File: hdf5filter.c

package info (click to toggle)
netcdf-parallel 1%3A4.7.4-1
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 105,352 kB
  • sloc: ansic: 229,114; sh: 11,180; yacc: 2,561; makefile: 1,390; lex: 1,173; xml: 173; awk: 2
file content (397 lines) | stat: -rw-r--r-- 12,648 bytes parent folder | download | duplicates (3)
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
/* Copyright 2003-2018, University Corporation for Atmospheric
 * Research. See the COPYRIGHT file for copying and redistribution
 * conditions.
 */
/**
 * @file @internal Internal netcdf-4 functions for filters
 *
 * This file contains functions internal to the netcdf4 library. None of
 * the functions in this file are exposed in the exetnal API. These
 * functions all relate to the manipulation of netcdf-4 filters
 *
 * @author Dennis Heimbigner
 */

#include "config.h"
#include <stdlib.h>
#include "hdf5internal.h"
#include "hdf5debug.h"

#define HAVE_H5_DEFLATE

/* Mnemonic */
#define FILTERACTIVE 1


/* WARNING: GLOBAL VARIABLE */

/* Define list of registered filters */
static NClist* NC4_registeredfilters = NULL; /** List<NC_FILTER_CLIENT_HDF5*> */

/**************************************************/
/* Filter registration support */

static int
filterlookup(unsigned int id)
{
    int i;
    if(NC4_registeredfilters == NULL)
	NC4_registeredfilters = nclistnew();
    for(i=0;i<nclistlength(NC4_registeredfilters);i++) {
	NC_FILTER_CLIENT_HDF5* x = nclistget(NC4_registeredfilters,i);
	if(x != NULL && x->id == id) return i; /* return position */
    }
    return -1;
}

static void
reclaiminfo(NC_FILTER_CLIENT_HDF5* info)
{
    nullfree(info);
}

static int
filterremove(int pos)
{
    NC_FILTER_CLIENT_HDF5* info = NULL;
    if(NC4_registeredfilters == NULL)
	return THROW(NC_EINVAL);
    if(pos < 0 || pos >= nclistlength(NC4_registeredfilters))
	return THROW(NC_EINVAL);
    info = nclistget(NC4_registeredfilters,pos);
    reclaiminfo(info);
    nclistremove(NC4_registeredfilters,pos);
    return NC_NOERR;
}

static NC_FILTER_CLIENT_HDF5*
dupfilterinfo(NC_FILTER_CLIENT_HDF5* info)
{
    NC_FILTER_CLIENT_HDF5* dup = NULL;
    if(info == NULL) goto fail;
    if((dup = calloc(1,sizeof(NC_FILTER_CLIENT_HDF5))) == NULL) goto fail;
    *dup = *info;
    return dup;
fail:
    reclaiminfo(dup);
    return NULL;
}

int
NC4_hdf5_addfilter(NC_VAR_INFO_T* var, int active, unsigned int id, size_t nparams, unsigned int* inparams)
{
    int stat = NC_NOERR;
    NC_FILTER_SPEC_HDF5* fi = NULL;
    unsigned int* params = NULL;

    if(var->filters == NULL) {
	if((var->filters = nclistnew())==NULL) return THROW(NC_ENOMEM);
    }

    if(nparams > 0 && inparams == NULL)
        return THROW(NC_EINVAL);
    if(inparams != NULL) {
        if((params = malloc(sizeof(unsigned int)*nparams)) == NULL)
	    return THROW(NC_ENOMEM);
        memcpy(params,inparams,sizeof(unsigned int)*nparams);
    }
    
    if((fi = calloc(1,sizeof(NC_FILTER_SPEC_HDF5))) == NULL)
    	{nullfree(params); return THROW(NC_ENOMEM);}

    fi->active = active;
    fi->filterid = id;
    fi->nparams = nparams;
    fi->params = params;
    nclistpush(var->filters,fi);
    return THROW(stat);
}

int
nc4_global_filter_action(int op, unsigned int id, NC_FILTER_OBJ_HDF5* infop)
{
    int stat = NC_NOERR;
    H5Z_class2_t* h5filterinfo = NULL;
    herr_t herr;
    int pos = -1;
    NC_FILTER_CLIENT_HDF5* dup = NULL;
    NC_FILTER_CLIENT_HDF5* elem = NULL;
    NC_FILTER_CLIENT_HDF5 ncf;

    switch (op) {
    case NCFILTER_CLIENT_REG: /* Ignore id argument */
        if(infop == NULL) {stat = NC_EINVAL; goto done;}
	assert(NC_FILTER_FORMAT_HDF5 == infop->hdr.format);
	assert(NC_FILTER_SORT_CLIENT == infop->sort);
	elem = (NC_FILTER_CLIENT_HDF5*)&infop->u.client;
        h5filterinfo = elem->info;
        /* Another sanity check */
        if(id != h5filterinfo->id)
	    {stat = NC_EINVAL; goto done;}
	/* See if this filter is already defined */
	if((pos = filterlookup(id)) >= 0)
	    {stat = NC_ENAMEINUSE; goto done;} /* Already defined */
	if((herr = H5Zregister(h5filterinfo)) < 0)
	    {stat = NC_EFILTER; goto done;}
	/* Save a copy of the passed in info */
	ncf.id = id;
	ncf.info = elem->info;
	if((dup=dupfilterinfo(&ncf)) == NULL)
	    {stat = NC_ENOMEM; goto done;}		
	nclistpush(NC4_registeredfilters,dup);	
	break;
    case NCFILTER_CLIENT_UNREG:
	if(id <= 0)
	    {stat = NC_ENOTNC4; goto done;}
	/* See if this filter is already defined */
	if((pos = filterlookup(id)) < 0)
	    {stat = NC_ENOFILTER; goto done;} /* Not defined */
	if((herr = H5Zunregister(id)) < 0)
	    {stat = NC_EFILTER; goto done;}
	if((stat=filterremove(pos))) goto done;
	break;
    case NCFILTER_CLIENT_INQ:
	if(infop == NULL) goto done;
        /* Look up the id in our local table */
   	if((pos = filterlookup(id)) < 0)
	    {stat = NC_ENOFILTER; goto done;} /* Not defined */
        elem = (NC_FILTER_CLIENT_HDF5*)nclistget(NC4_registeredfilters,pos);
	if(elem == NULL) {stat = NC_EINTERNAL; goto done;}
	if(infop != NULL) {
	    infop->u.client = *elem;
	}
	break;
    default:
	{stat = NC_EINTERNAL; goto done;}	
    }
done:
    return THROW(stat);
} 

/**
 * @internal Define filter settings. Called by nc_def_var_filter().
 *
 * @param ncid File ID.
 * @param varid Variable ID.
 * @param id Filter ID
 * @param nparams Number of parameters for filter.
 * @param parms Filter parameters.
 *
 * @returns ::NC_NOERR for success
 * @returns ::NC_EBADID Bad ncid.
 * @returns ::NC_ENOTVAR Invalid variable ID.
 * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
 * not netCDF-4/HDF5.
 * @returns ::NC_ELATEDEF Too late to change settings for this variable.
 * @returns ::NC_EFILTER Filter error.
 * @returns ::NC_EINVAL Invalid input
 * @author Dennis Heimbigner
 */
int
NC4_filter_actions(int ncid, int varid, int op, NC_Filterobject* args)
{
    int stat = NC_NOERR;
    NC_GRP_INFO_T *grp = NULL;
    NC_FILE_INFO_T *h5 = NULL;
    NC_VAR_INFO_T *var = NULL;
    NC_FILTER_OBJ_HDF5* obj = (NC_FILTER_OBJ_HDF5*)args;
    unsigned int id = 0;
    size_t nparams = 0;
    unsigned int* idp = NULL;
    size_t* nparamsp = NULL;
    size_t* nfiltersp = NULL;
    unsigned int* params = NULL;
    size_t nfilters = 0;
    unsigned int* filterids = NULL;

    LOG((2, "%s: ncid 0x%x varid %d op=%d", __func__, ncid, varid, op));

    if(args == NULL) return THROW(NC_EINVAL);
    if(args->format != NC_FILTER_FORMAT_HDF5) return THROW(NC_EFILTER);

    /* Find info for this file and group and var, and set pointer to each. */
    if ((stat = nc4_hdf5_find_grp_h5_var(ncid, varid, &h5, &grp, &var)))
	return THROW(stat);

    assert(h5 && var && var->hdr.id == varid);

    nfilters = nclistlength(var->filters);

    switch (op) {
    case NCFILTER_DEF: {
        if(obj->sort != NC_FILTER_SORT_SPEC) return THROW(NC_EFILTER);
        /* If the HDF5 dataset has already been created, then it is too
         * late to set all the extra stuff. */
        if (!(h5->flags & NC_INDEF)) return THROW(NC_EINDEFINE);
        if (!var->ndims) return NC_EINVAL; /* For scalars, complain */
        if (var->created)
             return THROW(NC_ELATEDEF);
        /* Can't turn on parallel and szip before HDF5 1.10.2. */
#ifdef USE_PARALLEL
#ifndef HDF5_SUPPORTS_PAR_FILTERS
        if (h5->parallel == NC_TRUE)
            return THROW(NC_EINVAL);
#endif /* HDF5_SUPPORTS_PAR_FILTERS */
#endif /* USE_PARALLEL */
	id = obj->u.spec.filterid;
	nparams = obj->u.spec.nparams;
	params = obj->u.spec.params;
#ifdef HAVE_H5_DEFLATE
        if(id == H5Z_FILTER_DEFLATE) {
	    int k;
	    int level;
            if(nparams != 1)
                return THROW(NC_EFILTER); /* incorrect no. of parameters */
	    level = (int)params[0];
            if (level < NC_MIN_DEFLATE_LEVEL ||
                level > NC_MAX_DEFLATE_LEVEL)
                return THROW(NC_EINVAL);
            /* If szip compression is already applied, return error. */
	    for(k=0;k<nclistlength(var->filters);k++) {
		NC_FILTER_SPEC_HDF5* f = nclistget(var->filters,k);
                if (f->filterid == H5Z_FILTER_SZIP)
                 return THROW(NC_EINVAL);
	    }
        }
#else /*!HAVE_H5_DEFLATE*/
        if(id == H5Z_FILTER_DEFLATE)
            return THROW(NC_EFILTER); /* Not allowed */
#endif
#ifdef HAVE_H5Z_SZIP
        if(id == H5Z_FILTER_SZIP) { /* Do error checking */
	    int k;
            if(nparams != 2)
                return THROW(NC_EFILTER); /* incorrect no. of parameters */
            /* Pixels per block must be an even number, < 32. */
            if (params[1] % 2 || params[1] > NC_MAX_PIXELS_PER_BLOCK)
                return THROW(NC_EINVAL);
            /* If zlib compression is already applied, return error. */
	    for(k=0;k<nclistlength(var->filters);k++) {
		NC_FILTER_SPEC_HDF5* f = nclistget(var->filters,k);
                if (f->filterid == H5Z_FILTER_DEFLATE)
                 return THROW(NC_EINVAL);
	    }
        }
#else /*!HAVE_H5Z_SZIP*/
        if(id == H5Z_FILTER_SZIP)
            return THROW(NC_EFILTER); /* Not allowed */
#endif
        /* Filter => chunking */
	var->storage = NC_CHUNKED;
        /* Determine default chunksizes for this variable unless already specified */
        if(var->chunksizes && !var->chunksizes[0]) {
	    /* Should this throw error? */
            if((stat = nc4_find_default_chunksizes2(grp, var)))
	        goto done;
            /* Adjust the cache. */
            if ((stat = nc4_adjust_var_cache(grp, var)))
                goto done;
        }
#ifdef HAVE_H5Z_SZIP
        if(id == H5Z_FILTER_SZIP) { /* szip X chunking error checking */
	    /* For szip, the pixels_per_block parameter must not be greater
	     * than the number of elements in a chunk of data. */
            size_t num_elem = 1;
            int d;
            for (d = 0; d < var->ndims; d++)
                num_elem *= var->dim[d]->len;
            /* Pixels per block must be <= number of elements. */
            if (params[1] > num_elem)
                return THROW(NC_EINVAL);
        }
#endif
	if((stat = NC4_hdf5_addfilter(var,!FILTERACTIVE,id,nparams,params)))
  	    goto done;
#ifdef USE_PARALLEL
#ifdef HDF5_SUPPORTS_PAR_FILTERS
        /* Switch to collective access. HDF5 requires collevtive access
         * for filter use with parallel I/O. */
        if (h5->parallel)
            var->parallel_access = NC_COLLECTIVE;
#else
        if (h5->parallel)
            return NC_EINVAL;
#endif /* HDF5_SUPPORTS_PAR_FILTERS */
#endif /* USE_PARALLEL */
	} break;
    case NCFILTER_INQ: {
        if (!var->ndims) return THROW(NC_EINVAL); /* For scalars, fail */
        if(obj->sort != NC_FILTER_SORT_SPEC) return THROW(NC_EFILTER);
	idp = &obj->u.spec.filterid;
	nparamsp = &obj->u.spec.nparams;
	params = obj->u.spec.params;
	if(nfilters > 0) {
	    /* Return info about var->filters[0] */
	    NC_FILTER_SPEC_HDF5* f = (NC_FILTER_SPEC_HDF5*)nclistget(var->filters,0);
	    if(idp) *idp = f->filterid;
	    if(nparamsp) {
		*nparamsp = (f->params == NULL ? 0 : f->nparams);
		if(params && f->params != NULL && f->nparams > 0)
		    memcpy(params,f->params,f->nparams*sizeof(unsigned int));
	    }
	} else {stat = NC_ENOFILTER; goto done;}
	} break;
    case NCFILTER_FILTERIDS: {
        if(obj->sort != NC_FILTER_SORT_IDS) return THROW(NC_EFILTER);
	nfiltersp = &obj->u.ids.nfilters;
	filterids = obj->u.ids.filterids;
        if(nfiltersp) *nfiltersp = nfilters;
	if(filterids) filterids[0] = 0;
        if(nfilters > 0 && filterids != NULL) {
	    int k;
	    for(k=0;k<nfilters;k++) {
		NC_FILTER_SPEC_HDF5* f = (NC_FILTER_SPEC_HDF5*)nclistget(var->filters,k);
		filterids[k] = f->filterid;
	    }
	}
	} break;
    case NCFILTER_INFO: {
	int k,found;
        if(obj->sort != NC_FILTER_SORT_SPEC) return THROW(NC_EFILTER);
	id = obj->u.spec.filterid;
        for(found=0,k=0;k<nfilters;k++) {
	    NC_FILTER_SPEC_HDF5* f = (NC_FILTER_SPEC_HDF5*)nclistget(var->filters,k);
	    if(f->filterid == id) {
	        obj->u.spec.nparams = f->nparams;
		if(obj->u.spec.params != NULL && f->params != NULL && f->nparams > 0)
		    memcpy(obj->u.spec.params,f->params,f->nparams*sizeof(unsigned int));
		found = 1;
		break;
	    }
	}
	if(!found) {stat = NC_ENOFILTER; goto done;}
	} break;
    case NCFILTER_REMOVE: {
	int k;
        if (!(h5->flags & NC_INDEF)) return THROW(NC_EINDEFINE);
        if(obj->sort != NC_FILTER_SORT_SPEC) return THROW(NC_EFILTER);
	id = obj->u.spec.filterid;
	/* Walk backwards */
        for(k=nfilters-1;k>=0;k--) {
	    NC_FILTER_SPEC_HDF5* f = (NC_FILTER_SPEC_HDF5*)nclistget(var->filters,k);
	    if(f->filterid == id) {
		if(f->active) {
		    /* Remove from variable */
		    if((stat = NC4_hdf5_remove_filter(var,id))) {stat = NC_ENOFILTER; goto done;}
		}
		nclistremove(var->filters,k);
		NC4_freefilterspec(f);
	    }
	}
	} break;
    default:
	{stat = NC_EINTERNAL; goto done;}	
    }

done:
    return THROW(stat);
}

void
NC4_freefilterspec(NC_FILTER_SPEC_HDF5* f)
{
    if(f) {
        if(f->params != NULL) {free(f->params);}
	free(f);
    }
}