk_construct
*
* Purpose: Constructs new chunked layout information for dataset
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, May 22, 2008
*
* Modifications:
* Vailin Choi; April 2009
* Reset address and pointer of the array struct for the chunked storage index
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_construct(H5F_t *f, H5D_t *dset)
{
const H5T_t *type = dset->shared->type; /* Convenience pointer to dataset's datatype */
hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
uint64_t chunk_size; /* Size of chunk in bytes */
int ndims; /* Rank of dataspace */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_construct)
/* Sanity checks */
HDassert(f);
HDassert(dset);
/* Set up layout information */
if((ndims = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get rank")
if(dset->shared->layout.u.chunk.ndims != (unsigned)ndims)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimensionality of chunks doesn't match the dataspace")
/* Increment # of chunk dimensions, to account for datatype size as last element */
dset->shared->layout.u.chunk.ndims++;
HDassert((unsigned)(dset->shared->layout.u.chunk.ndims) <= NELMTS(dset->shared->layout.u.chunk.dim));
/* Chunked storage is not compatible with external storage (currently) */
if(dset->shared->dcpl_cache.efl.nused > 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "external storage not supported with chunked layout")
/* Set the last dimension of the chunk size to the size of the datatype */
dset->shared->layout.u.chunk.dim[dset->shared->layout.u.chunk.ndims - 1] = H5T_GET_SIZE(type);
/* Get local copy of dataset dimensions (for sanity checking) */
if(H5S_get_simple_extent_dims(dset->shared->space, NULL, max_dim) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to query maximum dimensions")
/* Sanity check dimensions */
for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++)
/*
* The chunk size of a dimension with a fixed size cannot exceed
* the maximum dimension size
*/
if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < dset->shared->layout.u.chunk.dim[u])
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be <= maximum dimension size for fixed-sized dimensions")
/* Compute the total size of a chunk */
/* (Use 64-bit value to ensure that we can detect >4GB chunks) */
for(u = 1, chunk_size = (uint64_t)dset->shared->layout.u.chunk.dim[0]; u < dset->shared->layout.u.chunk.ndims; u++)
chunk_size *= (uint64_t)dset->shared->layout.u.chunk.dim[u];
/* Check for chunk larger than can be represented in 32-bits */
/* (Chunk size is encoded in 32-bit value in v1 B-tree records) */
if(chunk_size > (uint64_t)0xffffffff)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "chunk size must be < 4GB")
/* Retain computed chunk size */
H5_ASSIGN_OVERFLOW(dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t);
/* Reset address and pointer of the array struct for the chunked storage index */
if(H5D_chunk_idx_reset(&dset->shared->layout, TRUE) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to reset chunked storage index")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_construct() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_init
*
* Purpose: Initialize the raw data chunk cache for a dataset. This is
* called when the dataset is initialized.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Monday, May 18, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Convenience pointer to dataset's chunk cache */
H5P_genplist_t *dapl; /* Data access property list object pointer */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_init, FAIL)
/* Sanity check */
HDassert(f);
HDassert(dset);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id)))
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for fapl ID");
/* Use the properties in dapl_id if they have been set, otherwise use the properties from the file */
if(H5P_get(dapl, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &rdcc->nslots) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get data cache number of slots");
if(rdcc->nslots == H5D_CHUNK_CACHE_NSLOTS_DEFAULT)
rdcc->nslots = H5F_RDCC_NSLOTS(f);
if(H5P_get(dapl, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &rdcc->nbytes_max) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get data cache byte size");
if(rdcc->nbytes_max == H5D_CHUNK_CACHE_NBYTES_DEFAULT)
rdcc->nbytes_max = H5F_RDCC_NBYTES(f);
if(H5P_get(dapl, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &rdcc->w0) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET,FAIL, "can't get preempt read chunks");
if(rdcc->w0 < 0)
rdcc->w0 = H5F_RDCC_W0(f);
/* If nbytes_max or nslots is 0, set them both to 0 and avoid allocating space */
if(!rdcc->nbytes_max || !rdcc->nslots)
rdcc->nbytes_max = rdcc->nslots = 0;
else {
rdcc->slot = H5FL_SEQ_CALLOC(H5D_rdcc_ent_ptr_t, rdcc->nslots);
if(NULL == rdcc->slot)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&(rdcc->last));
} /* end else */
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Allocate any indexing structures */
if(dset->shared->layout.u.chunk.ops->init && (dset->shared->layout.u.chunk.ops->init)(&idx_info, dset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_init() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_is_space_alloc
*
* Purpose: Query if space is allocated for layout
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, January 15, 2009
*
*-------------------------------------------------------------------------
*/
hbool_t
H5D_chunk_is_space_alloc(const H5O_layout_t *layout)
{
hbool_t ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOFUNC(H5D_chunk_is_space_alloc)
/* Sanity checks */
HDassert(layout);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
/* Query index layer */
ret_value = (layout->u.chunk.ops->is_space_alloc)(layout);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_is_space_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_io_init
*
* Purpose: Performs initialization before any sort of I/O on the raw data
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, March 20, 2008
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm)
{
H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */
const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */
H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
htri_t file_space_normalized = FALSE; /* File dataspace was normalized */
hid_t f_tid = (-1); /* Temporary copy of file datatype for iteration */
hbool_t iter_init = FALSE; /* 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) */
H5SL_node_t *curr_node; /* Current node in skip list */
H5S_sel_type fsel_type; /* Selection type on disk */
char bogus; /* "bogus" buffer to pass to selection iterator */
unsigned u; /* Local index variable */
hbool_t sel_hyper_flag;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_init)
/* Get layout for dataset */
fm->layout = &(dataset->shared->layout);
fm->nelmts = nelmts;
/* Check if the memory space is scalar & make equivalent memory space */
if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number")
/* Set the number of dimensions for the memory dataspace */
H5_ASSIGN_OVERFLOW(fm->m_ndims, sm_ndims, int, unsigned);
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1;
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
/* Normalize hyperslab selections by adjusting them by the offset */
/* (It might be worthwhile to normalize both the file and memory dataspaces
* before any (contiguous, chunked, etc) file I/O operation, in order to
* speed up hyperslab calculations by removing the extra checks and/or
* additions involving the offset and the hyperslab selection -QAK)
*/
if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
/* Decide the number of chunks in each dimension*/
for(u = 0; u < f_ndims; u++) {
/* Keep the size of the chunk dimensions as hsize_t for various routines */
fm->chunk_dim[u] = fm->layout->u.chunk.dim[u];
/* Round up to the next integer # of chunks, to accomodate partial chunks */
fm->chunks[u] = ((fm->f_dims[u] + dataset->shared->layout.u.chunk.dim[u]) - 1) / dataset->shared->layout.u.chunk.dim[u];
} /* 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")
#ifdef H5_HAVE_PARALLEL
/* Calculate total chunk in file map*/
fm->select_chunk = NULL;
fm->total_chunks = 1;
for(u = 0; u < fm->f_ndims; u++)
fm->total_chunks = fm->total_chunks * fm->chunks[u];
if(io_info->using_mpi_vfd) {
H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t);
if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->total_chunks * sizeof(H5D_chunk_info_t *))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/* Initialize "last chunk" information */
fm->last_index = (hsize_t)-1;
fm->last_chunk_info = NULL;
/* Point at the dataspaces */
fm->file_space = file_space;
fm->mem_space = mem_space;
/* Special case for only one element in selection */
/* (usually appending a record) */
if(nelmts == 1
#ifdef H5_HAVE_PARALLEL
&& !(io_info->using_mpi_vfd)
#endif /* H5_HAVE_PARALLEL */
) {
/* Initialize skip list for chunk selections */
fm->sel_chunks = NULL;
fm->use_single = TRUE;
/* Initialize single chunk dataspace */
if(NULL == dataset->shared->cache.chunk.single_space) {
/* Make a copy of the dataspace for the dataset */
if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
/* Resize chunk's dataspace dimensions to size of chunk */
if(H5S_set_extent_real(dataset->shared->cache.chunk.single_space, fm->chunk_dim) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust chunk dimensions")
/* Set the single chunk dataspace to 'all' selection */
if(H5S_select_all(dataset->shared->cache.chunk.single_space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to set all selection")
} /* end if */
fm->single_space = dataset->shared->cache.chunk.single_space;
HDassert(fm->single_space);
/* Allocate the single chunk information */
if(NULL == dataset->shared->cache.chunk.single_chunk_info) {
if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
} /* end if */
fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info;
HDassert(fm->single_chunk_info);
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* Set up chunk mapping for single element */
if(H5D_create_chunk_map_single(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element")
} /* end if */
else {
/* Initialize skip list for chunk selections */
if(NULL == dataset->shared->cache.chunk.sel_chunks) {
if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections")
} /* end if */
fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks;
HDassert(fm->sel_chunks);
/* We are not using single element mode */
fm->use_single = FALSE;
/* Get type of selection on disk & in memory */
if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
/* If the selection is NONE or POINTS, set the flag to FALSE */
if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
sel_hyper_flag = FALSE;
else
sel_hyper_flag = TRUE;
/* Check if file selection is a not a hyperslab selection */
if(sel_hyper_flag) {
/* Build the file selection for each chunk */
if(H5D_create_chunk_file_map_hyper(fm, io_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Clean file chunks' hyperslab span "scratch" information */
curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
HDassert(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 skip list */
curr_node = H5SL_next(curr_node);
} /* end while */
} /* end if */
else {
/* Create temporary datatypes for selection iteration */
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
/* Spaces might not be the same shape, iterate over the file 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_info = NULL;
} /* end else */
/* Build the memory selection for each chunk */
if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
/* 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 */
/* Make a copy of equivalent memory space */
if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* 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")
/* Save chunk template information */
fm->mchunk_tmpl = tmp_mspace;
/* Create temporary datatypes for selection iteration */
if(f_tid < 0) {
if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype")
} /* end if */
/* Create selection iterator for memory selection */
if(0 == (elmt_size = H5T_get_size(mem_type)))
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* 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 = H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
HDassert(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 skip list */
curr_node = H5SL_next(curr_node);
} /* end while */
} /* end if */
} /* end else */
} /* end else */
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_chunk_io_term(fm) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
/* Reset the global dataspace info */
fm->file_space = NULL;
fm->mem_space = NULL;
if(iter_init) {
if(H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
} /* end if */
if(f_tid!=(-1)) {
if(H5I_dec_ref(f_tid, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
} /* end if */
if(file_space_normalized) {
/* (Casting away const OK -QAK) */
if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_io_init() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_alloc
*
* Purpose: Allocate space for a chunk in memory. This routine allocates
* memory space for non-filtered chunks from a block free list
* and uses malloc()/free() for filtered chunks.
*
* Return: Pointer to memory for chunk on success/NULL on failure
*
* Programmer: Quincey Koziol
* April 22, 2004
*
*-------------------------------------------------------------------------
*/
static void *
H5D_chunk_alloc(size_t size, const H5O_pline_t *pline)
{
void *ret_value = NULL; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_alloc)
HDassert(size);
HDassert(pline);
if(pline->nused > 0)
ret_value = H5MM_malloc(size);
else
ret_value = H5FL_BLK_MALLOC(chunk, size);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_xfree
*
* Purpose: Free space for a chunk in memory. This routine allocates
* memory space for non-filtered chunks from a block free list
* and uses malloc()/free() for filtered chunks.
*
* Return: NULL (never fails)
*
* Programmer: Quincey Koziol
* April 22, 2004
*
*-------------------------------------------------------------------------
*/
static void *
H5D_chunk_xfree(void *chk, const H5O_pline_t *pline)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_xfree)
HDassert(pline);
if(chk) {
if(pline->nused > 0)
H5MM_xfree(chk);
else
(void)H5FL_BLK_FREE(chunk, chk);
} /* end if */
FUNC_LEAVE_NOAPI(NULL)
} /* H5D_chunk_xfree() */
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
PURPOSE
Internal routine to destroy a chunk info node
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. Called by H5SL_free
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata)
{
H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info)
HDassert(chunk_info);
/* Close the chunk's file dataspace, if it's not shared */
if(!chunk_info->fspace_shared)
(void)H5S_close(chunk_info->fspace);
else
H5S_select_all(chunk_info->fspace, TRUE);
/* Close the chunk's memory dataspace, if it's not shared */
if(!chunk_info->mspace_shared)
(void)H5S_close(chunk_info->mspace);
/* Free the actual chunk info */
(void)H5FL_FREE(H5D_chunk_info_t, chunk_info);
FUNC_LEAVE_NOAPI(0)
} /* H5D_free_chunk_info() */
/*-------------------------------------------------------------------------
* Function: H5D_create_chunk_map_single
*
* Purpose: Create chunk selections when appending a single record
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 20, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */
hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map_single)
/* Sanity check */
HDassert(fm->f_ndims > 0);
/* Get coordinate for selection */
if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Initialize the 'single chunk' file & memory chunk information */
chunk_info = fm->single_chunk_info;
chunk_info->chunk_points = 1;
/* Set chunk location & hyperslab size */
for(u = 0; u < fm->f_ndims; u++) {
HDassert(sel_start[u] == sel_end[u]);
chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
} /* end for */
chunk_info->coords[fm->f_ndims] = 0;
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Copy selection for file's dataspace into chunk dataspace */
if(H5S_select_copy(fm->single_space, fm->file_space, FALSE) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection")
/* Move selection back to have correct offset in chunk */
if(H5S_SELECT_ADJUST_U(fm->single_space, chunk_info->coords) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
if(io_info->using_mpi_vfd)
fm->select_chunk[chunk_info->index] = chunk_info;
#endif /* H5_HAVE_PARALLEL */
/* Set the file dataspace for the chunk to the shared 'single' dataspace */
chunk_info->fspace = fm->single_space;
/* Indicate that the chunk's file dataspace is shared */
chunk_info->fspace_shared = TRUE;
/* Just point at the memory dataspace & selection */
/* (Casting away const OK -QAK) */
chunk_info->mspace = (H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory dataspace is shared */
chunk_info->mspace_shared = TRUE;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_create_chunk_map_single() */
/*-------------------------------------------------------------------------
* 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
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
#ifndef H5_HAVE_PARALLEL
UNUSED
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hsize_t sel_points; /* Number of elements in file selection */
hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */
hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
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);
/* Get number of elements selected in file */
sel_points = fm->nelmts;
/* Get bounding box for selection (to reduce the number of chunks to iterate over) */
if(H5S_SELECT_BOUNDS(fm->file_space, 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++) {
start_coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u];
coords[u] = start_coords[u];
end[u] = (coords[u] + fm->chunk_dim[u]) - 1;
} /* end for */
/* Calculate the index of this chunk */
if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, 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 */
/* (Casting away const OK - QAK) */
if(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
hssize_t schunk_points; /* Number of elements in chunk selection */
/* Create "temporary" chunk for selection operations (copy file space) */
if(NULL == (tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
if(H5S_hyper_convert(tmp_fchunk) < 0) {
(void)H5S_close(tmp_fchunk);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
} /* end if */
/* "AND" temporary chunk and current chunk */
if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,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,fm->chunk_dim) < 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_SELECT_ADJUST_U(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;
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
if(io_info->using_mpi_vfd)
fm->select_chunk[chunk_index] = new_chunk_info;
#endif /* H5_HAVE_PARALLEL */
/* Set the file chunk dataspace */
new_chunk_info->fspace = tmp_fchunk;
new_chunk_info->fspace_shared = FALSE;
/* Set the memory chunk dataspace */
new_chunk_info->mspace=NULL;
new_chunk_info->mspace_shared = FALSE;
/* Copy the chunk's coordinates */
for(u=0; u<fm->f_ndims; u++)
new_chunk_info->coords[u]=coords[u];
new_chunk_info->coords[fm->f_ndims]=0;
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) {
H5D_free_chunk_info(new_chunk_info, NULL, NULL);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list")
} /* end if */
/* Get number of elements selected in chunk */
if((schunk_points = H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points, schunk_points, hssize_t, uint32_t);
/* Decrement # of points left in file selection */
sel_points -= (hsize_t)schunk_points;
/* Leave if we are done */
if(sel_points == 0)
HGOTO_DONE(SUCCEED)
} /* 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(fm->chunk_dim[curr_dim],hsize_t,hssize_t);
coords[curr_dim]+=fm->chunk_dim[curr_dim];
end[curr_dim]+=fm->chunk_dim[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 */
end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
/* Decrement current dimension */
curr_dim--;
/* Increment chunk location in current dimension */
coords[curr_dim] += fm->chunk_dim[curr_dim];
end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
} 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->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
} /* end if */
} /* end while */
done:
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.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
{
H5SL_node_t *curr_node; /* Current node in skip list */
hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */
hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */
hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file 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)
/* Sanity check */
assert(fm->f_ndims>0);
/* Check for all I/O going to a single chunk */
if(H5SL_count(fm->sel_chunks)==1) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get the node */
curr_node=H5SL_first(fm->sel_chunks);
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
assert(chunk_info);
/* Just point at the memory dataspace & selection */
/* (Casting away const OK -QAK) */
chunk_info->mspace = (H5S_t *)fm->mem_space;
/* Indicate that the chunk's memory space is shared */
chunk_info->mspace_shared = TRUE;
} /* end if */
else {
/* Get bounding box for file selection */
if(H5S_SELECT_BOUNDS(fm->file_space, file_sel_start, file_sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
/* Get bounding box for memory selection */
if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound 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_sel_start[u],hsize_t,hssize_t);
H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t);
adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u];
} /* end for */
/* Iterate over each chunk in the chunk list */
curr_node=H5SL_first(fm->sel_chunks);
while(curr_node) {
H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
assert(chunk_info);
/* Copy the information */
/* Copy the memory dataspace */
if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == 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,FALSE) < 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(chunk_info->coords[u],hsize_t,hssize_t);
chunk_adjust[u]=adjust[u]-(hssize_t)chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */
} /* end for */
/* Adjust the selection */
if(H5S_hyper_adjust_s(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")
/* Get the next chunk node in the skip list */
curr_node=H5SL_next(curr_node);
} /* end while */
} /* end else */
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
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
{
H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
hsize_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(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
if(chunk_index==fm->last_index) {
/* If the chunk index is the same as the last chunk index we used,
* get the cached info to operate on.
*/
chunk_info=fm->last_chunk_info;
} /* end if */
else {
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the skip list.
*/
/* Get the chunk node from the skip list */
if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index))) {
H5S_t *fspace; /* Memory chunk's dataspace */
/* Allocate the file & memory chunk information */
if (NULL==(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 */
chunk_info->index=chunk_index;
/* Create a dataspace for the chunk */
if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) {
(void)H5FL_FREE(H5D_chunk_info_t,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);
(void)H5FL_FREE(H5D_chunk_info_t,chunk_info);
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace")
} /* end if */
/* Set the file chunk dataspace */
chunk_info->fspace = fspace;
chunk_info->fspace_shared = FALSE;
/* Set the memory chunk dataspace */
chunk_info->mspace = NULL;
chunk_info->mspace_shared = FALSE;
/* Set the number of selected elements in chunk to zero */
chunk_info->chunk_points = 0;
/* Compute the chunk's coordinates */
for(u = 0; u < fm->f_ndims; u++) {
H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u], hsize_t, hssize_t);
chunk_info->coords[u] = (coords[u] / (hssize_t)fm->layout->u.chunk.dim[u]) * (hssize_t)fm->layout->u.chunk.dim[u];
} /* end for */
chunk_info->coords[fm->f_ndims] = 0;
/* Insert the new chunk into the skip list */
if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) {
H5D_free_chunk_info(chunk_info,NULL,NULL);
HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list")
} /* end if */
} /* end if */
/* Update the "last chunk seen" information */
fm->last_index=chunk_index;
fm->last_chunk_info=chunk_info;
} /* 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->u.chunk.dim[u];
/* Add point to file selection for chunk */
if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
/* Increment the number of elemented selected in chunk */
chunk_info->chunk_points++;
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
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static herr_t
H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm)
{
H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */
H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */
hsize_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(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Find correct chunk in file & memory skip list */
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.
*/
chunk_info = fm->last_chunk_info;
} /* end if */
else {
/* If the chunk index is not the same as the last chunk index we used,
* find the chunk in the skip list.
*/
/* Get the chunk node from the skip list */
if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_index)))
HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list")
/* Check if the chunk already has a memory space */
if(NULL == chunk_info->mspace) {
/* Copy the template memory chunk dataspace */
if(NULL == (chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
} /* end else */
/* Update the "last chunk seen" information */
fm->last_index = chunk_index;
fm->last_chunk_info = chunk_info;
} /* 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(chunk_info->mspace, H5S_SELECT_APPEND, (size_t)1, coords_in_mem) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element")
} /* end if */
else {
if(H5S_hyper_add_span_element(chunk_info->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, (size_t)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() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cacheable
*
* Purpose: A small internal function to if it's possible to load the
* chunk into cache.
*
* Return: TRUE or FALSE
*
* Programmer: Raymond Lu
* 17 July 2007
*
*-------------------------------------------------------------------------
*/
htri_t
H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op)
{
const H5D_t *dataset = io_info->dset;
htri_t ret_value = FAIL;
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cacheable)
HDassert(io_info);
HDassert(dataset);
/* Must bring the whole chunk in if there are any filters */
if(dataset->shared->dcpl_cache.pline.nused > 0)
ret_value = TRUE;
else {
#ifdef H5_HAVE_PARALLEL
/* If MPI based VFD is used and the file is opened for write access, must
* bypass the chunk-cache scheme because other MPI processes could
* be writing to other elements in the same chunk. Do a direct
* write-through of only the elements requested.
*/
if(io_info->using_mpi_vfd && (H5F_ACC_RDWR & H5F_INTENT(dataset->oloc.file)))
ret_value = FALSE;
else {
#endif /* H5_HAVE_PARALLEL */
/* If the chunk is too large to keep in the cache and if we don't
* need to write the fill value, then don't load the chunk into the
* cache, just write the data to it directly.
*/
H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t);
if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes_max) {
if(write_op && !H5F_addr_defined(caddr)) {
const H5O_fill_t *fill = &(dataset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* Fill value status */
/* Revtrieve the fill value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If the fill value needs to be written then we will need
* to use the cache to write the fill value */
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET
&& fill_status == H5D_FILL_VALUE_USER_DEFINED))
ret_value = TRUE;
else
ret_value = FALSE;
} else
ret_value = FALSE;
} else
ret_value = TRUE;
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cacheable() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_in_cache
*
* Purpose: Check if a chunk is in the cache.
*
* Return: TRUE or FALSE
*
* Programmer: Quincey Koziol
* 1 April 2008
*
*-------------------------------------------------------------------------
*/
static hbool_t
H5D_chunk_in_cache(const H5D_t *dset, const hsize_t *chunk_offset,
hsize_t chunk_idx)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/
hbool_t found = FALSE; /*already in cache? */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_in_cache)
/* Sanity checks */
HDassert(dset);
HDassert(chunk_offset);
/* Check if the chunk is in the cache (but hasn't been written to disk yet) */
if(rdcc->nslots > 0) {
unsigned idx = H5D_CHUNK_HASH(dset->shared, chunk_idx); /* Cache entry index */
H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */
/* Potential match... */
if(ent) {
size_t u; /* Local index variable */
for(u = 0, found = TRUE; u < dset->shared->layout.u.chunk.ndims; u++) {
if(chunk_offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
} /* end for */
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI(found)
} /* end H5D_chunk_in_cache() */
/*-------------------------------------------------------------------------
* 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
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space,
H5D_chunk_map_t *fm)
{
H5SL_node_t *chunk_node; /* Current node in chunk skip list */
H5D_io_info_t nonexistent_io_info; /* "nonexistent" I/O info object */
H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */
H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */
H5D_io_info_t cpt_io_info; /* Compact I/O info object */
H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */
hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
uint32_t src_accessed_bytes = 0; /* Total accessed size in a chunk */
hbool_t skip_missing_chunks = FALSE; /* Whether to skip missing chunks */
unsigned idx_hint = 0; /* Cache index hint */
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
/* Sanity check */
HDassert(io_info);
HDassert(io_info->u.rbuf);
HDassert(type_info);
HDassert(fm);
/* Set up "nonexistent" I/O info object */
HDmemcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info));
nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT;
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
/* Initialize temporary contiguous storage info */
H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
/* Initialize temporary compact storage info */
cpt_store.compact.dirty = &cpt_dirty;
{
const H5O_fill_t *fill = &(io_info->dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* Fill value status */
/* Check the fill value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are never to return fill values, or if we would return them
* but they aren't set, set the flag to skip missing chunks.
*/
if(fill->fill_time == H5D_FILL_TIME_NEVER ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status != H5D_FILL_VALUE_USER_DEFINED))
skip_missing_chunks = TRUE;
}
/* Iterate through nodes in chunk skip list */
chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* Chunk information */
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
H5D_chunk_ud_t udata; /* B-tree pass-through */
htri_t cacheable; /* Whether the chunk is cacheable */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
/* Get the info for the chunk in the file */
if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
/* Check for non-existant chunk & skip it if appropriate */
if(H5F_addr_defined(udata.addr) || H5D_chunk_in_cache(io_info->dset, chunk_info->coords, chunk_info->index)
|| !skip_missing_chunks) {
/* Load the chunk into cache and lock it. */
if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, FALSE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable")
if(cacheable) {
/* Pass in chunk's coordinates in a union. */
io_info->store->chunk.offset = chunk_info->coords;
io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
src_accessed_bytes = chunk_info->chunk_points * type_info->src_type_size;
/* Lock the chunk into the cache */
if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
/* Point I/O info at contiguous I/O info for this chunk */
chk_io_info = &cpt_io_info;
} /* end if */
else if(H5F_addr_defined(udata.addr)) {
/* Set up the storage address information for this chunk */
ctg_store.contig.dset_addr = udata.addr;
/* No chunk cached */
chunk = NULL;
/* Point I/O info at temporary I/O info for this chunk */
chk_io_info = &ctg_io_info;
} /* end else if */
else {
/* No chunk cached */
chunk = NULL;
/* Point I/O info at "nonexistent" I/O info for this chunk */
chk_io_info = &nonexistent_io_info;
} /* end else */
/* Perform the actual read operation */
if((io_info->io_ops.single_read)(chk_io_info, type_info,
(hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed")
/* Release the cache lock on the chunk. */
if(chunk && H5D_chunk_unlock(io_info, &udata, FALSE, idx_hint, chunk, src_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
} /* end if */
/* Advance to next chunk in list */
chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
} /* end while */
done:
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
*
* Modification:Raymond Lu
* 4 Feb 2009
* One case that was considered cacheable was when the chunk
* was bigger than the cache size but not allocated on disk.
* I moved it to uncacheable branch to bypass the cache to
* improve performance.
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t UNUSED nelmts, const H5S_t UNUSED *file_space, const H5S_t UNUSED *mem_space,
H5D_chunk_map_t *fm)
{
H5SL_node_t *chunk_node; /* Current node in chunk skip list */
H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */
H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */
H5D_io_info_t cpt_io_info; /* Compact I/O info object */
H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */
hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */
uint32_t dst_accessed_bytes = 0; /* Total accessed size in a chunk */
unsigned idx_hint = 0; /* Cache index hint */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write)
/* Sanity check */
HDassert(io_info);
HDassert(io_info->u.wbuf);
HDassert(type_info);
HDassert(fm);
/* Set up contiguous I/O info object */
HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info));
ctg_io_info.store = &ctg_store;
ctg_io_info.layout_ops = *H5D_LOPS_CONTIG;
/* Initialize temporary contiguous storage info */
H5_ASSIGN_OVERFLOW(ctg_store.contig.dset_size, io_info->dset->shared->layout.u.chunk.size, uint32_t, hsize_t);
/* Set up compact I/O info object */
HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info));
cpt_io_info.store = &cpt_store;
cpt_io_info.layout_ops = *H5D_LOPS_COMPACT;
/* Initialize temporary compact storage info */
cpt_store.compact.dirty = &cpt_dirty;
/* Iterate through nodes in chunk skip list */
chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm);
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* Chunk information */
H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */
void *chunk; /* Pointer to locked chunk buffer */
H5D_chunk_ud_t udata; /* Index pass-through */
htri_t cacheable; /* Whether the chunk is cacheable */
/* Get the actual chunk information from the skip list node */
chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node);
/* Load the chunk into cache. But if the whole chunk is written,
* simply allocate space instead of load the chunk. */
if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
if((cacheable = H5D_chunk_cacheable(io_info, udata.addr, TRUE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable")
if(cacheable) {
hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */
/* Pass in chunk's coordinates in a union. */
io_info->store->chunk.offset = chunk_info->coords;
io_info->store->chunk.index = chunk_info->index;
/* Compute # of bytes accessed in chunk */
dst_accessed_bytes = chunk_info->chunk_points * type_info->dst_type_size;
/* Determine if we will access all the data in the chunk */
if(dst_accessed_bytes != ctg_store.contig.dset_size ||
(chunk_info->chunk_points * type_info->src_type_size) != ctg_store.contig.dset_size)
entire_chunk = FALSE;
/* Lock the chunk into the cache */
if(NULL == (chunk = H5D_chunk_lock(io_info, &udata, entire_chunk, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Set up the storage buffer information for this chunk */
cpt_store.compact.buf = chunk;
/* Point I/O info at main I/O info for this chunk */
chk_io_info = &cpt_io_info;
} /* end if */
else {
/* If the chunk hasn't been allocated on disk, do so now. */
if(!H5F_addr_defined(udata.addr)) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Compose chunked index info struct */
idx_info.f = io_info->dset->oloc.file;
idx_info.dxpl_id = io_info->dxpl_id;
idx_info.pline = &(io_info->dset->shared->dcpl_cache.pline);
idx_info.layout = &(io_info->dset->shared->layout);
/* Set up the size of chunk for user data */
udata.nbytes = io_info->dset->shared->layout.u.chunk.size;
/* Create the chunk */
if((io_info->dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
/* Make sure the address of the chunk is returned. */
if(!H5F_addr_defined(udata.addr))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
/* Cache the new chunk information */
H5D_chunk_cinfo_cache_update(&io_info->dset->shared->cache.chunk.last, &udata);
} /* end if */
/* Set up the storage address information for this chunk */
ctg_store.contig.dset_addr = udata.addr;
/* No chunk cached */
chunk = NULL;
/* Point I/O info at temporary I/O info for this chunk */
chk_io_info = &ctg_io_info;
} /* end else */
/* Perform the actual write operation */
if((io_info->io_ops.single_write)(chk_io_info, type_info,
(hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked write failed")
/* Release the cache lock on the chunk. */
if(chunk && H5D_chunk_unlock(io_info, &udata, TRUE, idx_hint, chunk, dst_accessed_bytes) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Advance to next chunk in list */
chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
} /* end while */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_write() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_io_term
*
* Purpose: Destroy I/O operation information.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Saturday, May 17, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_io_term(const H5D_chunk_map_t *fm)
{
herr_t ret_value = SUCCEED; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_io_term)
/* Single element I/O vs. multiple element I/O cleanup */
if(fm->use_single) {
/* Sanity checks */
HDassert(fm->sel_chunks == NULL);
HDassert(fm->single_chunk_info);
HDassert(fm->single_chunk_info->fspace_shared);
HDassert(fm->single_chunk_info->mspace_shared);
/* Reset the selection for the single element I/O */
H5S_select_all(fm->single_space, TRUE);
} /* end if */
else {
/* Release the nodes on the list of selected chunks */
if(fm->sel_chunks)
if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks")
} /* end else */
/* 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")
#ifdef H5_HAVE_PARALLEL
if(fm->select_chunk)
H5MM_xfree(fm->select_chunk);
#endif /* H5_HAVE_PARALLEL */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_io_term() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_idx_reset
*
* Purpose: Reset index information
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, January 15, 2009
*
* Modifications:
* Vailin Choi; April 2009
* Pass along RESET_ADDR: whether to reset the address of chunked storage index
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_idx_reset(H5O_layout_t *layout, hbool_t reset_addr)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_idx_reset, FAIL)
/* Sanity checks */
HDassert(layout);
HDassert(layout->u.chunk.ops);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
/* Reset index structures */
if((layout->u.chunk.ops->reset)(layout, reset_addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset chunk index info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_idx_reset() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_reset
*
* Purpose: Reset the cached chunk info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_reset)
/* Sanity check */
HDassert(last);
/* Indicate that the cached info is not valid */
last->valid = FALSE;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5D_chunk_cinfo_cache_reset() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_update
*
* Purpose: Update the cached chunk info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata)
{
unsigned u; /* Local index variable */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_update)
/* Sanity check */
HDassert(last);
HDassert(udata);
HDassert(udata->common.mesg);
HDassert(udata->common.offset);
/* Stored the information to cache */
for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
last->offset[u] = udata->common.offset[u];
last->nbytes = udata->nbytes;
last->filter_mask = udata->filter_mask;
last->addr = udata->addr;
/* Indicate that the cached info is valid */
last->valid = TRUE;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* H5D_chunk_cinfo_cache_update() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cinfo_cache_found
*
* Purpose: Look for chunk info in cache
*
* Return: TRUE/FALSE/FAIL
*
* Programmer: Quincey Koziol
* November 27, 2007
*
*-------------------------------------------------------------------------
*/
static hbool_t
H5D_chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata)
{
hbool_t ret_value = FALSE; /* Return value */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_cinfo_cache_found)
/* Sanity check */
HDassert(last);
HDassert(udata);
HDassert(udata->common.mesg);
HDassert(udata->common.offset);
/* Check if the cached information is what is desired */
if(last->valid) {
unsigned u; /* Local index variable */
/* Check that the offset is the same */
for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++)
if(last->offset[u] != udata->common.offset[u])
HGOTO_DONE(FALSE)
/* Retrieve the information from the cache */
udata->nbytes = last->nbytes;
udata->filter_mask = last->filter_mask;
udata->addr = last->addr;
/* Indicate that the data was found */
HGOTO_DONE(TRUE)
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_cinfo_cache_found() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_create
*
* Purpose: Creates a new chunked storage index and initializes the
* layout information with information about the storage. The
* layout info should be immediately written to the object header.
*
* Return: Non-negative on success (with the layout information initialized
* and ready to write to an object header). Negative on failure.
*
* Programmer: Quincey Koziol
* Thursday, May 22, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_create, FAIL)
/* Check args */
HDassert(dset);
HDassert(H5D_CHUNKED == dset->shared->layout.type);
HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
#ifndef NDEBUG
{
unsigned u; /* Local index variable */
for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
HDassert(dset->shared->layout.u.chunk.dim[u] > 0);
}
#endif
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Create the index for the chunks */
if((dset->shared->layout.u.chunk.ops->create)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_create() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_get_info
*
* Purpose: Get the info about a chunk if file space has been
* assigned. Save the retrieved information in the udata
* supplied.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Albert Cheng
* June 27, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_get_info(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset,
H5D_chunk_ud_t *udata)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_get_info)
HDassert(dset);
HDassert(dset->shared->layout.u.chunk.ndims > 0);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
HDassert(chunk_offset);
HDassert(udata);
/* Initialize the query information about the chunk we are looking for */
udata->common.mesg = &(dset->shared->layout);
udata->common.offset = chunk_offset;
/* Reset information about the chunk we are looking for */
udata->nbytes = 0;
udata->filter_mask = 0;
udata->addr = HADDR_UNDEF;
/* Check for cached information */
if(!H5D_chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Go get the chunk information */
if((dset->shared->layout.u.chunk.ops->get_addr)(&idx_info, udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address")
/* Cache the information retrieved */
H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_get_info() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_flush_entry
*
* Purpose: Writes a chunk to disk. If RESET is non-zero then the
* entry is cleared -- it's slightly faster to flush a chunk if
* the RESET flag is turned on because it results in one fewer
* memory copy.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
H5D_rdcc_ent_t *ent, hbool_t reset)
{
void *buf = NULL; /* Temporary buffer */
hbool_t point_of_no_return = FALSE;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_flush_entry)
HDassert(dset);
HDassert(dset->shared);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
HDassert(dxpl_cache);
HDassert(ent);
HDassert(!ent->locked);
buf = ent->chunk;
if(ent->dirty) {
H5D_chunk_ud_t udata; /* pass through B-tree */
hbool_t must_insert = FALSE; /* Whether the chunk must go through the "insert" method */
/* Set up user data for index callbacks */
udata.common.mesg = &dset->shared->layout;
udata.common.offset = ent->offset;
udata.filter_mask = 0;
udata.nbytes = dset->shared->layout.u.chunk.size;
udata.addr = ent->chunk_addr;
/* Should the chunk be filtered before writing it to disk? */
if(dset->shared->dcpl_cache.pline.nused) {
size_t alloc = udata.nbytes; /* Bytes allocated for BUF */
size_t nbytes; /* Chunk size (in bytes) */
if(!reset) {
/*
* Copy the chunk to a new buffer before running it through
* the pipeline because we'll want to save the original buffer
* for later.
*/
H5_ASSIGN_OVERFLOW(alloc, udata.nbytes, uint32_t, size_t);
if(NULL == (buf = H5MM_malloc(alloc)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline")
HDmemcpy(buf, ent->chunk, udata.nbytes);
} /* end if */
else {
/*
* If we are reseting and something goes wrong after this
* point then it's too late to recover because we may have
* destroyed the original data by calling H5Z_pipeline().
* The only safe option is to continue with the reset
* even if we can't write the data to disk.
*/
point_of_no_return = TRUE;
ent->chunk = NULL;
} /* end else */
H5_ASSIGN_OVERFLOW(nbytes, udata.nbytes, uint32_t, size_t);
if(H5Z_pipeline(&(dset->shared->dcpl_cache.pline), 0, &(udata.filter_mask), dxpl_cache->err_detect,
dxpl_cache->filter_cb, &nbytes, &alloc, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(nbytes > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
H5_ASSIGN_OVERFLOW(udata.nbytes, nbytes, size_t, uint32_t);
/* Indicate that the chunk must go through 'insert' method */
must_insert = TRUE;
} /* end if */
else if(!H5F_addr_defined(udata.addr))
/* Indicate that the chunk must go through 'insert' method */
must_insert = TRUE;
/* Check if the chunk needs to be 'inserted' (could exist already and
* the 'insert' operation could resize it)
*/
if(must_insert) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Create the chunk it if it doesn't exist, or reallocate the chunk
* if its size changed.
*/
if((dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk")
/* Update the chunk entry's address, in case it was allocated or relocated */
ent->chunk_addr = udata.addr;
} /* end if */
/* Write the data to the file */
HDassert(H5F_addr_defined(udata.addr));
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.nbytes, dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
/* Cache the chunk's info, in case it's accessed again shortly */
H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata);
/* Mark cache entry as clean */
ent->dirty = FALSE;
/* Check for SWMR writes to the file */
if(dset->shared->layout.u.chunk.ops->can_swim && H5F_INTENT(dset->oloc.file) & H5F_ACC_SWMR_WRITE) {
/* Mark the proxy entry in the cache as clean */
if(H5D_chunk_proxy_mark(dset, ent, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTMARKDIRTY, FAIL, "can't mark proxy for chunk from metadata cache as clean")
} /* end if */
/* Increment # of flushed entries */
dset->shared->cache.chunk.stats.nflushes++;
} /* end if */
/* Reset, but do not free or removed from list */
if(reset) {
point_of_no_return = FALSE;
if(buf == ent->chunk)
buf = NULL;
if(ent->chunk != NULL)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end if */
done:
/* Free the temp buffer only if it's different than the entry chunk */
if(buf != ent->chunk)
H5MM_xfree(buf);
/*
* If we reached the point of no return then we have no choice but to
* reset the entry. This can only happen if RESET is true but the
* output pipeline failed. Do not free the entry or remove it from the
* list.
*/
if(ret_value < 0 && point_of_no_return) {
if(ent->chunk)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_flush_entry() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cache_evict
*
* Purpose: Preempts the specified entry from the cache, flushing it to
* disk if necessary.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *dxpl_cache,
H5D_rdcc_ent_t *ent, hbool_t flush)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_evict)
HDassert(dset);
HDassert(dxpl_cache);
HDassert(ent);
HDassert(!ent->locked);
HDassert(ent->idx < rdcc->nslots);
if(flush) {
/* Flush */
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
/* Don't flush, just free chunk */
if(ent->chunk != NULL)
ent->chunk = (uint8_t *)H5D_chunk_xfree(ent->chunk, &(dset->shared->dcpl_cache.pline));
} /* end else */
/* Check for SWMR writes to the file */
if(dset->shared->layout.u.chunk.ops->can_swim && H5F_INTENT(dset->oloc.file) & H5F_ACC_SWMR_WRITE) {
/* Remove the proxy entry in the cache */
if(H5D_chunk_proxy_remove(dset, dxpl_id, ent) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "can't remove proxy for chunk from metadata cache")
} /* end if */
/* Unlink from list */
if(ent->prev)
ent->prev->next = ent->next;
else
rdcc->head = ent->next;
if(ent->next)
ent->next->prev = ent->prev;
else
rdcc->tail = ent->prev;
ent->prev = ent->next = NULL;
/* Remove from cache */
rdcc->slot[ent->idx] = NULL;
ent->idx = UINT_MAX;
rdcc->nbytes_used -= dset->shared->layout.u.chunk.size;
--rdcc->nused;
/* Free */
(void)H5FL_FREE(H5D_rdcc_ent_t, ent);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cache_evict() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_cache_prune
*
* Purpose: Prune the cache by preempting some things until the cache has
* room for something which is SIZE bytes. Only unlocked
* entries are considered for preemption.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_cache_prune(const H5D_t *dset, hid_t dxpl_id,
const H5D_dxpl_cache_t *dxpl_cache, size_t size)
{
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
size_t total = rdcc->nbytes_max;
const int nmeth = 2; /*number of methods */
int w[1]; /*weighting as an interval */
H5D_rdcc_ent_t *p[2], *cur; /*list pointers */
H5D_rdcc_ent_t *n[2]; /*list next pointers */
int nerrors = 0; /* Accumulated error count during preemptions */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_cache_prune)
/*
* Preemption is accomplished by having multiple pointers (currently two)
* slide down the list beginning at the head. Pointer p(N+1) will start
* traversing the list when pointer pN reaches wN percent of the original
* list. In other words, preemption method N gets to consider entries in
* approximate least recently used order w0 percent before method N+1
* where 100% means tha method N will run to completion before method N+1
* begins. The pointers participating in the list traversal are each
* given a chance at preemption before any of the pointers are advanced.
*/
w[0] = (int)(rdcc->nused * rdcc->w0);
p[0] = rdcc->head;
p[1] = NULL;
while((p[0] || p[1]) && (rdcc->nbytes_used + size) > total) {
int i; /* Local index variable */
/* Introduce new pointers */
for(i = 0; i < nmeth - 1; i++)
if(0 == w[i])
p[i + 1] = rdcc->head;
/* Compute next value for each pointer */
for(i = 0; i < nmeth; i++)
n[i] = p[i] ? p[i]->next : NULL;
/* Give each method a chance */
for(i = 0; i < nmeth && (rdcc->nbytes_used + size) > total; i++) {
if(0 == i && p[0] && !p[0]->locked &&
((0 == p[0]->rd_count && 0 == p[0]->wr_count) ||
(0 == p[0]->rd_count && dset->shared->layout.u.chunk.size == p[0]->wr_count) ||
(dset->shared->layout.u.chunk.size == p[0]->rd_count && 0 == p[0]->wr_count))) {
/*
* Method 0: Preempt entries that have been completely written
* and/or completely read but not entries that are partially
* written or partially read.
*/
cur = p[0];
} else if(1 == i && p[1] && !p[1]->locked) {
/*
* Method 1: Preempt the entry without regard to
* considerations other than being locked. This is the last
* resort preemption.
*/
cur = p[1];
} else {
/* Nothing to preempt at this point */
cur = NULL;
}
if(cur) {
int j; /* Local index variable */
for(j = 0; j < nmeth; j++) {
if(p[j] == cur)
p[j] = NULL;
if(n[j] == cur)
n[j] = cur->next;
} /* end for */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, cur, TRUE) < 0)
nerrors++;
} /* end if */
} /* end for */
/* Advance pointers */
for(i = 0; i < nmeth; i++)
p[i] = n[i];
for(i = 0; i < nmeth - 1; i++)
w[i] -= 1;
} /* end while */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to preempt one or more raw data cache entry")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_cache_prune() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_lock
*
* Purpose: Return a pointer to a dataset chunk. The pointer points
* directly into the chunk cache and should not be freed
* by the caller but will be valid until it is unlocked. The
* input value IDX_HINT is used to speed up cache lookups and
* it's output value should be given to H5D_chunk_unlock().
* IDX_HINT is ignored if it is out of range, and if it points
* to the wrong entry then we fall back to the normal search
* method.
*
* If RELAX is non-zero and the chunk isn't in the cache then
* don't try to read it from the file, but just allocate an
* uninitialized buffer to hold the result. This is intended
* for output functions that are about to overwrite the entire
* chunk.
*
* Return: Success: Ptr to a file chunk.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
void *
H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
hbool_t relax, unsigned *idx_hint/*in,out*/)
{
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
unsigned idx = 0; /*hash index number */
hbool_t found = FALSE; /*already in cache? */
haddr_t chunk_addr = HADDR_UNDEF; /* Address of chunk on disk */
size_t chunk_size; /*size of a chunk */
void *chunk = NULL; /*the file chunk */
unsigned u; /*counters */
void *ret_value; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_lock)
HDassert(io_info);
HDassert(io_info->dxpl_cache);
HDassert(io_info->store);
HDassert(udata);
HDassert(dset);
HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
/* Get the chunk's size */
HDassert(layout->u.chunk.size > 0);
H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
/* Search for the chunk in the cache */
if(rdcc->nslots > 0) {
idx = H5D_CHUNK_HASH(dset->shared, io_info->store->chunk.index);
ent = rdcc->slot[idx];
if(ent)
for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++)
if(io_info->store->chunk.offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
} /* end if */
if(found) {
/*
* Already in the cache. Count a hit.
*/
rdcc->stats.nhits++;
} /* end if */
else if(relax) {
/*
* Not in the cache, but we're about to overwrite the whole thing
* anyway, so just allocate a buffer for it but don't initialize that
* buffer with the file contents. Count this as a hit instead of a
* miss because we saved ourselves lots of work.
*/
rdcc->stats.nhits++;
if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
/* In the case that some dataset functions look through this data,
* clear it to all 0s. */
HDmemset(chunk, 0, chunk_size);
} /* end if */
else {
/*
* Not in the cache. Count this as a miss if it's in the file
* or an init if it isn't.
*/
/* Save the chunk address */
chunk_addr = udata->addr;
/* Check if the chunk exists on disk */
if(H5F_addr_defined(chunk_addr)) {
size_t chunk_alloc = 0; /*allocated chunk size */
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
H5_ASSIGN_OVERFLOW(chunk_alloc, udata->nbytes, uint32_t, size_t);
if(NULL == (chunk = H5D_chunk_alloc(chunk_alloc, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, chunk_alloc, io_info->dxpl_id, chunk) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
if(pline->nused) {
if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->filter_mask), io_info->dxpl_cache->err_detect,
io_info->dxpl_cache->filter_cb, &chunk_alloc, &chunk_alloc, &chunk) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed")
H5_ASSIGN_OVERFLOW(udata->nbytes, chunk_alloc, size_t, uint32_t);
} /* end if */
/* Increment # of cache misses */
rdcc->stats.nmisses++;
} /* end if */
else {
H5D_fill_value_t fill_status;
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined")
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
/*
* The chunk doesn't exist in the file. Replicate the fill
* value throughout the chunk, if the fill value is defined.
*/
/* Initialize the fill value buffer */
/* (use the compact dataset storage buffer as the fill value buffer) */
if(H5D_fill_init(&fb_info, chunk, FALSE,
NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info")
fb_info_init = TRUE;
/* Check for VL datatype & non-default fill value */
if(fb_info.has_vlen_fill_type)
/* Fill the buffer with VL datatype fill values */
if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "can't refill fill value buffer")
} /* end if */
else
HDmemset(chunk, 0, chunk_size);
/* Increment # of creations */
rdcc->stats.ninits++;
} /* end else */
} /* end else */
HDassert(found || chunk_size > 0);
if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes_max &&
(!ent || !ent->locked)) {
/*
* Add the chunk to the cache only if the slot is not already locked.
* Preempt enough things from the cache to make room.
*/
if(ent) {
if(H5D_chunk_cache_evict(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache")
} /* end if */
if(H5D_chunk_cache_prune(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, chunk_size) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache")
/* Create a new entry */
ent = H5FL_MALLOC(H5D_rdcc_ent_t);
ent->locked = 0;
ent->dirty = FALSE;
ent->chunk_addr = chunk_addr;
ent->proxy_addr = HADDR_UNDEF;
ent->proxy = NULL;
for(u = 0; u < layout->u.chunk.ndims; u++)
ent->offset[u] = io_info->store->chunk.offset[u];
H5_ASSIGN_OVERFLOW(ent->rd_count, chunk_size, size_t, uint32_t);
H5_ASSIGN_OVERFLOW(ent->wr_count, chunk_size, size_t, uint32_t);
ent->chunk = (uint8_t *)chunk;
/* Add it to the cache */
HDassert(NULL == rdcc->slot[idx]);
rdcc->slot[idx] = ent;
ent->idx = idx;
rdcc->nbytes_used += chunk_size;
rdcc->nused++;
/* Add it to the linked list */
ent->next = NULL;
if(rdcc->tail) {
rdcc->tail->next = ent;
ent->prev = rdcc->tail;
rdcc->tail = ent;
} /* end if */
else {
rdcc->head = rdcc->tail = ent;
ent->prev = NULL;
} /* end else */
/* Check for SWMR writes to the file */
if(io_info->dset->shared->layout.u.chunk.ops->can_swim
&& H5F_INTENT(io_info->dset->oloc.file) & H5F_ACC_SWMR_WRITE) {
/* Insert a proxy entry in the cache, to make certain that the
* flush dependencies are maintained in the proper way for SWMR
* access to work.
*/
if(H5D_chunk_proxy_create(io_info->dset, io_info->dxpl_id, (H5D_chunk_common_ud_t *)udata, ent) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert proxy for chunk in metadata cache")
} /* end if */
/* Indicate that the chunk is in the cache now */
found = TRUE;
} else if(!found) {
/*
* The chunk is larger than the entire cache so we don't cache it.
* This is the reason all those arguments have to be repeated for the
* unlock function.
*/
ent = NULL;
idx = UINT_MAX;
} else {
/*
* The chunk is not at the beginning of the cache; move it backward
* by one slot. This is how we implement the LRU preemption
* algorithm.
*/
HDassert(ent);
if(ent->next) {
if(ent->next->next)
ent->next->next->prev = ent;
else
rdcc->tail = ent;
ent->next->prev = ent->prev;
if(ent->prev)
ent->prev->next = ent->next;
else
rdcc->head = ent->next;
ent->prev = ent->next;
ent->next = ent->next->next;
ent->prev->next = ent;
} /* end if */
} /* end else */
/* Lock the chunk into the cache */
if(ent) {
HDassert(!ent->locked);
ent->locked = TRUE;
chunk = ent->chunk;
} /* end if */
if(idx_hint)
*idx_hint = idx;
/* Set return value */
ret_value = chunk;
done:
/* Release the fill buffer info, if it's been initialized */
if(fb_info_init && H5D_fill_term(&fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, NULL, "Can't release fill buffer info")
/* Release the chunk allocated, on error */
if(!ret_value)
if(chunk)
chunk = H5D_chunk_xfree(chunk, pline);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_lock() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_unlock
*
* Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and
* OFFSET arguments should be the same as for H5D_chunk_lock().
* The DIRTY argument should be set to non-zero if the chunk has
* been modified since it was locked. The IDX_HINT argument is
* the returned index hint from the lock operation and BUF is
* the return value from the lock.
*
* The NACCESSED argument should be the number of bytes accessed
* for reading or writing (depending on the value of DIRTY).
* It's only purpose is to provide additional information to the
* preemption policy.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata,
hbool_t dirty, unsigned idx_hint, void *chunk, uint32_t naccessed)
{
const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset layout */
const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk);
H5D_rdcc_ent_t *ent = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_unlock)
HDassert(io_info);
HDassert(udata);
if(UINT_MAX == idx_hint) {
/*
* It's not in the cache, probably because it's too big. If it's
* dirty then flush it to disk. In any case, free the chunk.
* Note: we have to copy the layout and filter messages so we
* don't discard the `const' qualifier.
*/
if(dirty) {
H5D_rdcc_ent_t fake_ent; /* "fake" chunk cache entry */
HDmemset(&fake_ent, 0, sizeof(fake_ent));
fake_ent.dirty = TRUE;
HDmemcpy(fake_ent.offset, io_info->store->chunk.offset, layout->u.chunk.ndims * sizeof(fake_ent.offset[0]));
HDassert(layout->u.chunk.size > 0);
fake_ent.chunk_addr = udata->addr;
fake_ent.chunk = (uint8_t *)chunk;
if(H5D_chunk_flush_entry(io_info->dset, io_info->dxpl_id, io_info->dxpl_cache, &fake_ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
if(chunk)
chunk = H5D_chunk_xfree(chunk, &(io_info->dset->shared->dcpl_cache.pline));
} /* end else */
} /* end if */
else {
/* Sanity check */
HDassert(idx_hint < rdcc->nslots);
HDassert(rdcc->slot[idx_hint]);
HDassert(rdcc->slot[idx_hint]->chunk == chunk);
/*
* It's in the cache so unlock it.
*/
ent = rdcc->slot[idx_hint];
HDassert(ent->locked);
if(dirty) {
ent->dirty = TRUE;
ent->wr_count -= MIN(ent->wr_count, naccessed);
/* Check for SWMR writes to the file */
if(io_info->dset->shared->layout.u.chunk.ops->can_swim
&& H5F_INTENT(io_info->dset->oloc.file) & H5F_ACC_SWMR_WRITE) {
/* Mark the proxy entry in the cache as dirty */
if(H5D_chunk_proxy_mark(io_info->dset, ent, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTMARKDIRTY, FAIL, "can't mark proxy for chunk from metadata cache as dirty")
} /* end if */
} /* end if */
else
ent->rd_count -= MIN(ent->rd_count, naccessed);
ent->locked = FALSE;
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_unlock() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_flush
*
* Purpose: Writes all dirty chunks to disk and optionally preempts them
* from the cache.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
{
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
unsigned nerrors = 0;
H5D_rdcc_ent_t *ent, *next;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_flush, FAIL)
/* 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")
/* Loop over all entries in the chunk cache */
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
if((flags & H5F_FLUSH_INVALIDATE)) {
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
nerrors++;
} else {
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
nerrors++;
}
} /* end for */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_flush() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocated_cb
*
* Purpose: Simply counts the number of chunks for a dataset.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
hsize_t *nbytes = (hsize_t *)_udata;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_allocated_cb)
*(hsize_t *)nbytes += chunk_rec->nbytes;
FUNC_LEAVE_NOAPI(H5_ITER_CONT)
} /* H5D_chunk_allocated_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocated
*
* Purpose: Return the number of bytes allocated in the file for storage
* of raw data in the chunked dataset
*
* Return: Success: Number of bytes stored in all chunks.
* Failure: 0
*
* Programmer: Quincey Koziol
* Tuesday, May 20, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
hsize_t chunk_bytes = 0; /* Number of bytes allocated for chunks */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_allocated, FAIL)
HDassert(dset);
HDassert(dset->shared);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
/* 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")
/* Search for cached chunks that haven't been written out */
for(ent = rdcc->head; ent; ent = ent->next) {
/* Flush the chunk out to disk, to make certain the size is correct later */
if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end for */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Iterate over the chunks */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_allocated_cb, &chunk_bytes) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
/* Set number of bytes for caller */
*nbytes = chunk_bytes;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_allocated() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_allocate
*
* Purpose: Allocate file space for all chunks that are not allocated yet.
* Return SUCCEED if all needed allocation succeed, otherwise
* FAIL.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Albert Cheng
* June 26, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
const H5D_chunk_ops_t *ops = dset->shared->layout.u.chunk.ops; /* Chunk operations */
hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
size_t orig_chunk_size; /* Original size of chunk in bytes */
unsigned filter_mask = 0; /* Filter mask for chunks that have them */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* The fill value status */
hbool_t should_fill = FALSE; /* Whether fill values should be written */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
#ifdef H5_HAVE_PARALLEL
MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank = (-1); /* This process's rank */
int mpi_code; /* MPI return code */
hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
int space_ndims; /* Dataset's space rank */
hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
hid_t data_dxpl_id; /* DXPL ID to use for raw data I/O operations */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_allocate, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == layout->type);
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
/* Retrieve the dataset dimensions */
if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
space_dim[space_ndims] = layout->u.chunk.dim[space_ndims];
#ifdef H5_HAVE_PARALLEL
/* Retrieve MPI parameters */
if(IS_H5FD_MPI(dset->oloc.file)) {
/* Get the MPI communicator */
if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file)))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator")
/* Get the MPI rank */
if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
/* Set the MPI-capable file driver flag */
using_mpi = TRUE;
/* Use the internal "independent" DXPL */
data_dxpl_id = H5AC_ind_dxpl_id;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
/* Use the DXPL we were given */
data_dxpl_id = dxpl_id;
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
/* Fill the DXPL cache values for later use */
if(H5D_get_dxpl_cache(data_dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Get original chunk size */
H5_ASSIGN_OVERFLOW(orig_chunk_size, layout->u.chunk.size, uint32_t, size_t);
/* Check the dataset's fill-value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are filling the dataset on allocation or "if set" and
* the fill value _is_ set, _and_ we are not overwriting the new blocks,
* or if there are any pipeline filters defined,
* set the "should fill" flag
*/
if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
|| pline->nused > 0)
should_fill = TRUE;
/* Check if fill values should be written to chunks */
if(should_fill) {
/* Initialize the fill value buffer */
/* (delay allocating fill buffer for VL datatypes until refilling) */
/* (casting away const OK - QAK) */
if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0),
(H5MM_allocate_t)H5D_chunk_alloc, (void *)pline,
(H5MM_free_t)H5D_chunk_xfree, (void *)pline,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
fb_info_init = TRUE;
/* Check if there are filters which need to be applied to the chunk */
/* (only do this in advance when the chunk info can be re-used (i.e.
* it doesn't contain any non-default VL datatype fill values)
*/
if(!fb_info.has_vlen_fill_type && pline->nused > 0) {
size_t buf_size = orig_chunk_size;
/* Push the chunk through the filters */
if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(orig_chunk_size > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
} /* end if */
} /* end if */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Reset the chunk offset indices */
HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0])));
/* Loop over all chunks */
carry = FALSE;
while(!carry) {
H5D_chunk_ud_t udata; /* User data for querying chunk info */
int i; /* Local index variable */
/* Get the chunk's info */
if(H5D_chunk_get_info(dset, dxpl_id, chunk_offset, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
/* Check if the chunk exists yet on disk */
if(!H5F_addr_defined(udata.addr)) {
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
H5D_rdcc_ent_t *ent; /* Cache entry */
hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
unsigned u; /* Local index variable */
/* Didn't find the chunk on disk */
chunk_exists = FALSE;
/* Look for chunk in cache */
for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
/* Assume a match */
chunk_exists = TRUE;
for(u = 0; u < layout->u.chunk.ndims; u++)
if(ent->offset[u] != chunk_offset[u]) {
chunk_exists = FALSE; /* Reset if no match */
break;
} /* end if */
} /* end for */
/* Chunk wasn't in cache either, create it now */
if(!chunk_exists) {
size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
/* Check for VL datatype & non-default fill value */
if(fb_info_init && fb_info.has_vlen_fill_type) {
/* Sanity check */
HDassert(should_fill);
/* Fill the buffer with VL datatype fill values */
if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
/* Check if there are filters which need to be applied to the chunk */
if(pline->nused > 0) {
size_t buf_size = orig_chunk_size;
size_t nbytes = fb_info.fill_buf_size;
/* Push the chunk through the filters */
if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(nbytes > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
/* Keep the number of bytes the chunk turned in to */
chunk_size = nbytes;
} /* end if */
else
H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
} /* end if */
else
chunk_size = orig_chunk_size;
/* Initialize the chunk information */
udata.common.mesg = layout;
udata.common.offset = chunk_offset;
H5_ASSIGN_OVERFLOW(udata.nbytes, chunk_size, size_t, uint32_t);
udata.filter_mask = filter_mask;
udata.addr = HADDR_UNDEF;
/* Allocate the chunk with all processes */
if((ops->insert)(&idx_info, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert record into chunk index")
HDassert(H5F_addr_defined(udata.addr));
/* Check if fill values should be written to chunks */
if(should_fill) {
/* Sanity check */
HDassert(fb_info_init);
HDassert(udata.nbytes == chunk_size);
#ifdef H5_HAVE_PARALLEL
/* Check if this file is accessed with an MPI-capable file driver */
if(using_mpi) {
/* Write the chunks out from only one process */
/* !! Use the internal "independent" DXPL!! -QAK */
if(H5_PAR_META_WRITE == mpi_rank)
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
/* Indicate that blocks are being written */
blocks_written = TRUE;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, chunk_size, data_dxpl_id, fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
#ifdef H5_HAVE_PARALLEL
} /* end else */
#endif /* H5_HAVE_PARALLEL */
} /* end if */
/* Release the fill buffer if we need to re-allocate it each time */
if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0)
H5D_fill_release(&fb_info);
} /* end if */
} /* end if */
/* Increment indices */
carry = TRUE;
for(i = (int)(space_ndims - 1); i >= 0; --i) {
chunk_offset[i] += layout->u.chunk.dim[i];
if(chunk_offset[i] >= space_dim[i])
chunk_offset[i] = 0;
else {
carry = FALSE;
break;
} /* end else */
} /* end for */
} /* end while */
#ifdef H5_HAVE_PARALLEL
/* Only need to block at the barrier if we actually initialized a chunk */
/* using an MPI-capable file driver */
if(using_mpi && blocks_written) {
/* Wait at barrier to avoid race conditions where some processes are
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
done:
/* Release the fill buffer info, if it's been initialized */
if(fb_info_init && H5D_fill_term(&fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_allocate() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_fill
*
* Purpose: Write the fill value to the parts of the chunk that are no
* longer part of the dataspace
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* March 26, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_chunk_prune_fill(const H5D_chunk_rec_t *chunk_rec, H5D_chunk_it_ud1_t *udata)
{
const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* Dataset rank */
H5S_sel_iter_t chunk_iter; /* Memory selection iteration info */
hssize_t sel_nelmts; /* Number of elements in selection */
hsize_t count[H5O_LAYOUT_NDIMS]; /* Element count of hyperslab */
void *chunk; /* The file chunk */
unsigned idx_hint; /* Which chunk we're dealing with */
H5D_chunk_ud_t chk_udata; /* User data for locking chunk */
uint32_t bytes_accessed; /* Bytes accessed in chunk */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_fill)
/* Initialize the fill value buffer, if necessary */
if(!udata->fb_info_init) {
H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t);
if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill,
dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk,
io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
udata->fb_info_init = TRUE;
} /* end if */
/* Compute the # of elements to leave with existing value, in each dimension */
for(u = 0; u < rank; u++) {
count[u] = MIN(layout->u.chunk.dim[u], (udata->dims[u] - chunk_rec->offset[u]));
HDassert(count[u] > 0);
} /* end for */
/* Select all elements in chunk, to begin with */
if(H5S_select_all(udata->chunk_space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select space")
/* "Subtract out" the elements to keep */
if(H5S_select_hyperslab(udata->chunk_space, H5S_SELECT_NOTB, udata->hyper_start, NULL, count, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select hyperslab")
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks,
&io_info->store->chunk.index) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index")
/* Lock the chunk into the cache, to get a pointer to the chunk buffer */
/* (Casting away const OK -QAK) */
io_info->store->chunk.offset = (hsize_t *)chunk_rec->offset;
chk_udata.common.mesg = layout;
chk_udata.common.offset = chunk_rec->offset;
chk_udata.nbytes = chunk_rec->nbytes;
chk_udata.filter_mask = chunk_rec->filter_mask;
chk_udata.addr = chunk_rec->chunk_addr;
if(NULL == (chunk = (void *)H5D_chunk_lock(udata->io_info, &chk_udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to lock raw data chunk")
/* Fill the selection in the memory buffer */
/* Use the size of the elements in the chunk directly instead of */
/* relying on the fill.size, which might be set to 0 if there is */
/* no fill-value defined for the dataset -QAK */
/* Get the number of elements in the selection */
sel_nelmts = H5S_GET_SELECT_NPOINTS(udata->chunk_space);
HDassert(sel_nelmts >= 0);
H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, size_t);
/* Check for VL datatype & non-default fill value */
if(udata->fb_info.has_vlen_fill_type)
/* Re-fill the buffer to use for this I/O operation */
if(H5D_fill_refill_vl(&udata->fb_info, (size_t)sel_nelmts, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
/* Create a selection iterator for scattering the elements to memory buffer */
if(H5S_select_iter_init(&chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunk selection information")
/* Scatter the data into memory */
if(H5D_scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, &chunk_iter, (size_t)sel_nelmts, io_info->dxpl_cache, chunk/*out*/) < 0) {
H5S_SELECT_ITER_RELEASE(&chunk_iter);
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed")
} /* end if */
/* Release the selection iterator */
if(H5S_SELECT_ITER_RELEASE(&chunk_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
/* The number of bytes accessed in the chunk */
/* (i.e. the bytes replaced with fill values) */
H5_CHECK_OVERFLOW(sel_nelmts, hssize_t, uint32_t);
bytes_accessed = (uint32_t)sel_nelmts * layout->u.chunk.dim[rank];
/* Release lock on chunk */
if(H5D_chunk_unlock(io_info, &chk_udata, TRUE, idx_hint, chunk, bytes_accessed) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_prune_fill */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_cb
*
* Purpose: Search for chunks that are no longer inside the pruned
* dataset's extent
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* March 26, 2002
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_prune_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud1_t *udata = (H5D_chunk_it_ud1_t *)_udata; /* User data */
H5D_chunk_prune_stack_t *stack_node = NULL; /* Stack node for chunk to remove */
unsigned rank; /* Current # of dimensions */
hbool_t should_delete = FALSE; /* Whether the chunk should be deleted */
hbool_t needs_fill = FALSE; /* Whether the chunk overlaps the new extent and needs fill valiues */
unsigned u; /* Local index variable */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_prune_cb)
/* Figure out what chunks are no longer in use for the specified extent and release them */
rank = udata->common.mesg->u.chunk.ndims - 1;
for(u = 0; u < rank; u++)
/* The chunk record points to a chunk of storage that contains the
* beginning of the logical address space represented by UDATA.
*/
if(udata->shrunk_dims[u]) {
if(chunk_rec->offset[u] >= udata->dims[u]) {
/* Indicate that the chunk will be deleted */
should_delete = TRUE;
/* Break out of loop, we know the chunk is outside the current dimensions */
break;
} /* end if */
/* Check for chunk that overlaps new extent and will need fill values */
else if((chunk_rec->offset[u] + udata->common.mesg->u.chunk.dim[u]) > udata->dims[u])
/* Indicate that the chunk needs filling */
/* (but continue in loop, since it could be outside the extent in
* another dimension -QAK)
*/
needs_fill = TRUE;
} /* end if */
/* Check for chunk to delete */
if(should_delete) {
/* Allocate space for the removal stack node */
if(NULL == (stack_node = H5FL_MALLOC(H5D_chunk_prune_stack_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for removal stack node")
/* Store the record for the chunk */
stack_node->rec = *chunk_rec;
/* Push the chunk description onto the stack */
stack_node->next = udata->rm_stack;
udata->rm_stack = stack_node;
} /* end if */
/* Check for chunk that overlaps the new dataset dimensions and needs filling */
else if(needs_fill)
/* Write the fill value */
if(H5D_chunk_prune_fill(chunk_rec, udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write fill value")
done:
/* It is currently impossible to fail after the stack node has been
* malloc'ed. No need to free it here on failure. */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_prune_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_prune_by_extent
*
* Purpose: This function searches for chunks that are no longer necessary
* both in the raw data cache and in the chunk index.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Algorithm: Robb Matzke
* March 27, 2002
*
* The algorithm is:
*
* For chunks that are no longer necessary:
*
* 1. Search in the raw data cache for each chunk
* 2. If found then preempt it from the cache
* 3. Search in the B-tree for each chunk
* 4. If found then remove it from the B-tree and deallocate file storage for the chunk
*
* This example shows a 2d dataset of 90x90 with a chunk size of 20x20.
*
*
* 0 20 40 60 80 90 100
* 0 +---------+---------+---------+---------+-----+...+
* |:::::X:::::::::::::: : : | :
* |:::::::X:::::::::::: : : | : Key
* |::::::::::X::::::::: : : | : --------
* |::::::::::::X::::::: : : | : +-+ Dataset
* 20+::::::::::::::::::::.........:.........:.....+...: | | Extent
* | :::::X::::: : : | : +-+
* | ::::::::::: : : | :
* | ::::::::::: : : | : ... Chunk
* | :::::::X::: : : | : : : Boundary
* 40+.........:::::::::::.........:.........:.....+...: :.:
* | : : : : | :
* | : : : : | : ... Allocated
* | : : : : | : ::: & Filled
* | : : : : | : ::: Chunk
* 60+.........:.........:.........:.........:.....+...:
* | : :::::::X::: : | : X Element
* | : ::::::::::: : | : Written
* | : ::::::::::: : | :
* | : ::::::::::: : | :
* 80+.........:.........:::::::::::.........:.....+...: O Fill Val
* | : : ::::::::::: | : Explicitly
* | : : ::::::X:::: | : Written
* 90+---------+---------+---------+---------+-----+ :
* : : : ::::::::::: :
* 100:.........:.........:.........:::::::::::.........:
*
*
* We have 25 total chunks for this dataset, 5 of which have space
* allocated in the file because they were written to one or more
* elements. These five chunks (and only these five) also have entries in
* the storage B-tree for this dataset.
*
* Now lets say we want to shrink the dataset down to 70x70:
*
*
* 0 20 40 60 70 80 90 100
* 0 +---------+---------+---------+----+----+-----+...+
* |:::::X:::::::::::::: : | : | :
* |:::::::X:::::::::::: : | : | : Key
* |::::::::::X::::::::: : | : | : --------
* |::::::::::::X::::::: : | : | : +-+ Dataset
* 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent
* | :::::X::::: : | : | : +-+
* | ::::::::::: : | : | :
* | ::::::::::: : | : | : ... Chunk
* | :::::::X::: : | : | : : : Boundary
* 40+.........:::::::::::.........:....+....:.....|...: :.:
* | : : : | : | :
* | : : : | : | : ... Allocated
* | : : : | : | : ::: & Filled
* | : : : | : | : ::: Chunk
* 60+.........:.........:.........:....+....:.....|...:
* | : :::::::X::: | : | : X Element
* | : ::::::::::: | : | : Written
* +---------+---------+---------+----+ : | :
* | : ::::::::::: : | :
* 80+.........:.........:::::::::X:.........:.....|...: O Fill Val
* | : : ::::::::::: | : Explicitly
* | : : ::::::X:::: | : Written
* 90+---------+---------+---------+---------+-----+ :
* : : : ::::::::::: :
* 100:.........:.........:.........:::::::::::.........:
*
*
* That means that the nine chunks along the bottom and right side should
* no longer exist. Of those nine chunks, (0,80), (20,80), (40,80),
* (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated
* that needs to be released.
* To release the chunks, we traverse the B-tree to obtain a list of unused
* allocated chunks, and then call H5B_remove() for each chunk.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_io_info_t chk_io_info; /* Chunked I/O info object */
H5D_storage_t chk_store; /* Chunk storage information */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Cache entries */
hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dataspace dimensions */
hbool_t shrunk_dims[H5O_LAYOUT_NDIMS]; /* Dimensions which have shrunk */
H5D_chunk_it_ud1_t udata; /* Chunk index iterator user data */
hbool_t udata_init = FALSE; /* Whether the chunk index iterator user data has been initialized */
hbool_t needs_fill; /* Whether we need to write the fill value */
H5D_chunk_prune_stack_t *fill_stack = NULL; /* Stack of chunks to fill */
H5D_chunk_prune_stack_t *tmp_stack; /* Temporary stack node pointer */
H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */
H5S_t *chunk_space = NULL; /* Dataspace for a chunk */
hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */
uint32_t elmts_per_chunk; /* Elements in chunk */
unsigned rank; /* Current # of dimensions */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_prune_by_extent, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == layout->type);
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
HDassert(dxpl_cache);
/* set the removal stack pointer in udata to NULL, so if the function fails
* early it will not try to free the nonexistent stack */
udata.rm_stack = NULL;
/* 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")
/* Go get the rank & dimensions (including the element size) */
rank = layout->u.chunk.ndims - 1;
if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
curr_dims[rank] = layout->u.chunk.dim[rank];
/* Round up to the next integer # of chunks, to accomodate partial chunks */
/* Use current dims because the indices have already been updated! -NAF */
/* (also compute the number of elements per chunk) */
/* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */
/* (also compute the dimensions which have been shrunk) */
elmts_per_chunk = 1;
for(u = 0; u < rank; u++) {
chunks[u] = ((curr_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u];
elmts_per_chunk *= layout->u.chunk.dim[u];
chunk_dims[u] = layout->u.chunk.dim[u];
shrunk_dims[u] = curr_dims[u] < old_dims[u];
} /* end for */
/* Get the "down" sizes for each dimension */
if(H5V_array_down(rank, chunks, down_chunks) < 0)
HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* Create a dataspace for a chunk & set the extent */
if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Reset hyperslab start array */
/* (hyperslabs will always start from origin) */
HDmemset(hyper_start, 0, sizeof(hyper_start));
/* Set up chunked I/O info object, for operations on chunks (in callback) */
/* (Casting away const OK -QAK) */
H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, dxpl_cache, dxpl_id, &chk_store, NULL);
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Initialize the user data for the iteration */
HDmemset(&udata, 0, sizeof udata);
udata.common.mesg = layout;
udata.io_info = &chk_io_info;
udata.idx_info = &idx_info;
udata.dims = curr_dims;
udata.shrunk_dims = shrunk_dims;
udata.down_chunks = down_chunks;
udata.elmts_per_chunk = elmts_per_chunk;
udata.chunk_space = chunk_space;
udata.hyper_start = hyper_start;
udata_init = TRUE;
/*-------------------------------------------------------------------------
* Figure out what chunks are no longer in use for the specified extent
* and release them from the linked list raw data cache
*-------------------------------------------------------------------------
*/
for(ent = rdcc->head; ent; ent = next) {
/* Get pointer to next extry in cache, in case this one is evicted */
next = ent->next;
needs_fill = FALSE;
/* Check for chunk offset outside of new dimensions */
for(u = 0; u < rank; u++) {
if((hsize_t)ent->offset[u] >= curr_dims[u]) {
/* Evict the entry from the cache, but do not flush it to disk */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
/* We don't need to write the fill value */
needs_fill = FALSE;
/* Break out of loop, chunk is evicted */
break;
} else if(!H5F_addr_defined(ent->chunk_addr) && shrunk_dims[u]
&& (ent->offset[u] + chunk_dims[u]) > curr_dims[u])
/* We need to write the fill value to the unused parts of chunk */
needs_fill = TRUE;
} /* end for */
if(needs_fill) {
/* Allocate space for the stack node */
if(NULL == (tmp_stack = H5FL_MALLOC(H5D_chunk_prune_stack_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for stack node")
/* Set up chunk record for fill routine */
tmp_stack->rec.nbytes = dset->shared->layout.u.chunk.size;
HDmemcpy(tmp_stack->rec.offset, ent->offset, sizeof(tmp_stack->rec.offset));
tmp_stack->rec.filter_mask = 0; /* Since the chunk is already in cache this doesn't matter */
tmp_stack->rec.chunk_addr = ent->chunk_addr;
/* Push the chunk description onto the stack */
tmp_stack->next = fill_stack;
fill_stack = tmp_stack;
} /* end if */
} /* end for */
/* Traverse the stack of chunks to be filled, filling each. We will free
* the nodes later in the "done" section. */
tmp_stack = fill_stack;
while(tmp_stack) {
/* Write the fill value */
if(H5D_chunk_prune_fill(&(tmp_stack->rec), &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write fill value")
/* Advance the stack pointer */
tmp_stack = tmp_stack->next;
} /* end while */
/* Iterate over the chunks */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_prune_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve prune chunks from index")
/* Traverse the stack of chunks to be deleted, removing each. We will free
* the nodes later in the "done" section. */
idx_udata.mesg = layout;
tmp_stack = udata.rm_stack;
while(tmp_stack) {
/* Update the offset in idx_udata */
idx_udata.offset = tmp_stack->rec.offset;
/* Remove the chunk from disk */
if((layout->u.chunk.ops->remove)(&idx_info, &idx_udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, H5_ITER_ERROR, "unable to remove chunk entry from index")
/* Advance the stack pointer */
tmp_stack = tmp_stack->next;
} /* end while */
/* Reset any cached chunk info for this dataset */
H5D_chunk_cinfo_cache_reset(&dset->shared->cache.chunk.last);
done:
/* Release resources */
if(chunk_space && H5S_close(chunk_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
if(udata_init) {
if(udata.fb_info_init && H5D_fill_term(&udata.fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
} /* end if */
/* Free stack of filled chunks */
tmp_stack = fill_stack;
while(tmp_stack) {
/* Free the stack node and advance the stack pointer */
tmp_stack = tmp_stack->next;
(void)H5FL_FREE(H5D_chunk_prune_stack_t, fill_stack);
fill_stack = tmp_stack;
} /* end while */
/* Free stack of removed chunks */
tmp_stack = udata.rm_stack;
while(tmp_stack) {
/* Free the stack node and advance the stack pointer */
tmp_stack = tmp_stack->next;
(void)H5FL_FREE(H5D_chunk_prune_stack_t, udata.rm_stack);
udata.rm_stack = tmp_stack;
} /* end while */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_prune_by_extent() */
#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5D_chunk_addrmap_cb
*
* Purpose: Callback when obtaining the chunk addresses for all existing chunks
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Kent Yang
* Tuesday, November 15, 2005
*
*-------------------------------------------------------------------------
*/
static int
H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud2_t *udata = (H5D_chunk_it_ud2_t *)_udata; /* User data for callback */
unsigned rank = udata->common.mesg->u.chunk.ndims - 1; /* # of dimensions of dataset */
hsize_t chunk_index;
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb)
/* Compute the index for this chunk */
if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index")
/* Set it in the userdata to return */
udata->chunk_addr[chunk_index] = chunk_rec->chunk_addr;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_chunk_addrmap_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_addrmap
*
* Purpose: Obtain the chunk addresses for all existing chunks
*
* Return: Success: Non-negative on succeed.
* Failure: negative value
*
* Programmer: Kent Yang
* November 15, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],
const hsize_t down_chunks[])
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_t *dset = io_info->dset; /* Local pointer to dataset info */
H5D_chunk_it_ud2_t udata; /* User data for iteration callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL)
HDassert(dset);
HDassert(dset->shared);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
HDassert(chunk_addr);
HDassert(down_chunks);
/* Set up user data for B-tree callback */
HDmemset(&udata, 0, sizeof(udata));
udata.common.mesg = &dset->shared->layout;
udata.down_chunks = down_chunks;
udata.chunk_addr = chunk_addr;
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = io_info->dxpl_id;
idx_info.layout = &dset->shared->layout;
/* Iterate over chunks to build mapping of chunk addresses */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_addrmap_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to iterate over chunk index to build address map")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_addrmap() */
#endif /* H5_HAVE_PARALLEL */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_delete
*
* Purpose: Delete raw data storage for entire dataset (i.e. all chunks)
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Thursday, March 20, 2003
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_layout_t *layout)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5O_pline_t pline; /* I/O pipeline message */
htri_t exists; /* Flag if header message of interest exists */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_delete, FAIL)
/* Sanity check */
HDassert(f);
HDassert(oh);
HDassert(layout);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
/* Check for I/O pipeline message */
if((exists = H5O_msg_exists_oh(oh, H5O_PLINE_ID)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header")
else if(exists) {
if(NULL == H5O_msg_read_oh(f, dxpl_id, oh, H5O_PLINE_ID, &pline))
HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "can't find I/O pipeline message")
} /* end else if */
else
HDmemset(&pline, 0, sizeof(pline));
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &pline;
idx_info.layout = layout;
/* Delete the chunked storage information in the file */
if((layout->u.chunk.ops->idx_delete)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk index")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_delete() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_update_cache
*
* Purpose: Update any cached chunks index values after the dataspace
* size has changed
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Quincey Koziol
* Saturday, May 29, 2004
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent, *next; /*cache entry */
H5D_rdcc_ent_t *old_ent; /* Old cache entry */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
unsigned rank; /*current # of dimensions */
hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */
hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */
unsigned u; /*counters */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_update_cache, FAIL)
/* Check args */
HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
/* Get the rank */
rank = dset->shared->layout.u.chunk.ndims-1;
HDassert(rank > 0);
/* 1-D dataset's chunks can't have their index change */
if(rank == 1)
HGOTO_DONE(SUCCEED)
/* Go get the dimensions */
if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
/* Round up to the next integer # of chunks, to accomodate partial chunks */
for(u = 0; u < rank; u++)
chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u];
/* Get the "down" sizes for each dimension */
if(H5V_array_down(rank, chunks, down_chunks) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* 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")
/* Recompute the index for each cached chunk that is in a dataset */
for(ent = rdcc->head; ent; ent = next) {
hsize_t idx; /* Chunk index */
unsigned old_idx; /* Previous index number */
/* Get the pointer to the next cache entry */
next = ent->next;
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
/* Compute the index for the chunk entry */
old_idx = ent->idx; /* Save for later */
ent->idx = H5D_CHUNK_HASH(dset->shared, idx);
if(old_idx != ent->idx) {
/* Check if there is already a chunk at this chunk's new location */
old_ent = rdcc->slot[ent->idx];
if(old_ent != NULL) {
HDassert(old_ent->locked == 0);
/* Check if we are removing the entry we would walk to next */
if(old_ent == next)
next = old_ent->next;
/* Remove the old entry from the cache */
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, old_ent, TRUE) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
} /* end if */
/* Insert this chunk into correct location in hash table */
rdcc->slot[ent->idx] = ent;
/* Null out previous location */
rdcc->slot[old_idx] = NULL;
} /* end if */
} /* end for */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_update_cache() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_copy_cb
*
* Purpose: Copy chunked raw data from source file and insert to the
* index in the destination file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Peter Cao
* August 20, 2005
*
*-------------------------------------------------------------------------
*/
static int
H5D_chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud3_t *udata = (H5D_chunk_it_ud3_t *)_udata; /* User data for callback */
H5D_chunk_ud_t udata_dst; /* User data about new destination chunk */
hbool_t is_vlen = FALSE; /* Whether datatype is variable-length */
hbool_t fix_ref = FALSE; /* Whether to fix up references in the dest. file */
/* General information about chunk copy */
void *bkg = udata->bkg; /* Background buffer for datatype conversion */
void *buf = udata->buf; /* Chunk buffer for I/O & datatype conversions */
size_t buf_size = udata->buf_size; /* Size of chunk buffer */
H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */
/* needed for commpressed variable length data */
hbool_t has_filters = FALSE; /* Whether chunk has filters */
size_t nbytes; /* Size of chunk in file (in bytes) */
H5Z_cb_t cb_struct; /* Filter failure callback struct */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_copy_cb)
/* Get 'size_t' local value for number of bytes in chunk */
H5_ASSIGN_OVERFLOW(nbytes, chunk_rec->nbytes, uint32_t, size_t);
/* Check parameter for type conversion */
if(udata->do_convert) {
if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0)
is_vlen = TRUE;
else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->idx_info_dst->f))
fix_ref = TRUE;
else
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
} /* end if */
/* Check for filtered chunks */
if(pline && pline->nused) {
has_filters = TRUE;
cb_struct.func = NULL; /* no callback function when failed */
} /* end if */
/* Resize the buf if it is too small to hold the data */
if(nbytes > buf_size) {
void *new_buf; /* New buffer for data */
/* Re-allocate memory for copying the chunk */
if(NULL == (new_buf = H5MM_realloc(udata->buf, nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
udata->buf = new_buf;
if(udata->bkg) {
if(NULL == (new_buf = H5MM_realloc(udata->bkg, nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5_ITER_ERROR, "memory allocation failed for raw data chunk")
udata->bkg = new_buf;
if(!udata->cpy_info->expand_ref)
HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size));
bkg = udata->bkg;
} /* end if */
buf = udata->buf;
udata->buf_size = buf_size = nbytes;
} /* end if */
/* read chunk data from the source file */
if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
/* Need to uncompress variable-length & reference data elements */
if(has_filters && (is_vlen || fix_ref)) {
unsigned filter_mask = chunk_rec->filter_mask;
if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "data pipeline read failed")
} /* end if */
/* Perform datatype conversion, if necessary */
if(is_vlen) {
H5T_path_t *tpath_src_mem = udata->tpath_src_mem;
H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst;
H5S_t *buf_space = udata->buf_space;
hid_t tid_src = udata->tid_src;
hid_t tid_dst = udata->tid_dst;
hid_t tid_mem = udata->tid_mem;
void *reclaim_buf = udata->reclaim_buf;
size_t reclaim_buf_size = udata->reclaim_buf_size;
/* Convert from source file to memory */
H5_CHECK_OVERFLOW(udata->nelmts, uint32_t, size_t);
if(H5T_convert(tpath_src_mem, tid_src, tid_mem, (size_t)udata->nelmts, (size_t)0, (size_t)0, buf, NULL, udata->idx_info_dst->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, reclaim_buf_size);
/* Set background buffer to all zeros */
HDmemset(bkg, 0, buf_size);
/* Convert from memory to destination file */
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, udata->nelmts, (size_t)0, (size_t)0, buf, bkg, udata->idx_info_dst->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed")
/* Reclaim space from variable length data */
if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data")
} /* end if */
else if(fix_ref) {
/* Check for expanding references */
/* (background buffer has already been zeroed out, if not expanding) */
if(udata->cpy_info->expand_ref) {
size_t ref_count;
/* Determine # of reference elements to copy */
ref_count = nbytes / H5T_get_size(udata->dt_src);
/* Copy the reference elements */
if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->dxpl_id, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
} /* end if */
/* After fix ref, copy the new reference elements to the buffer to write out */
HDmemcpy(buf, bkg, buf_size);
} /* end if */
/* Set up destination chunk callback information for insertion */
udata_dst.common.mesg = udata->idx_info_dst->layout;
udata_dst.common.offset = chunk_rec->offset;
udata_dst.nbytes = chunk_rec->nbytes;
udata_dst.filter_mask = chunk_rec->filter_mask;
udata_dst.addr = HADDR_UNDEF;
/* Need to compress variable-length & reference data elements before writing to file */
if(has_filters && (is_vlen || fix_ref) ) {
if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(nbytes > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
H5_ASSIGN_OVERFLOW(udata_dst.nbytes, nbytes, size_t, uint32_t);
udata->buf = buf;
udata->buf_size = buf_size;
} /* end if */
/* Insert chunk into the destination index */
if((udata->idx_info_dst->layout->u.chunk.ops->insert)(udata->idx_info_dst, &udata_dst) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk into index")
/* Write chunk data to destination file */
HDassert(H5F_addr_defined(udata_dst.addr));
if(H5F_block_write(udata->idx_info_dst->f, H5FD_MEM_DRAW, udata_dst.addr, nbytes, udata->idx_info_dst->dxpl_id, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to write raw data to file")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_copy_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_copy
*
* Purpose: Copy chunked storage from SRC file to DST file.
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Peter Cao
* August 20, 2005
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info,
H5O_pline_t *pline_src, hid_t dxpl_id)
{
H5D_chunk_it_ud3_t udata; /* User data for iteration callback */
H5D_chk_idx_info_t idx_info_dst; /* Dest. chunked index info */
H5D_chk_idx_info_t idx_info_src; /* Source chunked index info */
H5O_pline_t _pline; /* Temporary pipeline info */
H5O_pline_t *pline; /* Pointer to pipeline info to use */
H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */
hid_t tid_src = -1; /* Datatype ID for source datatype */
hid_t tid_dst = -1; /* Datatype ID for destination datatype */
hid_t tid_mem = -1; /* Datatype ID for memory datatype */
size_t buf_size; /* Size of copy buffer */
size_t reclaim_buf_size; /* Size of reclaim buffer */
void *buf = NULL; /* Buffer for copying data */
void *bkg = NULL; /* Buffer for background during type conversion */
void *reclaim_buf = NULL; /* Buffer for reclaiming data */
H5S_t *buf_space = NULL; /* Dataspace describing buffer */
hid_t sid_buf = -1; /* ID for buffer dataspace */
uint32_t nelmts = 0; /* Number of elements in buffer */
hbool_t do_convert = FALSE; /* Indicate that type conversions should be performed */
hbool_t copy_setup_done = FALSE; /* Indicate that 'copy setup' is done */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_copy, FAIL)
/* Check args */
HDassert(f_src);
HDassert(f_dst);
HDassert(layout_src && H5D_CHUNKED == layout_src->type);
HDassert((H5D_CHUNK_EARRAY == layout_src->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout_src->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout_src->u.chunk.idx_type &&
H5D_COPS_BTREE == layout_src->u.chunk.ops));
HDassert(layout_dst && H5D_CHUNKED == layout_dst->type);
HDassert((H5D_CHUNK_EARRAY == layout_dst->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout_dst->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout_dst->u.chunk.idx_type &&
H5D_COPS_BTREE == layout_dst->u.chunk.ops));
HDassert(dt_src);
/* Initialize the temporary pipeline info */
if(NULL == pline_src) {
HDmemset(&_pline, 0, sizeof(_pline));
pline = &_pline;
} /* end if */
else
pline = pline_src;
/* Compose source & dest chunked index info structs */
idx_info_src.f = f_src;
idx_info_src.dxpl_id = dxpl_id;
idx_info_src.pline = pline;
idx_info_src.layout = layout_src;
idx_info_dst.f = f_dst;
idx_info_dst.dxpl_id = dxpl_id;
idx_info_dst.pline = pline; /* Use same I/O filter pipeline for dest. */
idx_info_dst.layout = layout_dst;
/* Call the index-specific "copy setup" routine */
if((layout_src->u.chunk.ops->copy_setup)(&idx_info_src, &idx_info_dst) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up index-specific chunk copying information")
copy_setup_done = TRUE;
/* Create datatype ID for src datatype */
if((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
/* If there's a VLEN source datatype, set up type conversion information */
if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
H5T_t *dt_dst; /* Destination datatype */
H5T_t *dt_mem; /* Memory datatype */
size_t mem_dt_size; /* Memory datatype size */
size_t tmp_dt_size; /* Temp. datatype size */
size_t max_dt_size; /* Max atatype size */
hsize_t buf_dim; /* Dimension for buffer */
unsigned u;
/* create a memory copy of the variable-length datatype */
if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
/* create variable-length datatype at the destinaton file */
if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
/* Set up the conversion functions */
if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
/* Determine largest datatype size */
if(0 == (max_dt_size = H5T_get_size(dt_src)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(max_dt_size, mem_dt_size);
if(0 == (tmp_dt_size = H5T_get_size(dt_dst)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
max_dt_size = MAX(max_dt_size, tmp_dt_size);
/* Compute the number of elements per chunk */
nelmts = 1;
for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++)
nelmts *= layout_src->u.chunk.dim[u];
/* Create the space and set the initial extent */
buf_dim = nelmts;
if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
/* Atomize */
if((sid_buf = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) {
H5S_close(buf_space);
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
} /* end if */
/* Set initial buffer sizes */
buf_size = nelmts * max_dt_size;
reclaim_buf_size = nelmts * mem_dt_size;
/* Allocate memory for reclaim buf */
if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Indicate that type conversion should be performed */
do_convert = TRUE;
} /* end if */
else {
if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) {
/* Indicate that type conversion should be performed */
do_convert = TRUE;
} /* end if */
H5_ASSIGN_OVERFLOW(buf_size, layout_src->u.chunk.size, uint32_t, size_t);
reclaim_buf_size = 0;
} /* end else */
/* Set up conversion buffer, if appropriate */
if(do_convert) {
/* Allocate background memory for converting the chunk */
if(NULL == (bkg = H5MM_malloc(buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Check for reference datatype and no expanding references & clear background buffer */
if(!cpy_info->expand_ref &&
((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst)))
/* Reset value to zero */
HDmemset(bkg, 0, buf_size);
} /* end if */
/* Allocate memory for copying the chunk */
if(NULL == (buf = H5MM_malloc(buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk")
/* Initialize the callback structure for the source */
HDmemset(&udata, 0, sizeof udata);
udata.common.mesg = layout_src;
udata.file_src = f_src;
udata.idx_info_dst = &idx_info_dst;
udata.buf = buf;
udata.bkg = bkg;
udata.buf_size = buf_size;
udata.tid_src = tid_src;
udata.tid_mem = tid_mem;
udata.tid_dst = tid_dst;
udata.dt_src = dt_src;
udata.do_convert = do_convert;
udata.tpath_src_mem = tpath_src_mem;
udata.tpath_mem_dst = tpath_mem_dst;
udata.reclaim_buf = reclaim_buf;
udata.reclaim_buf_size = reclaim_buf_size;
udata.buf_space = buf_space;
udata.nelmts = nelmts;
udata.pline = pline;
udata.cpy_info = cpy_info;
/* Iterate over chunks to copy data */
if((layout_src->u.chunk.ops->iterate)(&idx_info_src, H5D_chunk_copy_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data")
/* I/O buffers may have been re-allocated */
buf = udata.buf;
bkg = udata.bkg;
done:
if(sid_buf > 0 && H5I_dec_ref(sid_buf, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't decrement temporary dataspace ID")
if(tid_src > 0)
if(H5I_dec_ref(tid_src, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_dst > 0)
if(H5I_dec_ref(tid_dst, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(tid_mem > 0)
if(H5I_dec_ref(tid_mem, FALSE) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")
if(buf)
H5MM_xfree(buf);
if(bkg)
H5MM_xfree(bkg);
if(reclaim_buf)
H5MM_xfree(reclaim_buf);
/* Clean up any index information */
if(copy_setup_done)
if((layout_src->u.chunk.ops->copy_shutdown)(layout_src, layout_dst, dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to shut down index copying info")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_copy() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_bh_size
*
* Purpose: Retrieve the amount of index storage for chunked dataset
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Vailin Choi
* June 8, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
const H5O_pline_t *pline, hsize_t *index_size)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_bh_info, FAIL)
/* Check args */
HDassert(f);
HDassert(layout);
HDassert((H5D_CHUNK_EARRAY == layout->u.chunk.idx_type &&
H5D_COPS_EARRAY == layout->u.chunk.ops) ||
(H5D_CHUNK_BTREE == layout->u.chunk.idx_type &&
H5D_COPS_BTREE == layout->u.chunk.ops));
HDassert(pline);
HDassert(index_size);
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = pline;
idx_info.layout = layout;
/* Get size of index structure */
if((layout->u.chunk.ops->size)(&idx_info, index_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_bh_info() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_iter_dump
*
* Purpose: If the UDATA.STREAM member is non-null then debugging
* information is written to that stream.
*
* Return: Success: Non-negative
*
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
/* ARGSUSED */
static int
H5D_chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_it_ud4_t *udata = (H5D_chunk_it_ud4_t *)_udata; /* User data from caller */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_dump_index_cb)
if(udata->stream) {
unsigned u; /* Local index variable */
/* Print header if not already displayed */
if(!udata->header_displayed) {
HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n");
HDfprintf(udata->stream, " ========== ======== ========== ==============================\n");
/* Set flag that the headers has been printed */
udata->header_displayed = TRUE;
} /* end if */
/* Print information about this chunk */
HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", chunk_rec->filter_mask, chunk_rec->nbytes, chunk_rec->chunk_addr);
for(u = 0; u < udata->ndims; u++)
HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), chunk_rec->offset[u]);
HDfputs("]\n", udata->stream);
} /* end if */
FUNC_LEAVE_NOAPI(H5_ITER_CONT)
} /* H5D_chunk_dump_index_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_dump_index
*
* Purpose: Prints information about the storage index to the specified
* stream.
*
* Return: Success: Non-negative
* Failure: negative
*
* Programmer: Robb Matzke
* Wednesday, April 28, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_dump_index, FAIL)
/* Sanity check */
HDassert(dset);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
/* Only display info if stream is defined */
if(stream) {
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_chunk_it_ud4_t udata; /* User data for callback */
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Display info for index */
if((dset->shared->layout.u.chunk.ops->dump)(&idx_info, stream) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to dump chunk index info")
/* Set up user data for callback */
udata.stream = stream;
udata.header_displayed = FALSE;
udata.ndims = dset->shared->layout.u.chunk.ndims;
/* Iterate over index and dump chunk info */
if((dset->shared->layout.u.chunk.ops->iterate)(&idx_info, H5D_chunk_dump_index_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to dump chunk info")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_dump_index() */
/*-------------------------------------------------------------------------
* Function: H5D_chunk_dest
*
* Purpose: Destroy the entire chunk cache by flushing dirty entries,
* preempting all entries, and freeing the cache itself.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Dataset's chunk cache */
H5D_rdcc_ent_t *ent = NULL, *next = NULL; /* Pointer to current & next cache entries */
int nerrors = 0; /* Accumulated count of errors */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_dest, FAIL)
HDassert(f);
HDassert(dset);
HDassert((H5D_CHUNK_EARRAY == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_EARRAY == dset->shared->layout.u.chunk.ops) ||
(H5D_CHUNK_BTREE == dset->shared->layout.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.u.chunk.ops));
/* 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")
/* Flush all the cached chunks */
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
nerrors++;
} /* end for */
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
/* Release cache structures */
if(rdcc->slot)
rdcc->slot = H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot);
HDmemset(rdcc, 0, sizeof(H5D_rdcc_t));
/* Compose chunked index info struct */
idx_info.f = f;
idx_info.dxpl_id = dxpl_id;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout;
/* Free any index structures */
if((dset->shared->layout.u.chunk.ops->dest)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_dest() */
#ifdef H5D_CHUNK_DEBUG
/*-------------------------------------------------------------------------
* Function: H5D_chunk_stats
*
* Purpose: Print raw data cache statistics to the debug stream. If
* HEADERS is non-zero then print table column headers,
* otherwise assume that the H5AC layer has already printed them.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_chunk_stats(const H5D_t *dset, hbool_t headers)
{
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
double miss_rate;
char ascii[32];
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_chunk_stats, FAIL)
if (!H5DEBUG(AC))
HGOTO_DONE(SUCCEED)
if (headers) {
fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n");
fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n",
"Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes");
fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n",
"-----", "----", "------", "--------", "-----", "-------");
}
#ifdef H5AC_DEBUG
if (H5DEBUG(AC)) headers = TRUE;
#endif
if (headers) {
if (rdcc->nhits>0 || rdcc->nmisses>0) {
miss_rate = 100.0 * rdcc->nmisses /
(rdcc->nhits + rdcc->nmisses);
} else {
miss_rate = 0.0;
}
if (miss_rate > 100) {
sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5));
} else {
sprintf(ascii, "%7.2f%%", miss_rate);
}
fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n",
"raw data chunks", rdcc->nhits, rdcc->nmisses, ascii,
rdcc->ninits, (long)(rdcc->nflushes)-(long)(rdcc->ninits));
}
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_chunk_stats() */
#endif /* H5D_CHUNK_DEBUG */
/*-------------------------------------------------------------------------
* Function: H5D_nonexistent_readvv
*
* Purpose: When the chunk doesn't exist on disk and the chunk is bigger
* than the cache size, performs fill value I/O operation on
* memory buffer, advancing through two I/O vectors, until one
* runs out.
*
* Note: This algorithm is pretty inefficient about initializing and
* terminating the fill buffer info structure and it would be
* faster to refactor this into a "real" initialization routine,
* and a "vectorized fill" routine. -QAK
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* 6 Feb 2009
*
*-------------------------------------------------------------------------
*/
static ssize_t
H5D_nonexistent_readvv(const H5D_io_info_t *io_info,
size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[])
{
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */
hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */
ssize_t bytes_processed = 0; /* Eventual return value */
size_t u, v; /* Local index variables */
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_nonexistent_readvv)
/* Check args */
HDassert(chunk_len_arr);
HDassert(chunk_offset_arr);
HDassert(mem_len_arr);
HDassert(mem_offset_arr);
/* Work through all the sequences */
for(u = *mem_curr_seq, v = *chunk_curr_seq; u < mem_max_nseq && v < chunk_max_nseq; ) {
unsigned char *buf; /* Temporary pointer into read buffer */
size_t size; /* Size of sequence in bytes */
/* Choose smallest buffer to write */
if(chunk_len_arr[v] < mem_len_arr[u])
size = chunk_len_arr[v];
else
size = mem_len_arr[u];
/* Compute offset in memory */
buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[u];
/* Initialize the fill value buffer */
if(H5D_fill_init(&fb_info, buf, FALSE,
NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, size, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
fb_info_init = TRUE;
/* Check for VL datatype & fill the buffer with VL datatype fill values */
if(fb_info.has_vlen_fill_type && H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
/* Release the fill buffer info */
if(H5D_fill_term(&fb_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
fb_info_init = FALSE;
/* Update source information */
chunk_len_arr[v] -= size;
chunk_offset_arr[v] += size;
if(chunk_len_arr[v] == 0)
v++;
/* Update destination information */
mem_len_arr[u] -= size;
mem_offset_arr[u] += size;
if(mem_len_arr[u] == 0)
u++;
/* Increment number of bytes copied */
bytes_processed += (ssize_t)size;
} /* end for */
/* Update current sequence vectors */
*mem_curr_seq = u;
*chunk_curr_seq = v;
/* Set return value */
ret_value = bytes_processed;
done:
/* Release the fill buffer info, if it's been initialized */
if(fb_info_init && H5D_fill_term(&fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info")
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_nonexistent_readvv() */
|