1: #include <petsc/private/dmmbimpl.h> /*I "petscdmmoab.h" I*/
2: #include <petsc/private/vecimpl.h>
4: #include <petscdmmoab.h>
5: #include <MBTagConventions.hpp>
7: static PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM,PetscInt*,PetscInt*,PetscInt*,PetscInt*,PetscBool);
11: PetscErrorCode DMCreateMatrix_Moab(DM dm,Mat *J) 12: {
13: PetscErrorCode ierr;
14: PetscInt innz=0,ionz=0,nlsiz;
15: DM_Moab *dmmoab=(DM_Moab*)dm->data;
16: PetscInt *nnz=0,*onz=0;
17: char *tmp=0;
18: Mat A;
19: MatType mtype;
25: /* next, need to allocate the non-zero arrays to enable pre-allocation */
26: mtype = dm->mattype;
27: PetscStrstr(mtype, "baij", &tmp);
28: nlsiz = (tmp ? dmmoab->nloc:dmmoab->nloc*dmmoab->numFields);
30: /* allocate the nnz, onz arrays based on block size and local nodes */
31: PetscCalloc2(nlsiz,&nnz,nlsiz,&onz);
33: /* compute the nonzero pattern based on MOAB connectivity data for local elements */
34: DMMoab_Compute_NNZ_From_Connectivity(dm,&innz,nnz,&ionz,onz,(tmp?PETSC_TRUE:PETSC_FALSE));
36: /* create the Matrix and set its type as specified by user */
37: MatCreate(dmmoab->pcomm->comm(), &A);
38: MatSetSizes(A, dmmoab->nloc*dmmoab->numFields, dmmoab->nloc*dmmoab->numFields, PETSC_DETERMINE, PETSC_DETERMINE);
39: MatSetType(A, mtype);
40: MatSetBlockSize(A, dmmoab->bs);
41: MatSetDM(A, dm); /* set DM reference */
42: MatSetFromOptions(A);
44: if (!dmmoab->ltog_map) SETERRQ(dmmoab->pcomm->comm(), PETSC_ERR_ORDER, "Cannot create a DMMoab Mat without calling DMSetUp first.");
45: MatSetLocalToGlobalMapping(A,dmmoab->ltog_map,dmmoab->ltog_map);
47: /* set preallocation based on different supported Mat types */
48: MatSeqAIJSetPreallocation(A, innz, nnz);
49: MatMPIAIJSetPreallocation(A, innz, nnz, ionz, onz);
50: MatSeqBAIJSetPreallocation(A, dmmoab->bs, innz, nnz);
51: MatMPIBAIJSetPreallocation(A, dmmoab->bs, innz, nnz, ionz, onz);
53: /* clean up temporary memory */
54: PetscFree2(nnz,onz);
56: /* set up internal matrix data-structures */
57: MatSetUp(A);
59: *J = A;
60: return(0);
61: }
66: PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM dm,PetscInt* innz,PetscInt* nnz,PetscInt* ionz,PetscInt* onz,PetscBool isbaij) 67: {
68: PetscInt i,f,nloc,vpere,bs,ivtx,n_nnz,n_onz;
69: PetscInt ibs,jbs,inbsize,iobsize,nfields,nlsiz;
70: DM_Moab *dmmoab = (DM_Moab*)dm->data;
71: const moab::EntityHandle *connect;
72: moab::Range adjs,found,allvlocal,allvghost;
73: moab::Range::iterator iter,jter;
74: std::vector<moab::EntityHandle> storage;
75: PetscBool isinterlaced;
76: moab::EntityHandle vtx;
77: moab::ErrorCode merr;
80: bs = dmmoab->bs;
81: nloc = dmmoab->nloc;
82: nfields = dmmoab->numFields;
83: isinterlaced=(isbaij || bs==nfields ? PETSC_TRUE : PETSC_FALSE);
84: nlsiz = (isinterlaced ? nloc:nloc*nfields);
86: /* find the truly user-expected layer of ghosted entities to decipher NNZ pattern */
87: merr = dmmoab->mbiface->get_entities_by_type(dmmoab->fileset,moab::MBVERTEX,allvlocal,true);MBERRNM(merr);
88: merr = dmmoab->pcomm->filter_pstatus(allvlocal,PSTATUS_NOT_OWNED,PSTATUS_NOT,-1,&adjs);MBERRNM(merr);
89: allvghost = moab::subtract(allvlocal, adjs);
91: /* loop over the locally owned vertices and figure out the NNZ pattern using connectivity information */
92: for(iter = dmmoab->vowned->begin(),ivtx=0; iter != dmmoab->vowned->end(); iter++,ivtx++) {
94: vtx = *iter;
95: adjs.clear();
96: /* Get adjacency information for current vertex - i.e., all elements of dimension (dim) that connects
97: to the current vertex. We can then decipher if a vertex is ghosted or not and compute the
98: non-zero pattern accordingly. */
99: merr = dmmoab->mbiface->get_adjacencies(&vtx,1,dmmoab->dim,false,adjs,moab::Interface::INTERSECT);
101: /* reset counters */
102: n_nnz=n_onz=0;
103: found.clear();
105: /* loop over vertices and update the number of connectivity */
106: for(jter = adjs.begin(); jter != adjs.end(); jter++) {
108: /* Get connectivity information in canonical ordering for the local element */
109: merr = dmmoab->mbiface->get_connectivity(*jter,connect,vpere,false,&storage);MBERRNM(merr);
111: /* loop over each element connected to the adjacent vertex and update as needed */
112: for (i=0; i<vpere; ++i) {
113: if (connect[i] == vtx || found.find(connect[i]) != found.end()) continue; /* make sure we don't double count shared vertices */
114: if (allvghost.find(connect[i]) != allvghost.end()) n_onz++; /* update out-of-proc onz */
115: else n_nnz++; /* else local vertex */
116: found.insert(connect[i]);
117: }
118: }
120: if (isbaij) {
121: nnz[ivtx]=n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
122: if (onz) {
123: onz[ivtx]=n_onz; /* add ghost non-owned nodes */
124: }
125: }
126: else { /* AIJ matrices */
127: if (!isinterlaced) {
128: for (f=0;f<nfields;f++) {
129: nnz[f*nloc+ivtx]=n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
130: if (onz)
131: onz[f*nloc+ivtx]=n_onz; /* add ghost non-owned nodes */
132: }
133: }
134: else {
135: for (f=0;f<nfields;f++) {
136: nnz[nfields*ivtx+f]=n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
137: if (onz)
138: onz[nfields*ivtx+f]=n_onz; /* add ghost non-owned nodes */
139: }
140: }
141: }
142: }
144: for (i=0;i<nlsiz;i++)
145: nnz[i]+=1; /* self count the node */
147: for (ivtx=0;ivtx<nloc;ivtx++) {
148: if (!isbaij) {
149: for (ibs=0; ibs<nfields; ibs++) {
150: if (dmmoab->dfill) { /* first address the diagonal block */
151: /* just add up the ints -- easier/faster rather than branching based on "1" */
152: for (jbs=0,inbsize=0; jbs<nfields; jbs++)
153: inbsize += dmmoab->dfill[ibs*nfields+jbs];
154: }
155: else inbsize=nfields; /* dense coupling since user didn't specify the component fill explicitly */
156: if (isinterlaced) nnz[ivtx*nfields+ibs]*=inbsize;
157: else nnz[ibs*nloc+ivtx]*=inbsize;
159: if (onz) {
160: if (dmmoab->ofill) { /* next address the off-diagonal block */
161: /* just add up the ints -- easier/faster rather than branching based on "1" */
162: for (jbs=0,iobsize=0; jbs<nfields; jbs++)
163: iobsize += dmmoab->dfill[ibs*nfields+jbs];
164: }
165: else iobsize=nfields; /* dense coupling since user didn't specify the component fill explicitly */
166: if (isinterlaced) onz[ivtx*nfields+ibs]*=iobsize;
167: else onz[ibs*nloc+ivtx]*=iobsize;
168: }
169: }
170: }
171: else {
172: /* check if we got overzealous in our nnz and onz computations */
173: nnz[ivtx]=(nnz[ivtx]>dmmoab->nloc?dmmoab->nloc:nnz[ivtx]);
174: if (onz) onz[ivtx]=(onz[ivtx]>dmmoab->nloc?dmmoab->nloc:onz[ivtx]);
175: }
176: }
177: /* update innz and ionz based on local maxima */
178: if (innz || ionz) {
179: if (innz) *innz=0;
180: if (ionz) *ionz=0;
181: for (i=0;i<nlsiz;i++) {
182: if (innz && (nnz[i]>*innz)) *innz=nnz[i];
183: if ((ionz && onz) && (onz[i]>*ionz)) *ionz=onz[i];
184: }
185: }
186: return(0);
187: }
192: static PetscErrorCode DMMoabSetBlockFills_Private(PetscInt w,const PetscInt *fill,PetscInt **rfill)193: {
195: PetscInt i,j,*ifill;
198: if (!fill) return(0);
199: PetscMalloc1(w*w,&ifill);
200: for (i=0;i<w;i++) {
201: for (j=0; j<w; j++)
202: ifill[i*w+j]=fill[i*w+j];
203: }
205: *rfill = ifill;
206: return(0);
207: }
212: /*@
213: DMMoabSetBlockFills - Sets the fill pattern in each block for a multi-component problem
214: of the matrix returned by DMCreateMatrix().
216: Logically Collective on DMDA218: Input Parameter:
219: + dm - the DMMoab object
220: . dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
221: - ofill - the fill pattern in the off-diagonal blocks
223: Level: developer
225: Notes: This only makes sense when you are doing multicomponent problems but using the
226: MPIAIJ matrix format
228: The format for dfill and ofill is a 2 dimensional dof by dof matrix with 1 entries
229: representing coupling and 0 entries for missing coupling. For example
230: $ dfill[9] = {1, 0, 0,
231: $ 1, 1, 0,
232: $ 0, 1, 1}
233: means that row 0 is coupled with only itself in the diagonal block, row 1 is coupled with
234: itself and row 0 (in the diagonal block) and row 2 is coupled with itself and row 1 (in the
235: diagonal block).
237: DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then
238: can be represented in the dfill, ofill format
240: Contributed by Glenn Hammond
242: .seealso DMCreateMatrix(), DMDASetGetMatrix(), DMSetMatrixPreallocateOnly()
244: @*/
245: PetscErrorCodeDMMoabSetBlockFills(DM dm,const PetscInt *dfill,const PetscInt *ofill)246: {
247: DM_Moab *dmmoab=(DM_Moab*)dm->data;
252: DMMoabSetBlockFills_Private(dmmoab->numFields,dfill,&dmmoab->dfill);
253: DMMoabSetBlockFills_Private(dmmoab->numFields,ofill,&dmmoab->ofill);
254: return(0);
255: }