1 #define PETSCMAT_DLL 2 3 #include "src/mat/impls/aij/mpi/mpiaij.h" 4 5 EXTERN PetscErrorCode CreateColmap_MPIAIJ_Private(Mat); 6 EXTERN PetscErrorCode MatGetColumnIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscInt*,PetscInt*[],PetscInt*[],PetscTruth*); 7 EXTERN PetscErrorCode MatRestoreColumnIJ_SeqAIJ(Mat,PetscInt,PetscTruth,PetscInt*,PetscInt*[],PetscInt*[],PetscTruth*); 8 9 #undef __FUNCT__ 10 #define __FUNCT__ "MatFDColoringCreate_MPIAIJ" 11 PetscErrorCode MatFDColoringCreate_MPIAIJ(Mat mat,ISColoring iscoloring,MatFDColoring c) 12 { 13 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 14 PetscErrorCode ierr; 15 PetscMPIInt size,*ncolsonproc,*disp,nn; 16 PetscInt i,*is,n,nrows,j,k,m,*rows = 0,*A_ci,*A_cj,ncols,col; 17 PetscInt nis = iscoloring->n,nctot,*cols,*B_ci,*B_cj; 18 PetscInt *rowhit,M = mat->rmap.n,cstart = mat->cmap.rstart,cend = mat->cmap.rend,colb; 19 PetscInt *columnsforrow,l; 20 IS *isa; 21 PetscTruth done,flg; 22 ISLocalToGlobalMapping map = mat->mapping; 23 PetscInt *ltog = map->indices,ctype=c->ctype; 24 25 PetscFunctionBegin; 26 if (!mat->assembled) { 27 SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Matrix must be assembled first; MatAssemblyBegin/End();"); 28 } 29 30 ierr = ISColoringGetIS(iscoloring,PETSC_IGNORE,&isa);CHKERRQ(ierr); 31 c->M = mat->rmap.N; /* set the global rows and columns and local rows */ 32 c->N = mat->cmap.N; 33 c->m = mat->rmap.n; 34 c->rstart = mat->rmap.rstart; 35 36 c->ncolors = nis; 37 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->ncolumns);CHKERRQ(ierr); 38 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columns);CHKERRQ(ierr); 39 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->nrows);CHKERRQ(ierr); 40 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->rows);CHKERRQ(ierr); 41 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columnsforrow);CHKERRQ(ierr); 42 ierr = PetscLogObjectMemory(c,5*nis*sizeof(PetscInt));CHKERRQ(ierr); 43 44 /* Allow access to data structures of local part of matrix */ 45 if (!aij->colmap) { 46 ierr = CreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 47 } 48 /* 49 Calls the _SeqAIJ() version of these routines to make sure it does not 50 get the reduced (by inodes) version of I and J 51 */ 52 ierr = MatGetColumnIJ_SeqAIJ(aij->A,0,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 53 ierr = MatGetColumnIJ_SeqAIJ(aij->B,0,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 54 55 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&rowhit);CHKERRQ(ierr); 56 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&columnsforrow);CHKERRQ(ierr); 57 58 for (i=0; i<nis; i++) { 59 ierr = ISGetLocalSize(isa[i],&n);CHKERRQ(ierr); 60 ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr); 61 c->ncolumns[i] = n; 62 if (n) { 63 ierr = PetscMalloc(n*sizeof(PetscInt),&c->columns[i]);CHKERRQ(ierr); 64 ierr = PetscLogObjectMemory(c,n*sizeof(PetscInt));CHKERRQ(ierr); 65 ierr = PetscMemcpy(c->columns[i],is,n*sizeof(PetscInt));CHKERRQ(ierr); 66 } else { 67 c->columns[i] = 0; 68 } 69 70 if (ctype == IS_COLORING_LOCAL){ 71 /* Determine the total (parallel) number of columns of this color */ 72 ierr = MPI_Comm_size(mat->comm,&size);CHKERRQ(ierr); 73 ierr = PetscMalloc(2*size*sizeof(PetscInt*),&ncolsonproc);CHKERRQ(ierr); 74 disp = ncolsonproc + size; 75 76 nn = (PetscMPIInt)n; 77 ierr = MPI_Allgather(&nn,1,MPI_INT,ncolsonproc,1,MPI_INT,mat->comm);CHKERRQ(ierr); 78 nctot = 0; for (j=0; j<size; j++) {nctot += ncolsonproc[j];} 79 if (!nctot) { 80 ierr = PetscInfo(mat,"Coloring of matrix has some unneeded colors with no corresponding rows\n");CHKERRQ(ierr); 81 } 82 83 disp[0] = 0; 84 for (j=1; j<size; j++) { 85 disp[j] = disp[j-1] + ncolsonproc[j-1]; 86 } 87 88 /* Get complete list of columns for color on each processor */ 89 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 90 ierr = MPI_Allgatherv(is,n,MPIU_INT,cols,ncolsonproc,disp,MPIU_INT,mat->comm);CHKERRQ(ierr); 91 ierr = PetscFree(ncolsonproc);CHKERRQ(ierr); 92 } else if (ctype == IS_COLORING_GHOSTED){ 93 /* Determine local number of columns of this color on this process, including ghost points */ 94 nctot = n; 95 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 96 ierr = PetscMemcpy(cols,is,n*sizeof(PetscInt));CHKERRQ(ierr); 97 } else { 98 SETERRQ(PETSC_ERR_SUP,"Not provided for this MatFDColoring type"); 99 } 100 101 /* 102 Mark all rows affect by these columns 103 */ 104 /* Temporary option to allow for debugging/testing */ 105 ierr = PetscOptionsHasName(PETSC_NULL,"-matfdcoloring_slow",&flg);CHKERRQ(ierr); 106 if (!flg) {/*-----------------------------------------------------------------------------*/ 107 /* crude, fast version */ 108 ierr = PetscMemzero(rowhit,M*sizeof(PetscInt));CHKERRQ(ierr); 109 /* loop over columns*/ 110 for (j=0; j<nctot; j++) { 111 if (ctype == IS_COLORING_GHOSTED) { 112 col = ltog[cols[j]]; 113 } else { 114 col = cols[j]; 115 } 116 if (col >= cstart && col < cend) { 117 /* column is in diagonal block of matrix */ 118 rows = A_cj + A_ci[col-cstart]; 119 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 120 } else { 121 #if defined (PETSC_USE_CTABLE) 122 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr) 123 colb --; 124 #else 125 colb = aij->colmap[col] - 1; 126 #endif 127 if (colb == -1) { 128 m = 0; 129 } else { 130 rows = B_cj + B_ci[colb]; 131 m = B_ci[colb+1] - B_ci[colb]; 132 } 133 } 134 /* loop over columns marking them in rowhit */ 135 for (k=0; k<m; k++) { 136 rowhit[*rows++] = col + 1; 137 } 138 } 139 140 /* count the number of hits */ 141 nrows = 0; 142 for (j=0; j<M; j++) { 143 if (rowhit[j]) nrows++; 144 } 145 c->nrows[i] = nrows; 146 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 147 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 148 ierr = PetscLogObjectMemory(c,2*(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 149 nrows = 0; 150 for (j=0; j<M; j++) { 151 if (rowhit[j]) { 152 c->rows[i][nrows] = j; 153 c->columnsforrow[i][nrows] = rowhit[j] - 1; 154 nrows++; 155 } 156 } 157 } else {/*-------------------------------------------------------------------------------*/ 158 /* slow version, using rowhit as a linked list */ 159 PetscInt currentcol,fm,mfm; 160 rowhit[M] = M; 161 nrows = 0; 162 /* loop over columns*/ 163 for (j=0; j<nctot; j++) { 164 if (ctype == IS_COLORING_GHOSTED) { 165 col = ltog[cols[j]]; 166 } else { 167 col = cols[j]; 168 } 169 if (col >= cstart && col < cend) { 170 /* column is in diagonal block of matrix */ 171 rows = A_cj + A_ci[col-cstart]; 172 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 173 } else { 174 #if defined (PETSC_USE_CTABLE) 175 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 176 colb --; 177 #else 178 colb = aij->colmap[col] - 1; 179 #endif 180 if (colb == -1) { 181 m = 0; 182 } else { 183 rows = B_cj + B_ci[colb]; 184 m = B_ci[colb+1] - B_ci[colb]; 185 } 186 } 187 188 /* loop over columns marking them in rowhit */ 189 fm = M; /* fm points to first entry in linked list */ 190 for (k=0; k<m; k++) { 191 currentcol = *rows++; 192 /* is it already in the list? */ 193 do { 194 mfm = fm; 195 fm = rowhit[fm]; 196 } while (fm < currentcol); 197 /* not in list so add it */ 198 if (fm != currentcol) { 199 nrows++; 200 columnsforrow[currentcol] = col; 201 /* next three lines insert new entry into linked list */ 202 rowhit[mfm] = currentcol; 203 rowhit[currentcol] = fm; 204 fm = currentcol; 205 /* fm points to present position in list since we know the columns are sorted */ 206 } else { 207 SETERRQ(PETSC_ERR_PLIB,"Invalid coloring of matrix detected"); 208 } 209 } 210 } 211 c->nrows[i] = nrows; 212 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 213 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 214 ierr = PetscLogObjectMemory(c,(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 215 /* now store the linked list of rows into c->rows[i] */ 216 nrows = 0; 217 fm = rowhit[M]; 218 do { 219 c->rows[i][nrows] = fm; 220 c->columnsforrow[i][nrows++] = columnsforrow[fm]; 221 fm = rowhit[fm]; 222 } while (fm < M); 223 } /* ---------------------------------------------------------------------------------------*/ 224 ierr = PetscFree(cols);CHKERRQ(ierr); 225 } 226 227 /* Optimize by adding the vscale, and scaleforrow[][] fields */ 228 /* 229 vscale will contain the "diagonal" on processor scalings followed by the off processor 230 */ 231 if (ctype == IS_COLORING_LOCAL) { 232 ierr = VecCreateGhost(mat->comm,aij->A->rmap.n,PETSC_DETERMINE,aij->B->cmap.n,aij->garray,&c->vscale);CHKERRQ(ierr); 233 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 234 for (k=0; k<c->ncolors; k++) { 235 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 236 for (l=0; l<c->nrows[k]; l++) { 237 col = c->columnsforrow[k][l]; 238 if (col >= cstart && col < cend) { 239 /* column is in diagonal block of matrix */ 240 colb = col - cstart; 241 } else { 242 /* column is in "off-processor" part */ 243 #if defined (PETSC_USE_CTABLE) 244 ierr = PetscTableFind(aij->colmap,col+1,&colb);CHKERRQ(ierr); 245 colb --; 246 #else 247 colb = aij->colmap[col] - 1; 248 #endif 249 colb += cend - cstart; 250 } 251 c->vscaleforrow[k][l] = colb; 252 } 253 } 254 } else if (ctype == IS_COLORING_GHOSTED) { 255 /* Get gtol mapping */ 256 PetscInt N = mat->cmap.N, *gtol; 257 ierr = PetscMalloc((N+1)*sizeof(PetscInt),>ol);CHKERRQ(ierr); 258 for (i=0; i<N; i++) gtol[i] = -1; 259 for (i=0; i<map->n; i++) gtol[ltog[i]] = i; 260 261 c->vscale = 0; /* will be created in MatFDColoringApply() */ 262 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 263 for (k=0; k<c->ncolors; k++) { 264 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 265 for (l=0; l<c->nrows[k]; l++) { 266 col = c->columnsforrow[k][l]; /* global column index */ 267 c->vscaleforrow[k][l] = gtol[col]; /* local column index */ 268 } 269 } 270 ierr = PetscFree(gtol);CHKERRQ(ierr); 271 } 272 ierr = ISColoringRestoreIS(iscoloring,&isa);CHKERRQ(ierr); 273 274 ierr = PetscFree(rowhit);CHKERRQ(ierr); 275 ierr = PetscFree(columnsforrow);CHKERRQ(ierr); 276 ierr = MatRestoreColumnIJ_SeqAIJ(aij->A,0,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 277 ierr = MatRestoreColumnIJ_SeqAIJ(aij->B,0,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 278 PetscFunctionReturn(0); 279 } 280 281 282 283 284 285 286