summaryrefslogtreecommitdiffstats
path: root/testpar/t_mdset.c
blob: 11f81af09222f1b42a6aa9fc1ec280d6a267790d (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
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
 * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/* $Id$ */

#include "testphdf5.h"

#define DIM  2
#define SIZE 32
#define NDATASET 4
#define GROUP_DEPTH 128
enum obj_type { is_group, is_dset };
 
void write_dataset(hid_t, hid_t, hid_t);
int  read_dataset(hid_t, hid_t, hid_t);
void create_group_recursive(hid_t, hid_t, hid_t, int);
void recursive_read_group(hid_t, hid_t, hid_t, int);
void group_dataset_read(hid_t fid, int mpi_rank, int m);
void write_attribute(hid_t, int, int);
int  read_attribute(hid_t, int, int);
int  check_value(DATATYPE *, DATATYPE *);
void get_slab(hssize_t[], hsize_t[], hsize_t[], hsize_t[]);

/*
 * Example of using PHDF5 to create ndatasets datasets.  Each process write
 * a slab of array to the file.
 */
void multiple_dset_write(char *filename, int ndatasets)
{
    int i, j, n, mpi_size, mpi_rank;
    hid_t iof, plist, dataset, memspace, filespace;
    hid_t dcpl;                         /* Dataset creation property list */
    hbool_t use_gpfs = FALSE;           /* Use GPFS hints */
    hssize_t chunk_origin [DIM];
    hsize_t chunk_dims [DIM], file_dims [DIM];
    hsize_t count[DIM]={1,1};
    double outme [SIZE][SIZE];
    double fill=1.0;                    /* Fill value */
    char dname [100];
    herr_t ret;

    MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);

    VRFY((mpi_size <= SIZE), "mpi_size <= SIZE");

    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    VRFY((plist>=0), "create_faccess_plist succeeded");
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
    VRFY((iof>=0), "H5Fcreate succeeded");
    ret = H5Pclose (plist);
    VRFY((ret>=0), "H5Pclose succeeded");

    /* decide the hyperslab according to process number. */
    get_slab(chunk_origin, chunk_dims, count, file_dims);  

    memspace = H5Screate_simple (DIM, chunk_dims, NULL);
    filespace = H5Screate_simple (DIM, file_dims, NULL);
    ret = H5Sselect_hyperslab (filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims);
    VRFY((ret>=0), "mdata hyperslab selection");

    /* Create a dataset creation property list */
    dcpl = H5Pcreate(H5P_DATASET_CREATE);
    VRFY((dcpl>=0), "dataset creation property list succeeded");

    ret=H5Pset_fill_value(dcpl, H5T_NATIVE_DOUBLE, &fill);
    VRFY((ret>=0), "set fill-value succeeded");

    for (n = 0; n < ndatasets; n++) {
	sprintf (dname, "dataset %d", n);
	dataset = H5Dcreate (iof, dname, H5T_NATIVE_DOUBLE, filespace, dcpl);
	VRFY((dataset > 0), dname); 

	/* calculate data to write */
	for (i = 0; i < SIZE; i++)
	    for (j = 0; j < SIZE; j++)
	        outme [i][j] = n*1000 + mpi_rank;

	H5Dwrite (dataset, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT, outme);

	H5Dclose (dataset);
#ifdef BARRIER_CHECKS
	if (! ((n+1) % 10)) {
	    printf("created %d datasets\n", n+1);
	    MPI_Barrier(MPI_COMM_WORLD);
	}
#endif /* BARRIER_CHECKS */
    }

    H5Sclose (filespace);
    H5Sclose (memspace);
    H5Pclose (dcpl);
    H5Fclose (iof);
}

/* Example of using PHDF5 to create, write, and read compact dataset.  
 */
void compact_dataset(char *filename)
{
    int i, j, mpi_size, mpi_rank, err_num=0;
    hbool_t use_gpfs = FALSE;
    hid_t iof, plist, dcpl, dxpl, dataset, filespace;
    hsize_t file_dims [DIM]={SIZE,SIZE};
    double outme [SIZE][SIZE], inme[SIZE][SIZE];
    char dname[]="dataset";
    herr_t ret;
                                
    MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);

    VRFY((mpi_size <= SIZE), "mpi_size <= SIZE");

    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);

    /* Define data space */
    filespace = H5Screate_simple (DIM, file_dims, NULL);

    /* Create a compact dataset */
    dcpl = H5Pcreate(H5P_DATASET_CREATE);
    VRFY((dcpl>=0), "dataset creation property list succeeded");
    ret=H5Pset_layout(dcpl, H5D_COMPACT);
    VRFY((dcpl >= 0), "set property list for compact dataset");
    ret=H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY);
    VRFY((ret >= 0), "set space allocation time for compact dataset");

    dataset = H5Dcreate (iof, dname, H5T_NATIVE_DOUBLE, filespace, dcpl);
    VRFY((dataset >= 0), "H5Dcreate succeeded");        

    /* set up the collective transfer properties list */
    dxpl = H5Pcreate (H5P_DATASET_XFER);
    VRFY((dxpl >= 0), "");
    ret=H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
    VRFY((ret >= 0), "H5Pcreate xfer succeeded");

    /* Recalculate data to write.  Each process writes the same data. */
    for (i = 0; i < SIZE; i++)
         for (j = 0; j < SIZE; j++)
              outme [i][j] = (i+j)*1000;

    ret=H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, outme);
    VRFY((ret >= 0), "H5Dwrite succeeded");

    H5Pclose (dcpl);
    H5Pclose (plist);
    H5Dclose (dataset);
    H5Sclose (filespace);
    H5Fclose (iof);

    /* Open the file and dataset, read and compare the data. */
    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    iof = H5Fopen(filename, H5F_ACC_RDONLY, plist);
    VRFY((iof >= 0), "H5Fopen succeeded");

    /* set up the collective transfer properties list */
    dxpl = H5Pcreate (H5P_DATASET_XFER);
    VRFY((dxpl >= 0), "");
    ret=H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
    VRFY((ret >= 0), "H5Pcreate xfer succeeded");

    dataset = H5Dopen(iof, dname);
    VRFY((dataset >= 0), "H5Dcreate succeeded");

    ret = H5Dread(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, inme);
    VRFY((ret >= 0), "H5Dread succeeded");

    /* Verify data value */
    for (i = 0; i < SIZE; i++)
        for (j = 0; j < SIZE; j++)
            if(inme[i][j] != outme[i][j])
                if(err_num++ < MAX_ERR_REPORT || verbose)
                    printf("Dataset Verify failed at [%d][%d]: expect %f, got %f\n", i, j, outme[i][j], inme[i][j]); 
                                                            
    H5Pclose(plist);
    H5Pclose(dxpl);
    H5Dclose(dataset);
    H5Fclose(iof);
}

/* Example of using PHDF5 to create "large" datasets.  (>2GB, >4GB, >8GB)
 * Actual data is _not_ written to these datasets.  Dataspaces are exact
 * sizes (2GB, 4GB, etc.), but the metadata for the file pushes the file over
 * the boundary of interest.
 */
void big_dataset(const char *filename)
{
    int mpi_size, mpi_rank;     /* MPI info */
    hbool_t use_gpfs = FALSE;   /* Don't use GPFS stuff for this test */
    hid_t iof,                  /* File ID */
        fapl,                   /* File access property list ID */
        dataset,                /* Dataset ID */
        filespace;              /* Dataset's dataspace ID */
    hsize_t file_dims [4];      /* Dimensions of dataspace */
    char dname[]="dataset";     /* Name of dataset */
    MPI_Offset file_size;       /* Size of file on disk */
    herr_t ret;                 /* Generic return value */
                                
    MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);

    VRFY((mpi_size <= SIZE), "mpi_size <= SIZE");

    fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    VRFY((fapl >= 0), "create_faccess_plist succeeded");        

    /*
     * Create >2GB HDF5 file
     */
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
    VRFY((iof >= 0), "H5Fcreate succeeded");        

    /* Define dataspace for 2GB dataspace */
    file_dims[0]= 2;
    file_dims[1]= 1024;
    file_dims[2]= 1024;
    file_dims[3]= 1024;
    filespace = H5Screate_simple (4, file_dims, NULL);
    VRFY((filespace >= 0), "H5Screate_simple succeeded");        

    dataset = H5Dcreate (iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT);
    VRFY((dataset >= 0), "H5Dcreate succeeded");        

    /* Close all file objects */
    ret=H5Dclose (dataset);
    VRFY((ret >= 0), "H5Dclose succeeded");        
    ret=H5Sclose (filespace);
    VRFY((ret >= 0), "H5Sclose succeeded");        
    ret=H5Fclose (iof);
    VRFY((ret >= 0), "H5Fclose succeeded");        

    /* Check that file of the correct size was created */
    file_size=h5_mpi_get_file_size(filename, MPI_COMM_WORLD, MPI_INFO_NULL);
    VRFY((file_size == 2147485696ULL), "File is correct size");        

    /*
     * Create >4GB HDF5 file
     */
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
    VRFY((iof >= 0), "H5Fcreate succeeded");        

    /* Define dataspace for 4GB dataspace */
    file_dims[0]= 4;
    file_dims[1]= 1024;
    file_dims[2]= 1024;
    file_dims[3]= 1024;
    filespace = H5Screate_simple (4, file_dims, NULL);
    VRFY((filespace >= 0), "H5Screate_simple succeeded");        

    dataset = H5Dcreate (iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT);
    VRFY((dataset >= 0), "H5Dcreate succeeded");        

    /* Close all file objects */
    ret=H5Dclose (dataset);
    VRFY((ret >= 0), "H5Dclose succeeded");        
    ret=H5Sclose (filespace);
    VRFY((ret >= 0), "H5Sclose succeeded");        
    ret=H5Fclose (iof);
    VRFY((ret >= 0), "H5Fclose succeeded");        

    /* Check that file of the correct size was created */
    file_size=h5_mpi_get_file_size(filename, MPI_COMM_WORLD, MPI_INFO_NULL);
    VRFY((file_size == 4294969344ULL), "File is correct size");        

    /*
     * Create >8GB HDF5 file
     */
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
    VRFY((iof >= 0), "H5Fcreate succeeded");        

    /* Define dataspace for 8GB dataspace */
    file_dims[0]= 8;
    file_dims[1]= 1024;
    file_dims[2]= 1024;
    file_dims[3]= 1024;
    filespace = H5Screate_simple (4, file_dims, NULL);
    VRFY((filespace >= 0), "H5Screate_simple succeeded");        

    dataset = H5Dcreate (iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT);
    VRFY((dataset >= 0), "H5Dcreate succeeded");        

    /* Close all file objects */
    ret=H5Dclose (dataset);
    VRFY((ret >= 0), "H5Dclose succeeded");        
    ret=H5Sclose (filespace);
    VRFY((ret >= 0), "H5Sclose succeeded");        
    ret=H5Fclose (iof);
    VRFY((ret >= 0), "H5Fclose succeeded");        

    /* Check that file of the correct size was created */
    file_size=h5_mpi_get_file_size(filename, MPI_COMM_WORLD, MPI_INFO_NULL);
    VRFY((file_size == 8589936640ULL), "File is correct size");        

    /* Close fapl */
    ret=H5Pclose (fapl);
    VRFY((ret >= 0), "H5Pclose succeeded");        
}

/* Example of using PHDF5 to read "short" datasets.  These datasets don't have
 * actual data written to the entire raw data area and rely on the "fill with
 * zeros" code in the VFL driver read routine to work correctly.
 */
void short_dataset(const char *filename)
{
    int mpi_size, mpi_rank;     /* MPI info */
    hbool_t use_gpfs = FALSE;   /* Don't use GPFS stuff for this test */
    int err_num;                /* Number of errors */
    hid_t iof,                  /* File ID */
        fapl,                   /* File access property list ID */
        dxpl,                   /* Data transfer property list ID */
        dataset,                /* Dataset ID */
        memspace,               /* Memory dataspace ID */
        filespace;              /* Dataset's dataspace ID */
    char dname[]="dataset";     /* Name of dataset */
    hsize_t     dset_size[4] = {0, 6, 7, 8};
    hssize_t    req_start[4] = {0, 0, 0, 0};
    hsize_t     req_count[4] = {1, 6, 7, 8};
    int *rdata, *wdata;         /* Buffers for data to read and write */
    int *tdata, *tdata2;        /* Temporary pointer into buffer */
    int acc, i, j, k, l;        /* Local index variables */
    herr_t ret;                 /* Generic return value */
                                
    MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);

    VRFY((mpi_size <= SIZE), "mpi_size <= SIZE");

    /* Allocate space for the buffers */
    dset_size[0]=mpi_size+1;
    rdata=HDmalloc((size_t)(dset_size[0]*dset_size[1]*dset_size[2]*dset_size[3]*sizeof(int)));
    VRFY((rdata != NULL), "HDcalloc succeeded for read buffer");
    wdata=HDmalloc((size_t)(dset_size[0]*dset_size[1]*dset_size[2]*dset_size[3]*sizeof(int)));
    VRFY((wdata != NULL), "HDmalloc succeeded for write buffer");

    /* Initialize write buffer */
    HDmemset(rdata,2,(size_t)(dset_size[0]*dset_size[1]*dset_size[2]*dset_size[3]*sizeof(int)));
    tdata=wdata;
    for (i=0, acc=0; i<(int)dset_size[0]; i++)
        for (j=0; j<(int)dset_size[1]; j++)
            for (k=0; k<(int)dset_size[2]; k++)
                for (l=0; l<(int)dset_size[3]; l++)
                    *tdata++ = acc++;

    fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    VRFY((fapl >= 0), "create_faccess_plist succeeded");

    /*
     * Create HDF5 file
     */
    iof = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
    VRFY((iof >= 0), "H5Fcreate succeeded");

    filespace = H5Screate_simple(4, dset_size, NULL);
    VRFY((filespace >= 0), "File H5Screate_simple succeeded");

    dataset = H5Dcreate(iof, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT);
    VRFY((dataset >= 0), "H5Dcreate succeeded");

    memspace = H5Screate_simple(4, dset_size, NULL);
    VRFY((memspace >= 0), "Memory H5Screate_simple succeeded");

    /* Create hyperslabs in memory and file dataspaces */
    req_start[0]=mpi_rank;
    ret=H5Sselect_hyperslab(filespace, H5S_SELECT_SET, req_start, NULL, req_count, NULL);
    VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace");
    ret=H5Sselect_hyperslab(memspace, H5S_SELECT_SET, req_start, NULL, req_count, NULL);
    VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace");

    /* Create DXPL for collective I/O */
    dxpl = H5Pcreate (H5P_DATASET_XFER);
    VRFY((dxpl >= 0), "H5Pcreate succeeded");

    ret=H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
    VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");

    /* Collectively write a hyperslab of data to the dataset */
    ret=H5Dwrite(dataset, H5T_NATIVE_INT, memspace, filespace, dxpl, wdata);
    VRFY((ret >= 0), "H5Dwrite succeeded");

    /* Barrier here, to allow MPI-posix I/O to sync */
    MPI_Barrier(MPI_COMM_WORLD);

    /* Independently read the entire dataset back */
    ret=H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
    VRFY((ret >= 0), "H5Dread succeeded");

    /* Verify correct data read */
    tdata=wdata;
    tdata2=rdata;
    err_num=0;
    for (i=0; i<(int)dset_size[0]; i++)
        for (j=0; j<(int)dset_size[1]; j++)
            for (k=0; k<(int)dset_size[2]; k++)
                for (l=0; l<(int)dset_size[3]; l++, tdata++, tdata2++)
                    if(i<mpi_size) {
                        if( *tdata != *tdata2 )
                            if(err_num++ < MAX_ERR_REPORT || verbose)
                                printf("Dataset Verify failed at [%d][%d][%d][%d]: expect %d, got %d\n", i,j,k,l, *tdata, *tdata2); 
                    } /* end if */
                    else {
                        if( *tdata2 != 0)
                            if(err_num++ < MAX_ERR_REPORT || verbose)
                                printf("Dataset Verify failed at [%d][%d][%d][%d]: expect 0, got %d\n", i,j,k,l, *tdata2);
                    } /* end else */
    if(err_num > MAX_ERR_REPORT && !verbose)
        printf("[more errors ...]\n");
    if(err_num){
        printf("%d errors found in check_value\n", err_num);
	nerrors++;
    }

    /* Close all file objects */
    ret=H5Dclose (dataset);
    VRFY((ret >= 0), "H5Dclose succeeded");        
    ret=H5Sclose (filespace);
    VRFY((ret >= 0), "H5Sclose succeeded");        
    ret=H5Fclose (iof);
    VRFY((ret >= 0), "H5Fclose succeeded");        

    /* Close memory dataspace */
    ret=H5Sclose (memspace);
    VRFY((ret >= 0), "H5Sclose succeeded");

    /* Close dxpl */
    ret=H5Pclose (dxpl);
    VRFY((ret >= 0), "H5Pclose succeeded");

    /* Close fapl */
    ret=H5Pclose (fapl);
    VRFY((ret >= 0), "H5Pclose succeeded");
}

/* Write multiple groups with a chunked dataset in each group collectively. 
 * These groups and datasets are for testing independent read later.
 */
void collective_group_write(char *filename, int ngroups)
{
    int mpi_rank, mpi_size;
    int i, j, m;
    hbool_t use_gpfs = FALSE;
    char gname[64], dname[32];
    hid_t fid, gid, did, plist, dcpl, memspace, filespace;
    DATATYPE outme[SIZE][SIZE];
    hssize_t chunk_origin[DIM];
    hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
    const hsize_t chunk_size[2] = {SIZE/2, SIZE/2};  /* Chunk dimensions */
    herr_t ret1, ret2;

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
    H5Pclose(plist);

    /* decide the hyperslab according to process number. */
    get_slab(chunk_origin, chunk_dims, count, file_dims);  

    /* select hyperslab in memory and file spaces.  These two operations are
     * identical since the datasets are the same. */
    memspace  = H5Screate_simple(DIM, file_dims, NULL);
    ret1 = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, 
                               chunk_dims, count, chunk_dims);
    filespace = H5Screate_simple(DIM, file_dims,  NULL);
    ret2 = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, 
                               chunk_dims, count, chunk_dims);
    VRFY((memspace>=0), "memspace");
    VRFY((filespace>=0), "filespace");
    VRFY((ret1>=0), "mgroup memspace selection");
    VRFY((ret2>=0), "mgroup filespace selection");   
    
    dcpl = H5Pcreate(H5P_DATASET_CREATE);
    ret1 = H5Pset_chunk (dcpl, 2, chunk_size);
    VRFY((dcpl>=0), "dataset creation property");
    VRFY((ret1>=0), "set chunk for dataset creation property");
        
    /* creates ngroups groups under the root group, writes chunked 
     * datasets in parallel. */
    for(m = 0; m < ngroups; m++) {
        sprintf(gname, "group%d", m);
        gid = H5Gcreate(fid, gname, 0);
        VRFY((gid > 0), gname);

        sprintf(dname, "dataset%d", m);
        did = H5Dcreate(gid, dname, H5T_NATIVE_INT, filespace, dcpl);
        VRFY((did > 0), dname);

        for(i=0; i < SIZE; i++)
            for(j=0; j < SIZE; j++)
     	        outme[i][j] = (i+j)*1000 + mpi_rank;

        H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, 
                 outme);

        H5Dclose(did);
        H5Gclose(gid);

#ifdef BARRIER_CHECKS
        if(! ((m+1) % 10)) {
            printf("created %d groups\n", m+1);
            MPI_Barrier(MPI_COMM_WORLD);
	}
#endif /* BARRIER_CHECKS */
    }
   
    H5Pclose(dcpl);
    H5Sclose(filespace);
    H5Sclose(memspace);
    H5Fclose(fid);
}

/* Let two sets of processes open and read different groups and chunked 
 * datasets independently. 
 */
void independent_group_read(char *filename, int ngroups)
{
    int      mpi_rank, m;
    hid_t    plist, fid;
    hbool_t  use_gpfs = FALSE;

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    
    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    fid = H5Fopen(filename, H5F_ACC_RDONLY, plist);
    H5Pclose(plist);

    /* open groups and read datasets. Odd number processes read even number 
     * groups from the end; even number processes read odd number groups 
     * from the beginning. */
    if(mpi_rank%2==0) {
        for(m=ngroups-1; m==0; m-=2) 
            group_dataset_read(fid, mpi_rank, m);
    } else {
        for(m=0; m<ngroups; m+=2)
            group_dataset_read(fid, mpi_rank, m);
    }

    H5Fclose(fid);
}

/* Open and read datasets and compare data */
void group_dataset_read(hid_t fid, int mpi_rank, int m)
{
    int      ret, i, j;
    char     gname[64], dname[32];
    hid_t    gid, did;
    DATATYPE *outdata, *indata;

    indata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));
    outdata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));
    
    /* open every group under root group. */
    sprintf(gname, "group%d", m);
    gid = H5Gopen(fid, gname);
    VRFY((gid > 0), gname);

    /* check the data. */
    sprintf(dname, "dataset%d", m);
    did = H5Dopen(gid, dname);
    VRFY((did>0), dname);

    H5Dread(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, indata);

    /* this is the original value */
    for(i=0; i<SIZE; i++)
       for(j=0; j<SIZE; j++) { 
           *outdata = (i+j)*1000 + mpi_rank;
           outdata++;
       }
    outdata -= SIZE*SIZE;

    /* compare the original value(outdata) to the value in file(indata).*/
    ret = check_value(indata, outdata);
    VRFY((ret==0), "check the data");

    H5Dclose(did);
    H5Gclose(gid);
}

/*
 * Example of using PHDF5 to create multiple groups.  Under the root group, 
 * it creates ngroups groups.  Under the first group just created, it creates 
 * recursive subgroups of depth GROUP_DEPTH.  In each created group, it 
 * generates NDATASETS datasets.  Each process write a hyperslab of an array
 * into the file.  The structure is like
 *               
 *                             root group
 *                                 |
 *            ---------------------------- ... ... ------------------------
 *           |          |         |        ... ...  |                      |
 *       group0*+'   group1*+' group2*+'   ... ...             group ngroups*+'
 *           |
 *      1st_child_group*' 
 *           |
 *      2nd_child_group*'
 *           |
 *           :
 *           :
 *           |
 * GROUP_DEPTHth_child_group*'
 *
 *      * means the group has dataset(s).
 *      + means the group has attribute(s).
 *      ' means the datasets in the groups have attribute(s).
 */
void multiple_group_write(char *filename, int ngroups)
{
    int mpi_rank, mpi_size;
    int m;
    hbool_t use_gpfs = FALSE;
    char gname[64];
    hid_t fid, gid, plist, memspace, filespace;
    hssize_t chunk_origin[DIM];
    hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
    herr_t ret;

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
    H5Pclose(plist);

    /* decide the hyperslab according to process number. */
    get_slab(chunk_origin, chunk_dims, count, file_dims);  

    /* select hyperslab in memory and file spaces.  These two operations are
     * identical since the datasets are the same. */
    memspace  = H5Screate_simple(DIM, file_dims, NULL);
    VRFY((memspace>=0), "memspace");
    ret = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, 
                               chunk_dims, count, chunk_dims);
    VRFY((ret>=0), "mgroup memspace selection");

    filespace = H5Screate_simple(DIM, file_dims,  NULL);
    VRFY((filespace>=0), "filespace");
    ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, 
                               chunk_dims, count, chunk_dims);
    VRFY((ret>=0), "mgroup filespace selection");   

    /* creates ngroups groups under the root group, writes datasets in 
     * parallel. */
    for(m = 0; m < ngroups; m++) {
        sprintf(gname, "group%d", m);
        gid = H5Gcreate(fid, gname, 0);
        VRFY((gid > 0), gname);

        /* create attribute for these groups. */   
	write_attribute(gid, is_group, m);
           
        if(m != 0)
	    write_dataset(memspace, filespace, gid);

        H5Gclose(gid);

#ifdef BARRIER_CHECKS
        if(! ((m+1) % 10)) {
            printf("created %d groups\n", m+1);
            MPI_Barrier(MPI_COMM_WORLD);
	}
#endif /* BARRIER_CHECKS */
    }
    
    /* recursively creates subgroups under the first group. */
    gid = H5Gopen(fid, "group0");
    create_group_recursive(memspace, filespace, gid, 0);
    ret = H5Gclose(gid);
    VRFY((ret>=0), "H5Gclose");
    
    ret = H5Sclose(filespace);
    VRFY((ret>=0), "H5Sclose");
    ret = H5Sclose(memspace);
    VRFY((ret>=0), "H5Sclose");
    ret = H5Fclose(fid);
    VRFY((ret>=0), "H5Fclose");
}

/* 
 * In a group, creates NDATASETS datasets.  Each process writes a hyperslab
 * of a data array to the file.
 */ 
void write_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
    int i, j, n;
    int mpi_rank, mpi_size;
    char dname[32];
    DATATYPE outme[SIZE][SIZE];
    hid_t did;

  
    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    for(n=0; n < NDATASET; n++) {
         sprintf(dname, "dataset%d", n);
         did = H5Dcreate(gid, dname, H5T_NATIVE_INT, filespace, 
                         H5P_DEFAULT);
         VRFY((did > 0), dname);

         for(i=0; i < SIZE; i++)
             for(j=0; j < SIZE; j++)
     	         outme[i][j] = n*1000 + mpi_rank;

         H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, 
                  outme);

         /* create attribute for these datasets.*/
         write_attribute(did, is_dset, n);
	 
         H5Dclose(did);
    }
}

/* 
 * Creates subgroups of depth GROUP_DEPTH recursively.  Also writes datasets
 * in parallel in each group.
 */
void create_group_recursive(hid_t memspace, hid_t filespace, hid_t gid, 
                            int counter)
{ 
   hid_t child_gid;
   int   mpi_rank;
   char  gname[64];
  
   MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);

#ifdef BARRIER_CHECKS
   if(! ((counter+1) % 10)) {
        printf("created %dth child groups\n", counter+1);
        MPI_Barrier(MPI_COMM_WORLD);
   }
#endif /* BARRIER_CHECKS */
 
   sprintf(gname, "%dth_child_group", counter+1);   
   child_gid = H5Gcreate(gid, gname, 0);
   VRFY((child_gid > 0), gname);

   /* write datasets in parallel. */
   write_dataset(memspace, filespace, gid);  

   if( counter < GROUP_DEPTH ) 
       create_group_recursive(memspace, filespace, child_gid, counter+1);

   H5Gclose(child_gid);
}

/* 
 * This function is to verify the data from multiple group testing.  It opens
 * every dataset in every group and check their correctness.  
 */
void multiple_group_read(char *filename, int ngroups)
{
    int      mpi_rank, mpi_size, error_num;
    int      m;
    hbool_t  use_gpfs = FALSE;
    char     gname[64];
    hid_t    plist, fid, gid, memspace, filespace;
    hssize_t chunk_origin[DIM];
    hsize_t  chunk_dims[DIM], file_dims[DIM], count[DIM];

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
    fid = H5Fopen(filename, H5F_ACC_RDONLY, plist);
    H5Pclose(plist);

    /* decide hyperslab for each process */
    get_slab(chunk_origin, chunk_dims, count, file_dims);

    /* select hyperslab for memory and file space */
    memspace  = H5Screate_simple(DIM, file_dims, NULL);
    H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims,
                        count, chunk_dims);
    filespace = H5Screate_simple(DIM, file_dims, NULL);
    H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, 
                        count, chunk_dims);
    
    /* open every group under root group. */
    for(m=0; m<ngroups; m++) {
        sprintf(gname, "group%d", m);
        gid = H5Gopen(fid, gname);
        VRFY((gid > 0), gname);
         
        /* check the data. */
        if(m != 0)
            if( (error_num = read_dataset(memspace, filespace, gid))>0)
	        nerrors += error_num;
        
        /* check attribute.*/ 
        error_num = 0;        
        if( (error_num = read_attribute(gid, is_group, m))>0 )
	    nerrors += error_num;

        H5Gclose(gid);

#ifdef BARRIER_CHECKS
        if(!((m+1)%10))
            MPI_Barrier(MPI_COMM_WORLD);
#endif /* BARRIER_CHECKS */
    }

    /* open all the groups in vertical direction. */
    gid = H5Gopen(fid, "group0");
    VRFY((gid>0), "group0");
    recursive_read_group(memspace, filespace, gid, 0);
    H5Gclose(gid);

    H5Sclose(filespace);
    H5Sclose(memspace);
    H5Fclose(fid);

}

/* 
 * This function opens all the datasets in a certain, checks the data using 
 * dataset_vrfy function.
 */
int read_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
    int i, j, n, mpi_rank, mpi_size, attr_errors=0, vrfy_errors=0;
    char dname[32];
    DATATYPE *outdata, *indata;
    hid_t did;

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    indata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));
    outdata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));

    for(n=0; n<NDATASET; n++) {
        sprintf(dname, "dataset%d", n);
        did = H5Dopen(gid, dname);
        VRFY((did>0), dname);

        H5Dread(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, 
                indata);

        /* this is the original value */
        for(i=0; i<SIZE; i++)
	    for(j=0; j<SIZE; j++) { 
	         *outdata = n*1000 + mpi_rank;
                 outdata++;
	    }
        outdata -= SIZE*SIZE;

        /* compare the original value(outdata) to the value in file(indata).*/
        vrfy_errors = check_value(indata, outdata);

        /* check attribute.*/  
        if( (attr_errors = read_attribute(did, is_dset, n))>0 )
            vrfy_errors += attr_errors; 
	       
        H5Dclose(did);
    }

    free(indata);
    free(outdata);

    return vrfy_errors;
}

/* 
 * This recursive function opens all the groups in vertical direction and 
 * checks the data.
 */
void recursive_read_group(hid_t memspace, hid_t filespace, hid_t gid, 
                          int counter)
{
    hid_t child_gid;
    int   mpi_rank, err_num=0;
    char  gname[64];

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#ifdef BARRIER_CHECKS
    if((counter+1) % 10) 
        MPI_Barrier(MPI_COMM_WORLD);
#endif /* BARRIER_CHECKS */

    if( (err_num = read_dataset(memspace, filespace, gid)) )
        nerrors += err_num;

    if( counter < GROUP_DEPTH ) {
        sprintf(gname, "%dth_child_group", counter+1);
        child_gid = H5Gopen(gid, gname);
        VRFY((child_gid>0), gname);
        recursive_read_group(memspace, filespace, child_gid, counter+1);
        H5Gclose(child_gid);
    }
}

/* Create and write attribute for a group or a dataset.  For groups, attribute
 * is a scalar datum; for dataset, it is a one-dimensional array.
 */ 
void write_attribute(hid_t obj_id, int this_type, int num)
{
    hid_t   sid, aid;
    hsize_t dspace_dims[1]={8};
    int     i, mpi_rank, attr_data[8], dspace_rank=1;
    char    attr_name[32];

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
        
    if(this_type == is_group) {
        sprintf(attr_name, "Group Attribute %d", num);
        sid = H5Screate(H5S_SCALAR);
        aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
        H5Awrite(aid, H5T_NATIVE_INT,  &num);
        H5Aclose(aid);
        H5Sclose(sid);
    }
    else if(this_type == is_dset) {
        sprintf(attr_name, "Dataset Attribute %d", num);
        for(i=0; i<8; i++)
            attr_data[i] = i;
        sid = H5Screate_simple(dspace_rank, dspace_dims, NULL);
        aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
        H5Awrite(aid, H5T_NATIVE_INT, attr_data);   
        H5Aclose(aid);
        H5Sclose(sid);
    }

}

/* Read and verify attribute for group or dataset. */
int read_attribute(hid_t obj_id, int this_type, int num)
{
    hid_t aid;
    hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
    int  i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
    char attr_name[32];
   
    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    
    if(this_type == is_group) {
        sprintf(attr_name, "Group Attribute %d", num);
        aid = H5Aopen_name(obj_id, attr_name);
        if(MAINPROCESS) {
            H5Aread(aid, H5T_NATIVE_INT, &in_num);
            vrfy_errors =  dataset_vrfy(NULL, NULL, NULL, group_block, 
                                        &in_num, &num);
	}
        H5Aclose(aid);
    }
    else if(this_type == is_dset) {
        sprintf(attr_name, "Dataset Attribute %d", num);  
        for(i=0; i<8; i++)
            out_data[i] = i;
        aid = H5Aopen_name(obj_id, attr_name);
        if(MAINPROCESS) {
            H5Aread(aid, H5T_NATIVE_INT, in_data);
            vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data,
                                       out_data);
	}
        H5Aclose(aid);
    }       
    
    return vrfy_errors;
}

/* This functions compares the original data with the read-in data for its 
 * hyperslab part only by process ID. */
int check_value(DATATYPE *indata, DATATYPE *outdata) 
{
    int mpi_rank, mpi_size, err_num=0;
    hsize_t i, j;
    hssize_t chunk_origin[DIM];
    hsize_t  chunk_dims[DIM], count[DIM];

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
    
    get_slab(chunk_origin, chunk_dims, count, NULL);

    indata += chunk_origin[0]*SIZE;
    outdata += chunk_origin[0]*SIZE;
    for(i=chunk_origin[0]; i<(chunk_origin[0]+chunk_dims[0]); i++)
         for(j=chunk_origin[1]; j<(chunk_origin[1]+chunk_dims[1]); j++) {
              if( *indata != *outdata )
	          if(err_num++ < MAX_ERR_REPORT || verbose)
		      printf("Dataset Verify failed at [%ld][%ld](row %ld, col%ld): expect %d, got %d\n", (long)i, (long)j, (long)i, (long)j, *outdata, *indata); 
	 }
    if(err_num > MAX_ERR_REPORT && !verbose)
        printf("[more errors ...]\n");
    if(err_num)
        printf("%d errors found in check_value\n", err_num);
    return err_num;
}

/* Decide the portion of data chunk in dataset by process ID. */
void get_slab(hssize_t chunk_origin[], hsize_t chunk_dims[], hsize_t count[],
              hsize_t file_dims[])
{
    int mpi_rank, mpi_size;
    
    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);

    if(chunk_origin != NULL) {
        chunk_origin[0] = mpi_rank * (SIZE/mpi_size);
        chunk_origin[1] = 0;
    }
    if(chunk_dims != NULL) {
        chunk_dims[0]   = SIZE/mpi_size;
        chunk_dims[1]   = SIZE;
    }
    if(file_dims != NULL) 
        file_dims[0] = file_dims[1] = SIZE;
    if(count != NULL) 
        count[0] = count[1] = 1;
}

/*=============================================================================
 *                         End of t_mdset.c
 *===========================================================================*/