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
|
<html>
<head>
<title>
HDF5 Draft Disk-Format Specification
</title>
</head>
<body>
<center><h1>HDF5: Disk Format Implementation</h1></center>
<ol type=I>
<li><a href="#BootBlock">
Disk Format Level 0 - File Signature and Boot Block</a>
<li><a href="#ObjectDir">
Disk Format Level 1 - File Infrastructure</a>
<ol type=A>
<li><a href="#Btrees">
Disk Format Level 1A - B-link Trees</a>
<li><a href="#SymbolTable">
Disk Format Level 1B - Symbol Table</a>
<li><a href="#SymbolTableEntry">
Disk Format Level 1C - Symbol Table Entry</a>
<li><a href="#LocalHeap">
Disk Format Level 1D - Local Heaps</a>
<li><a href="#GlobalHeap">
Disk Format Level 1E - Global Heap</a>
<li><a href="#FreeSpaceIndex">
Disk Format Level 1F - Free-Space Index</a>
</ol>
<li><a href="#DataObject">
Disk Format Level 2 - Data Objects</a>
<ol type=A>
<li><a href="#ObjectHeader">
Disk Format Level 2a - Data Object Headers</a>
<ol type=1>
<li><a href="#NILMessage"> <!-- 0x0000 -->
Name: NIL</a>
<li><a href="#SimpleDataSpace"> <!-- 0x0001 -->
Name: Simple Data Space</a>
<li><a href="#DataSpaceMessage"> <!-- 0x0002 -->
Name: Data-Space</a>
<li><a href="#DataTypeMessage"> <!-- 0x0003 -->
Name: Data-Type</a>
<li><a href="#ReservedMessage_0004"> <!-- 0x0004 -->
Name: Reserved - not assigned yet</a>
<li><a href="#ReservedMessage_0005"> <!-- 0x0005 -->
Name: Reserved - not assigned yet</a>
<li><a href="#CompactDataStorageMessage"> <!-- 0x0006 -->
Name: Data Storage - Compact</a>
<li><a href="#ExternalFileListMessage"> <!-- 0x0007 -->
Name: Data Storage - External Data Files</a>
<li><a href="#LayoutMessage"> <!-- 0x0008 -->
Name: Data Storage - Layout</a>
<li><a href="#ReservedMessage_0009"> <!-- 0x0009 -->
Name: Reserved - not assigned yet</a>
<li><a href="#ReservedMessage_000A"> <!-- 0x000a -->
Name: Reserved - not assigned yet</a>
<li><a href="#CompressionMessage"> <!-- 0x000b -->
Name: Data Storage - Compressed</a>
<li><a href="#AttributeMessage"> <!-- 0x000c -->
Name: Attribute</a>
<li><a href="#NameMessage"> <!-- 0x000d -->
Name: Object Name</a>
<li><a href="#ModifiedMessage"> <!-- 0x000e -->
Name: Object Modification Date & Time</a>
<li><a href="#SharedMessage"> <!-- 0x000f -->
Name: Shared Object Message</a>
<li><a href="#ContinuationMessage"> <!-- 0x0010 -->
Name: Object Header Continuation</a>
<li><a href="#SymbolTableMessage"> <!-- 0x0011 -->
Name: Symbol Table Message</a>
</ol>
<li><a href="#SharedObjectHeader">
Disk Format: Level 2b - Shared Data Object Headers</a>
<li><a href="#DataStorage">
Disk Format: Level 2c - Data Object Data Storage</a>
</ol>
</ol>
<h2>Disk Format Implementation</h2>
<P>The format of a HDF5 file on disk encompasses several
key ideas of the current HDF4 & AIO file formats as well as
addressing some short-comings therein. The new format will be
more self-describing than the HDF4 format and will be more
uniformly applied to data objects in the file.
<P>Three levels of information compose the file format. The level
0 contains basic information for identifying and
"boot-strapping" the file. Level 1 information is composed of
the object directory (stored as a B-tree) and is used as the
index for all the objects in the file. The rest of the file is
composed of data-objects at level 2, with each object
partitioned into header (or "meta") information and data
information.
<p>The sizes of various fields in the following layout tables are
determined by looking at the number of columns the field spans
in the table. There are three exceptions: (1) The size may be
overridden by specifying a size in parentheses, (2) the size of
addresses is determined by the <em>Size of Addresses</em> field
in the boot block, and (3) the size of size fields is determined
by the <em>Size of Sizes</em> field in the boot block.
<h3><a name="BootBlock">
Disk Format: Level 0 - File Signature and Boot Block</a></h3>
<P>The boot block may begin at certain predefined offsets within
the HDF5 file, allowing a block of unspecified content for
users to place additional information at the beginning (and
end) of the HDF5 file without limiting the HDF5 library's
ability to manage the objects within the file itself. This
feature was designed to accommodate wrapping an HDF5 file in
another file format or adding descriptive information to the
file without requiring the modification of the actual file's
information. The boot-block is located by searching for the
HDF5 file signature at byte offset 0, byte offset 512 and at
successive locations in the file, each a multiple of two of
the previous location, i.e. 0, 512, 1024, 2048, etc.
<P>The boot-block is composed of a file signature, followed by
boot block and object directory version numbers, information
about the sizes of offset and length values used to describe
items within the file, the size of each object directory page,
and a symbol table entry for the root object in the file.
<p>
<center>
<table border align=center cellpadding=4 width="80%">
<caption align=top>
<B>HDF5 Boot Block Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>HDF5 File Signature (8 bytes)<br><br></td>
</tr>
<tr align=center>
<td>Version # of Boot Block</td>
<td>Version # of Global Free-Space Storage</td>
<td>Version # of Object Directory</td>
<td>Reserved</td>
</tr>
<tr align=center>
<td>Version # of Shared Header Message Format</td>
<td>Size of Addresses</td>
<td>Size of Sizes</td>
<td>Reserved (zero)</td>
</tr>
<tr align=center>
<td colspan=2>Symbol Table Leaf Node K</td>
<td colspan=2>Symbol Table Internal Node K</td>
</tr>
<tr align=center>
<td colspan=4>File Consistency Flags</td>
</tr>
<tr align=center>
<td colspan=4>Base Address</td>
</tr>
<tr align=center>
<td colspan=4>Address of Global Free-Space Heap</td>
</tr>
<tr align=center>
<td colspan=4>End of File Address</td>
</tr>
<tr align=center>
<td colspan=4>Reserved Address</td>
</tr>
<tr align=center>
<td colspan=4><br>Root Group Symbol Table Entry<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>File Signature</td>
<td>This field contains a constant value and can be used to
quickly identify a file as being an HDF5 file. The
constant value is designed to allow easy identification of
an HDF5 file and to allow certain types of data corruption
to be detected. The file signature of a HDF5 file always
contain the following values:
<br><br><center>
<table border align=center cellpadding=4 width="80%">
<tr align=center>
<td>decimal</td>
<td width="8%">137</td>
<td width="8%">72</td>
<td width="8%">68</td>
<td width="8%">70</td>
<td width="8%">13</td>
<td width="8%">10</td>
<td width="8%">26</td>
<td width="8%">10</td>
</tr>
<tr align=center>
<td>hexadecimal</td>
<td width="8%">89</td>
<td width="8%">48</td>
<td width="8%">44</td>
<td width="8%">46</td>
<td width="8%">0d</td>
<td width="8%">0a</td>
<td width="8%">1a</td>
<td width="8%">0a</td>
</tr>
<tr align=center>
<td>ASCII C Notation</td>
<td width="8%">\211</td>
<td width="8%">H</td>
<td width="8%">D</td>
<td width="8%">F</td>
<td width="8%">\r</td>
<td width="8%">\n</td>
<td width="8%">\032</td>
<td width="8%">\n</td>
</tr>
</table>
</center>
<br>
This signature both identifies the file as a HDF5 file
and provides for immediate detection of common
file-transfer problems. The first two bytes distinguish
HDF5 files on systems that expect the first two bytes to
identify the file type uniquely. The first byte is
chosen as a non-ASCII value to reduce the probability
that a text file may be misrecognized as a HDF5 file;
also, it catches bad file transfers that clear bit
7. Bytes two through four name the format. The CR-LF
sequence catches bad file transfers that alter newline
sequences. The control-Z character stops file display
under MS-DOS. The final line feed checks for the inverse
of the CR-LF translation problem. (This is a direct
descendent of the PNG file signature.)</td>
</tr>
<tr valign=top>
<td>Version # of the Boot Block</td>
<td>This value is used to determine the format of the
information in the boot block. When the format of the
information in the boot block is changed, the version #
is incremented to the next integer and can be used to
determine how the information in the boot block is
formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Global Free-Space Storage</td>
<td>This value is used to determine the format of the
information in the Global Free-Space Heap. Currently,
this is implemented as a B-tree of length/offset pairs
to locate free space in the file, but future advances in
the file-format could change the method of finding
global free-space. When the format of the information
is changed, the version # is incremented to the next
integer and can be used to determine how the information
is formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Object Directory</td>
<td>This value is used to determine the format of the
information in the Object Directory. When the format of
the information in the Object Directory is changed, the
version # is incremented to the next integer and can be
used to determine how the information in the Object
Directory is formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Shared Header Message Format</td>
<td>This value is used to determine the format of the
information in a shared object header message, which is
stored in the global small-data heap. Since the format
of the shared header messages differ from the private
header messages, a version # is used to identify changes
in the format.</td>
</tr>
<tr valign=top>
<td>Size of Addresses</td>
<td>This value contains the number of bytes used for
addresses in the file. The values for the addresses of
objects in the file are relative to a base address,
usually the address of the boot block signature. This
allows a wrapper to be added after the file is created
without invalidating the internal offset locations.</td>
</tr>
<tr valign=top>
<td>Size of Sizes</td>
<td>This value contains the number of bytes used to store
the size of an object.</td>
</tr>
<tr valign=top>
<td>Symbol Table Leaf Node K</td>
<td>Each leaf node of a symbol table B-tree will have at
least this many entries but not more than twice this
many. If a symbol table has a single leaf node then it
may have fewer entries.</td>
</tr>
<tr valign=top>
<td>Symbol Table Internal Node K</td>
<td>Each internal node of a symbol table B-tree will have
at least K pointers to other nodes but not more than 2K
pointers. If the symbol table has only one internal
node then it might have fewer than K pointers.</td>
</tr>
<tr valign=top>
<td>Bytes per B-Tree Page</td>
<td>This value contains the # of bytes used for symbol
pairs per page of the B-Trees used in the file. All
B-Tree pages will have the same size per page. <br>(For
32-bit file offsets, 340 objects is the maximum per 4KB
page, and for 64-bit file offset, 254 objects will fit
per 4KB page. In general, the equation is: <br> <#
of objects> = FLOOR((<page size>-<offset
size>)/(<Symbol size>+<offset size>))-1 )</td>
</tr>
<tr valign=top>
<td>File Consistency Flags</td>
<td>This value contains flags to indicate information
about the consistency of the information contained
within the file. Currently, the following bit flags are
defined: bit 0 set indicates that the file is opened for
write-access and bit 1 set indicates that the file has
been verified for consistency and is guaranteed to be
consistent with the format defined in this document.
Bits 2-31 are reserved for future use. Bit 0 should be
set as the first action when a file is opened for write
access and should be cleared only as the final action
when closing a file. Bit 1 should be cleared during
normal access to a file and only set after the file's
consistency is guaranteed by the library or a
consistency utility.</td>
</tr>
<tr valign=top>
<td>Base Address</td>
<td>This is the absolute file address of the first byte of
the hdf5 data within the file. Unless otherwise noted,
all other file addresses are relative to this base
address.</td>
</tr>
<tr valign=top>
<td>Address of Global Free-Space Heap</td>
<td>This value contains the relative address of the B-Tree
used to manage the blocks of data which are unused in the
file currently. The free-space heap is used to manage the
blocks of bytes at the file-level which become unused with
objects are moved within the file.</td>
</tr>
<tr valign=top>
<td>End of File Address</td>
<td>This is the relative file address of the first byte past
the end of all HDF5 data. It is used to determine if a
file has been accidently truncated and as an address where
file memory allocation can occur if the free list is not
used.</td>
</tr>
<tr valign=top>
<td>Reserved Address</td>
<td>This address field is present for alignment purposes and
is always set to the undefined address value (all bits
set).</td>
</tr>
<tr valign=top>
<td>Root Group Symbol Table Entry</td>
<td>This symbol-table entry (described later in this
document) refers to the entry point into the group
graph. If the file contains a single object, then that
object can be the root object and no groups are used.</td>
</tr>
</table>
</center>
<h3><a name="Btrees">Disk Format: Level 1A - B-link Trees</a></h3>
<p>B-link trees allow flexible storage for objects which tend to grow
in ways that cause the object to be stored discontiguously. B-trees
are described in various algorithms books including "Introduction to
Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald
L. Rivest. The B-link tree, in which the sibling nodes at a
particular level in the tree are stored in a doubly-linked list,
is described in the "Efficient Locking for Concurrent Operations
on B-trees" paper by Phillip Lehman and S. Bing Yao as published
in the <em>ACM Transactions on Database Systems</em>, Vol. 6,
No. 4, December 1981.
<p>The B-link trees implemented by the file format contain one more
key than the number of children. In other words, each child
pointer out of a B-tree node has a left key and a right key.
The pointers out of internal nodes point to sub-trees while
the pointers out of leaf nodes point to other file data types.
Notwithstanding that difference, internal nodes and leaf nodes
are identical.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>B-tree Nodes</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Node Signature</td>
<tr align=center>
<td>Node Type</td>
<td>Node Level</td>
<td colspan=2>Entries Used</td>
<tr align=center>
<td colspan=4>Address of Left Sibling</td>
<tr align=center>
<td colspan=4>Address of Right Sibling</td>
<tr align=center>
<td colspan=4>Key 0 (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 0</td>
<tr align=center>
<td colspan=4>Key 1 (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 1</td>
<tr align=center>
<td colspan=4>...</td>
<tr align=center>
<td colspan=4>Key 2<em>K</em> (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 2<em>K</em></td>
<tr align=center>
<td colspan=4>Key 2<em>K</em>+1 (variable size)</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Node Signature</td>
<td>The value ASCII 'TREE' is used to indicate the
beginning of a B-link tree node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file.</td>
</tr>
<tr valign=top>
<td>Node Type</td>
<td>Each B-link tree points to a particular type of data.
This field indicates the type of data as well as
implying the maximum degree <em>K</em> of the tree and
the size of each Key field.
<br>
<dl compact>
<dt>0
<dd>This tree points to symbol table nodes.
<dt>1
<dd>This tree points to a (partial) linear address space.
</dl>
</td>
</tr>
<tr valign=top>
<td>Node Level</td>
<td>The node level indicates the level at which this node
appears in the tree (leaf nodes are at level zero). Not
only does the level indicate whether child pointers
point to sub-trees or to data, but it can also be used
to help file consistency checking utilities reconstruct
damanged trees.</td>
</tr>
<tr valign=top>
<td>Entries Used</td>
<td>This determines the number of children to which this
node points. All nodes of a particular type of tree
have the same maximum degree, but most nodes will point
to less than that number of children. The valid child
pointers and keys appear at the beginning of the node
and the unused pointers and keys appear at the end of
the node. The unused pointers and keys have undefined
values.</td>
</tr>
<tr valign=top>
<td>Address of Left Sibling</td>
<td>This is the file address of the left sibling of the
current node relative to the boot block. If the current
node is the left-most node at this level then this field
is the undefined address (all bits set).</td>
</tr>
<tr valign=top>
<td>Address of Right Sibling</td>
<td>This is the file address of the right sibling of the
current node relative to the boot block. If the current
node is the right-most node at this level then this
field is the undefined address (all bits set).</td>
</tr>
<tr valign=top>
<td>Keys and Child Pointers</td>
<td>Each tree has 2<em>K</em>+1 keys with 2<em>K</em>
child pointers interleaved between the keys. The number
of keys and child pointers actually containing valid
values is determined by the `Entries Used' field. If
that field is <em>N</em> then the B-link tree contains
<em>N</em> child pointers and <em>N</em>+1 keys.</td>
</tr>
<tr valign=top>
<td>Key</td>
<td>The format and size of the key values is determined by
the type of data to which this tree points. The keys are
ordered and are boundaries for the contents of the child
pointer. That is, the key values represented by child
<em>N</em> fall between Key <em>N</em> and Key
<em>N</em>+1. Whether the interval is open or closed on
each end is determined by the type of data to which the
tree points.</td>
</tr>
<tr valign=top>
<td>Address of Children</td>
<td>The tree node contains file addresses of subtrees or
data depending on the node level (0 implies data
addresses).</td>
</tr>
</table>
</center>
<h3><a name="SymbolTable">Disk Format: Level 1B - Symbol Table</a></h3>
<p>A symbol table is a group internal to the file that allows
arbitrary nesting of objects (including other symbol
tables). A symbol table maps a set of names to a set of file
address relative to the file boot block. Certain meta data
for an object to which the symbol table points can be cached
in the symbol table in addition to (or in place of?) the
object header.
<p>An HDF5 object name space can be stored hierarchically by
partitioning the name into components and storing each
component in a symbol table. The symbol table entry for a
non-ultimate component points to the symbol table containing
the next component. The symbol table entry for the last
component points to the object being named.
<p>A symbol table is a collection of symbol table nodes pointed
to by a B-link tree. Each symbol table node contains entries
for one or more symbols. If an attempt is made to add a
symbol to an already full symbol table node containing
2<em>K</em> entries, then the node is split and one node
contains <em>K</em> symbols and the other contains
<em>K</em>+1 symbols.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Node</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Node Signature</td>
<tr align=center>
<td>Version Number</td>
<td>Reserved for Future Use</td>
<td colspan=2>Number of Symbols</td>
<tr align=center>
<td colspan=4><br><br>Symbol Table Entries<br><br><br></td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Node Signature</td>
<td>The value ASCII 'SNOD' is used to indicate the
beginning of a symbol table node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file.</td>
</tr>
<tr valign=top>
<td>Version Number</td>
<td>The version number for the symbol table node. This
document describes version 1.</td>
</tr>
<tr valign=top>
<td>Number of Symbols</td>
<td>Although all symbol table nodes have the same length,
most contain fewer than the maximum possible number of
symbol entries. This field indicates how many entries
contain valid data. The valid entries are packed at the
beginning of the symbol table node while the remaining
entries contain undefined values.</td>
</tr>
<tr valign=top>
<td>Symbol Table Entries</td>
<td>Each symbol has an entry in the symbol table node.
The format of the entry is described below.</td>
</tr>
</table>
</center>
<h3><a name="SymbolTableEntry">
Disk Format: Level 1C - Symbol-Table Entry </a></h3>
<p>Each symbol table entry in a symbol table node is designed to allow
for very fast browsing of commonly stored scientific objects.
Toward that design goal, the format of the symbol-table entries
includes space for caching certain constant meta data from the
object header.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Entry</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Name Offset (<size> bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Object Header Address</td>
</tr>
<tr align=center>
<td colspan=4>Symbol-Type</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br><br>Scratch-pad Space (16 bytes)<br><br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Name Offset</td>
<td>This is the byte offset into the symbol table local
heap for the name of the symbol. The name is null
terminated.</td>
</tr>
<tr valign=top>
<td>Object Header Address</td>
<td>Every object has an object header which serves as a
permanent home for the object's meta data. In addition
to appearing in the object header, the meta data can be
cached in the scratch-pad space.</td>
</tr>
<tr valign=top>
<td>Symbol-Type</td>
<td>The symbol type is determined from the object header.
It also determines the format for the scratch-pad space.
The value zero indicates that no object header meta data
is cached in the symbol table entry.
<br>
<dl compact>
<dt>0
<dd>No data is cached by the symbol table entry. This
is guaranteed to be the case when an object header
has a link count greater than one.
<dt>1
<dd>Symbol table meta data is cached in the symbol
table entry. This implies that the symbol table
entry refers to another symbol table.
<dt>2
<dd>The entry is a symbolic link. The first four bytes
of the scratch pad space are the offset into the local
heap for the link value. The object header address
will be undefined.
<dt><em>N</em>
<dd>Other cache values can be defined later and
libraries that don't understand the new values will
still work properly.
</dl>
</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>These for bytes are present so that the scratch pad
space is aligned on an eight-byte boundary. They are
always set to zero.</td>
</tr>
<tr valign=top>
<td>Scratch-Pad Space</td>
<td>This space is used for different purposes, depending
on the value of the Symbol Type field. Any meta-data
about a dataset object represented in the scratch-pad
space is duplicated in the object header for that
dataset. Furthermore, no data is cached in the symbol
table entry scratch-pad space if the object header for
the symbol table entry has a link count greater than
one.</td>
</tr>
</table>
</center>
<p>The symbol table entry scratch-pad space is formatted
according to the value of the Symbol Type field. If the
Symbol Type field has the value zero then no information is
stored in the scratch pad space.
<p>If the Symbol Type field is one, then the scratch pad space
contains cached meta data for another symbol table with the format:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Scratch-Pad Format</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Address of B-tree</td>
<tr align=center>
<td colspan=4>Address of Name Heap</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Address of B-tree</td>
<td>This is the file address for the symbol table's
B-tree.</td>
</tr>
<tr valign=top>
<td>Address of Name Heap</td>
<td>This is the file address for the symbol table's local
heap that stores the symbol names.</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbolic Link Scratch-Pad Format</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Offset to Link Value</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Offset to Link Value</td>
<td>The value of a symbolic link (that is, the name of the
thing to which it points) is stored in the local heap.
This field is the 4-byte offset into the local heap for
the start of the link value, which is null terminated.</td>
</tr>
</table>
</center>
<h3><a name="LocalHeap">Disk Format: Level 1D - Local Heaps</a></h3>
<p>A heap is a collection of small heap objects. Objects can be
inserted and removed from the heap at any time and the address
of a heap doesn't change once the heap is created. Note: this
is the "local" version of the heap mostly intended for the
storage of names in a symbol table. The storage of small
objects in a global heap is described below.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Local Heaps</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Heap Signature</td>
</tr>
<tr align=center>
<td colspan=4>Reserved (zero)</td>
</tr>
<tr align=center>
<td colspan=4>Data Segment Size</td>
</tr>
<tr align=center>
<td colspan=4>Offset to Head of Free-list (<size> bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Address of Data Segment</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Heap Signature</td>
<td>The valid ASCII 'HEAP' is used to indicate the
beginning of a heap. This gives file consistency
checking utilities a better chance of reconstructing a
damaged file.</td>
</tr>
<tr valign=top>
<td>Data Segment Size</td>
<td>The total amount of disk memory allocated for the heap
data. This may be larger than the amount of space
required by the object stored in the heap. The extra
unused space holds a linked list of free blocks.</td>
</tr>
<tr valign=top>
<td>Offset to Head of Free-list</td>
<td>This is the offset within the heap data segment of the
first free block (or all 0xff bytes if there is no free
block). The free block contains <size> bytes that
are the offset of the next free chunk (or all 0xff bytes
if this is the last free chunk) followed by <size>
bytes that store the size of this free chunk.</td>
</tr>
<tr valign=top>
<td>Address of Data Segment</td>
<td>The data segment originally starts immediately after
the heap header, but if the data segment must grow as a
result of adding more objects, then the data segment may
be relocated to another part of the file.</td>
</tr>
</table>
</center>
<p>Objects within the heap should be aligned on an 8-byte boundary.
<h3><a name="GlobalHeap">Disk Format: Level 1E - Global Heap</a></h3>
<p>Each HDF5 file has a global heap which stores various types of
information which is typically shared between datasets. The
global heap was designed to satisfy these goals:
<ol type="A">
<li>Repeated access to a heap object must be efficient without
resulting in repeated file I/O requests. Since global heap
objects will typically be shared among several datasets it's
probable that the object will be accessed repeatedly.
<br><br>
<li>Collections of related global heap objects should result in
fewer and larger I/O requests. For instance, a dataset of
void pointers will have a global heap object for each
pointer. Reading the entire set of void pointer objects
should result in a few large I/O requests instead of one small
I/O request for each object.
<br><br>
<li>It should be possible to remove objects from the global heap
and the resulting file hole should be eligible to be reclaimed
for other uses.
<br><br>
</ol>
<p>The implementation of the heap makes use of the memory
management already available at the file level and combines that
with a new top-level object called a <em>collection</em> to
achieve Goal B. The global heap is the set of all collections.
Each global heap object belongs to exactly one collection and
each collection contains one or more global heap objects. For
the purposes of disk I/O and caching, a collection is treated as
an atomic object.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Global Heap Collection</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Magic Number</td>
</tr>
<tr align=center>
<td>Version</td>
<td colspan=3>Reserved</td>
</td>
<tr align=center>
<td colspan=4>Collection Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Object 1<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object 2<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>...<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object <em>N</em><br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object 0 (free space)<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Magic Number</td>
<td>The magic number for global heap collections are the
four bytes `G', `C', `O', `L'.</td>
</tr>
<tr valign=top>
<td>Version</td>
<td>Each collection has its own version number so that new
collections can be added to old files. This document
describes version zero of the collections.
</tr>
<tr valign=top>
<td>Collection Data Size</td>
<td>This is the size in bytes of the entire collection
including this field. The default (and minimum)
collection size is 4096 bytes which is a typical file
system block size and which allows for 170 16-byte heap
objects plus their overhead.</td>
</tr>
<tr valign=top>
<td>Object <em>i</em> for positive <em>i</em></td> <td>The
objects are stored in any order with no intervening unused
space.</td>
</tr>
<tr valign=top>
<td>Object 0</td>
<td>Object zero, when present, represents the free space in
the collection. Free space always appears at the end of
the collection. If the free space is too small to store
the header for object zero (described below) then the
header is implied.
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Global Heap Object</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=2>Object ID</td>
<td colspan=2>Reference Count</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Object Total Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Object Data<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Object ID</td>
<td>Each object has a unique identification number within a
collection. The identification numbers are chosen so that
new objects have the smallest value possible with the
exception that the identifier `0' always refers to the
object which represents all free space within the
collection.</td>
</tr>
<tr valign=top>
<td>Reference Count</td>
<td>All heap objects have a reference count field. An
object which is referenced from some other part of the
file will have a positive reference count. The reference
count for Object zero is always zero.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>Zero padding to align next field on an 8-byte
boundary.</td>
</tr>
<tr valign=top>
<td>Object Total Size</td>
<td>This is the total size in bytes of the object. It
includes all fields listed in this table.</td>
</tr>
<tr valign=top>
<td>Object Data</td>
<td>The object data is treated as a one-dimensional array
of bytes to be interpreted by the caller.</td>
</tr>
</table>
</center>
<h3><a name="FreeSpaceIndex">Disk Format: Level 1F - Free-Space
Index (NOT FULLY DEFINED)</a></h3>
<p>The Free-Space Index is a collection of blocks of data,
dispersed throughout the file, which are currently not used by
any file objects. The blocks of data are indexed by a B-tree of
their length within the file.
<p>Each B-Tree page is composed of the following entries and
B-tree management information, organized as follows:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Free-Space Heap Page</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Free-Space Heap Signature</td>
<tr align=center>
<td colspan=4>B-Tree Left-Link Offset</td>
<tr align=center>
<td colspan=4><br>Length of Free-Block #1<br> <br></td>
<tr align=center>
<td colspan=4><br>Offset of Free-Block #1<br> <br></td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4><br>Length of Free-Block #n<br> <br></td>
<tr align=center>
<td colspan=4><br>Offset of Free-Block #n<br> <br></td>
<tr align=center>
<td colspan=4>"High" Offset</td>
<tr align=center>
<td colspan=4>Right-Link Offset</td>
</table>
</center>
<p>
<dl>
<dt> The elements of the free-space heap page are described below:
<dd>
<dl>
<dt>Free-Space Heap Signature: (4 bytes)
<dd>The value ASCII: 'FREE' is used to indicate the
beginning of a free-space heap B-Tree page. This gives
file consistency checking utilities a better chance of
reconstructing a damaged file.
<dt>B-Tree Left-Link Offset: (<offset> bytes)
<dd>This value is used to indicate the offset of all offsets
in the B-link-tree which are smaller than the value of the
offset in entry #1. This value is also used to indicate a
leaf node in the B-link-tree by being set to all ones.
<dt>Length of Free-Block #n: (<length> bytes)
<dd>This value indicates the length of an un-used block in
the file.
<dt>Offset of Free-Block #n: (<offset> bytes)
<dd>This value indicates the offset in the file of an
un-used block in the file.
<dt>"High" Offset: (4-bytes)
<dd>This offset is used as the upper bound on offsets
contained within a page when the page has been split.
<dt>Right-link Offset: (<offset> bytes)
<dd>This value is used to indicate the offset of the next
child to the right of the parent of this object directory
page. When there is no node to the right, this value is
all zeros.
</dl>
</dl>
<p>The algorithms for searching and inserting objects in the
B-tree pages are described fully in the Lehman & Yao paper,
which should be read to provide a full description of the
B-Tree's usage.
<h3><a name="DataObject">Disk Format: Level 2 - Data Objects </a></h3>
<p>Data objects contain the real information in the file. These
objects compose the scientific data and other information which
are generally thought of as "data" by the end-user. All the
other information in the file is provided as a framework for
these data objects.
<p>A data object is composed of header information and data
information. The header information contains the information
needed to interpret the data information for the data object as
well as additional "meta-data" or pointers to additional
"meta-data" used to describe or annotate each data object.
<h3><a name="ObjectHeader">
Disk Format: Level 2a - Data Object Headers</a></h3>
<p>The header information of an object is designed to encompass
all the information about an object which would be desired to be
known, except for the data itself. This information includes
the dimensionality, number-type, information about how the data
is stored on disk (in external files, compressed, broken up in
blocks, etc.), as well as other information used by the library
to speed up access to the data objects or maintain a file's
integrity. The header of each object is not necessarily located
immediately prior to the object's data in the file and in fact
may be located in any position in the file.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Object Headers</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=1 width="25%">Version # of Object Header</td>
<td colspan=1 width="25%">Reserved</td>
<td colspan=2 width="50%">Number of Header Messages</td>
</tr>
<tr align=center>
<td colspan=4>Object Reference Count</td>
</tr>
<tr align=center>
<td colspan=4><br>Total Object-Header Size<br><br></td>
</tr>
<tr align=center>
<td colspan=2>Header Message Type #1</td>
<td colspan=2>Size of Header Message Data #1</td>
</tr>
<tr align=center>
<td>Flags</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br>Header Message Data #1<br><br></td>
</tr>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr align=center>
<td colspan=2>Header Message Type #n</td>
<td colspan=2>Size of Header Message Data #n</td>
</tr>
<tr align=center>
<td>Flags</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br>Header Message Data #n<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Version # of the object header</td>
<td>This value is used to determine the format of the
information in the object header. When the format of the
information in the object header is changed, the version #
is incremented and can be used to determine how the
information in the object header is formatted.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>Always set to zero.</td>
</tr>
<tr valign=top>
<td>Number of header messages</td>
<td>This value determines the number of messages listed in
this object header. This provides a fast way for software
to prepare storage for the messages in the header.</td>
</tr>
<tr valign=top>
<td>Object Reference Count</td>
<td>This value specifies the number of references to this
object within the current file. References to the
data-object from external files are not tracked.</td>
</tr>
<tr valign=top>
<td>Total Object-Header Size</td>
<td>This value specifies the total number of bytes of header
message data following this length field for the current
message as well as any continuation data located elsewhere
in the file.</td>
</tr>
<tr valign=top>
<td>Header Message Type</td>
<td>The header message type specifies the type of
information included in the header message data following
the type along with a small amount of other information.
Bit 15 of the message type is set if the message is
constant (constant messages cannot be changed since they
may be cached in symbol table entries throughout the
file). The header message types for the pre-defined
header messages will be included in further discussion
below.</td>
</tr>
<tr valign=top>
<td>Size of Header Message Data</td>
<td>This value specifies the number of bytes of header
message data following the header message type and length
information for the current message. The size includes
padding bytes to make the message a multiple of eight
bytes.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>This is a bit field with the following definition:
<dl>
<dt><code>0</code>
<dd>If set, the message data is constant. This is used
for messages like the data type message of a dataset.
<dt><code>1</code>
<dd>If set, the message is stored in the global heap and
the Header Message Data field contains a Shared Object
message. and the Size of Header Message Data field
contains the size of that Shared Object message.
<dt><code>2-7</code>
<dd>Reserved
</dl>
</td>
<tr valign=top>
<td>Header Message Data</td>
<td>The format and length of this field is determined by the
header message type and size respectively. Some header
message types do not require any data and this information
can be eliminated by setting the length of the message to
zero. The data is padded with enough zeros to make the
size a multiple of eight.</td>
</tr>
</table>
</center>
<p>The header message types and the message data associated with
them compose the critical "meta-data" about each object. Some
header messages are required for each object while others are
optional. Some optional header messages may also be repeated
several times in the header itself, the requirements and number
of times allowed in the header will be noted in each header
message description below.
<P>The following is a list of currently defined header messages:
<hr>
<h3><a name="NILMessage">Name: NIL</a></h3>
<b>Type: </b>0x0000<br>
<b>Length:</b> varies<br>
<b>Status:</b> Optional, may be repeated.<br>
<b>Purpose and Description:</b> The NIL message is used to
indicate a message
which is to be ignored when reading the header messages for a data object.
[Probably one which has been deleted for some reason.]<br>
<b>Format of Data:</b> Unspecified.<br>
<b>Examples:</b> None.
<hr>
<h3><a name="SimpleDataSpace">Name: Simple Data Space</a></h3>
<b>Type: </b>0x0001<br>
<b>Length:</b> varies<br>
<b>Status:</b> One of the <em>Simple Data Space</em> or
<em>Data-Space</em> messages is required (but not both) and may
not be repeated.<br>
<p>The <em>Simple Dimensionality</em> message describes the number
of dimensions and size of each dimension that the data object
has. This message is only used for datasets which have a
simple, rectilinear grid layout, datasets requiring a more
complex layout (irregularly or unstructured grids, etc) must use
the <em>Data-Space</em> message for expressing the space the
dataset inhabits.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Simple Data Space Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Version</td>
<td>Dimensionality</td>
<td>Flags</td>
<td>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Dimension Size #1 (<size> bytes)</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Dimension Size #n (<size> bytes)</td>
<tr align=center>
<td colspan=4>Dimension Maximum #1 (<size> bytes)</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Dimension Maximum #n (<size> bytes)</td>
<tr align=center>
<td colspan=4>Permutation Index #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Permutation Index #n</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Dimensionality</td>
<td>This value is the number of dimensions that the data
object has.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>This field is used to store flags to indicate the
presence of parts of this message. Bit 0 (the least
significant bit) is used to indicate that maximum
dimensions are present. Bit 1 is used to indicate that
permutation indices are present for each dimension.</td>
</tr>
<tr valign=top>
<td>Dimension Size #n (<size> bytes)</td>
<td>This value is the current size of the dimension of the
data as stored in the file. The first dimension stored in
the list of dimensions is the slowest changing dimension
and the last dimension stored is the fastest changing
dimension.</td>
</tr>
<tr valign=top>
<td>Dimension Maximum #n (<size> bytes)</td>
<td>This value is the maximum size of the dimension of the
data as stored in the file. This value may be the special
value <UNLIMITED> (all bits set) which indicates
that the data may expand along this dimension
indefinitely. If these values are not stored, the maximum
value of each dimension is assumed to be the same as the
current size value.</td>
</tr>
<tr valign=top>
<td>Permutation Index #n (4 bytes)</td>
<td>This value is the index permutation used to map
each dimension from the canonical representation to an
alternate axis for each dimension. If these values are
not stored, the first dimension stored in the list of
dimensions is the slowest changing dimension and the last
dimension stored is the fastest changing dimension.</td>
</tr>
</table>
</center>
<h4>Examples</h4>
<dl>
<dt> Example #1
<dd>A sample 640 horizontally by 480 vertically raster image
dimension header. The number of dimensions would be set to 2
and the first dimension's size and maximum would both be set
to 480. The second dimension's size and maximum would both be
set to 640
.
<dt>Example #2
<dd>A sample 4 dimensional scientific dataset which is composed
of 30x24x3 slabs of data being written out in an unlimited
series every several minutes as timestep data (currently there
are five slabs). The number of dimensions is 4. The first
dimension size is 5 and it's maximum is <UNLIMITED>. The
second through fourth dimensions' size and maximum value are
set to 3, 24, and 30 respectively.
<dt>Example #3
<dd>A sample unlimited length text string, currently of length
83. The number of dimensions is 1, the size of the first
dimension is 83 and the maximum of the first dimension is set
to <UNLIMITED>, allowing further text data to be
appended to the string or possibly the string to be replaced
with another string of a different size. (This could also be
stored as a scalar dataset with number-type set to "string")
</dl>
<hr>
<h3><a name="DataSpaceMessage">Name: Data-Space (Fiber Bundle?)</a></h3>
<b>Type: </b>0x0002<br>
<b>Length:</b> varies<br>
<b>Status:</b> One of the <em>Simple Dimensionality</em> or
<em>Data-Space</em> messages is required (but not both) and may
not be repeated.<br> <b>Purpose and Description:</b> The
<em>Data-Space</em> message describes space that the dataset is
mapped onto in a more comprehensive way than the <em>Simple
Dimensionality</em> message is capable of handling. The
data-space of a dataset encompasses the type of coordinate system
used to locate the dataset's elements as well as the structure and
regularity of the coordinate system. The data-space also
describes the number of dimensions which the dataset inhabits as
well as a possible higher dimensional space in which the dataset
is located within.
<br>
<b>Format of Data:</b>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Message Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Mesh Type</td>
<tr align=center>
<td colspan=4>Logical Dimensionality</td>
</table>
</center>
<p>
<dl>
<dt>The elements of the dimensionality message are described below:
<dd>
<dl>
<dt>Mesh Type: (unsigned 32-bit integer)
<dd>This value indicates whether the grid is
polar/spherical/cartesion,
structured/unstructured and regular/irregular. <br>
The mesh type value is broken up as follows: <br>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Mesh-Type Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=1>Mesh Embedding</td>
<td colspan=1>Coordinate System</td>
<td colspan=1>Structure</td>
<td colspan=1>Regularity</td>
</table>
</center>
The following are the definitions of mesh-type bytes:
<dl>
<dt>Mesh Embedding
<dd>This value indicates whether the dataset data-space
is located within
another dataspace or not:
<dl> <dl>
<dt><STANDALONE>
<dd>The dataset mesh is self-contained and is not
embedded in another mesh.
<dt><EMBEDDED>
<dd>The dataset's data-space is located within
another data-space, as
described in information below.
</dl> </dl>
<dt>Coordinate System
<dd>This value defines the type of coordinate system
used for the mesh:
<dl> <dl>
<dt><POLAR>
<dd>The last two dimensions are in polar
coordinates, higher dimensions are
cartesian.
<dt><SPHERICAL>
<dd>The last three dimensions are in spherical
coordinates, higher dimensions
are cartesian.
<dt><CARTESIAN>
<dd>All dimensions are in cartesian coordinates.
</dl> </dl>
<dt>Structure
<dd>This value defines the locations of the grid-points
on the axes:
<dl> <dl>
<dt><STRUCTURED>
<dd>All grid-points are on integral, sequential
locations, starting from 0.
<dt><UNSTRUCTURED>
<dd>Grid-points locations in each dimension are
explicitly defined and
may be of any numeric data-type.
</dl> </dl>
<dt>Regularity
<dd>This value defines the locations of the dataset
points on the grid:
<dl> <dl>
<dt><REGULAR>
<dd>All dataset elements are located at the
grid-points defined.
<dt><IRREGULAR>
<dd>Each dataset element has a particular
grid-location defined.
</dl> </dl>
</dl>
<p>The following grid combinations are currently allowed:
<dl> <dl>
<dt><POLAR-STRUCTURED-REGULAR>
<dt><SPHERICAL-STRUCTURED-REGULAR>
<dt><CARTESIAN-STRUCTURED-REGULAR>
<dt><POLAR-UNSTRUCTURED-REGULAR>
<dt><SPHERICAL-UNSTRUCTURED-REGULAR>
<dt><CARTESIAN-UNSTRUCTURED-REGULAR>
<dt><CARTESIAN-UNSTRUCTURED-IRREGULAR>
</dl> </dl>
All of the above grid types can be embedded within another
data-space.
<br> <br>
<dt>Logical Dimensionality: (unsigned 32-bit integer)
<dd>This value is the number of dimensions that the dataset occupies.
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Embedded Dimensionality Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Embedded Dimensionality</td>
<tr align=center>
<td colspan=4>Embedded Dimension Size #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Embedded Dimension Size #n</td>
<tr align=center>
<td colspan=4>Embedded Origin Location #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Embedded Origin Location #n</td>
</table>
</center>
<dt>Embedded Dimensionality: (unsigned 32-bit integer)
<dd>This value is the number of dimensions of the space the
dataset is located
within. i.e. a planar dataset located within a 3-D space,
or a 3-D dataset
which is a subset of another 3-D space, etc.
<dt>Embedded Dimension Size: (unsigned 32-bit integer)
<dd>These values are the sizes of the dimensions of the
embedded data-space
that the dataset is located within.
<dt>Embedded Origin Location: (unsigned 32-bit integer)
<dd>These values comprise the location of the dataset's
origin within the embedded data-space.
</dl>
</dl>
[Comment: need some way to handle different orientations of the
dataset data-space
within the embedded data-space]<br>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Structured/Regular Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Logical Dimension Size #1</td>
<tr align=center>
<td colspan=4>Logical Dimension Maximum #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Logical Dimension Size #n</td>
<tr align=center>
<td colspan=4>Logical Dimension Maximum #n</td>
</table>
</center>
<p>
<dl>
<dt>The elements of the dimensionality message are described below:
<dd>
<dl>
<dt>Logical Dimension Size #n: (unsigned 32-bit integer)
<dd>This value is the current size of the dimension of the
data as stored in
the file. The first dimension stored in the list of
dimensions is the slowest
changing dimension and the last dimension stored is the
fastest changing
dimension.
<dt>Logical Dimension Maximum #n: (unsigned 32-bit integer)
<dd>This value is the maximum size of the dimension of the
data as stored in
the file. This value may be the special value
<UNLIMITED> which
indicates that the data may expand along this dimension
indefinitely.
</dl>
</dl>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Structured/Irregular Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4># of Grid Points in Dimension #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4># of Grid Points in Dimension #n</td>
<tr align=center>
<td colspan=4>Data-Type of Grid Point Locations</td>
<tr align=center>
<td colspan=4>Location of Grid Points in Dimension #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Location of Grid Points in Dimension #n</td>
</table>
</center>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Unstructured Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4># of Grid Points</td>
<tr align=center>
<td colspan=4>Data-Type of Grid Point Locations</td>
<tr align=center>
<td colspan=4>Grid Point Locations<br>.<br>.<br></td>
</table>
</center>
<h4><a name="DataSpaceExample">Examples:</a></h4>
Need some good examples, this is complex!
<hr>
<h3><a name="DataTypeMessage">Name: Data Type</a></h3>
<b>Type:</b> 0x0003<br>
<b>Length:</b> variable<br>
<b>Status:</b> One required per dataset<br>
<p>The data type message defines the data type for each data point
of a dataset. A data type can describe an atomic type like a
fixed- or floating-point type or a compound type like a C
struct. A data type does not, however, describe how data points
are combined to produce a dataset. Data types are stored on disk
as a data type message, which is a list of data type classes and
their associated properties.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Data Type Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Type Class and Version</td>
<td colspan=3>Class Bit Field</td>
</tr>
<tr align=center>
<td colspan=4>Size in Bytes (4 bytes)</td>
</tr>
<tr align=center>
<td colspan=4><br><br>Properties<br><br><br></td>
</tr>
</table>
</center>
<p>The Class Bit Field and Properties fields vary depending
on the Type Class, which is the low-order four bits of the Type
Class and Version field (the high-order four byte are the
version which should be set to the value one). The type class
is one of: 0 (fixed-point number), 1 (floating-point number), 2
(date and time), 3 (text string), 4 (bit field), 5 (opaque), 6
(compound). The Class Bit Field is zero and the size of the
Properties field is zero except for the cases noted here.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Bit Field for Fixed-Point Numbers (Class 0)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<td>1, 2</td>
<td><b>Padding type.</b> Bit 1 is the lo_pad type and bit 2
is the hi_pad type. If a datum has unused bits at either
end, then the lo_pad or hi_pad bit is copied to those
locations.</td>
</tr>
<tr>
<td>3</td>
<td><b>Signed.</b> If this bit is set then the fixed-point
number is in 2's complement form.</td>
</tr>
<tr>
<td>4-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Properties for Fixed-Point Numbers (Class 0)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Bit Field for Floating-Point Numbers (Class 1)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<td>1, 2, 3</td>
<td><b>Padding type.</b> Bit 1 is the low bits pad type, bit 2
is the high bits pad type, and bit 3 is the internal bits
pad type. If a datum has unused bits at either or between
the sign bit, exponent, or mantissa, then the value of bit
1, 2, or 3 is copied to those locations.</td>
</tr>
<tr>
<td>4-5</td>
<td><b>Normalization.</b> The value can be 0 if there is no
normalization, 1 if the most significant bit of the
mantissa is always set (except for 0.0), and 2 if the most
signficant bit of the mantissa is not stored but is
implied to be set. The value 3 is reserved and will not
appear in this field.</td>
</tr>
<tr>
<td>6-7</td>
<td>Reserved (zero).</td>
</tr>
<tr>
<td>8-15</td>
<td><b>Sign.</b> This is the bit position of the sign
bit.</td>
</tr>
<tr>
<td>16-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Properties for Floating-Point Numbers (Class 1)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
<tr align=center>
<td>Exponent Location</td>
<td>Exponent Size in Bits</td>
<td>Mantissa Location</td>
<td>Mantissa Size in Bits</td>
</tr>
<tr align=center>
<td colspan=4>Exponent Bias</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Bit Field for Compound Types (Class 6)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0-15</td>
<td><b>Number of Members.</b> This field contains the number
of members defined for the compound data type. The member
definitions are listed in the Properties field of the data
type message.
</tr>
<tr>
<td>15-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>The Properties field of a compound data type is a list of the
member definitions of the compound data type. The member
definitions appear one after another with no intervening bytes.
The member types are described with a recursive data type
message.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Properties for Compound Types (Class 6)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=4><br><br>Name (null terminated, multiple of
eight bytes)<br><br><br></td>
</tr>
<tr align=center>
<td colspan=4>Byte Offset of Member in Compound Instance</td>
</tr>
<tr align=center>
<td>Dimensionality</td>
<td colspan=3>reserved</td>
</tr>
<tr align=center>
<td colspan=4>Dimension Permutation</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 0 (required)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 1 (required)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 2 (required)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 3 (required)</td>
</tr>
<tr align=center>
<td colspan=4><br><br>Member Type Message<br><br><br></td>
</tr>
</table>
</center>
<p>Data type examples are <a href="Datatypes.html">here</a>.
<hr>
<h3><a name="ReservedMessage_0004">Name: Reserved - Not Assigned
Yet</a></h3>
<b>Type:</b> 0x0004<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<hr>
<h3><a name="ReservedMessage_0005">Name: Reserved - Not Assigned
Yet</a></h3>
<b>Type:</b> 0x0005<br>
<b>Length:</b> N/A<br>
<b>Status:</b> N/A<br>
<hr>
<h3><a name="CompactDataStorageMessage">Name: Data Storage - Compact</a></h3>
<b>Type:</b> 0x0006<br>
<b>Length:</b> varies<br>
<b>Status:</b> Optional, may not be repeated.<br>
<p>This message indicates that the data for the data object is
stored within the current HDF file by including the actual
data within the header data for this message. The data is
stored internally in
the "normal" format, i.e. in one chunk, un-compressed, etc.
<P>Note that one and only one of the "Data Storage" headers can be
stored for each data object.
<P><b>Format of Data:</b> The message data is actually composed
of dataset data, so the format will be determined by the dataset
format.
<h4><a name="CompactDataStorageExample">Examples:</a></h4>
[very straightforward]
<hr>
<h3><a name="ExternalFileListMessage">Name: Data Storage -
External Data Files</a></h3>
<b>Type:</b> 0x0007<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may not be repeated.<BR>
<p><b>Purpose and Description:</b> The external object message
indicates that the data for an object is stored outside the HDF5
file. The filename of the object is stored as a Universal
Resource Location (URL) of the actual filename containing the
data. An external file list record also contains the byte offset
of the start of the data within the file and the amount of space
reserved in the file for that data.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>External File List Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Version</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=2>Allocated Slots</td>
<td colspan=2>Used Slots</td>
</tr>
<tr align=center>
<td colspan=4><br>Heap Address<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Slot Definitions...<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Heap Address</td>
<td>This is the address of a local name heap which contains
the names for the external files. The name at offset zero
in the heap is always the empty string.</td>
</tr>
<tr valign=top>
<td>Allocated Slots</td>
<td>The total number of slots allocated in the message. Its
value must be at least as large as the value contained in
the Used Slots field.</td>
</tr>
<tr valign=top>
<td>Used Slots</td>
<td>The number of initial slots which contain valid
information. The remaining slots are zero filled.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>This field is reserved for future use.</td>
</tr>
<tr valign=top>
<td>Slot Definitions</td>
<td>The slot definitions are stored in order according to
the array addresses they represent. If more slots have
been allocated than what has been used then the defined
slots are all at the beginning of the list.</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>External File List Slot</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>Name Offset (<size> bytes)<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>File Offset (<size> bytes)<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Size<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Name Offset (<size> bytes)</td>
<td>The byte offset within the local name heap for the name
of the file. File names are stored as a URL which has a
protocol name, a host name, a port number, and a file
name:
<code><em>protocol</em>:<em>port</em>//<em>host</em>/<em>file</em></code>.
If the protocol is omitted then "file:" is assumed. If
the port number is omitted then a default port for that
protocol is used. If both the protocol and the port
number are omitted then the colon can also be omitted. If
the double slash and host name are omitted then
"localhost" is assumed. The file name is the only
mandatory part, and if the leading slash is missing then
it is relative to the application's current working
directory (the use of relative names is not
recommended).</td>
</tr>
<tr valign=top>
<td>File Offset (<size> bytes)</td>
<td>This is the byte offset to the start of the data in the
specified file. For files that contain data for a single
dataset this will usually be zero.</td>
</tr>
<tr valign=top>
<td>Size</td>
<td>This is the total number of bytes reserved in the
specified file for raw data storage. For a file that
contains exactly one complete dataset which is not
extendable, the size will usually be the exact size of the
dataset. However, by making the size larger one allows
HDF5 to extend the dataset. The size can be set to a value
larger than the entire file since HDF5 will read zeros
past the end of the file without failing.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="LayoutMessage">Name: Data Storage - Layout</a></h3>
<b>Type:</b> 0x0008<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Required for datasets, may not be repeated.
<p><b>Purpose and Description:</b> Data layout describes how the
elements of a multi-dimensional array are arranged in the linear
address space of the file. Two types of data layout are
supported:
<ol>
<li>The array can be stored in one contiguous area of the file.
The layout requires that the size of the array be constant and
does not permit chunking or compression. The message stores
the total size of the array and the offset of an element from
the beginning of the storage area is computed as in C.
<li>The array domain can be regularly decomposed into chunks and
each chunk is allocated separately. This layout supports
arbitrary element traversals and compression and the chunks
can be distributed across external raw data files (these
features are described in other messages). The message stores
the size of a chunk instead of the size of the entire array;
the size of the entire array can be calculated by traversing
the B-tree that stores the chunk addresses.
</ol>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Data Layout Message</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Version</td>
<td>Dimensionality</td>
<td>Layout Class</td>
<td>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br>Address<br><br></td>
</tr>
<tr align=center>
<td colspan=4>Dimension 0 (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Dimension 1 (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>...</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Version</td>
<td>A version number for the layout message. This
documentation describes version one.</td>
</tr>
<tr valign=top>
<td>Dimensionality</td>
<td>An array has a fixed dimensionality. This field
specifies the number of dimension size fields later in the
message.</td>
</tr>
<tr valign=top>
<td>Layout Class</td>
<td>The layout class specifies how the other fields of the
layout message are to be interpreted. A value of one
indicates contiguous storage while a value of two
indicates chunked storage. Other values will be defined
in the future.</td>
</tr>
<tr valign=top>
<td>Address</td>
<td>For contiguous storage, this is the address of the first
byte of storage. For chunked storage this is the address
of the B-tree that is used to look up the addresses of the
chunks.</td>
</tr>
<tr valign=top>
<td>Dimensions</td>
<td>For contiguous storage the dimensions define the entire
size of the array while for chunked storage they define
the size of a single chunk.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="ReservedMessage_0009">Name: Reserved - Not Assigned Yet</a></h3>
<b>Type:</b> 0x0009<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Purpose and Description:</b> N/A<BR>
<b>Format of Data:</b> N/A
<hr>
<h3><a name="ReservedMessage_000A">Name: Reserved - Not Assigned Yet</a></h3>
<b>Type:</b> 0x000A<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Purpose and Description:</b> N/A<BR>
<b>Format of Data:</b> N/A
<hr>
<h3><a name="CompressionMessage">Name: Data Storage - Compressed</a></h3>
<b>Type:</b> 0x000B<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may not be repeated.
<p><b>Purpose and Description:</b> Compressed objects are
datasets which are stored in an HDF file after they have been
compressed. The encoding algorithm and its parameters are
stored in a Compression Message in the object header of the
dataset.
<p>
<center>
<table border align=center cellpadding=4 witdh="80%">
<caption align=top>
<b>Compression Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Method</td>
<td>Flags</td>
<td colspan=2>Client Data Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Client Data<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Method</td>
<td>The compression method is a value between zero and 255,
inclusive, that is used as a index into a compression
method lookup table. The value zero indicates no
compression. The values one through 15, inclusive, are
reserved for methods defined by NCSA. All other values
are user-defined compression methods.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>Eight bits of flags which are passed to the compression
algorithm. There meaning depends on the compression
method.</td>
</tr>
<tr valign=top>
<td>Client Data Size</td>
<td>The size in bytes of the optional Client Data
field.</td>
</tr>
<tr valign=top>
<td>Client Data</td>
<td>Additional information needed by the compression method
can be stored in this field. The data will be passed to
the compression algorithm as a void pointer.</td>
</tr>
</table>
</center>
<p>Sometimes additional redundancy can be added to the data before
it's compressed to result in a better compression ratio. The
library doesn't specifically support modeling methods to add
redundancy, but the effect can be achieved through the use of
user-defined data types.
<p>The library uses the following compression methods.
<center>
<table align=center width="80%">
<tr valign=top>
<td><code>0</code></td>
<td>No compression: The blocks of data are stored in
their raw format.</td>
</tr>
<tr valign=top>
<td><code>1</code></td>
<td>Deflation: This is the same algorithm used by
GNU gzip which is a combination Huffman and LZ77
dictionary encoder. The <code>libz</code> library version
1.1.2 or later must be available.</td>
</tr>
<tr valign=top>
<td><code>2</code></td>
<td>Run length encoding: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>3</code></td>
<td>Adaptive Huffman: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>4</code></td>
<td>Adaptive Arithmetic: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>5</code></td>
<td>LZ78 Dictionary Encoding: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>6</code></td>
<td>Adaptive Lempel-Ziv: Similar to Unix
<code>compress</code>. Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>7-15</code></td>
<td>Reserved for future use.</td>
</tr>
<tr valign=top>
<td><code>16-255</code></td>
<td>User-defined.</td>
</tr>
</table>
</center>
<p>The compression is applied independently to each chunk of
storage (after data space and data type conversions). If the
compression is unable to make the chunk smaller than it would
normally be, the chunk is stored without compression. At the
library's discretion, chunks which fail the compression can also
be stored in their raw format.
<hr>
<h3><a name="AttributeMessage">Name: Attribute</a></h3>
<b>Type:</b> 0x000C<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may be repeated.<BR>
<p><b>Purpose and Description:</b> The <em>Attribute</em>
message is used to list objects in the HDF file which are used
as attributes, or "meta-data" about the current object. An
attribute is a small dataset; it has a name, a data type, a data
space, and raw data. Since attributes are stored in the object
header they must be relatively small (<64kb) and can be
associated with any type of object which has an object header
(groups, datasets, named types and spaces, etc.).
<p><b>Format of Data:</b>
<p>
<center>
<table border align=center cellpadding=4 width="80%">
<caption align=top>
<b>Attribute Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Version</td>
<td>Reserved</td>
<td colspan=2>Name Size</td>
</tr>
<tr align=center>
<td colspan=2>Type Size</td>
<td colspan=2>Space Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Name<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Type<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Space<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Data<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Version</td>
<td>Version number for the message. This document describes
version 1 of attribute messages.</td>
</tr>
<tr valign=top>
<td>Name Size</td>
<td>The length of the attribute name in bytes including the
null terminator. Note that the Name field below may
contain additional padding not represented by this
field.</td>
</tr>
<tr valign=top>
<td>Type Size</td>
<td>The length of the data type description in the Type
field below. Note that the Type field may contain
additional padding not represented by this field.</td>
</tr>
<tr valign=top>
<td>Space Size</td>
<td>The length of the data space description in the Space
field below. Note that the Space field may contain
additional padding not represented by this field.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>This field is reserved for later use and is set to
zero.</td>
</tr>
<tr valign=top>
<td>Name</td>
<td>The null-terminated attribute name. This field is
padded with additional null characters to make it a
multiple of eight bytes.</td>
</tr>
<tr valign=top>
<td>Type</td>
<td>The data type description follows the same format as
described for the data type object header message. This
field is padded with additional zero bytes to make it a
multiple of eight bytes.</td>
</tr>
<tr valign=top>
<td>Space</td>
<td>The data space description follows the same format as
described for the data space object header message. This
field is padded with additional zero bytes to make it a
multiple of eight bytes.</td>
</tr>
<tr valign=top>
<td>Data</td>
<td>The raw data for the attribute. The size is determined
from the data type and data space descriptions. This
field is <em>not</em> padded with additional zero
bytes.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="NameMessage">Name: Object Name</a></h3>
<b>Type:</b> 0x000D<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional [required?], may not be repeated.<BR>
<b>Purpose and Description:</b> The object name is designed to be a short
description of the instance of the data object (the class may be a short
description of the "type" of the object). An object name is a sequence of
non-zero ('\0') ASCII characters with no other formatting included by the
library.<BR>
<b>Format of Data:</b>The data for the object name is just a sequence of ASCII
characters with no special formatting.
<hr>
<h3><a name="ModifiedMessage">Name: Object Modification Date & Time</a></h3>
<b>Type:</b> 0x000E<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Required?, may not be repeated.<BR>
<b>Purpose and Description:</b> The object modification date and time is a
timestamp which indicates (using ISO8601 date and time format) the last
modification of a data object.<BR>
<b>Format of Data:</b>
The date is represented as a fixed length ASCII string according to the
"complete calendar date representation, without hyphens" listed in the ISO8601
standard.<br>
The time of day is represented as a fixed length ASCII string according
to the "complete local time of day representation, without hyphens"
listed in the ISO8601 standard.
<h4><a name="ModifiedExample">Examples:</a></h4>
"February 14, 1993, 1:10pm and 30 seconds" is represented as "19930214131030" in
the ISO standard format.
<hr>
<h3><a name="SharedMessage">Name: Shared Object Message</a></h3>
<b>Type:</b> 0x000F<br>
<b>Length:</b> 4 Bytes<br>
<b>Status:</b> Optional, may be repeated.
<p>A constant message can be shared among several object headers
by writing that message in the global heap and having the object
headers all point to it. The pointing is accomplished with a
Shared Object message which is understood directly by the object
header layer of the library. It is also possible to have a
message of one object header point to a message in some other
object header, but care must be exercised to prevent cycles.
<p>If a message is shared, then the message appears in the global
heap and its message ID appears in the Header Message Type
field of the object header. Also, the Flags field in the object
header for that message will have bit two set (the
<code>H5O_FLAG_SHARED</code> bit). The message body in the
object header will be that of a Shared Object message defined
here and not that of the pointed-to message.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Shared Message Message</b>
</caption>
<tr align=center>
<th width="25%">byte</td>
<th width="25%">byte</td>
<th width="25%">byte</td>
<th width="25%">byte</td>
</tr>
<tr align=center>
<td>Version</td>
<td>Flags</td>
<td colspan=2>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br>Pointer<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Version</td>
<td>The version number for the message. This document
describes version one of shared messages.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>The Shared Message message points to a message which is
shared among multiple object headers. The Flags field
describes the type of sharing:
<dl>
<dt><code>Bit 0</code>
<dd>If this bit is clear then the actual message is the
first message in some other object header; otherwise
the actual message is stored in the global heap.
<dt><code>Bits 2-7</code>
<dd>Reserved (always zero)
</dl>
</tr>
<tr valign=top>
<td>Pointer</td>
<td>This field points to the actual message. The format of
the pointer depends on the value of the Flags field. If
the actual message is in the global heap then the pointer
is the file address of the global heap collection that
holds the message, and a four-byte index into that
collection. Otherwise the pointer is a symbol table entry
that points to some other object header.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="ContinuationMessage">Name: Object Header Continuation</a></h3>
<b>Type:</b> 0x0010<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Optional, may be repeated.<BR>
<b>Purpose and Description:</b> The object header continuation is the location
in the file of more header messages for the current data object. This can be
used when header blocks are large, or likely to change over time.<BR>
<b>Format of Data:</b><p>
The object header continuation is formatted as follows (assuming a 4-byte
length & offset are being used in the current file):
<P>
<center>
<table border cellpadding=4 width=60%>
<caption align=bottom>
<B>HDF5 Object Header Continuation Message Layout</B>
</caption>
<tr align=center>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<tr align=center>
<td colspan=4>Header Continuation Offset</td>
<tr align=center>
<td colspan=4>Header Continuation Length</td>
</table>
</center>
<P>
<dl>
<dt>The elements of the Header Continuation Message are described below:
<dd>
<dl>
<dt>Header Continuation Offset: (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file where the
header continuation information is located.
<dt>Header Continuation Length: (<length> bytes)
<dd>This value is the length in bytes of the header continuation information in
the file.
</dl>
</dl>
<h4><a name="ContinuationExample">Examples:</a></h4>
[straightforward]
<hr>
<h3><a name="SymbolTableMessage">Name: Symbol Table Message</a></h3>
<b>Type:</b> 0x0011<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Required for symbol tables, may not be repeated.<BR>
<b>Purpose and Description:</b> Each symbol table has a B-tree and a
name heap which are pointed to by this message.<BR>
<b>Format of data:</b>
<p>The symbol table message is formatted as follows:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<b>HDF5 Object Header Symbol Table Message Layout</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>B-Tree Address</td>
<tr align=center>
<td colspan=4>Heap Address</td>
</table>
</center>
<P>
<dl>
<dt>The elements of the Symbol Table Message are described below:
<dd>
<dl>
<dt>B-tree Address (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the B-tree is located.
<dt>Heap Address (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the symbol table name heap is located.
</dl>
</dl>
<h3><a name="SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a></h3>
<P>In order to share header messages between several dataset objects, object
header messages may be placed into the global small-data heap. Since these
messages require additional information beyond the basic object header message
information, the format of the shared message is detailed below.
<BR> <BR>
<center>
<table border cellpadding=4 width=60%>
<caption align=bottom>
<B>HDF5 Shared Object Header Message</B>
</caption>
<tr align=center>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<tr align=center>
<td colspan=4>Reference Count of Shared Header Message</td>
<tr align=center>
<td colspan=4><br> Shared Object Header Message<br> <br></td>
</table>
</center>
<p>
<dl>
<dt> The elements of the shared object header message are described below:
<dd>
<dl>
<dt>Reference Count of Shared Header Message: (32-bit unsigned integer)
<dd>This value is used to keep a count of the number of dataset objects which
refer to this message from their dataset headers. When this count reaches zero,
the shared message header may be removed from the global small-data heap.
<dt>Shared Object Header Message: (various lengths)
<dd>The data stored for the shared object header message is formatted in the
same way as the private object header messages described in the object header
description earlier in this document and begins with the header message Type.
</dl>
</dl>
<h3><a name="DataStorage">Disk Format: Level 2c - Data Object Data Storage</a></h3>
<P>The data information for an object is stored separately from the header
information in the file and may not actually be located in the HDF5 file
itself if the header indicates that the data is stored externally. The
information for each record in the object is stored according to the
dimensionality of the object (indicated in the dimensionality header message).
Multi-dimensional data is stored in C order [same as current scheme], i.e. the
"last" dimension changes fastest.
<P>Data whose elements are composed of simple number-types are stored in
native-endian IEEE format, unless they are specifically defined as being stored
in a different machine format with the architecture-type information from the
number-type header message. This means that each architecture will need to
[potentially] byte-swap data values into the internal representation for that
particular machine.
<P> Data with a "variable" sized number-type is stored in an data heap
internal to the HDF file [which should not be user-modifiable].
<P>Data whose elements are composed of pointer number-types are stored in several
different ways depending on the particular pointer type involved. Simple
pointers are just stored as the dataset offset of the object being pointed to with the
size of the pointer being the same number of bytes as offsets in the file.
Partial-object pointers are stored as a heap-ID which points to the following
information within the file-heap: an offset of the object pointed to, number-type
information (same format as header message), dimensionality information (same
format as header message), sub-set start and end information (i.e. a coordinate
location for each), and field start and end names (i.e. a [pointer to the]
string indicating the first field included and a [pointer to the] string name
for the last field).
Browse pointers are stored as an heap-ID (for the name in the file-heap)
followed by a offset of the data object being referenced.
<P>Data of a compound data-type is stored as a contiguous stream of the items
in the structure, with each item formatted according to it's
data-type.
<hr>
<address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
<address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
<!-- hhmts start -->
Last modified: Mon Jul 20 13:49:08 EDT 1998
<!-- hhmts end -->
</body>
</html>
|
