Actual source code: dmmbmat.cxx

petsc-3.6.1 2015-08-06
Report Typos and Errors
  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 DMDA

218:     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: PetscErrorCode  DMMoabSetBlockFills(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: }