summaryrefslogtreecommitdiffstats
path: root/tools/h5repack/h5repack_copy.c
blob: b41f7be15256162af62fe3ef39892feeb1b64f1b (plain)
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
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"

/*-------------------------------------------------------------------------
 * typedefs
 *-------------------------------------------------------------------------
 */

/*-------------------------------------------------------------------------
 * globals
 *-------------------------------------------------------------------------
 */

/*-------------------------------------------------------------------------
 * macros
 *-------------------------------------------------------------------------
 */

/* size of buffer/# of bytes to xfer at a time when copying userblock */
#define USERBLOCK_XFER_SIZE     512

/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf)  {  \
    H5E_BEGIN_TRY {  \
        if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) {  \
            hid_t _err_num = 0; \
            char _msg[80]; \
            H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
            H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
            error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
            HGOTO_DONE(_fail) \
        } \
    } H5E_END_TRY; \
}

/*-------------------------------------------------------------------------
 * local functions
 *-------------------------------------------------------------------------
 */
static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
        size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
        pack_opt_t *options);
static int copy_user_block(const char *infile, const char *outfile,
        hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
#endif
static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);

/* get the major number from the error stack. */
static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
    if (err_desc)
        *((hid_t *) udata) = err_desc->maj_num;

    return 0;
}

/*-------------------------------------------------------------------------
 * Function: copy_objects
 *
 * Purpose:  duplicate all HDF5 objects in the file
 *
 * Return:   0, ok,
 *          -1 no
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: October, 23, 2003
 *
 *-------------------------------------------------------------------------
 */

int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
{
    int           ret_value = 0;          /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
    hid_t         fidin;
    hid_t         fidout = -1;
    trav_table_t  *travt = NULL;
    hsize_t       ub_size = 0;            /* size of user block */
    hid_t         fcpl = H5P_DEFAULT;     /* file creation property list ID */
    hid_t         fapl = H5P_DEFAULT;     /* file access property list ID */
    unsigned      crt_order_flags;        /* group creation order flag */

    /*-------------------------------------------------------------------------
     * open input file
     *-------------------------------------------------------------------------
     */
    if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
        error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
    }

    /* get user block size and file space strategy/threshold */
    {
        hid_t fcpl_in; /* file creation property list ID for input file */
        hid_t grp_in = -1;   /* group ID */
        hid_t gcpl_in = -1;  /* group creation property list */

        if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
            error_msg("failed to retrieve file creation property list\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }

        if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
            error_msg("failed to retrieve userblock size\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }

        /* open root group */
        if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");

        /* get root group creation property list */
        if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");

        /* query and set the group creation properties */
        if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");

        if (H5Pclose(fcpl_in) < 0) {
            error_msg("failed to close property list\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /* Check if we need to create a non-default file creation property list */
    if (options->latest || ub_size > 0) {
        /* Create file creation property list */
        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
            error_msg("fail to create a file creation property list\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }

        if (ub_size > 0) {
            if (H5Pset_userblock(fcpl, ub_size) < 0) {
                error_msg("failed to set non-default userblock size\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }
        }

        if (options->latest) {
            unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];

            /* Adjust group creation parameters for root group */
            /* (So that it is created in "dense storage" form) */
            if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
                        (unsigned) options->grp_indexed) < 0) {
                error_msg("fail to adjust group creation parameters for root group\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }

            for (i = 0; i < 5; i++) {
                if (options->msg_size[i] > 0) {
                    switch (i) {
                        case 0:
                            mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
                            break;

                        case 1:
                            mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
                            break;

                        case 2:
                            mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
                            break;

                        case 3:
                            mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
                            break;

                        case 4:
                            mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
                            break;

                        default:
                            break;
                    } /* end switch */
                    min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];

                    nindex++;
                } /* end if */
            } /* end for */

            if (nindex > 0) {
                if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
                    error_msg("fail to set the number of shared object header message indexes\n");
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                }

                /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
                for (i = 0; i < (nindex - 1); i++) {
                    if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
                        error_msg("fail to configure the specified shared object header message index\n");
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                    } /* end if */
                } /* end for */
            } /* if (nindex>0) */

            /* Create file access property list */
            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
                error_msg("Could not create file access property list\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            } /* end if */

            if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
                error_msg("Could not set property for using latest version of the format\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            } /* end if */
        } /* end if */
    } /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
print_user_block(fnamein, fidin);
#endif

    /*-------------------------------------------------------------------------
     * set the new user userblock options in the FCPL (before H5Fcreate )
     *-------------------------------------------------------------------------
     */
    if (options->ublock_size > 0) {
        /* either use the FCPL already created or create a new one */
        if (fcpl == H5P_DEFAULT) {
            /* create a file creation property list */
            if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
                error_msg("fail to create a file creation property list\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }
        }

        /* set user block size */
        if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
            error_msg("failed to set userblock size\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /*-------------------------------------------------------------------------
     * set alignment options
     *-------------------------------------------------------------------------
     */
    if (options->alignment > 0) {
        /* either use the FAPL already created or create a new one */
        if (fapl == H5P_DEFAULT) {
            /* create a file access property list */
            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
                error_msg("Could not create file access property list\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }
        }

        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
            error_msg("failed to set alignment\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /*-------------------------------------------------------------------------
     * set metadata block size option
     *-------------------------------------------------------------------------
     */
    if (options->meta_block_size > 0) {
        /* either use the FAPL already created or create a new one */
        if (fapl == H5P_DEFAULT) {
            /* create a file access property list */
            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
                error_msg("Could not create file access property list\n");
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }
        }

        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
            error_msg("failed to set metadata block size\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /*-------------------------------------------------------------------------
     * set free-space strategy options
     *-------------------------------------------------------------------------
     */

    /* either use the FCPL already created or create a new one */
    if (fcpl == H5P_DEFAULT) {
        /* create a file creation property list */
        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
            error_msg("fail to create a file creation property list\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");

    /*-------------------------------------------------------------------------
     * create the output file
     *-------------------------------------------------------------------------
     */
    if (options->verbose)
        printf("Making file <%s>...\n", fnameout);

    if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
        error_msg("<%s>: Could not create file\n", fnameout);
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
    }

    /*-------------------------------------------------------------------------
     * write a new user block if requested
     *-------------------------------------------------------------------------
     */
    if (options->ublock_size > 0) {
        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
            error_msg("Could not copy user block. Exiting...\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /*-------------------------------------------------------------------------
     * get list of objects
     *-------------------------------------------------------------------------
     */

    /* Initialize indexing options */
    h5trav_set_index(sort_by, sort_order);
    /* init table */
    trav_table_init(&travt);

    /* get the list of objects in the file */
    if (h5trav_gettable(fidin, travt) < 0)
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");

    /*-------------------------------------------------------------------------
     * do the copy
     *-------------------------------------------------------------------------
     */
    if (do_copy_objects(fidin, fidout, travt, options) < 0) {
        error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
    } /* end if */

    /*-------------------------------------------------------------------------
     * do the copy of referenced objects
     * and create hard links
     *-------------------------------------------------------------------------
     */
    if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
        printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
    }

    /*-------------------------------------------------------------------------
     * close
     *-------------------------------------------------------------------------
     */

    if (fapl > 0)
        H5Pclose(fapl);

    if (fcpl > 0)
        H5Pclose(fcpl);

    H5Fclose(fidin);
    H5Fclose(fidout);

    /* free table */
    trav_table_free(travt);
    travt = NULL;

    /*-------------------------------------------------------------------------
     * write only the input file user block if there is no user block file input
     *-------------------------------------------------------------------------
     */

    if (ub_size > 0 && options->ublock_size == 0) {
        if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
            error_msg("Could not copy user block. Exiting...\n");
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    return 0;

    /*-------------------------------------------------------------------------
     * out
     *-------------------------------------------------------------------------
     */

done:
    H5E_BEGIN_TRY {
        H5Pclose(fapl);
        H5Pclose(fcpl);
        H5Fclose(fidin);
        H5Fclose(fidout);
    } H5E_END_TRY;
    if (travt)
        trav_table_free(travt);

    return ret_value;
}

/*-------------------------------------------------------------------------
 * Function: Get_hyperslab
 *
 * Purpose: Calulate a hyperslab from a dataset for higher performance.
 *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
 *          Return the hyperslab dimentions and size in byte.
 *
 * Return: 0 - SUCCEED, -1 FAILED
 *
 * Parameters:
 *   dcpl_id : [IN] dataset creation property.
 *   rank_dset : [IN] dataset rank
 *   dims_dset[] : [IN] dataset dimentions
 *   size_datum : [IN] size of a data element in byte
 *   dims_hslab[] : [OUT] calculated hyperslab dimentions
 *   * hslab_nbytes_p : [OUT] total byte of the hyperslab
 *
 * Programmer: Jonathan Kim
 * Date: Feburary, 2012
 * Update:
 *   The hyperslab calucation would be depend on if the dataset is chunked
 *   or not.
 *
 *   There care 3 conditions to cover:
 *   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
 *      collection and the boundary would be dataset's dims.
 *   2. If chunked but a chunk doesn't fit in buffer, each data element would
 *      be a unit of collection and the boundary would be the chunk itself.
 *   3. If not chunked, each data element would be a unit of collection and
 *      the boundary would be dataset's dims.
 *
 *   The calulation starts from the last dimention (h5dump dims output).
 *
 * Note:
 *   Added for JIRA HDFFV-7862.
 *-----------------------------------------*/

int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
        size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
{
    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
    int     k;
    H5D_layout_t dset_layout;
    int     rank_chunk;
    hsize_t dims_chunk[H5S_MAX_RANK];
    hsize_t size_chunk = 1;
    hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
    hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
    hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
    hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
    hsize_t hslab_nbytes; /* size of hyperslab in byte */

    /* init to set as size of a data element */
    hslab_nbytes = size_datum;

    /* get layout of dataset */
    dset_layout = H5Pget_layout(dcpl_id);

    /* if dataset is chunked */
    if (dset_layout == H5D_CHUNKED) {
        /* get chunk dims */
        rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
        if (rank_chunk < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");

        for (k = rank_dset; k > 0; --k)
            size_chunk *= dims_chunk[k - 1];

        /* figure out how many chunks can fit in the hyperslab buffer */
        nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;

        /* 1. if a chunk fit in hyperslab buffer */
        if (nchunk_fit >= 1) {
            /* Calulate a hyperslab that contains as many chunks that can fit
             * in hyperslab buffer. Hyperslab will be increased starting from
             * the last dimention of the dataset (see h5dump's dims output).
             * The calculation boundary is dataset dims.
             * In the loop, used mapping from a datum to a chunk to figure out
             * chunk based hyperslab.
             */
            for (k = rank_dset; k > 0; --k) {
                /* map dataset dimentions with a chunk dims */
                chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];

                /* if reminder exist, increse by 1 to cover partial edge chunks */
                if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
                    chunk_dims_map[k - 1]++;

                /* get mapped hyperslab dims */
                hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);

                /* prepare next round */
                nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
                /* if a chunk is bigger than the rest of buffer */
                if (nchunk_fit == 0)
                    nchunk_fit = 1;

                /* get hyperslab dimentions as unmapping to actual size */
                dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);

                /* calculate total size for the hyperslab */
                hslab_nbytes *= dims_hslab[k - 1];
            }
        }
        /* 2. if a chunk is bigger than hyperslab buffer */
        else {
            /* Calulate a hyperslab that contains as many data elements that
             * can fit in hyperslab buffer. Hyperslab will be increased
             * starting from the last dimention of the chunk (see h5dump's dims
             * output).
             * The calculation boundary is a chunk dims.
             */
            for (k = rank_dset; k > 0; --k) {
                ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;

                /* if a datum is bigger than rest of buffer */
                if (ndatum_fit == 0)
                    ndatum_fit = 1;
                /* get hyperslab dimentions within a chunk boundary */
                dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);

                /* calculate total size for the hyperslab */
                hslab_nbytes *= dims_hslab[k - 1];

                if (hslab_nbytes <= 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
            }
        }
    }
    /* 3. if dataset is not chunked */
    else {
        /* Calulate a hyperslab that contains as many data elements that can
         * fit in hyperslab buffer. Hyperslab will be increased starting from
         * the last dimention of the dataset (see h5dump's dims output).
         * The calculation boundary is dataset dims.
         */
        for (k = rank_dset; k > 0; --k) {
            ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;

            /* if a datum is bigger than rest of buffer */
            if (ndatum_fit == 0)
                ndatum_fit = 1;
            /* get hyperslab dimentions within dataset boundary */
            dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);

            /* calculate total size for the hyperslab */
            hslab_nbytes *= dims_hslab[k - 1];

            if (hslab_nbytes <= 0)
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
        }
    }

    /* pass out the hyperslab size*/
    *hslab_nbytes_p = hslab_nbytes;

done:
    return ret_value;
}

/*-------------------------------------------------------------------------
 * Function: do_copy_objects
 *
 * Purpose: duplicate all HDF5 objects in the file
 *
 * Return: 0, ok, -1 no
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: October, 23, 2003
 *
 * Modifications:
 *
 *  July 2004:     Introduced the extra EC or NN option for SZIP
 *
 *  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
 *                  with the requested filter, use the input one
 *
 *  October 2006:  Read/write using the file type by default.
 *
 *  October 2006:  Read by hyperslabs for big datasets.
 *
 *  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
 *  i.e., if the memory needed to read a dataset is greater than this limit,
 *  then hyperslab I/O is done instead of one operation I/O
 *  For each dataset, the memory needed is calculated according to
 *
 *  memory needed = number of elements * size of each element
 *
 *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
 *  are done
 *
 *  H5Dread( input_dataset1 )
 *  H5Dread( input_dataset2 )
 *
 *  with all elements in the datasets selected. If the memory needed is greater than
 *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
 *
 *  a strip mine is defined for each dimension k (a strip mine is defined as a
 *  hyperslab whose size is memory manageable) according to the formula
 *
 *  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
 *
 *  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
 *  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
 *  mine size k is simply defined as its dimension k, but for larger datasets the
 *  hyperslab size is still memory manageable.
 *  a cycle is done until the number of elements in the dataset is reached. In each
 *  iteration, two parameters are defined for the function H5Sselect_hyperslab,
 *  the start and size of each hyperslab, according to
 *
 *  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
 *
 *  where hyperslab_offset [k] is initially set to zero, and later incremented in
 *  hyperslab_size[k] offsets. The reason for the operation
 *
 *  dimension[k] - hyperslab_offset[k]
 *
 *  in (2) is that, when using the strip mine size, it assures that the "remaining" part
 *  of the dataset that does not fill an entire strip mine is processed.
 *
 *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
 *   H5Ocopy or not is if a change of filters or layout is requested by the user
 *   then use read/write else use H5Ocopy.
 *
 * May, 1, 2008: Add a printing of the compression ratio of old size / new size
 *
 * Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
 * Programmer: Jonathan Kim
 *
 *  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
 *  i.e., if the memory needed to read a dataset is greater than this limit,
 *  then hyperslab I/O is done instead of one operation I/O
 *  For each dataset, the memory needed is calculated according to
 *
 *  memory needed = number of elements * size of each element
 *
 *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
 *  are done
 *
 *  H5Dread( input_dataset )
 *  H5Dwrite( output_dataset )
 *
 *  with all elements in the datasets selected. If the memory needed is greater than
 *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
 *
 *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
 *  2. Calculate the hyperslab selections as the selection is moving forward.
 *     Selection would be same as the hyperslab except for the remaining edge portion
 *     of the dataset. The code take care of the remaining portion if exist.
 *
 *-------------------------------------------------------------------------
 */

int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
        pack_opt_t *options) /* repack options */
{
    int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
    hid_t grp_in = -1;   /* group ID */
    hid_t grp_out = -1;  /* group ID */
    hid_t dset_in = -1;  /* read dataset ID */
    hid_t dset_out = -1; /* write dataset ID */
    hid_t gcpl_in = -1;  /* group creation property list */
    hid_t gcpl_out = -1; /* group creation property list */
    hid_t type_in = -1;  /* named type ID */
    hid_t type_out = -1; /* named type ID */
    hid_t dcpl_in = -1;  /* dataset creation property list ID */
    hid_t dcpl_out = -1; /* dataset creation property list ID */
    hid_t f_space_id = -1; /* file space ID */
    hid_t ftype_id = -1; /* file type ID */
    hid_t wtype_id = -1; /* read/write type ID */
    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
    size_t msize;        /* size of type */
    hsize_t nelmts;      /* number of elements in dataset */
    H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
    int rank;            /* rank of dataset */
    hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
    hsize_t dsize_in;    /* input dataset size before filter */
    hsize_t dsize_out;   /* output dataset size after filter */
    int apply_s;         /* flag for apply filter to small dataset sizes */
    int apply_f;         /* flag for apply filter to return error on H5Dcreate */
    void *buf = NULL;    /* buffer for raw data */
    void *hslab_buf = NULL; /* hyperslab buffer for raw data */
    int has_filter;      /* current object has a filter */
    int req_filter;      /* there was a request for a filter */
    int req_obj_layout = 0; /* request layout to current object */
    unsigned crt_order_flags; /* group creation order flag */
    unsigned i;
    unsigned u;
    int is_ref = 0;
    htri_t is_named;
    hbool_t limit_maxdims;
    hsize_t size_dset;

    /*-------------------------------------------------------------------------
     * copy the suppplied object list
     *-------------------------------------------------------------------------
     */

    if (options->verbose) {
        printf("-----------------------------------------\n");
        printf(" Type     Filter (Compression)     Name\n");
        printf("-----------------------------------------\n");
    }

    for (i = 0; i < travt->nobjs; i++) {
        /* init variables per obj */
        buf = NULL;
        limit_maxdims = FALSE;

        switch (travt->objs[i].type) {
            case H5TRAV_TYPE_UNKNOWN:
                HDassert(0);
                break;

                /*-------------------------------------------------------------------------
                 * H5TRAV_TYPE_GROUP
                 *-------------------------------------------------------------------------
                 */
            case H5TRAV_TYPE_GROUP:
                if (options->verbose)
                    printf(FORMAT_OBJ, "group", travt->objs[i].name);

                /* open input group */
                if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");

                /* get input group creation property list */
                if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");

                /* query and set the group creation properties */
                if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");

                /* set up group creation property list */
                if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");

                if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");

                /*-------------------------------------------------------------------------
                 * the root is a special case, we get an ID for the root group
                 * and copy its attributes using that ID
                 *-------------------------------------------------------------------------
                 */
                if (HDstrcmp(travt->objs[i].name, "/") == 0) {
                    if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
                }
                else {
                    if (options->grp_compact > 0 || options->grp_indexed > 0)
                        if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");

                    if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed");
                }

                /*-------------------------------------------------------------------------
                 * copy attrs
                 *-------------------------------------------------------------------------
                 */
                if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");

                if (H5Pclose(gcpl_out) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                if (H5Pclose(gcpl_in) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                if (H5Gclose(grp_out) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
                if (H5Gclose(grp_in) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");

                break;

                /*-------------------------------------------------------------------------
                 * H5TRAV_TYPE_DATASET
                 *-------------------------------------------------------------------------
                 */
            case H5TRAV_TYPE_DATASET:
                has_filter = 0;
                req_filter = 0;

                /* check if global filters were requested */
                if (options->n_filter_g)
                    req_filter = 1;

                /* check if filters were requested for individual objects */
                for (u = 0; u < options->op_tbl->nelems; u++)
                    if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
                        if (options->op_tbl->objs[u].filter->filtn > 0)
                            req_filter = 1;

                /* check if layout change requested individual object */
                if (options->layout_g != H5D_LAYOUT_ERROR) {
                    pack_info_t *pckinfo;

                    /* any dataset is specified */
                    if (options->op_tbl->nelems > 0) {
                        /* check if object exist */
                        pckinfo = options_get_object(travt->objs[i].name, options->op_tbl);
                        if (pckinfo)
                            req_obj_layout = 1;
                    }
                }

                /* early detection of references */
                if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                if ((ftype_id = H5Dget_type(dset_in)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
                if (H5T_REFERENCE == H5Tget_class(ftype_id))
                    is_ref = 1;

                /* Check if the datatype is committed */
                if ((is_named = H5Tcommitted(ftype_id)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
                if (is_named)
                    if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");

                if (H5Tclose(ftype_id) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                if (H5Dclose(dset_in) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");

                /*-------------------------------------------------------------------------
                 * check if we should use H5Ocopy or not
                 * if there is a request for filters/layout, we read/write the object
                 * otherwise we do a copy using H5Ocopy
                 *-------------------------------------------------------------------------
                 */
                if (options->op_tbl->nelems || options->all_filter == 1
                        || options->all_layout == 1 || is_ref || is_named) {

                    int j;

                    if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                    if ((f_space_id = H5Dget_space(dset_in)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
                    if ((ftype_id = H5Dget_type(dset_in)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
                    if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
                    if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
                    if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
                    HDmemset(dims, 0, sizeof dims);
                    if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
                    if (H5Dget_space_status(dset_in, &space_status) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");

                    nelmts = 1;
                    for (j = 0; j < rank; j++)
                        nelmts *= dims[j];

                    /* wtype_id will have already been set if using a named dtype */
                    if (!is_named) {
                        if (options->use_native == 1)
                            wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
                        else
                            wtype_id = H5Tcopy(ftype_id);
                    } /* end if */

                    if ((msize = H5Tget_size(wtype_id)) == 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");

                    /* size of current dset */
                    size_dset = nelmts * msize;

                    /*-------------------------------------------------------------------------
                     * check if the dataset creation property list has filters that
                     * are not registered in the current configuration
                     * 1) the external filters GZIP and SZIP might not be available
                     * 2) the internal filters might be turned off
                     *-------------------------------------------------------------------------
                     */
                    if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
                        apply_s = 1;
                        apply_f = 1;

                        /*-------------------------------------------------------------------------
                         * references are a special case
                         * we cannot just copy the buffers, but instead we recreate the reference
                         * in a second traversal of the output file
                         *-------------------------------------------------------------------------
                         */
                        if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
                            /* get the storage size of the input dataset */
                            dsize_in = H5Dget_storage_size(dset_in);

                            /* check for small size datasets (less than 1k) except
                             * changing to COMPACT. For the reference, COMPACT is limited
                             * by size 64K by library.
                             */
                            if (options->layout_g != H5D_COMPACT)
                                if (size_dset < options->min_comp)
                                    apply_s = 0;

                            /* apply the filter */
                            if (apply_s)
                                if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0)
                                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");

                            /* only if layout change requested for entire file or
                             * individual obj */
                            if (options->all_layout > 0 || req_obj_layout == 1)
                                /*-------------------------------------------------
                                 * Unset the unlimited max dims if convert to other
                                 * than chunk layouts, because unlimited max dims
                                 * only can be applied to chunk layout.
                                 * Also perform only for targeted dataset
                                 * Also check for size limit to convert to compact
                                 *-------------------------------------------------*/
                                if (options->layout_g != H5D_CHUNKED) {
                                    /* any dataset is specified */
                                    if (options->op_tbl->nelems > 0) {
                                        /* if current obj match specified obj */
                                        if (options_get_object(travt->objs[i].name, options->op_tbl))
                                            limit_maxdims = TRUE;
                                    }
                                    else  /* no dataset is specified */
                                        limit_maxdims = TRUE;

                                    /* if convert to COMPACT */
                                    if (options->layout_g == H5D_COMPACT)
                                        /* should be smaller than 64K */
                                        if (size_dset > MAX_COMPACT_DSIZE)
                                            limit_maxdims = FALSE;

                                    /* unset unlimited max dims */
                                    if (limit_maxdims)
                                        H5Sset_extent_simple(f_space_id, rank, dims, NULL);
                                }

                            /*-------------------------------------------------------------------------
                             * create the output dataset;
                             * disable error checking in case the dataset cannot be created with the
                             * modified dcpl; in that case use the original instead
                             *-------------------------------------------------------------------------
                             */
                            dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
                            if (dset_out == FAIL) {
                                H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
                                if (options->verbose)
                                    printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);

                                if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
                                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
                                apply_f = 0;
                            }

                            /*-------------------------------------------------------------------------
                             * read/write
                             *-------------------------------------------------------------------------
                             */
                            if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
                                size_t need = (size_t)(nelmts * msize); /* bytes needed */

                                /* have to read the whole dataset if there is only one element in the dataset */
                                if (need < H5TOOLS_MALLOCSIZE)
                                    buf = HDmalloc(need);

                                if (buf != NULL) {
                                    /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
                                    CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
                                    CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);

                                    /* Check if we have VL data in the dataset's
                                     * datatype that must be reclaimed */
                                    if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
                                        if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
                                }
                                else { /* possibly not enough memory, read/write by hyperslabs */
                                    size_t p_type_nbytes = msize; /*size of memory type */
                                    hsize_t p_nelmts = nelmts; /*total elements */
                                    hsize_t elmtno; /*counter  */
                                    int carry; /*counter carry value */
                                    unsigned int vl_data = 0; /*contains VL datatypes */

                                    /* hyperslab info */
                                    hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
                                    hsize_t hslab_nbytes; /*bytes per hyperslab */
                                    hsize_t hslab_nelmts; /*elements per hyperslab*/
                                    hid_t hslab_space; /*hyperslab data space */

                                    /* hyperslab selection info */
                                    hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
                                    hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
                                    hsize_t hs_select_nelmts; /* selected elements */
                                    hsize_t zero[8]; /*vector of zeros */
                                    int k;
                                    H5D_layout_t dset_layout;
                                    hid_t dcpl_tmp = -1; /* dataset creation property list ID */

                                    /* check if we have VL data in the dataset's datatype */
                                    if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
                                        vl_data = TRUE;

                                    /* check first if writing dataset is chunked,
                                     * if so use its chunk layout for better performance. */
                                    dset_layout = H5Pget_layout(dcpl_out);
                                    if (dset_layout == H5D_CHUNKED)
                                        dcpl_tmp = dcpl_out; /* writing dataset */
                                    else { /* if reading dataset is chunked */
                                        dset_layout = H5Pget_layout(dcpl_in);
                                        if (dset_layout == H5D_CHUNKED)
                                            dcpl_tmp = dcpl_in; /* reading dataset */
                                    }

                                    /* get hyperslab dims and size in byte */
                                    if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");

                                    hslab_buf = HDmalloc((size_t)hslab_nbytes);

                                    hslab_nelmts = hslab_nbytes / p_type_nbytes;
                                    hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);

                                    /* the hyperslab selection loop */
                                    HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
                                    HDmemset(zero, 0, sizeof zero);

                                    for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) {
                                        if (rank > 0) {
                                            /* calculate the hyperslab selections.
                                             * The selection would be same as the hyperslab
                                             * except for remaining edge portion of the dataset
                                             * which is smaller then the hyperslab.
                                             */
                                            for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
                                                /* MIN() is used to get the remaining edge portion if exist.
                                                 * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
                                                hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
                                                hs_select_nelmts *= hs_sel_count[k];
                                            }

                                            if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
                                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
                                            if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
                                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
                                        }
                                        else {
                                            H5Sselect_all(f_space_id);
                                            H5Sselect_all(hslab_space);
                                            hs_select_nelmts = 1;
                                        } /* rank */

                                        /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
                                        CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
                                        CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);

                                        /* reclaim any VL memory, if necessary */
                                        if (vl_data)
                                            H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);

                                        /* calculate the next hyperslab offset */
                                        for (k = rank, carry = 1; k > 0 && carry; --k) {
                                            hs_sel_offset[k - 1] += hs_sel_count[k - 1];
                                            /* if reached the end of a dim */
                                            if (hs_sel_offset[k - 1] == dims[k - 1])
                                                hs_sel_offset[k - 1] = 0;
                                            else
                                                carry = 0;
                                        } /* k */
                                    } /* elmtno */

                                    H5Sclose(hslab_space);
                                    /* free */
                                    if (hslab_buf != NULL) {
                                        HDfree(hslab_buf);
                                        hslab_buf = NULL;
                                    }
                                } /* hyperslab read */
                            } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */

                            /*-------------------------------------------------------------------------
                             * amount of compression used
                             *-------------------------------------------------------------------------
                             */
                            if (options->verbose) {
                                double ratio = 0;

                                /* only print the compression ration if there was a filter request */
                                if (apply_s && apply_f && req_filter) {
                                    /* get the storage size of the output dataset */
                                    dsize_out = H5Dget_storage_size(dset_out);

                                    /* compression ratio = uncompressed size /  compressed size */
                                    if (dsize_out != 0)
                                        ratio = (double) dsize_in / (double) dsize_out;
                                    print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1);
                                }
                                else
                                    print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0);

                                /* print a message that the filter was not applied
                                 (in case there was a filter)
                                 */
                                if (has_filter && apply_s == 0)
                                    printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);

                                if (has_filter && apply_f == 0)
                                    printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
                            } /* verbose */

                            /*-------------------------------------------------------------------------
                             * copy attrs
                             *-------------------------------------------------------------------------
                             */
                            if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");

                            /*close */
                            if (H5Dclose(dset_out) < 0)
                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
                        }/*!H5T_REFERENCE*/
                    }/*h5tools_canreadf*/

                    /*-------------------------------------------------------------------------
                     * close
                     *-------------------------------------------------------------------------
                     */
                    if (H5Tclose(ftype_id) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                    if (H5Tclose(wtype_id) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                    if (H5Pclose(dcpl_in) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                    if (H5Pclose(dcpl_out) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
                    if (H5Sclose(f_space_id) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
                    if (H5Dclose(dset_in) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
                }
                /*-------------------------------------------------------------------------
                 * we do not have request for filter/chunking use H5Ocopy instead
                 *-------------------------------------------------------------------------
                 */
                else {
                    hid_t pid;

                    /* create property to pass copy options */
                    if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");

                    /* set options for object copy */
                    if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");

                    /*-------------------------------------------------------------------------
                     * do the copy
                     *-------------------------------------------------------------------------
                     */

                    if (H5Ocopy(fidin, /* Source file or group identifier */
                            travt->objs[i].name, /* Name of the source object to be copied */
                            fidout, /* Destination file or group identifier  */
                            travt->objs[i].name, /* Name of the destination object  */
                            pid, /* Properties which apply to the copy   */
                            H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");

                    /* close property */
                    if (H5Pclose(pid) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");

                    /*-------------------------------------------------------------------------
                     * copy attrs manually
                     *-------------------------------------------------------------------------
                     */
                    if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                    if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                    if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
                    if (H5Dclose(dset_in) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
                    if (H5Dclose(dset_out) < 0)
                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");

                    if (options->verbose)
                        printf(FORMAT_OBJ, "dset", travt->objs[i].name);

                } /* end do we have request for filter/chunking */
                break;

            /*-------------------------------------------------------------------------
             * H5TRAV_TYPE_NAMED_DATATYPE
             *-------------------------------------------------------------------------
             */
            case H5TRAV_TYPE_NAMED_DATATYPE:
                if (options->verbose)
                    printf(FORMAT_OBJ, "type", travt->objs[i].name);

                if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");

                /* Copy the datatype anonymously */
                if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");

                /* Link in to group structure */
                if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed");

                /*-------------------------------------------------------------------------
                 * copy attrs
                 *-------------------------------------------------------------------------
                 */
                if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");

                if (H5Tclose(type_in) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                if (H5Tclose(type_out) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");

                break;

            /*-------------------------------------------------------------------------
             * H5TRAV_TYPE_LINK
             * H5TRAV_TYPE_UDLINK
             *
             * Only handles external links; H5Lcopy will fail for other UD link types
             * since we don't have creation or copy callbacks for them.
             *-------------------------------------------------------------------------
             */
            case H5TRAV_TYPE_LINK:
            case H5TRAV_TYPE_UDLINK:
                if (options->verbose)
                    printf(FORMAT_OBJ, "link", travt->objs[i].name);

                if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed");

                if (options->verbose)
                    printf(FORMAT_OBJ, "link", travt->objs[i].name);
                break;

            default:
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
        } /* switch */

        /* free */
        if (buf != NULL) {
            HDfree(buf);
            buf = NULL;
        }
    } /* i */

    /* Finalize (link) the stack of named datatypes (if any) */
    named_datatype_free(&named_dt_head, 0);

    return ret_value;

done:
    H5E_BEGIN_TRY
    {
        H5Gclose(grp_in);
        H5Gclose(grp_out);
        H5Pclose(dcpl_in);
        H5Pclose(gcpl_in);
        H5Pclose(gcpl_out);
        H5Sclose(f_space_id);
        H5Dclose(dset_in);
        H5Dclose(dset_out);
        H5Tclose(ftype_id);
        H5Tclose(wtype_id);
        H5Tclose(type_in);
        H5Tclose(type_out);
        named_datatype_free(&named_dt_head, 1);
    }H5E_END_TRY;

    /* free */
    if (buf != NULL)
        HDfree(buf);
    if (hslab_buf != NULL)
        HDfree(hslab_buf);

    return ret_value;
}

/*-------------------------------------------------------------------------
 * Function: print_dataset_info
 *
 * Purpose: print name, filters, percentage compression of a dataset
 *
 *-------------------------------------------------------------------------
 */
static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
{
    char     strfilter[255];
#if defined (PRINT_DEBUG )
    char     temp[255];
#endif
    int      nfilters;       /* number of filters */
    unsigned filt_flags;     /* filter flags */
    H5Z_filter_t filtn;      /* filter identification number */
    unsigned cd_values[20];  /* filter client data values */
    size_t   cd_nelmts;      /* filter client number of values */
    char     f_objname[256]; /* filter objname */
    int     i;

    HDstrcpy(strfilter, "\0");

    /* get information about input filters */
    if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
        return;

    for (i = 0; i < nfilters; i++) {
        cd_nelmts = NELMTS(cd_values);

        filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
                        cd_values, sizeof(f_objname), f_objname, NULL);

        switch (filtn) {
            case H5Z_FILTER_NONE:
                HDstrcat(strfilter, "NONE ");
                break;

            case H5Z_FILTER_DEFLATE:
                HDstrcat(strfilter, "GZIP ");

#if defined (PRINT_DEBUG)
                {
                    unsigned level = cd_values[0];

                    sprintf(temp,"(%d)", level);
                    HDstrcat(strfilter, temp);
                }
#endif
                break;

            case H5Z_FILTER_SZIP:
                HDstrcat(strfilter, "SZIP ");

#if defined (PRINT_DEBUG)
                {
                    unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/
                    unsigned ppb = cd_values[1];

                    sprintf(temp,"(%d,", ppb);
                    HDstrcat(strfilter, temp);
                    if (options_mask & H5_SZIP_EC_OPTION_MASK)
                        HDstrcpy(temp, "EC) ");
                    else if (options_mask & H5_SZIP_NN_OPTION_MASK)
                        HDstrcpy(temp, "NN) ");
                }
                HDstrcat(strfilter, temp);
#endif
                break;

            case H5Z_FILTER_SHUFFLE:
                HDstrcat(strfilter, "SHUF ");
                break;

            case H5Z_FILTER_FLETCHER32:
                HDstrcat(strfilter, "FLET ");
                break;

            case H5Z_FILTER_NBIT:
                HDstrcat(strfilter, "NBIT ");
                break;

            case H5Z_FILTER_SCALEOFFSET:
                HDstrcat(strfilter, "SCALEOFFSET ");
                break;

            default:
                HDstrcat(strfilter, "UD ");
                break;
        } /* switch */
    }/*i*/

    if (!pr)
        printf(FORMAT_OBJ, "dset", objname);
    else {
        char str[255], temp[28];

        HDstrcpy(str, "dset     ");
        HDstrcat(str, strfilter);
        sprintf(temp, "  (%.3f:1)", ratio);
        HDstrcat(str, temp);
        printf(FORMAT_OBJ, str, objname);
    }
}

/*-------------------------------------------------------------------------
 * Function: copy_user_block
 *
 * Purpose: copy user block from one file to another
 *
 * Return: 0, ok, -1 no
 *
 * Programmer: Peter Cao
 *
 * Date: October, 25, 2007
 *
 *-------------------------------------------------------------------------
 */
static int copy_user_block(const char *infile, const char *outfile, hsize_t size)
{
    int ret_value = 0;           /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
    int infid = -1, outfid = -1; /* File descriptors */

    /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
    HDassert(size > 0);

    /* Open files */
    if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
    if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");

    /* Copy the userblock from the input file to the output file */
    while (size > 0) {
        ssize_t nread, nbytes; /* # of bytes transfered, etc. */
        char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
        const char *wbuf; /* Pointer into buffer, for writing */

        /* Read buffer from source file */
        if (size > USERBLOCK_XFER_SIZE)
            nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
        else
            nread = HDread(infid, rbuf, (size_t)size);
        if (nread < 0)
            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");

        /* Write buffer to destination file */
        /* (compensating for interrupted writes & checking for errors, etc.) */
        nbytes = nread;
        wbuf = rbuf;
        while (nbytes > 0) {
            ssize_t nwritten; /* # of bytes written */

            do {
                nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
            } while (-1 == nwritten && EINTR == errno);
            if (-1 == nwritten)  /* error */
                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed");
            HDassert(nwritten > 0);
            HDassert(nwritten <= nbytes);

            /* Update # of bytes left & offset in buffer */
            nbytes -= nwritten;
            wbuf += nwritten;
            HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
        } /* end while */

        /* Update size of userblock left to transfer */
        size = size - (hsize_t) nread;
    } /* end while */

done:
    if (infid > 0)
        HDclose(infid);
    if (outfid > 0)
        HDclose(outfid);

    return ret_value;
}

/*-------------------------------------------------------------------------
 * Function: print_user_block
 *
 * Purpose: print user block
 *
 * Return: 0, ok, -1 no
 *
 * Programmer: Pedro Vicente
 *
 * Date: August, 20, 2008
 *
 *-------------------------------------------------------------------------
 */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static
void print_user_block(const char *filename, hid_t fid)
{
    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
    int     fh;   /* file handle  */
    hsize_t ub_size; /* user block size */
    hsize_t size; /* size read */
    hid_t   fcpl; /* file creation property list ID for HDF5 file */
    int     i;

    /* get user block size */
    if(( fcpl = H5Fget_create_plist(fid)) < 0) {
        error_msg("failed to retrieve file creation property list\n");
        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
    }

    if(H5Pget_userblock(fcpl, &ub_size) < 0) {
        error_msg("failed to retrieve userblock size\n");
        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
    }

    if(H5Pclose(fcpl) < 0) {
        error_msg("failed to close property list\n");
        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
    }

    /* open file */
    if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
    }

    size = ub_size;

    /* read file */
    while(size > 0) {
        ssize_t nread; /* # of bytes read */
        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */

        /* read buffer */
        if(size > USERBLOCK_XFER_SIZE)
            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
        else
            nread = HDread(fh, rbuf, (size_t)size);

        for(i = 0; i < nread; i++) {

            printf("%c ", rbuf[i]);

        }
        printf("\n");

        if(nread < 0) {
            HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
        }

        /* update size of userblock left to transfer */
        size -= nread;
    }

done:
    if(fh > 0)
        HDclose(fh);

    return;
}
#endif