Actual source code: hierarchical.c
petsc-3.13.6 2020-09-29
2: #include <../src/mat/impls/adj/mpi/mpiadj.h>
3: #include <petscsf.h>
4: #include <petsc/private/matimpl.h>
6: /*
7: It is a hierarchical partitioning. The partitioner has two goals:
8: (1) Most of current partitioners fail at a large scale. The hierarchical partitioning
9: strategy is trying to produce large number of subdomains when number of processor cores is large.
10: (2) PCGASM needs one 'big' subdomain across multi-cores. The partitioner provides two
11: consistent partitions, coarse parts and fine parts. A coarse part is a 'big' subdomain consisting
12: of several small subdomains.
13: */
15: PetscErrorCode MatPartitioningHierarchical_DetermineDestination(MatPartitioning,IS,PetscInt,PetscInt,IS*);
16: PetscErrorCode MatPartitioningHierarchical_AssembleSubdomain(Mat,IS,IS,IS*,Mat*,ISLocalToGlobalMapping*);
17: PetscErrorCode MatPartitioningHierarchical_ReassembleFineparts(Mat,IS,ISLocalToGlobalMapping,IS*);
19: typedef struct {
20: char* fineparttype; /* partitioner on fine level */
21: char* coarseparttype; /* partitioner on coarse level */
22: PetscInt nfineparts; /* number of fine parts on each coarse subdomain */
23: PetscInt ncoarseparts; /* number of coarse parts */
24: IS coarseparts; /* partitioning on coarse level */
25: IS fineparts; /* partitioning on fine level */
26: MatPartitioning coarseMatPart; /* MatPartititioning on coarse level (first level) */
27: MatPartitioning fineMatPart; /* MatPartitioning on fine level (second level) */
28: MatPartitioning improver; /* Improve the quality of a partition */
29: } MatPartitioning_Hierarchical;
31: /*
32: Uses a hierarchical partitioning strategy to partition the matrix in parallel.
33: Use this interface to make the partitioner consistent with others
34: */
35: static PetscErrorCode MatPartitioningApply_Hierarchical(MatPartitioning part,IS *partitioning)
36: {
37: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
38: const PetscInt *fineparts_indices, *coarseparts_indices;
39: PetscInt *fineparts_indices_tmp;
40: PetscInt *parts_indices,i,j,mat_localsize, *offsets;
41: Mat mat = part->adj,adj,sadj;
42: PetscReal *part_weights;
43: PetscBool flg;
44: PetscInt bs = 1;
45: PetscInt *coarse_vertex_weights = 0;
46: PetscMPIInt size,rank;
47: MPI_Comm comm,scomm;
48: IS destination,fineparts_temp, vweights, svweights;
49: PetscInt nsvwegihts,*fp_vweights;
50: const PetscInt *svweights_indices;
51: ISLocalToGlobalMapping mapping;
52: const char *prefix;
53: PetscBool use_edge_weights;
54: PetscErrorCode ierr;
57: PetscObjectGetComm((PetscObject)part,&comm);
58: MPI_Comm_size(comm,&size);
59: MPI_Comm_rank(comm,&rank);
60: PetscObjectTypeCompare((PetscObject)mat,MATMPIADJ,&flg);
61: if (flg) {
62: adj = mat;
63: PetscObjectReference((PetscObject)adj);
64: }else {
65: /* bs indicates if the converted matrix is "reduced" from the original and hence the
66: resulting partition results need to be stretched to match the original matrix */
67: MatConvert(mat,MATMPIADJ,MAT_INITIAL_MATRIX,&adj);
68: if (adj->rmap->n > 0) bs = mat->rmap->n/adj->rmap->n;
69: }
70: /* local size of mat */
71: mat_localsize = adj->rmap->n;
72: /* check parameters */
73: /* how many small subdomains we want from a given 'big' suddomain */
74: if(!hpart->nfineparts) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," must set number of small subdomains for each big subdomain \n");
75: if(!hpart->ncoarseparts && !part->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE," did not either set number of coarse parts or total number of parts \n");
77: /* Partitioning the domain into one single subdomain is a trivial case, and we should just return */
78: if (part->n==1) {
79: PetscCalloc1(bs*adj->rmap->n,&parts_indices);
80: ISCreateGeneral(comm,bs*adj->rmap->n,parts_indices,PETSC_OWN_POINTER,partitioning);
81: hpart->ncoarseparts = 1;
82: hpart->nfineparts = 1;
83: PetscStrallocpy("NONE",&hpart->coarseparttype);
84: PetscStrallocpy("NONE",&hpart->fineparttype);
85: MatDestroy(&adj);
86: return(0);
87: }
89: if(part->n){
90: hpart->ncoarseparts = part->n/hpart->nfineparts;
92: if (part->n%hpart->nfineparts != 0) hpart->ncoarseparts++;
93: }else{
94: part->n = hpart->ncoarseparts*hpart->nfineparts;
95: }
97: PetscMalloc1(hpart->ncoarseparts+1, &offsets);
98: PetscMalloc1(hpart->ncoarseparts, &part_weights);
100: offsets[0] = 0;
101: if (part->n%hpart->nfineparts != 0) offsets[1] = part->n%hpart->nfineparts;
102: else offsets[1] = hpart->nfineparts;
104: part_weights[0] = ((PetscReal)offsets[1])/part->n;
106: for (i=2; i<=hpart->ncoarseparts; i++) {
107: offsets[i] = hpart->nfineparts;
108: part_weights[i-1] = ((PetscReal)offsets[i])/part->n;
109: }
111: offsets[0] = 0;
112: for (i=1;i<=hpart->ncoarseparts; i++)
113: offsets[i] += offsets[i-1];
115: /* If these exists a mat partitioner, we should delete it */
116: MatPartitioningDestroy(&hpart->coarseMatPart);
117: MatPartitioningCreate(comm,&hpart->coarseMatPart);
118: PetscObjectGetOptionsPrefix((PetscObject)part,&prefix);
119: PetscObjectSetOptionsPrefix((PetscObject)hpart->coarseMatPart,prefix);
120: PetscObjectAppendOptionsPrefix((PetscObject)hpart->coarseMatPart,"hierarch_coarse_");
121: /* if did not set partitioning type yet, use parmetis by default */
122: if (!hpart->coarseparttype){
123: #if defined(PETSC_HAVE_PARMETIS)
124: MatPartitioningSetType(hpart->coarseMatPart,MATPARTITIONINGPARMETIS);
125: PetscStrallocpy(MATPARTITIONINGPARMETIS,&hpart->coarseparttype);
126: #elif defined(PETSC_HAVE_PTSCOTCH)
127: MatPartitioningSetType(hpart->coarseMatPart,MATPARTITIONINGPTSCOTCH);
128: PetscStrallocpy(MATPARTITIONINGPTSCOTCH,&hpart->coarseparttype);
129: #else
130: SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Requires PETSc be installed with ParMetis or run with -mat_partitioning_hierarchical_coarseparttype partitiontype");
131: #endif
132: } else {
133: MatPartitioningSetType(hpart->coarseMatPart,hpart->coarseparttype);
134: }
135: MatPartitioningSetAdjacency(hpart->coarseMatPart,adj);
136: MatPartitioningSetNParts(hpart->coarseMatPart, hpart->ncoarseparts);
137: /* copy over vertex weights */
138: if(part->vertex_weights){
139: PetscMalloc1(mat_localsize,&coarse_vertex_weights);
140: PetscArraycpy(coarse_vertex_weights,part->vertex_weights,mat_localsize);
141: MatPartitioningSetVertexWeights(hpart->coarseMatPart,coarse_vertex_weights);
142: }
143: /* Copy use_edge_weights flag from part to coarse part */
144: MatPartitioningGetUseEdgeWeights(part,&use_edge_weights);
145: MatPartitioningSetUseEdgeWeights(hpart->coarseMatPart,use_edge_weights);
147: MatPartitioningSetPartitionWeights(hpart->coarseMatPart, part_weights);
148: MatPartitioningApply(hpart->coarseMatPart,&hpart->coarseparts);
150: /* Wrap the original vertex weights into an index set so that we can extract the corresponding
151: * vertex weights for each big subdomain using ISCreateSubIS().
152: * */
153: if (part->vertex_weights) {
154: ISCreateGeneral(comm,mat_localsize,part->vertex_weights,PETSC_COPY_VALUES,&vweights);
155: }
157: PetscCalloc1(mat_localsize, &fineparts_indices_tmp);
158: for(i=0; i<hpart->ncoarseparts; i+=size){
159: /* Determine where we want to send big subdomains */
160: MatPartitioningHierarchical_DetermineDestination(part,hpart->coarseparts,i,i+size,&destination);
161: /* Assemble a submatrix and its vertex weights for partitioning subdomains */
162: MatPartitioningHierarchical_AssembleSubdomain(adj,part->vertex_weights? vweights:NULL,destination,part->vertex_weights? &svweights:NULL,&sadj,&mapping);
163: /* We have to create a new array to hold vertex weights since coarse partitioner needs to own the vertex-weights array */
164: if (part->vertex_weights) {
165: ISGetLocalSize(svweights,&nsvwegihts);
166: PetscMalloc1(nsvwegihts,&fp_vweights);
167: ISGetIndices(svweights,&svweights_indices);
168: PetscArraycpy(fp_vweights,svweights_indices,nsvwegihts);
169: ISRestoreIndices(svweights,&svweights_indices);
170: ISDestroy(&svweights);
171: }
173: ISDestroy(&destination);
174: PetscObjectGetComm((PetscObject)sadj,&scomm);
176: /*
177: * If the number of big subdomains is smaller than the number of processor cores, the higher ranks do not
178: * need to do partitioning
179: * */
180: if((i+rank)<hpart->ncoarseparts) {
181: MatPartitioningDestroy(&hpart->fineMatPart);
182: /* create a fine partitioner */
183: MatPartitioningCreate(scomm,&hpart->fineMatPart);
184: PetscObjectSetOptionsPrefix((PetscObject)hpart->fineMatPart,prefix);
185: PetscObjectAppendOptionsPrefix((PetscObject)hpart->fineMatPart,"hierarch_fine_");
186: /* if do not set partitioning type, use parmetis by default */
187: if(!hpart->fineparttype){
188: #if defined(PETSC_HAVE_PARMETIS)
189: MatPartitioningSetType(hpart->fineMatPart,MATPARTITIONINGPARMETIS);
190: PetscStrallocpy(MATPARTITIONINGPARMETIS,&hpart->fineparttype);
191: #elif defined(PETSC_HAVE_PTSCOTCH)
192: MatPartitioningSetType(hpart->fineMatPart,MATPARTITIONINGPTSCOTCH);
193: PetscStrallocpy(MATPARTITIONINGPTSCOTCH,&hpart->fineparttype);
194: #elif defined(PETSC_HAVE_CHACO)
195: MatPartitioningSetType(hpart->fineMatPart,MATPARTITIONINGCHACO);
196: PetscStrallocpy(MATPARTITIONINGCHACO,&hpart->fineparttype);
197: #elif defined(PETSC_HAVE_PARTY)
198: MatPartitioningSetType(hpart->fineMatPart,MATPARTITIONINGPARTY);
199: PetscStrallocpy(PETSC_HAVE_PARTY,&hpart->fineparttype);
200: #else
201: SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Requires PETSc be installed with ParMetis or run with -mat_partitioning_hierarchical_coarseparttype partitiontype");
202: #endif
203: } else {
204: MatPartitioningSetType(hpart->fineMatPart,hpart->fineparttype);
205: }
206: MatPartitioningSetUseEdgeWeights(hpart->fineMatPart,use_edge_weights);
207: MatPartitioningSetAdjacency(hpart->fineMatPart,sadj);
208: MatPartitioningSetNParts(hpart->fineMatPart, offsets[rank+1+i]-offsets[rank+i]);
209: if (part->vertex_weights) {
210: MatPartitioningSetVertexWeights(hpart->fineMatPart,fp_vweights);
211: }
212: MatPartitioningApply(hpart->fineMatPart,&fineparts_temp);
213: } else {
214: ISCreateGeneral(scomm,0,NULL,PETSC_OWN_POINTER,&fineparts_temp);
215: }
217: MatDestroy(&sadj);
219: /* Send partition back to the original owners */
220: MatPartitioningHierarchical_ReassembleFineparts(adj,fineparts_temp,mapping,&hpart->fineparts);
221: ISGetIndices(hpart->fineparts,&fineparts_indices);
222: for (j=0;j<mat_localsize;j++)
223: if (fineparts_indices[j] >=0) fineparts_indices_tmp[j] = fineparts_indices[j];
225: ISRestoreIndices(hpart->fineparts,&fineparts_indices);
226: ISDestroy(&hpart->fineparts);
227: ISDestroy(&fineparts_temp);
228: ISLocalToGlobalMappingDestroy(&mapping);
229: }
231: if (part->vertex_weights) {
232: ISDestroy(&vweights);
233: }
235: ISCreateGeneral(comm,mat_localsize,fineparts_indices_tmp,PETSC_OWN_POINTER,&hpart->fineparts);
236: ISGetIndices(hpart->fineparts,&fineparts_indices);
237: ISGetIndices(hpart->coarseparts,&coarseparts_indices);
238: PetscMalloc1(bs*adj->rmap->n,&parts_indices);
239: /* Modify the local indices to the global indices by combing the coarse partition and the fine partitions */
240: for(i=0; i<adj->rmap->n; i++){
241: for(j=0; j<bs; j++){
242: parts_indices[bs*i+j] = fineparts_indices[i]+offsets[coarseparts_indices[i]];
243: }
244: }
245: ISRestoreIndices(hpart->fineparts,&fineparts_indices);
246: ISRestoreIndices(hpart->coarseparts,&coarseparts_indices);
247: PetscFree(offsets);
248: ISCreateGeneral(comm,bs*adj->rmap->n,parts_indices,PETSC_OWN_POINTER,partitioning);
249: MatDestroy(&adj);
250: return(0);
251: }
254: PetscErrorCode MatPartitioningHierarchical_ReassembleFineparts(Mat adj, IS fineparts, ISLocalToGlobalMapping mapping, IS *sfineparts)
255: {
256: PetscInt *local_indices, *global_indices,*sfineparts_indices,localsize,i;
257: const PetscInt *ranges,*fineparts_indices;
258: PetscMPIInt rank,*owners;
259: MPI_Comm comm;
260: PetscLayout rmap;
261: PetscSFNode *remote;
262: PetscSF sf;
263: PetscErrorCode ierr;
267: PetscObjectGetComm((PetscObject)adj,&comm);
268: MPI_Comm_rank(comm,&rank);
269: MatGetLayouts(adj,&rmap,NULL);
270: ISGetLocalSize(fineparts,&localsize);
271: PetscMalloc2(localsize,&global_indices,localsize,&local_indices);
272: for (i=0; i<localsize; i++){
273: local_indices[i] = i;
274: }
275: /* map local indices back to global so that we can permulate data globally */
276: ISLocalToGlobalMappingApply(mapping,localsize,local_indices,global_indices);
277: PetscCalloc1(localsize,&owners);
278: /* find owners for global indices */
279: for(i=0; i<localsize; i++){
280: PetscLayoutFindOwner(rmap,global_indices[i],&owners[i]);
281: }
282: PetscLayoutGetRanges(rmap,&ranges);
283: PetscMalloc1(ranges[rank+1]-ranges[rank],&sfineparts_indices);
285: for (i=0; i<ranges[rank+1]-ranges[rank]; i++) {
286: sfineparts_indices[i] = -1;
287: }
289: ISGetIndices(fineparts,&fineparts_indices);
290: PetscSFCreate(comm,&sf);
291: PetscMalloc1(localsize,&remote);
292: for(i=0; i<localsize; i++){
293: remote[i].rank = owners[i];
294: remote[i].index = global_indices[i]-ranges[owners[i]];
295: }
296: PetscSFSetType(sf,PETSCSFBASIC);
297: /* not sure how to add prefix to sf */
298: PetscSFSetFromOptions(sf);
299: PetscSFSetGraph(sf,localsize,localsize,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
300: PetscSFReduceBegin(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);
301: PetscSFReduceEnd(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);
302: PetscSFDestroy(&sf);
303: ISRestoreIndices(fineparts,&fineparts_indices);
304: ISCreateGeneral(comm,ranges[rank+1]-ranges[rank],sfineparts_indices,PETSC_OWN_POINTER,sfineparts);
305: PetscFree2(global_indices,local_indices);
306: PetscFree(owners);
307: return(0);
308: }
311: PetscErrorCode MatPartitioningHierarchical_AssembleSubdomain(Mat adj,IS vweights, IS destination,IS *svweights,Mat *sadj,ISLocalToGlobalMapping *mapping)
312: {
313: IS irows,icols;
314: PetscInt irows_ln;
315: PetscMPIInt rank;
316: const PetscInt *irows_indices;
317: MPI_Comm comm;
318: PetscErrorCode ierr;
321: PetscObjectGetComm((PetscObject)adj,&comm);
322: MPI_Comm_rank(comm,&rank);
323: /* figure out where data comes from */
324: ISBuildTwoSided(destination,NULL,&irows);
325: ISDuplicate(irows,&icols);
326: ISGetLocalSize(irows,&irows_ln);
327: ISGetIndices(irows,&irows_indices);
328: ISLocalToGlobalMappingCreate(comm,1,irows_ln,irows_indices,PETSC_COPY_VALUES,mapping);
329: ISRestoreIndices(irows,&irows_indices);
330: MatCreateSubMatrices(adj,1,&irows,&icols,MAT_INITIAL_MATRIX,&sadj);
331: if (vweights && svweights) {
332: ISCreateSubIS(vweights,irows,svweights);
333: }
334: ISDestroy(&irows);
335: ISDestroy(&icols);
336: return(0);
337: }
340: PetscErrorCode MatPartitioningHierarchical_DetermineDestination(MatPartitioning part, IS partitioning, PetscInt pstart, PetscInt pend, IS *destination)
341: {
342: MPI_Comm comm;
343: PetscMPIInt rank,size,target;
344: PetscInt plocalsize,*dest_indices,i;
345: const PetscInt *part_indices;
346: PetscErrorCode ierr;
349: PetscObjectGetComm((PetscObject)part,&comm);
350: MPI_Comm_rank(comm,&rank);
351: MPI_Comm_size(comm,&size);
352: if((pend-pstart)>size) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"range [%D, %D] should be smaller than or equal to size %D",pstart,pend,size);
353: if(pstart>pend) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP," pstart %D should be smaller than pend %D",pstart,pend);
354: ISGetLocalSize(partitioning,&plocalsize);
355: PetscMalloc1(plocalsize,&dest_indices);
356: ISGetIndices(partitioning,&part_indices);
357: for (i=0; i<plocalsize; i++){
358: /* compute target */
359: target = part_indices[i]-pstart;
360: /* mark out of range entity as -1 */
361: if (part_indices[i]<pstart || part_indices[i]>=pend) target = -1;
362: dest_indices[i] = target;
363: }
364: ISCreateGeneral(comm,plocalsize,dest_indices,PETSC_OWN_POINTER,destination);
365: return(0);
366: }
369: PetscErrorCode MatPartitioningView_Hierarchical(MatPartitioning part,PetscViewer viewer)
370: {
371: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
372: PetscErrorCode ierr;
373: PetscMPIInt rank;
374: PetscBool iascii;
375: PetscViewer sviewer;
378: MPI_Comm_rank(PetscObjectComm((PetscObject)part),&rank);
379: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
380: if(iascii){
381: PetscViewerASCIIPrintf(viewer," Number of coarse parts: %D\n",hpart->ncoarseparts);
382: PetscViewerASCIIPrintf(viewer," Coarse partitioner: %s\n",hpart->coarseparttype);
383: if (hpart->coarseMatPart) {
384: PetscViewerASCIIPushTab(viewer);
385: MatPartitioningView(hpart->coarseMatPart,viewer);
386: PetscViewerASCIIPopTab(viewer);
387: }
388: PetscViewerASCIIPrintf(viewer," Number of fine parts: %D\n",hpart->nfineparts);
389: PetscViewerASCIIPrintf(viewer," Fine partitioner: %s\n",hpart->fineparttype);
390: PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);
391: if (!rank && hpart->fineMatPart) {
392: PetscViewerASCIIPushTab(viewer);
393: MatPartitioningView(hpart->fineMatPart,sviewer);
394: PetscViewerASCIIPopTab(viewer);
395: }
396: PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);
397: }
398: return(0);
399: }
402: PetscErrorCode MatPartitioningHierarchicalGetFineparts(MatPartitioning part,IS *fineparts)
403: {
404: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
405: PetscErrorCode ierr;
408: *fineparts = hpart->fineparts;
409: PetscObjectReference((PetscObject)hpart->fineparts);
410: return(0);
411: }
413: PetscErrorCode MatPartitioningHierarchicalGetCoarseparts(MatPartitioning part,IS *coarseparts)
414: {
415: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
416: PetscErrorCode ierr;
419: *coarseparts = hpart->coarseparts;
420: PetscObjectReference((PetscObject)hpart->coarseparts);
421: return(0);
422: }
424: PetscErrorCode MatPartitioningHierarchicalSetNcoarseparts(MatPartitioning part, PetscInt ncoarseparts)
425: {
426: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
429: hpart->ncoarseparts = ncoarseparts;
430: return(0);
431: }
433: PetscErrorCode MatPartitioningHierarchicalSetNfineparts(MatPartitioning part, PetscInt nfineparts)
434: {
435: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
438: hpart->nfineparts = nfineparts;
439: return(0);
440: }
442: PetscErrorCode MatPartitioningSetFromOptions_Hierarchical(PetscOptionItems *PetscOptionsObject,MatPartitioning part)
443: {
444: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
446: char value[1024];
447: PetscBool flag = PETSC_FALSE;
450: PetscOptionsHead(PetscOptionsObject,"Set hierarchical partitioning options");
451: PetscOptionsString("-mat_partitioning_hierarchical_coarseparttype","coarse part type",NULL,NULL,value,1024,&flag);
452: if (flag){
453: PetscStrallocpy(value,&hpart->coarseparttype);
454: }
455: PetscOptionsString("-mat_partitioning_hierarchical_fineparttype","fine part type",NULL,NULL,value,1024,&flag);
456: if (flag){
457: PetscStrallocpy(value,&hpart->fineparttype);
458: }
459: PetscOptionsInt("-mat_partitioning_hierarchical_ncoarseparts","number of coarse parts",NULL,hpart->ncoarseparts,&hpart->ncoarseparts,&flag);
460: PetscOptionsInt("-mat_partitioning_hierarchical_nfineparts","number of fine parts",NULL,hpart->nfineparts,&hpart->nfineparts,&flag);
461: PetscOptionsTail();
462: return(0);
463: }
466: PetscErrorCode MatPartitioningDestroy_Hierarchical(MatPartitioning part)
467: {
468: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
469: PetscErrorCode ierr;
472: if(hpart->coarseparttype) {PetscFree(hpart->coarseparttype);}
473: if(hpart->fineparttype) {PetscFree(hpart->fineparttype);}
474: ISDestroy(&hpart->fineparts);
475: ISDestroy(&hpart->coarseparts);
476: MatPartitioningDestroy(&hpart->coarseMatPart);
477: MatPartitioningDestroy(&hpart->fineMatPart);
478: MatPartitioningDestroy(&hpart->improver);
479: PetscFree(hpart);
480: return(0);
481: }
483: /*
484: Improves the quality of a partition
485: */
486: static PetscErrorCode MatPartitioningImprove_Hierarchical(MatPartitioning part, IS *partitioning)
487: {
488: PetscErrorCode ierr;
489: MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
490: Mat mat = part->adj, adj;
491: PetscBool flg;
492: PetscInt *vertex_weights;
493: const char *prefix;
496: PetscObjectTypeCompare((PetscObject)mat,MATMPIADJ,&flg);
497: if (flg) {
498: adj = mat;
499: PetscObjectReference((PetscObject)adj);
500: }else {
501: /* bs indicates if the converted matrix is "reduced" from the original and hence the
502: resulting partition results need to be stretched to match the original matrix */
503: MatConvert(mat,MATMPIADJ,MAT_INITIAL_MATRIX,&adj);
504: }
506: /* If there exists a mat partitioner, we should delete it */
507: MatPartitioningDestroy(&hpart->improver);
508: MatPartitioningCreate(PetscObjectComm((PetscObject)part),&hpart->improver);
509: PetscObjectGetOptionsPrefix((PetscObject)part,&prefix);
510: PetscObjectSetOptionsPrefix((PetscObject)hpart->improver,prefix);
511: PetscObjectAppendOptionsPrefix((PetscObject)hpart->improver,"hierarch_improver_");
512: /* Only parmetis supports to refine a partition */
513: #if defined(PETSC_HAVE_PARMETIS)
514: MatPartitioningSetType(hpart->improver,MATPARTITIONINGPARMETIS);
515: #else
516: SETERRQ(PetscObjectComm((PetscObject)adj),PETSC_ERR_SUP,"Requires PETSc be installed with ParMetis\n");
517: #endif
519: MatPartitioningSetAdjacency(hpart->improver,adj);
520: MatPartitioningSetNParts(hpart->improver, part->n);
521: /* copy over vertex weights */
522: if(part->vertex_weights){
523: PetscMalloc1(adj->rmap->n,&vertex_weights);
524: PetscArraycpy(vertex_weights,part->vertex_weights,adj->rmap->n);
525: MatPartitioningSetVertexWeights(hpart->improver,vertex_weights);
526: }
527: MatPartitioningImprove(hpart->improver,partitioning);
528: MatDestroy(&adj);
529: return(0);
530: }
533: /*MC
534: MATPARTITIONINGHIERARCH - Creates a partitioning context via hierarchical partitioning strategy.
535: The graph is partitioned into a number of subgraphs, and each subgraph is further split into a few smaller
536: subgraphs. The idea can be applied in a recursive manner. It is useful when you want to partition the graph
537: into a large number of subgraphs (often more than 10K) since partitions obtained with existing partitioners
538: such as ParMETIS and PTScotch are far from ideal. The hierarchical partitioning also tries to avoid off-node
539: communication as much as possible for multi-core processor. Another user case for the hierarchical partitioning
540: is to improve PCGASM convergence by generating multi-rank connected subdomain.
542: Collective
544: Input Parameter:
545: . part - the partitioning context
547: Options Database Keys:
548: + -mat_partitioning_hierarchical_coarseparttype - partitioner type at the first level and parmetis is used by default
549: . -mat_partitioning_hierarchical_fineparttype - partitioner type at the second level and parmetis is used by default
550: . -mat_partitioning_hierarchical_ncoarseparts - number of subgraphs is required at the first level, which is often the number of compute nodes
551: - -mat_partitioning_hierarchical_nfineparts - number of smaller subgraphs for each subgraph, which is often the number of cores per compute node
553: Level: beginner
555: References:
556: 1. Fande Kong, Xiao-Chuan Cai, A highly scalable multilevel Schwarz method with boundary geometry preserving coarse spaces for 3D elasticity
557: problems on domains with complex geometry, SIAM Journal on Scientific Computing 38 (2), C73-C95, 2016
558: 2. Fande Kong, Roy H. Stogner, Derek Gaston, John W. Peterson, Cody J. Permann, Andrew E. Slaughter, and Richard C. Martineau,
559: A general-purpose hierarchical mesh partitioning method with node balancing strategies for large-scale numerical simulations,
560: arXiv preprint arXiv:1809.02666CoRR, 2018.
562: .seealso: MatPartitioningSetType(), MatPartitioningType
564: M*/
566: PETSC_EXTERN PetscErrorCode MatPartitioningCreate_Hierarchical(MatPartitioning part)
567: {
568: PetscErrorCode ierr;
569: MatPartitioning_Hierarchical *hpart;
572: PetscNewLog(part,&hpart);
573: part->data = (void*)hpart;
575: hpart->fineparttype = 0; /* fine level (second) partitioner */
576: hpart->coarseparttype = 0; /* coarse level (first) partitioner */
577: hpart->nfineparts = 1; /* we do not further partition coarse partition any more by default */
578: hpart->ncoarseparts = 0; /* number of coarse parts (first level) */
579: hpart->coarseparts = 0;
580: hpart->fineparts = 0;
581: hpart->coarseMatPart = 0;
582: hpart->fineMatPart = 0;
584: part->ops->apply = MatPartitioningApply_Hierarchical;
585: part->ops->view = MatPartitioningView_Hierarchical;
586: part->ops->destroy = MatPartitioningDestroy_Hierarchical;
587: part->ops->setfromoptions = MatPartitioningSetFromOptions_Hierarchical;
588: part->ops->improve = MatPartitioningImprove_Hierarchical;
589: return(0);
590: }