Actual source code: data_bucket.c
petsc-3.11.4 2019-09-28
1: #include "../src/dm/impls/swarm/data_bucket.h"
3: /* string helpers */
4: PetscErrorCode DMSwarmDataFieldStringInList(const char name[],const PetscInt N,const DMSwarmDataField gfield[],PetscBool *val)
5: {
6: PetscInt i;
10: *val = PETSC_FALSE;
11: for (i = 0; i < N; ++i) {
12: PetscBool flg;
13: PetscStrcmp(name, gfield[i]->name, &flg);
14: if (flg) {
15: *val = PETSC_TRUE;
16: return(0);
17: }
18: }
19: return(0);
20: }
22: PetscErrorCode DMSwarmDataFieldStringFindInList(const char name[],const PetscInt N,const DMSwarmDataField gfield[],PetscInt *index)
23: {
24: PetscInt i;
28: *index = -1;
29: for (i = 0; i < N; ++i) {
30: PetscBool flg;
31: PetscStrcmp(name, gfield[i]->name, &flg);
32: if (flg) {
33: *index = i;
34: return(0);
35: }
36: }
37: return(0);
38: }
40: PetscErrorCode DMSwarmDataFieldCreate(const char registration_function[],const char name[],const size_t size,const PetscInt L,DMSwarmDataField *DF)
41: {
42: DMSwarmDataField df;
43: PetscErrorCode ierr;
46: PetscMalloc(sizeof(struct _p_DMSwarmDataField), &df);
47: PetscMemzero(df, sizeof(struct _p_DMSwarmDataField));
48: PetscStrallocpy(registration_function, &df->registration_function);
49: PetscStrallocpy(name, &df->name);
50: df->atomic_size = size;
51: df->L = L;
52: df->bs = 1;
53: /* allocate something so we don't have to reallocate */
54: PetscMalloc(size * L, &df->data);
55: PetscMemzero(df->data, size * L);
56: *DF = df;
57: return(0);
58: }
60: PetscErrorCode DMSwarmDataFieldDestroy(DMSwarmDataField *DF)
61: {
62: DMSwarmDataField df = *DF;
63: PetscErrorCode ierr;
66: PetscFree(df->registration_function);
67: PetscFree(df->name);
68: PetscFree(df->data);
69: PetscFree(df);
70: *DF = NULL;
71: return(0);
72: }
74: /* data bucket */
75: PetscErrorCode DMSwarmDataBucketCreate(DMSwarmDataBucket *DB)
76: {
77: DMSwarmDataBucket db;
78: PetscErrorCode ierr;
81: PetscMalloc(sizeof(struct _p_DMSwarmDataBucket), &db);
82: PetscMemzero(db, sizeof(struct _p_DMSwarmDataBucket));
84: db->finalised = PETSC_FALSE;
85: /* create empty spaces for fields */
86: db->L = -1;
87: db->buffer = 1;
88: db->allocated = 1;
89: db->nfields = 0;
90: PetscMalloc1(1, &db->field);
91: *DB = db;
92: return(0);
93: }
95: PetscErrorCode DMSwarmDataBucketDestroy(DMSwarmDataBucket *DB)
96: {
97: DMSwarmDataBucket db = *DB;
98: PetscInt f;
99: PetscErrorCode ierr;
102: /* release fields */
103: for (f = 0; f < db->nfields; ++f) {
104: DMSwarmDataFieldDestroy(&db->field[f]);
105: }
106: /* this will catch the initially allocated objects in the event that no fields are registered */
107: if (db->field != NULL) {
108: PetscFree(db->field);
109: }
110: PetscFree(db);
111: *DB = NULL;
112: return(0);
113: }
115: PetscErrorCode DMSwarmDataBucketQueryForActiveFields(DMSwarmDataBucket db,PetscBool *any_active_fields)
116: {
117: PetscInt f;
120: *any_active_fields = PETSC_FALSE;
121: for (f = 0; f < db->nfields; ++f) {
122: if (db->field[f]->active) {
123: *any_active_fields = PETSC_TRUE;
124: return(0);
125: }
126: }
127: return(0);
128: }
130: PetscErrorCode DMSwarmDataBucketRegisterField(
131: DMSwarmDataBucket db,
132: const char registration_function[],
133: const char field_name[],
134: size_t atomic_size, DMSwarmDataField *_gfield)
135: {
136: PetscBool val;
137: DMSwarmDataField fp;
141: /* check we haven't finalised the registration of fields */
142: /*
143: if(db->finalised==PETSC_TRUE) {
144: printf("ERROR: DMSwarmDataBucketFinalize() has been called. Cannot register more fields\n");
145: ERROR();
146: }
147: */
148: /* check for repeated name */
149: DMSwarmDataFieldStringInList(field_name, db->nfields, (const DMSwarmDataField*) db->field, &val);
150: if (val == PETSC_TRUE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Field %s already exists. Cannot add same field twice",field_name);
151: /* create new space for data */
152: PetscRealloc(sizeof(DMSwarmDataField)*(db->nfields+1), &db->field);
153: /* add field */
154: DMSwarmDataFieldCreate(registration_function, field_name, atomic_size, db->allocated, &fp);
155: db->field[db->nfields] = fp;
156: db->nfields++;
157: if (_gfield != NULL) {
158: *_gfield = fp;
159: }
160: return(0);
161: }
163: /*
164: #define DMSwarmDataBucketRegisterField(db,name,size,k) {\
165: char *location;\
166: asprintf(&location,"Registered by %s() at line %d within file %s", __FUNCTION__, __LINE__, __FILE__);\
167: _DMSwarmDataBucketRegisterField( (db), location, (name), (size), (k) );\
168: PetscFree(location);\
169: }
170: */
172: PetscErrorCode DMSwarmDataBucketGetDMSwarmDataFieldByName(DMSwarmDataBucket db,const char name[],DMSwarmDataField *gfield)
173: {
174: PetscInt idx;
175: PetscBool found;
179: DMSwarmDataFieldStringInList(name,db->nfields,(const DMSwarmDataField*)db->field,&found);
180: if (!found) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot find DMSwarmDataField with name %s",name);
181: DMSwarmDataFieldStringFindInList(name,db->nfields,(const DMSwarmDataField*)db->field,&idx);
182: *gfield = db->field[idx];
183: return(0);
184: }
186: PetscErrorCode DMSwarmDataBucketQueryDMSwarmDataFieldByName(DMSwarmDataBucket db,const char name[],PetscBool *found)
187: {
191: *found = PETSC_FALSE;
192: DMSwarmDataFieldStringInList(name,db->nfields,(const DMSwarmDataField*)db->field,found);
193: return(0);
194: }
196: PetscErrorCode DMSwarmDataBucketFinalize(DMSwarmDataBucket db)
197: {
199: db->finalised = PETSC_TRUE;
200: return(0);
201: }
203: PetscErrorCode DMSwarmDataFieldGetNumEntries(DMSwarmDataField df,PetscInt *sum)
204: {
206: *sum = df->L;
207: return(0);
208: }
210: PetscErrorCode DMSwarmDataFieldSetBlockSize(DMSwarmDataField df,PetscInt blocksize)
211: {
213: df->bs = blocksize;
214: return(0);
215: }
217: PetscErrorCode DMSwarmDataFieldSetSize(DMSwarmDataField df,const PetscInt new_L)
218: {
222: if (new_L < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot set size of DMSwarmDataField to be < 0");
223: if (new_L == df->L) return(0);
224: if (new_L > df->L) {
225: PetscRealloc(df->atomic_size * (new_L), &df->data);
226: /* init new contents */
227: PetscMemzero(( ((char*)df->data)+df->L*df->atomic_size), (new_L-df->L)*df->atomic_size);
228: } else {
229: /* reallocate pointer list, add +1 in case new_L = 0 */
230: PetscRealloc(df->atomic_size * (new_L+1), &df->data);
231: }
232: df->L = new_L;
233: return(0);
234: }
236: PetscErrorCode DMSwarmDataFieldZeroBlock(DMSwarmDataField df,const PetscInt start,const PetscInt end)
237: {
241: if (start > end) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot zero a block of entries if start(%D) > end(%D)",start,end);
242: if (start < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot zero a block of entries if start(%D) < 0",start);
243: if (end > df->L) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot zero a block of entries if end(%D) >= array size(%D)",end,df->L);
244: PetscMemzero((((char*)df->data)+start*df->atomic_size), (end-start)*df->atomic_size);
245: return(0);
246: }
248: /*
249: A negative buffer value will simply be ignored and the old buffer value will be used.
250: */
251: PetscErrorCode DMSwarmDataBucketSetSizes(DMSwarmDataBucket db,const PetscInt L,const PetscInt buffer)
252: {
253: PetscInt current_allocated,new_used,new_unused,new_buffer,new_allocated,f;
254: PetscBool any_active_fields;
258: if (db->finalised == PETSC_FALSE) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"You must call DMSwarmDataBucketFinalize() before DMSwarmDataBucketSetSizes()");
259: DMSwarmDataBucketQueryForActiveFields(db,&any_active_fields);
260: if (any_active_fields) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot safely re-size as at least one DMSwarmDataField is currently being accessed");
262: current_allocated = db->allocated;
263: new_used = L;
264: new_unused = current_allocated - new_used;
265: new_buffer = db->buffer;
266: if (buffer >= 0) { /* update the buffer value */
267: new_buffer = buffer;
268: }
269: new_allocated = new_used + new_buffer;
270: /* action */
271: if (new_allocated > current_allocated) {
272: /* increase size to new_used + new_buffer */
273: for (f=0; f<db->nfields; f++) {
274: DMSwarmDataFieldSetSize(db->field[f], new_allocated);
275: }
276: db->L = new_used;
277: db->buffer = new_buffer;
278: db->allocated = new_used + new_buffer;
279: } else {
280: if (new_unused > 2 * new_buffer) {
281: /* shrink array to new_used + new_buffer */
282: for (f = 0; f < db->nfields; ++f) {
283: DMSwarmDataFieldSetSize(db->field[f], new_allocated);
284: }
285: db->L = new_used;
286: db->buffer = new_buffer;
287: db->allocated = new_used + new_buffer;
288: } else {
289: db->L = new_used;
290: db->buffer = new_buffer;
291: }
292: }
293: /* zero all entries from db->L to db->allocated */
294: for (f = 0; f < db->nfields; ++f) {
295: DMSwarmDataField field = db->field[f];
296: DMSwarmDataFieldZeroBlock(field, db->L,db->allocated);
297: }
298: return(0);
299: }
301: PetscErrorCode DMSwarmDataBucketSetInitialSizes(DMSwarmDataBucket db,const PetscInt L,const PetscInt buffer)
302: {
303: PetscInt f;
307: DMSwarmDataBucketSetSizes(db,L,buffer);
308: for (f = 0; f < db->nfields; ++f) {
309: DMSwarmDataField field = db->field[f];
310: DMSwarmDataFieldZeroBlock(field,0,db->allocated);
311: }
312: return(0);
313: }
315: PetscErrorCode DMSwarmDataBucketGetSizes(DMSwarmDataBucket db,PetscInt *L,PetscInt *buffer,PetscInt *allocated)
316: {
318: if (L) {*L = db->L;}
319: if (buffer) {*buffer = db->buffer;}
320: if (allocated) {*allocated = db->allocated;}
321: return(0);
322: }
324: PetscErrorCode DMSwarmDataBucketGetGlobalSizes(MPI_Comm comm,DMSwarmDataBucket db,PetscInt *L,PetscInt *buffer,PetscInt *allocated)
325: {
326: PetscInt ierr;
329: if (L) { MPI_Allreduce(&db->L,L,1,MPIU_INT,MPI_SUM,comm); }
330: if (buffer) { MPI_Allreduce(&db->buffer,buffer,1,MPIU_INT,MPI_SUM,comm); }
331: if (allocated) { MPI_Allreduce(&db->allocated,allocated,1,MPIU_INT,MPI_SUM,comm); }
332: return(0);
333: }
335: PetscErrorCode DMSwarmDataBucketGetDMSwarmDataFields(DMSwarmDataBucket db,PetscInt *L,DMSwarmDataField *fields[])
336: {
338: if (L) {*L = db->nfields;}
339: if (fields) {*fields = db->field;}
340: return(0);
341: }
343: PetscErrorCode DMSwarmDataFieldGetAccess(const DMSwarmDataField gfield)
344: {
346: if (gfield->active) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Field \"%s\" is already active. You must call DMSwarmDataFieldRestoreAccess()",gfield->name);
347: gfield->active = PETSC_TRUE;
348: return(0);
349: }
351: PetscErrorCode DMSwarmDataFieldAccessPoint(const DMSwarmDataField gfield,const PetscInt pid,void **ctx_p)
352: {
354: *ctx_p = NULL;
355: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
356: /* debug mode */
357: /* check point is valid */
358: if (pid < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
359: if (pid >= gfield->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",gfield->L);
360: if (gfield->active == PETSC_FALSE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Field \"%s\" is not active. You must call DMSwarmDataFieldGetAccess() before point data can be retrivied",gfield->name);
361: #endif
362: *ctx_p = DMSWARM_DATAFIELD_point_access(gfield->data,pid,gfield->atomic_size);
363: return(0);
364: }
366: PetscErrorCode DMSwarmDataFieldAccessPointOffset(const DMSwarmDataField gfield,const size_t offset,const PetscInt pid,void **ctx_p)
367: {
369: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
370: /* debug mode */
371: /* check point is valid */
372: /* if( offset < 0 ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"offset must be >= 0");*/
373: /* Note compiler realizes this can never happen with an unsigned PetscInt */
374: if (offset >= gfield->atomic_size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"offset must be < %zu",gfield->atomic_size);
375: /* check point is valid */
376: if (pid < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
377: if (pid >= gfield->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",gfield->L);
378: if (gfield->active == PETSC_FALSE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Field \"%s\" is not active. You must call DMSwarmDataFieldGetAccess() before point data can be retrivied",gfield->name);
379: #endif
380: *ctx_p = DMSWARM_DATAFIELD_point_access_offset(gfield->data,pid,gfield->atomic_size,offset);
381: return(0);
382: }
384: PetscErrorCode DMSwarmDataFieldRestoreAccess(DMSwarmDataField gfield)
385: {
387: if (gfield->active == PETSC_FALSE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Field \"%s\" is not active. You must call DMSwarmDataFieldGetAccess()", gfield->name);
388: gfield->active = PETSC_FALSE;
389: return(0);
390: }
392: PetscErrorCode DMSwarmDataFieldVerifyAccess(const DMSwarmDataField gfield,const size_t size)
393: {
395: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
396: if (gfield->atomic_size != size) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_USER,"Field \"%s\" must be mapped to %zu bytes, your intended structure is %zu bytes in length.",gfield->name, gfield->atomic_size, size );
397: #endif
398: return(0);
399: }
401: PetscErrorCode DMSwarmDataFieldGetAtomicSize(const DMSwarmDataField gfield,size_t *size)
402: {
404: if (size) {*size = gfield->atomic_size;}
405: return(0);
406: }
408: PetscErrorCode DMSwarmDataFieldGetEntries(const DMSwarmDataField gfield,void **data)
409: {
411: if (data) {*data = gfield->data;}
412: return(0);
413: }
415: PetscErrorCode DMSwarmDataFieldRestoreEntries(const DMSwarmDataField gfield,void **data)
416: {
418: if (data) {*data = NULL;}
419: return(0);
420: }
422: /* y = x */
423: PetscErrorCode DMSwarmDataBucketCopyPoint(const DMSwarmDataBucket xb,const PetscInt pid_x,
424: const DMSwarmDataBucket yb,const PetscInt pid_y)
425: {
426: PetscInt f;
430: for (f = 0; f < xb->nfields; ++f) {
431: void *dest;
432: void *src;
434: DMSwarmDataFieldGetAccess(xb->field[f]);
435: if (xb != yb) { DMSwarmDataFieldGetAccess( yb->field[f]); }
436: DMSwarmDataFieldAccessPoint(xb->field[f],pid_x, &src);
437: DMSwarmDataFieldAccessPoint(yb->field[f],pid_y, &dest);
438: PetscMemcpy(dest, src, xb->field[f]->atomic_size);
439: DMSwarmDataFieldRestoreAccess(xb->field[f]);
440: if (xb != yb) {DMSwarmDataFieldRestoreAccess(yb->field[f]);}
441: }
442: return(0);
443: }
445: PetscErrorCode DMSwarmDataBucketCreateFromSubset(DMSwarmDataBucket DBIn,const PetscInt N,const PetscInt list[],DMSwarmDataBucket *DB)
446: {
447: PetscInt nfields;
448: DMSwarmDataField *fields;
449: PetscInt f,L,buffer,allocated,p;
453: DMSwarmDataBucketCreate(DB);
454: /* copy contents of DBIn */
455: DMSwarmDataBucketGetDMSwarmDataFields(DBIn,&nfields,&fields);
456: DMSwarmDataBucketGetSizes(DBIn,&L,&buffer,&allocated);
457: for (f = 0; f < nfields; ++f) {
458: DMSwarmDataBucketRegisterField(*DB,"DMSwarmDataBucketCreateFromSubset",fields[f]->name,fields[f]->atomic_size,NULL);
459: }
460: DMSwarmDataBucketFinalize(*DB);
461: DMSwarmDataBucketSetSizes(*DB,L,buffer);
462: /* now copy the desired guys from DBIn => DB */
463: for (p = 0; p < N; ++p) {
464: DMSwarmDataBucketCopyPoint(DBIn,list[p], *DB,p);
465: }
466: return(0);
467: }
469: /* insert into an exisitng location */
470: PetscErrorCode DMSwarmDataFieldInsertPoint(const DMSwarmDataField field,const PetscInt index,const void *ctx)
471: {
475: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
476: /* check point is valid */
477: if (index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
478: if (index >= field->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",field->L);
479: #endif
480: PetscMemcpy(DMSWARM_DATAFIELD_point_access(field->data,index,field->atomic_size), ctx, field->atomic_size);
481: return(0);
482: }
484: /* remove data at index - replace with last point */
485: PetscErrorCode DMSwarmDataBucketRemovePointAtIndex(const DMSwarmDataBucket db,const PetscInt index)
486: {
487: PetscInt f;
488: PetscBool any_active_fields;
492: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
493: /* check point is valid */
494: if (index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
495: if (index >= db->allocated) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",db->L+db->buffer);
496: #endif
497: DMSwarmDataBucketQueryForActiveFields(db,&any_active_fields);
498: if (any_active_fields) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Cannot safely remove point as at least one DMSwarmDataField is currently being accessed");
499: if (index >= db->L) { /* this point is not in the list - no need to error, but I will anyway */
500: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"You should not be trying to remove point at index=%D since it's < db->L = %D", index, db->L);
501: }
502: if (index != db->L-1) { /* not last point in list */
503: for (f = 0; f < db->nfields; ++f) {
504: DMSwarmDataField field = db->field[f];
506: /* copy then remove */
507: DMSwarmDataFieldCopyPoint(db->L-1, field, index, field);
508: /* DMSwarmDataFieldZeroPoint(field,index); */
509: }
510: }
511: /* decrement size */
512: /* this will zero out an crap at the end of the list */
513: DMSwarmDataBucketRemovePoint(db);
514: return(0);
515: }
517: /* copy x into y */
518: PetscErrorCode DMSwarmDataFieldCopyPoint(const PetscInt pid_x,const DMSwarmDataField field_x,
519: const PetscInt pid_y,const DMSwarmDataField field_y )
520: {
524: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
525: /* check point is valid */
526: if (pid_x < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"(IN) index must be >= 0");
527: if (pid_x >= field_x->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"(IN) index must be < %D",field_x->L);
528: if (pid_y < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"(OUT) index must be >= 0");
529: if (pid_y >= field_y->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"(OUT) index must be < %D",field_y->L);
530: if( field_y->atomic_size != field_x->atomic_size ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"atomic size must match");
531: #endif
532: PetscMemcpy(DMSWARM_DATAFIELD_point_access(field_y->data,pid_y,field_y->atomic_size),DMSWARM_DATAFIELD_point_access(field_x->data,pid_x,field_x->atomic_size),field_y->atomic_size);
533: return(0);
534: }
537: /* zero only the datafield at this point */
538: PetscErrorCode DMSwarmDataFieldZeroPoint(const DMSwarmDataField field,const PetscInt index)
539: {
543: #if defined(DMSWARM_DATAFIELD_POINT_ACCESS_GUARD)
544: /* check point is valid */
545: if (index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
546: if (index >= field->L) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",field->L);
547: #endif
548: PetscMemzero(DMSWARM_DATAFIELD_point_access(field->data,index,field->atomic_size), field->atomic_size);
549: return(0);
550: }
552: /* zero ALL data for this point */
553: PetscErrorCode DMSwarmDataBucketZeroPoint(const DMSwarmDataBucket db,const PetscInt index)
554: {
555: PetscInt f;
559: /* check point is valid */
560: if (index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be >= 0");
561: if (index >= db->allocated) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"index must be < %D",db->allocated);
562: for (f = 0; f < db->nfields; ++f) {
563: DMSwarmDataField field = db->field[f];
564: DMSwarmDataFieldZeroPoint(field,index);
565: }
566: return(0);
567: }
569: /* increment */
570: PetscErrorCode DMSwarmDataBucketAddPoint(DMSwarmDataBucket db)
571: {
575: DMSwarmDataBucketSetSizes(db,db->L+1,DMSWARM_DATA_BUCKET_BUFFER_DEFAULT);
576: return(0);
577: }
579: /* decrement */
580: PetscErrorCode DMSwarmDataBucketRemovePoint(DMSwarmDataBucket db)
581: {
585: DMSwarmDataBucketSetSizes(db,db->L-1,DMSWARM_DATA_BUCKET_BUFFER_DEFAULT);
586: return(0);
587: }
589: PetscErrorCode DMSwarmDataBucketView_stdout(MPI_Comm comm,DMSwarmDataBucket db)
590: {
591: PetscInt f;
592: double memory_usage_total,memory_usage_total_local = 0.0;
594:
596: PetscPrintf(comm,"DMSwarmDataBucketView: \n");
597: PetscPrintf(comm," L = %D \n", db->L);
598: PetscPrintf(comm," buffer = %D \n", db->buffer);
599: PetscPrintf(comm," allocated = %D \n", db->allocated);
600: PetscPrintf(comm," nfields registered = %D \n", db->nfields);
601:
602: for (f = 0; f < db->nfields; ++f) {
603: double memory_usage_f = (double)(db->field[f]->atomic_size * db->allocated) * 1.0e-6;
604: memory_usage_total_local += memory_usage_f;
605: }
606: MPI_Allreduce(&memory_usage_total_local,&memory_usage_total,1,MPI_DOUBLE,MPI_SUM,comm);
607:
608: for (f = 0; f < db->nfields; ++f) {
609: double memory_usage_f = (double)(db->field[f]->atomic_size * db->allocated) * 1.0e-6;
610: PetscPrintf(comm," [%3D] %15s : Mem. usage = %1.2e (MB) [rank0]\n", f, db->field[f]->name, memory_usage_f );
611: PetscPrintf(comm," blocksize = %D \n", db->field[f]->bs);
612: if (db->field[f]->bs != 1) {
613: PetscPrintf(comm," atomic size = %zu [full block, bs=%D]\n", db->field[f]->atomic_size,db->field[f]->bs);
614: PetscPrintf(comm," atomic size/item = %zu \n", db->field[f]->atomic_size/db->field[f]->bs);
615: } else {
616: PetscPrintf(comm," atomic size = %zu \n", db->field[f]->atomic_size);
617: }
618: }
619: PetscPrintf(comm," Total mem. usage = %1.2e (MB) (collective)\n", memory_usage_total);
620: return(0);
621: }
623: PetscErrorCode DMSwarmDataBucketView_SEQ(MPI_Comm comm,DMSwarmDataBucket db,const char filename[],DMSwarmDataBucketViewType type)
624: {
628: switch (type) {
629: case DATABUCKET_VIEW_STDOUT:
630: DMSwarmDataBucketView_stdout(PETSC_COMM_SELF,db);
631: break;
632: case DATABUCKET_VIEW_ASCII:
633: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for ascii output");
634: break;
635: case DATABUCKET_VIEW_BINARY:
636: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for binary output");
637: break;
638: case DATABUCKET_VIEW_HDF5:
639: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for HDF5 output");
640: break;
641: default: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown viewer method requested");
642: }
643: return(0);
644: }
646: PetscErrorCode DMSwarmDataBucketView_MPI(MPI_Comm comm,DMSwarmDataBucket db,const char filename[],DMSwarmDataBucketViewType type)
647: {
651: switch (type) {
652: case DATABUCKET_VIEW_STDOUT:
653: DMSwarmDataBucketView_stdout(comm,db);
654: break;
655: case DATABUCKET_VIEW_ASCII:
656: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for ascii output");
657: break;
658: case DATABUCKET_VIEW_BINARY:
659: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for binary output");
660: break;
661: case DATABUCKET_VIEW_HDF5:
662: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for HDF5 output");
663: break;
664: default: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown viewer method requested");
665: }
666: return(0);
667: }
669: PetscErrorCode DMSwarmDataBucketView(MPI_Comm comm,DMSwarmDataBucket db,const char filename[],DMSwarmDataBucketViewType type)
670: {
671: PetscMPIInt size;
675: MPI_Comm_size(comm,&size);
676: if (size == 1) {
677: DMSwarmDataBucketView_SEQ(comm,db,filename,type);
678: } else {
679: DMSwarmDataBucketView_MPI(comm,db,filename,type);
680: }
681: return(0);
682: }
684: PetscErrorCode DMSwarmDataBucketDuplicateFields(DMSwarmDataBucket dbA,DMSwarmDataBucket *dbB)
685: {
686: DMSwarmDataBucket db2;
687: PetscInt f;
688: PetscErrorCode ierr;
691: DMSwarmDataBucketCreate(&db2);
692: /* copy contents from dbA into db2 */
693: for (f = 0; f < dbA->nfields; ++f) {
694: DMSwarmDataField field;
695: size_t atomic_size;
696: char *name;
698: field = dbA->field[f];
699: atomic_size = field->atomic_size;
700: name = field->name;
701: DMSwarmDataBucketRegisterField(db2,"DMSwarmDataBucketDuplicateFields",name,atomic_size,NULL);
702: }
703: DMSwarmDataBucketFinalize(db2);
704: DMSwarmDataBucketSetInitialSizes(db2,0,1000);
705: *dbB = db2;
706: return(0);
707: }
709: /*
710: Insert points from db2 into db1
711: db1 <<== db2
712: */
713: PetscErrorCode DMSwarmDataBucketInsertValues(DMSwarmDataBucket db1,DMSwarmDataBucket db2)
714: {
715: PetscInt n_mp_points1,n_mp_points2;
716: PetscInt n_mp_points1_new,p;
720: DMSwarmDataBucketGetSizes(db1,&n_mp_points1,0,0);
721: DMSwarmDataBucketGetSizes(db2,&n_mp_points2,0,0);
722: n_mp_points1_new = n_mp_points1 + n_mp_points2;
723: DMSwarmDataBucketSetSizes(db1,n_mp_points1_new,DMSWARM_DATA_BUCKET_BUFFER_DEFAULT);
724: for (p = 0; p < n_mp_points2; ++p) {
725: /* db1 <<== db2 */
726: DMSwarmDataBucketCopyPoint(db2,p, db1,(n_mp_points1 + p));
727: }
728: return(0);
729: }
731: /* helpers for parallel send/recv */
732: PetscErrorCode DMSwarmDataBucketCreatePackedArray(DMSwarmDataBucket db,size_t *bytes,void **buf)
733: {
734: PetscInt f;
735: size_t sizeof_marker_contents;
736: void *buffer;
740: sizeof_marker_contents = 0;
741: for (f = 0; f < db->nfields; ++f) {
742: DMSwarmDataField df = db->field[f];
743: sizeof_marker_contents += df->atomic_size;
744: }
745: PetscMalloc(sizeof_marker_contents, &buffer);
746: PetscMemzero(buffer, sizeof_marker_contents);
747: if (bytes) {*bytes = sizeof_marker_contents;}
748: if (buf) {*buf = buffer;}
749: return(0);
750: }
752: PetscErrorCode DMSwarmDataBucketDestroyPackedArray(DMSwarmDataBucket db,void **buf)
753: {
757: if (buf) {
758: PetscFree(*buf);
759: *buf = NULL;
760: }
761: return(0);
762: }
764: PetscErrorCode DMSwarmDataBucketFillPackedArray(DMSwarmDataBucket db,const PetscInt index,void *buf)
765: {
766: PetscInt f;
767: void *data, *data_p;
768: size_t asize, offset;
772: offset = 0;
773: for (f = 0; f < db->nfields; ++f) {
774: DMSwarmDataField df = db->field[f];
776: asize = df->atomic_size;
777: data = (void*)( df->data );
778: data_p = (void*)( (char*)data + index*asize );
779: PetscMemcpy((void*)((char*)buf + offset), data_p, asize);
780: offset = offset + asize;
781: }
782: return(0);
783: }
785: PetscErrorCode DMSwarmDataBucketInsertPackedArray(DMSwarmDataBucket db,const PetscInt idx,void *data)
786: {
787: PetscInt f;
788: void *data_p;
789: size_t offset;
793: offset = 0;
794: for (f = 0; f < db->nfields; ++f) {
795: DMSwarmDataField df = db->field[f];
797: data_p = (void*)( (char*)data + offset );
798: DMSwarmDataFieldInsertPoint(df, idx, (void*)data_p);
799: offset = offset + df->atomic_size;
800: }
801: return(0);
802: }