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,n,nrows,j,k,m,*rows = 0,*A_ci,*A_cj,ncols,col; 15 const PetscInt *is; 16 PetscInt nis = iscoloring->n,nctot,*cols,*B_ci,*B_cj; 17 PetscInt *rowhit,M,cstart,cend,colb; 18 PetscInt *columnsforrow,l; 19 IS *isa; 20 PetscTruth done,flg; 21 ISLocalToGlobalMapping map = mat->mapping; 22 PetscInt *ltog = (map ? map->indices : (PetscInt*) PETSC_NULL) ,ctype=c->ctype; 23 24 PetscFunctionBegin; 25 if (!mat->assembled) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Matrix must be assembled first; MatAssemblyBegin/End();"); 26 if (ctype == IS_COLORING_GHOSTED && !map) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_INCOMP,"When using ghosted differencing matrix must have local to global mapping provided with MatSetLocalToGlobalMapping"); 27 28 ierr = ISColoringGetIS(iscoloring,PETSC_IGNORE,&isa);CHKERRQ(ierr); 29 30 M = mat->rmap->n; 31 cstart = mat->cmap->rstart; 32 cend = mat->cmap->rend; 33 c->M = mat->rmap->N; /* set the global rows and columns and local rows */ 34 c->N = mat->cmap->N; 35 c->m = mat->rmap->n; 36 c->rstart = mat->rmap->rstart; 37 38 c->ncolors = nis; 39 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->ncolumns);CHKERRQ(ierr); 40 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columns);CHKERRQ(ierr); 41 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->nrows);CHKERRQ(ierr); 42 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->rows);CHKERRQ(ierr); 43 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columnsforrow);CHKERRQ(ierr); 44 ierr = PetscLogObjectMemory(c,5*nis*sizeof(PetscInt));CHKERRQ(ierr); 45 46 /* Allow access to data structures of local part of matrix */ 47 if (!aij->colmap) { 48 ierr = CreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 49 } 50 ierr = MatGetColumnIJ(aij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 51 ierr = MatGetColumnIJ(aij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 52 53 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&rowhit);CHKERRQ(ierr); 54 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&columnsforrow);CHKERRQ(ierr); 55 56 for (i=0; i<nis; i++) { 57 ierr = ISGetLocalSize(isa[i],&n);CHKERRQ(ierr); 58 ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr); 59 c->ncolumns[i] = n; 60 if (n) { 61 ierr = PetscMalloc(n*sizeof(PetscInt),&c->columns[i]);CHKERRQ(ierr); 62 ierr = PetscLogObjectMemory(c,n*sizeof(PetscInt));CHKERRQ(ierr); 63 ierr = PetscMemcpy(c->columns[i],is,n*sizeof(PetscInt));CHKERRQ(ierr); 64 } else { 65 c->columns[i] = 0; 66 } 67 68 if (ctype == IS_COLORING_GLOBAL){ 69 /* Determine the total (parallel) number of columns of this color */ 70 ierr = MPI_Comm_size(((PetscObject)mat)->comm,&size);CHKERRQ(ierr); 71 ierr = PetscMalloc2(size,PetscMPIInt,&ncolsonproc,size,PetscMPIInt,&disp);CHKERRQ(ierr); 72 73 nn = PetscMPIIntCast(n); 74 ierr = MPI_Allgather(&nn,1,MPI_INT,ncolsonproc,1,MPI_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 75 nctot = 0; for (j=0; j<size; j++) {nctot += ncolsonproc[j];} 76 if (!nctot) { 77 ierr = PetscInfo(mat,"Coloring of matrix has some unneeded colors with no corresponding rows\n");CHKERRQ(ierr); 78 } 79 80 disp[0] = 0; 81 for (j=1; j<size; j++) { 82 disp[j] = disp[j-1] + ncolsonproc[j-1]; 83 } 84 85 /* Get complete list of columns for color on each processor */ 86 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 87 ierr = MPI_Allgatherv((void*)is,n,MPIU_INT,cols,ncolsonproc,disp,MPIU_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 88 ierr = PetscFree2(ncolsonproc,disp);CHKERRQ(ierr); 89 } else if (ctype == IS_COLORING_GHOSTED){ 90 /* Determine local number of columns of this color on this process, including ghost points */ 91 nctot = n; 92 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 93 ierr = PetscMemcpy(cols,is,n*sizeof(PetscInt));CHKERRQ(ierr); 94 } else { 95 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not provided for this MatFDColoring type"); 96 } 97 98 /* 99 Mark all rows affect by these columns 100 */ 101 /* Temporary option to allow for debugging/testing */ 102 flg = PETSC_FALSE; 103 ierr = PetscOptionsGetTruth(PETSC_NULL,"-matfdcoloring_slow",&flg,PETSC_NULL);CHKERRQ(ierr); 104 if (!flg) {/*-----------------------------------------------------------------------------*/ 105 /* crude, fast version */ 106 ierr = PetscMemzero(rowhit,M*sizeof(PetscInt));CHKERRQ(ierr); 107 /* loop over columns*/ 108 for (j=0; j<nctot; j++) { 109 if (ctype == IS_COLORING_GHOSTED) { 110 col = ltog[cols[j]]; 111 } else { 112 col = cols[j]; 113 } 114 if (col >= cstart && col < cend) { 115 /* column is in diagonal block of matrix */ 116 rows = A_cj + A_ci[col-cstart]; 117 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 118 } else { 119 #if defined (PETSC_USE_CTABLE) 120 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 121 colb --; 122 #else 123 colb = aij->colmap[col] - 1; 124 #endif 125 if (colb == -1) { 126 m = 0; 127 } else { 128 rows = B_cj + B_ci[colb]; 129 m = B_ci[colb+1] - B_ci[colb]; 130 } 131 } 132 /* loop over columns marking them in rowhit */ 133 for (k=0; k<m; k++) { 134 rowhit[*rows++] = col + 1; 135 } 136 } 137 138 /* count the number of hits */ 139 nrows = 0; 140 for (j=0; j<M; j++) { 141 if (rowhit[j]) nrows++; 142 } 143 c->nrows[i] = nrows; 144 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 145 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 146 ierr = PetscLogObjectMemory(c,2*(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 147 nrows = 0; 148 for (j=0; j<M; j++) { 149 if (rowhit[j]) { 150 c->rows[i][nrows] = j; 151 c->columnsforrow[i][nrows] = rowhit[j] - 1; 152 nrows++; 153 } 154 } 155 } else {/*-------------------------------------------------------------------------------*/ 156 /* slow version, using rowhit as a linked list */ 157 PetscInt currentcol,fm,mfm; 158 rowhit[M] = M; 159 nrows = 0; 160 /* loop over columns*/ 161 for (j=0; j<nctot; j++) { 162 if (ctype == IS_COLORING_GHOSTED) { 163 col = ltog[cols[j]]; 164 } else { 165 col = cols[j]; 166 } 167 if (col >= cstart && col < cend) { 168 /* column is in diagonal block of matrix */ 169 rows = A_cj + A_ci[col-cstart]; 170 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 171 } else { 172 #if defined (PETSC_USE_CTABLE) 173 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 174 colb --; 175 #else 176 colb = aij->colmap[col] - 1; 177 #endif 178 if (colb == -1) { 179 m = 0; 180 } else { 181 rows = B_cj + B_ci[colb]; 182 m = B_ci[colb+1] - B_ci[colb]; 183 } 184 } 185 186 /* loop over columns marking them in rowhit */ 187 fm = M; /* fm points to first entry in linked list */ 188 for (k=0; k<m; k++) { 189 currentcol = *rows++; 190 /* is it already in the list? */ 191 do { 192 mfm = fm; 193 fm = rowhit[fm]; 194 } while (fm < currentcol); 195 /* not in list so add it */ 196 if (fm != currentcol) { 197 nrows++; 198 columnsforrow[currentcol] = col; 199 /* next three lines insert new entry into linked list */ 200 rowhit[mfm] = currentcol; 201 rowhit[currentcol] = fm; 202 fm = currentcol; 203 /* fm points to present position in list since we know the columns are sorted */ 204 } else { 205 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid coloring of matrix detected"); 206 } 207 } 208 } 209 c->nrows[i] = nrows; 210 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 211 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 212 ierr = PetscLogObjectMemory(c,(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 213 /* now store the linked list of rows into c->rows[i] */ 214 nrows = 0; 215 fm = rowhit[M]; 216 do { 217 c->rows[i][nrows] = fm; 218 c->columnsforrow[i][nrows++] = columnsforrow[fm]; 219 fm = rowhit[fm]; 220 } while (fm < M); 221 } /* ---------------------------------------------------------------------------------------*/ 222 ierr = PetscFree(cols);CHKERRQ(ierr); 223 } 224 225 /* Optimize by adding the vscale, and scaleforrow[][] fields */ 226 /* 227 vscale will contain the "diagonal" on processor scalings followed by the off processor 228 */ 229 if (ctype == IS_COLORING_GLOBAL) { 230 ierr = VecCreateGhost(((PetscObject)mat)->comm,aij->A->rmap->n,PETSC_DETERMINE,aij->B->cmap->n,aij->garray,&c->vscale);CHKERRQ(ierr); 231 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 232 for (k=0; k<c->ncolors; k++) { 233 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 234 for (l=0; l<c->nrows[k]; l++) { 235 col = c->columnsforrow[k][l]; 236 if (col >= cstart && col < cend) { 237 /* column is in diagonal block of matrix */ 238 colb = col - cstart; 239 } else { 240 /* column is in "off-processor" part */ 241 #if defined (PETSC_USE_CTABLE) 242 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 243 colb --; 244 #else 245 colb = aij->colmap[col] - 1; 246 #endif 247 colb += cend - cstart; 248 } 249 c->vscaleforrow[k][l] = colb; 250 } 251 } 252 } else if (ctype == IS_COLORING_GHOSTED) { 253 /* Get gtol mapping */ 254 PetscInt N = mat->cmap->N, *gtol; 255 ierr = PetscMalloc((N+1)*sizeof(PetscInt),>ol);CHKERRQ(ierr); 256 for (i=0; i<N; i++) gtol[i] = -1; 257 for (i=0; i<map->n; i++) gtol[ltog[i]] = i; 258 259 c->vscale = 0; /* will be created in MatFDColoringApply() */ 260 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 261 for (k=0; k<c->ncolors; k++) { 262 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 263 for (l=0; l<c->nrows[k]; l++) { 264 col = c->columnsforrow[k][l]; /* global column index */ 265 c->vscaleforrow[k][l] = gtol[col]; /* local column index */ 266 } 267 } 268 ierr = PetscFree(gtol);CHKERRQ(ierr); 269 } 270 ierr = ISColoringRestoreIS(iscoloring,&isa);CHKERRQ(ierr); 271 272 ierr = PetscFree(rowhit);CHKERRQ(ierr); 273 ierr = PetscFree(columnsforrow);CHKERRQ(ierr); 274 ierr = MatRestoreColumnIJ(aij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 275 ierr = MatRestoreColumnIJ(aij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 276 PetscFunctionReturn(0); 277 } 278 279 280 281 282 283 284