1 #define PETSCMAT_DLL 2 3 #include "src/mat/impls/aij/mpi/mpiaij.h" 4 5 EXTERN PetscErrorCode CreateColmap_MPIAIJ_Private(Mat); 6 7 #undef __FUNCT__ 8 #define __FUNCT__ "MatFDColoringCreate_MPIAIJ" 9 PetscErrorCode MatFDColoringCreate_MPIAIJ(Mat mat,ISColoring iscoloring,MatFDColoring c) 10 { 11 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 12 PetscErrorCode ierr; 13 PetscMPIInt size,*ncolsonproc,*disp,nn; 14 PetscInt i,*is,n,nrows,j,k,m,*rows = 0,*A_ci,*A_cj,ncols,col; 15 PetscInt nis = iscoloring->n,nctot,*cols,*B_ci,*B_cj; 16 PetscInt *rowhit,M = mat->rmap.n,cstart = mat->cmap.rstart,cend = mat->cmap.rend,colb; 17 PetscInt *columnsforrow,l; 18 IS *isa; 19 PetscTruth done,flg; 20 ISLocalToGlobalMapping map = mat->mapping; 21 PetscInt *ltog = (map ? map->indices : PETSC_NULL) ,ctype=c->ctype; 22 23 PetscFunctionBegin; 24 if (!mat->assembled) { 25 SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Matrix must be assembled first; MatAssemblyBegin/End();"); 26 } 27 if (ctype == IS_COLORING_GHOSTED && !map) SETERRQ(PETSC_ERR_ARG_INCOMP,"When using ghosted differencing matrix must have local to global mapping provided with MatSetLocalToGlobalMapping"); 28 29 ierr = ISColoringGetIS(iscoloring,PETSC_IGNORE,&isa);CHKERRQ(ierr); 30 c->M = mat->rmap.N; /* set the global rows and columns and local rows */ 31 c->N = mat->cmap.N; 32 c->m = mat->rmap.n; 33 c->rstart = mat->rmap.rstart; 34 35 c->ncolors = nis; 36 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->ncolumns);CHKERRQ(ierr); 37 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columns);CHKERRQ(ierr); 38 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->nrows);CHKERRQ(ierr); 39 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->rows);CHKERRQ(ierr); 40 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columnsforrow);CHKERRQ(ierr); 41 ierr = PetscLogObjectMemory(c,5*nis*sizeof(PetscInt));CHKERRQ(ierr); 42 43 /* Allow access to data structures of local part of matrix */ 44 if (!aij->colmap) { 45 ierr = CreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 46 } 47 /* 48 Calls the _SeqAIJ() version of these routines to make sure it does not 49 get the reduced (by inodes) version of I and J 50 */ 51 ierr = MatGetColumnIJ_SeqAIJ(aij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 52 ierr = MatGetColumnIJ_SeqAIJ(aij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 53 54 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&rowhit);CHKERRQ(ierr); 55 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&columnsforrow);CHKERRQ(ierr); 56 57 for (i=0; i<nis; i++) { 58 ierr = ISGetLocalSize(isa[i],&n);CHKERRQ(ierr); 59 ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr); 60 c->ncolumns[i] = n; 61 if (n) { 62 ierr = PetscMalloc(n*sizeof(PetscInt),&c->columns[i]);CHKERRQ(ierr); 63 ierr = PetscLogObjectMemory(c,n*sizeof(PetscInt));CHKERRQ(ierr); 64 ierr = PetscMemcpy(c->columns[i],is,n*sizeof(PetscInt));CHKERRQ(ierr); 65 } else { 66 c->columns[i] = 0; 67 } 68 69 if (ctype == IS_COLORING_GLOBAL){ 70 /* Determine the total (parallel) number of columns of this color */ 71 ierr = MPI_Comm_size(((PetscObject)mat)->comm,&size);CHKERRQ(ierr); 72 ierr = PetscMalloc(2*size*sizeof(PetscInt*),&ncolsonproc);CHKERRQ(ierr); 73 disp = ncolsonproc + size; 74 75 nn = PetscMPIIntCast(n); 76 ierr = MPI_Allgather(&nn,1,MPI_INT,ncolsonproc,1,MPI_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 77 nctot = 0; for (j=0; j<size; j++) {nctot += ncolsonproc[j];} 78 if (!nctot) { 79 ierr = PetscInfo(mat,"Coloring of matrix has some unneeded colors with no corresponding rows\n");CHKERRQ(ierr); 80 } 81 82 disp[0] = 0; 83 for (j=1; j<size; j++) { 84 disp[j] = disp[j-1] + ncolsonproc[j-1]; 85 } 86 87 /* Get complete list of columns for color on each processor */ 88 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 89 ierr = MPI_Allgatherv(is,n,MPIU_INT,cols,ncolsonproc,disp,MPIU_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 90 ierr = PetscFree(ncolsonproc);CHKERRQ(ierr); 91 } else if (ctype == IS_COLORING_GHOSTED){ 92 /* Determine local number of columns of this color on this process, including ghost points */ 93 nctot = n; 94 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 95 ierr = PetscMemcpy(cols,is,n*sizeof(PetscInt));CHKERRQ(ierr); 96 } else { 97 SETERRQ(PETSC_ERR_SUP,"Not provided for this MatFDColoring type"); 98 } 99 100 /* 101 Mark all rows affect by these columns 102 */ 103 /* Temporary option to allow for debugging/testing */ 104 ierr = PetscOptionsHasName(PETSC_NULL,"-matfdcoloring_slow",&flg);CHKERRQ(ierr); 105 if (!flg) {/*-----------------------------------------------------------------------------*/ 106 /* crude, fast version */ 107 ierr = PetscMemzero(rowhit,M*sizeof(PetscInt));CHKERRQ(ierr); 108 /* loop over columns*/ 109 for (j=0; j<nctot; j++) { 110 if (ctype == IS_COLORING_GHOSTED) { 111 col = ltog[cols[j]]; 112 } else { 113 col = cols[j]; 114 } 115 if (col >= cstart && col < cend) { 116 /* column is in diagonal block of matrix */ 117 rows = A_cj + A_ci[col-cstart]; 118 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 119 } else { 120 #if defined (PETSC_USE_CTABLE) 121 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr) 122 colb --; 123 #else 124 colb = aij->colmap[col] - 1; 125 #endif 126 if (colb == -1) { 127 m = 0; 128 } else { 129 rows = B_cj + B_ci[colb]; 130 m = B_ci[colb+1] - B_ci[colb]; 131 } 132 } 133 /* loop over columns marking them in rowhit */ 134 for (k=0; k<m; k++) { 135 rowhit[*rows++] = col + 1; 136 } 137 } 138 139 /* count the number of hits */ 140 nrows = 0; 141 for (j=0; j<M; j++) { 142 if (rowhit[j]) nrows++; 143 } 144 c->nrows[i] = nrows; 145 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 146 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 147 ierr = PetscLogObjectMemory(c,2*(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 148 nrows = 0; 149 for (j=0; j<M; j++) { 150 if (rowhit[j]) { 151 c->rows[i][nrows] = j; 152 c->columnsforrow[i][nrows] = rowhit[j] - 1; 153 nrows++; 154 } 155 } 156 } else {/*-------------------------------------------------------------------------------*/ 157 /* slow version, using rowhit as a linked list */ 158 PetscInt currentcol,fm,mfm; 159 rowhit[M] = M; 160 nrows = 0; 161 /* loop over columns*/ 162 for (j=0; j<nctot; j++) { 163 if (ctype == IS_COLORING_GHOSTED) { 164 col = ltog[cols[j]]; 165 } else { 166 col = cols[j]; 167 } 168 if (col >= cstart && col < cend) { 169 /* column is in diagonal block of matrix */ 170 rows = A_cj + A_ci[col-cstart]; 171 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 172 } else { 173 #if defined (PETSC_USE_CTABLE) 174 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 175 colb --; 176 #else 177 colb = aij->colmap[col] - 1; 178 #endif 179 if (colb == -1) { 180 m = 0; 181 } else { 182 rows = B_cj + B_ci[colb]; 183 m = B_ci[colb+1] - B_ci[colb]; 184 } 185 } 186 187 /* loop over columns marking them in rowhit */ 188 fm = M; /* fm points to first entry in linked list */ 189 for (k=0; k<m; k++) { 190 currentcol = *rows++; 191 /* is it already in the list? */ 192 do { 193 mfm = fm; 194 fm = rowhit[fm]; 195 } while (fm < currentcol); 196 /* not in list so add it */ 197 if (fm != currentcol) { 198 nrows++; 199 columnsforrow[currentcol] = col; 200 /* next three lines insert new entry into linked list */ 201 rowhit[mfm] = currentcol; 202 rowhit[currentcol] = fm; 203 fm = currentcol; 204 /* fm points to present position in list since we know the columns are sorted */ 205 } else { 206 SETERRQ(PETSC_ERR_PLIB,"Invalid coloring of matrix detected"); 207 } 208 } 209 } 210 c->nrows[i] = nrows; 211 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 212 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 213 ierr = PetscLogObjectMemory(c,(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 214 /* now store the linked list of rows into c->rows[i] */ 215 nrows = 0; 216 fm = rowhit[M]; 217 do { 218 c->rows[i][nrows] = fm; 219 c->columnsforrow[i][nrows++] = columnsforrow[fm]; 220 fm = rowhit[fm]; 221 } while (fm < M); 222 } /* ---------------------------------------------------------------------------------------*/ 223 ierr = PetscFree(cols);CHKERRQ(ierr); 224 } 225 226 /* Optimize by adding the vscale, and scaleforrow[][] fields */ 227 /* 228 vscale will contain the "diagonal" on processor scalings followed by the off processor 229 */ 230 if (ctype == IS_COLORING_GLOBAL) { 231 ierr = VecCreateGhost(((PetscObject)mat)->comm,aij->A->rmap.n,PETSC_DETERMINE,aij->B->cmap.n,aij->garray,&c->vscale);CHKERRQ(ierr); 232 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 233 for (k=0; k<c->ncolors; k++) { 234 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 235 for (l=0; l<c->nrows[k]; l++) { 236 col = c->columnsforrow[k][l]; 237 if (col >= cstart && col < cend) { 238 /* column is in diagonal block of matrix */ 239 colb = col - cstart; 240 } else { 241 /* column is in "off-processor" part */ 242 #if defined (PETSC_USE_CTABLE) 243 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 244 colb --; 245 #else 246 colb = aij->colmap[col] - 1; 247 #endif 248 colb += cend - cstart; 249 } 250 c->vscaleforrow[k][l] = colb; 251 } 252 } 253 } else if (ctype == IS_COLORING_GHOSTED) { 254 /* Get gtol mapping */ 255 PetscInt N = mat->cmap.N, *gtol; 256 ierr = PetscMalloc((N+1)*sizeof(PetscInt),>ol);CHKERRQ(ierr); 257 for (i=0; i<N; i++) gtol[i] = -1; 258 for (i=0; i<map->n; i++) gtol[ltog[i]] = i; 259 260 c->vscale = 0; /* will be created in MatFDColoringApply() */ 261 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 262 for (k=0; k<c->ncolors; k++) { 263 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 264 for (l=0; l<c->nrows[k]; l++) { 265 col = c->columnsforrow[k][l]; /* global column index */ 266 c->vscaleforrow[k][l] = gtol[col]; /* local column index */ 267 } 268 } 269 ierr = PetscFree(gtol);CHKERRQ(ierr); 270 } 271 ierr = ISColoringRestoreIS(iscoloring,&isa);CHKERRQ(ierr); 272 273 ierr = PetscFree(rowhit);CHKERRQ(ierr); 274 ierr = PetscFree(columnsforrow);CHKERRQ(ierr); 275 ierr = MatRestoreColumnIJ_SeqAIJ(aij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 276 ierr = MatRestoreColumnIJ_SeqAIJ(aij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 277 PetscFunctionReturn(0); 278 } 279 280 281 282 283 284 285