1 2 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 3 #include <petsc-private/vecimpl.h> 4 #include <petscblaslapack.h> 5 #include <petscsf.h> 6 7 /*MC 8 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 9 10 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 11 and MATMPIAIJ otherwise. As a result, for single process communicators, 12 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 13 for communicators controlling multiple processes. It is recommended that you call both of 14 the above preallocation routines for simplicity. 15 16 Options Database Keys: 17 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 18 19 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 20 enough exist. 21 22 Level: beginner 23 24 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ,MATMPIAIJ 25 M*/ 26 27 /*MC 28 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 29 30 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 31 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 32 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 33 for communicators controlling multiple processes. It is recommended that you call both of 34 the above preallocation routines for simplicity. 35 36 Options Database Keys: 37 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 38 39 Level: beginner 40 41 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 42 M*/ 43 44 #undef __FUNCT__ 45 #define __FUNCT__ "MatFindNonzeroRows_MPIAIJ" 46 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 51 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 52 const PetscInt *ia,*ib; 53 const MatScalar *aa,*bb; 54 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 55 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 56 57 PetscFunctionBegin; 58 *keptrows = 0; 59 ia = a->i; 60 ib = b->i; 61 for (i=0; i<m; i++) { 62 na = ia[i+1] - ia[i]; 63 nb = ib[i+1] - ib[i]; 64 if (!na && !nb) { 65 cnt++; 66 goto ok1; 67 } 68 aa = a->a + ia[i]; 69 for (j=0; j<na; j++) { 70 if (aa[j] != 0.0) goto ok1; 71 } 72 bb = b->a + ib[i]; 73 for (j=0; j <nb; j++) { 74 if (bb[j] != 0.0) goto ok1; 75 } 76 cnt++; 77 ok1:; 78 } 79 ierr = MPI_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 80 if (!n0rows) PetscFunctionReturn(0); 81 ierr = PetscMalloc((M->rmap->n-cnt)*sizeof(PetscInt),&rows);CHKERRQ(ierr); 82 cnt = 0; 83 for (i=0; i<m; i++) { 84 na = ia[i+1] - ia[i]; 85 nb = ib[i+1] - ib[i]; 86 if (!na && !nb) continue; 87 aa = a->a + ia[i]; 88 for (j=0; j<na;j++) { 89 if (aa[j] != 0.0) { 90 rows[cnt++] = rstart + i; 91 goto ok2; 92 } 93 } 94 bb = b->a + ib[i]; 95 for (j=0; j<nb; j++) { 96 if (bb[j] != 0.0) { 97 rows[cnt++] = rstart + i; 98 goto ok2; 99 } 100 } 101 ok2:; 102 } 103 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 104 PetscFunctionReturn(0); 105 } 106 107 #undef __FUNCT__ 108 #define __FUNCT__ "MatFindZeroDiagonals_MPIAIJ" 109 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 110 { 111 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 112 PetscErrorCode ierr; 113 PetscInt i,rstart,nrows,*rows; 114 115 PetscFunctionBegin; 116 *zrows = NULL; 117 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 118 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 119 for (i=0; i<nrows; i++) rows[i] += rstart; 120 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 121 PetscFunctionReturn(0); 122 } 123 124 #undef __FUNCT__ 125 #define __FUNCT__ "MatGetColumnNorms_MPIAIJ" 126 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 127 { 128 PetscErrorCode ierr; 129 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 130 PetscInt i,n,*garray = aij->garray; 131 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 132 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 133 PetscReal *work; 134 135 PetscFunctionBegin; 136 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 137 ierr = PetscMalloc(n*sizeof(PetscReal),&work);CHKERRQ(ierr); 138 ierr = PetscMemzero(work,n*sizeof(PetscReal));CHKERRQ(ierr); 139 if (type == NORM_2) { 140 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 141 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 142 } 143 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 144 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 145 } 146 } else if (type == NORM_1) { 147 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 148 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 149 } 150 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 151 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 152 } 153 } else if (type == NORM_INFINITY) { 154 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 155 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 156 } 157 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 158 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 159 } 160 161 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 162 if (type == NORM_INFINITY) { 163 ierr = MPI_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,A->hdr.comm);CHKERRQ(ierr); 164 } else { 165 ierr = MPI_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,A->hdr.comm);CHKERRQ(ierr); 166 } 167 ierr = PetscFree(work);CHKERRQ(ierr); 168 if (type == NORM_2) { 169 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 170 } 171 PetscFunctionReturn(0); 172 } 173 174 #undef __FUNCT__ 175 #define __FUNCT__ "MatDistribute_MPIAIJ" 176 /* 177 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 178 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 179 180 Only for square matrices 181 182 Used by a preconditioner, hence PETSC_EXTERN 183 */ 184 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 185 { 186 PetscMPIInt rank,size; 187 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz,*gmataj,cnt,row,*ld,bses[2]; 188 PetscErrorCode ierr; 189 Mat mat; 190 Mat_SeqAIJ *gmata; 191 PetscMPIInt tag; 192 MPI_Status status; 193 PetscBool aij; 194 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 195 196 PetscFunctionBegin; 197 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 198 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 199 if (!rank) { 200 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 201 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 202 } 203 if (reuse == MAT_INITIAL_MATRIX) { 204 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 205 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 206 if (!rank) { 207 bses[0] = gmat->rmap->bs; 208 bses[1] = gmat->cmap->bs; 209 } 210 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 211 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 212 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 213 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&rowners);CHKERRQ(ierr); 214 ierr = PetscMalloc2(m,PetscInt,&dlens,m,PetscInt,&olens);CHKERRQ(ierr); 215 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 216 217 rowners[0] = 0; 218 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 219 rstart = rowners[rank]; 220 rend = rowners[rank+1]; 221 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 222 if (!rank) { 223 gmata = (Mat_SeqAIJ*) gmat->data; 224 /* send row lengths to all processors */ 225 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 226 for (i=1; i<size; i++) { 227 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 228 } 229 /* determine number diagonal and off-diagonal counts */ 230 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 231 ierr = PetscMalloc(m*sizeof(PetscInt),&ld);CHKERRQ(ierr); 232 ierr = PetscMemzero(ld,m*sizeof(PetscInt));CHKERRQ(ierr); 233 jj = 0; 234 for (i=0; i<m; i++) { 235 for (j=0; j<dlens[i]; j++) { 236 if (gmata->j[jj] < rstart) ld[i]++; 237 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 238 jj++; 239 } 240 } 241 /* send column indices to other processes */ 242 for (i=1; i<size; i++) { 243 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 244 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 245 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 246 } 247 248 /* send numerical values to other processes */ 249 for (i=1; i<size; i++) { 250 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 251 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 252 } 253 gmataa = gmata->a; 254 gmataj = gmata->j; 255 256 } else { 257 /* receive row lengths */ 258 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 259 /* receive column indices */ 260 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 261 ierr = PetscMalloc2(nz,PetscScalar,&gmataa,nz,PetscInt,&gmataj);CHKERRQ(ierr); 262 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 263 /* determine number diagonal and off-diagonal counts */ 264 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 265 ierr = PetscMalloc(m*sizeof(PetscInt),&ld);CHKERRQ(ierr); 266 ierr = PetscMemzero(ld,m*sizeof(PetscInt));CHKERRQ(ierr); 267 jj = 0; 268 for (i=0; i<m; i++) { 269 for (j=0; j<dlens[i]; j++) { 270 if (gmataj[jj] < rstart) ld[i]++; 271 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 272 jj++; 273 } 274 } 275 /* receive numerical values */ 276 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 277 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 278 } 279 /* set preallocation */ 280 for (i=0; i<m; i++) { 281 dlens[i] -= olens[i]; 282 } 283 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 284 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 285 286 for (i=0; i<m; i++) { 287 dlens[i] += olens[i]; 288 } 289 cnt = 0; 290 for (i=0; i<m; i++) { 291 row = rstart + i; 292 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 293 cnt += dlens[i]; 294 } 295 if (rank) { 296 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 297 } 298 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 299 ierr = PetscFree(rowners);CHKERRQ(ierr); 300 301 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 302 303 *inmat = mat; 304 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 305 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 306 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 307 mat = *inmat; 308 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 309 if (!rank) { 310 /* send numerical values to other processes */ 311 gmata = (Mat_SeqAIJ*) gmat->data; 312 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 313 gmataa = gmata->a; 314 for (i=1; i<size; i++) { 315 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 316 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 317 } 318 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 319 } else { 320 /* receive numerical values from process 0*/ 321 nz = Ad->nz + Ao->nz; 322 ierr = PetscMalloc(nz*sizeof(PetscScalar),&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 323 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 324 } 325 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 326 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 327 ad = Ad->a; 328 ao = Ao->a; 329 if (mat->rmap->n) { 330 i = 0; 331 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 332 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 333 } 334 for (i=1; i<mat->rmap->n; i++) { 335 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 336 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 337 } 338 i--; 339 if (mat->rmap->n) { 340 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 341 } 342 if (rank) { 343 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 344 } 345 } 346 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 347 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 348 PetscFunctionReturn(0); 349 } 350 351 /* 352 Local utility routine that creates a mapping from the global column 353 number to the local number in the off-diagonal part of the local 354 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 355 a slightly higher hash table cost; without it it is not scalable (each processor 356 has an order N integer array but is fast to acess. 357 */ 358 #undef __FUNCT__ 359 #define __FUNCT__ "MatCreateColmap_MPIAIJ_Private" 360 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 361 { 362 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 363 PetscErrorCode ierr; 364 PetscInt n = aij->B->cmap->n,i; 365 366 PetscFunctionBegin; 367 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 368 #if defined(PETSC_USE_CTABLE) 369 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 370 for (i=0; i<n; i++) { 371 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 372 } 373 #else 374 ierr = PetscMalloc((mat->cmap->N+1)*sizeof(PetscInt),&aij->colmap);CHKERRQ(ierr); 375 ierr = PetscLogObjectMemory(mat,mat->cmap->N*sizeof(PetscInt));CHKERRQ(ierr); 376 ierr = PetscMemzero(aij->colmap,mat->cmap->N*sizeof(PetscInt));CHKERRQ(ierr); 377 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 378 #endif 379 PetscFunctionReturn(0); 380 } 381 382 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv) \ 383 { \ 384 if (col <= lastcol1) low1 = 0; \ 385 else high1 = nrow1; \ 386 lastcol1 = col;\ 387 while (high1-low1 > 5) { \ 388 t = (low1+high1)/2; \ 389 if (rp1[t] > col) high1 = t; \ 390 else low1 = t; \ 391 } \ 392 for (_i=low1; _i<high1; _i++) { \ 393 if (rp1[_i] > col) break; \ 394 if (rp1[_i] == col) { \ 395 if (addv == ADD_VALUES) ap1[_i] += value; \ 396 else ap1[_i] = value; \ 397 goto a_noinsert; \ 398 } \ 399 } \ 400 if (value == 0.0 && ignorezeroentries) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 401 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 402 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 403 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 404 N = nrow1++ - 1; a->nz++; high1++; \ 405 /* shift up all the later entries in this row */ \ 406 for (ii=N; ii>=_i; ii--) { \ 407 rp1[ii+1] = rp1[ii]; \ 408 ap1[ii+1] = ap1[ii]; \ 409 } \ 410 rp1[_i] = col; \ 411 ap1[_i] = value; \ 412 a_noinsert: ; \ 413 ailen[row] = nrow1; \ 414 } 415 416 417 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv) \ 418 { \ 419 if (col <= lastcol2) low2 = 0; \ 420 else high2 = nrow2; \ 421 lastcol2 = col; \ 422 while (high2-low2 > 5) { \ 423 t = (low2+high2)/2; \ 424 if (rp2[t] > col) high2 = t; \ 425 else low2 = t; \ 426 } \ 427 for (_i=low2; _i<high2; _i++) { \ 428 if (rp2[_i] > col) break; \ 429 if (rp2[_i] == col) { \ 430 if (addv == ADD_VALUES) ap2[_i] += value; \ 431 else ap2[_i] = value; \ 432 goto b_noinsert; \ 433 } \ 434 } \ 435 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 436 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 437 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 438 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 439 N = nrow2++ - 1; b->nz++; high2++; \ 440 /* shift up all the later entries in this row */ \ 441 for (ii=N; ii>=_i; ii--) { \ 442 rp2[ii+1] = rp2[ii]; \ 443 ap2[ii+1] = ap2[ii]; \ 444 } \ 445 rp2[_i] = col; \ 446 ap2[_i] = value; \ 447 b_noinsert: ; \ 448 bilen[row] = nrow2; \ 449 } 450 451 #undef __FUNCT__ 452 #define __FUNCT__ "MatSetValuesRow_MPIAIJ" 453 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 454 { 455 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 456 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 457 PetscErrorCode ierr; 458 PetscInt l,*garray = mat->garray,diag; 459 460 PetscFunctionBegin; 461 /* code only works for square matrices A */ 462 463 /* find size of row to the left of the diagonal part */ 464 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 465 row = row - diag; 466 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 467 if (garray[b->j[b->i[row]+l]] > diag) break; 468 } 469 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 470 471 /* diagonal part */ 472 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 473 474 /* right of diagonal part */ 475 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 476 PetscFunctionReturn(0); 477 } 478 479 #undef __FUNCT__ 480 #define __FUNCT__ "MatSetValues_MPIAIJ" 481 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 482 { 483 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 484 PetscScalar value; 485 PetscErrorCode ierr; 486 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 487 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 488 PetscBool roworiented = aij->roworiented; 489 490 /* Some Variables required in the macro */ 491 Mat A = aij->A; 492 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 493 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 494 MatScalar *aa = a->a; 495 PetscBool ignorezeroentries = a->ignorezeroentries; 496 Mat B = aij->B; 497 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 498 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 499 MatScalar *ba = b->a; 500 501 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 502 PetscInt nonew; 503 MatScalar *ap1,*ap2; 504 505 PetscFunctionBegin; 506 if (v) PetscValidScalarPointer(v,6); 507 for (i=0; i<m; i++) { 508 if (im[i] < 0) continue; 509 #if defined(PETSC_USE_DEBUG) 510 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 511 #endif 512 if (im[i] >= rstart && im[i] < rend) { 513 row = im[i] - rstart; 514 lastcol1 = -1; 515 rp1 = aj + ai[row]; 516 ap1 = aa + ai[row]; 517 rmax1 = aimax[row]; 518 nrow1 = ailen[row]; 519 low1 = 0; 520 high1 = nrow1; 521 lastcol2 = -1; 522 rp2 = bj + bi[row]; 523 ap2 = ba + bi[row]; 524 rmax2 = bimax[row]; 525 nrow2 = bilen[row]; 526 low2 = 0; 527 high2 = nrow2; 528 529 for (j=0; j<n; j++) { 530 if (v) { 531 if (roworiented) value = v[i*n+j]; 532 else value = v[i+j*m]; 533 } else value = 0.0; 534 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES)) continue; 535 if (in[j] >= cstart && in[j] < cend) { 536 col = in[j] - cstart; 537 nonew = a->nonew; 538 MatSetValues_SeqAIJ_A_Private(row,col,value,addv); 539 } else if (in[j] < 0) continue; 540 #if defined(PETSC_USE_DEBUG) 541 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 542 #endif 543 else { 544 if (mat->was_assembled) { 545 if (!aij->colmap) { 546 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 547 } 548 #if defined(PETSC_USE_CTABLE) 549 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 550 col--; 551 #else 552 col = aij->colmap[in[j]] - 1; 553 #endif 554 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 555 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 556 col = in[j]; 557 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 558 B = aij->B; 559 b = (Mat_SeqAIJ*)B->data; 560 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 561 rp2 = bj + bi[row]; 562 ap2 = ba + bi[row]; 563 rmax2 = bimax[row]; 564 nrow2 = bilen[row]; 565 low2 = 0; 566 high2 = nrow2; 567 bm = aij->B->rmap->n; 568 ba = b->a; 569 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", im[i], in[j]); 570 } else col = in[j]; 571 nonew = b->nonew; 572 MatSetValues_SeqAIJ_B_Private(row,col,value,addv); 573 } 574 } 575 } else { 576 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 577 if (!aij->donotstash) { 578 mat->assembled = PETSC_FALSE; 579 if (roworiented) { 580 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 581 } else { 582 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 583 } 584 } 585 } 586 } 587 PetscFunctionReturn(0); 588 } 589 590 #undef __FUNCT__ 591 #define __FUNCT__ "MatGetValues_MPIAIJ" 592 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 593 { 594 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 595 PetscErrorCode ierr; 596 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 597 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 598 599 PetscFunctionBegin; 600 for (i=0; i<m; i++) { 601 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 602 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 603 if (idxm[i] >= rstart && idxm[i] < rend) { 604 row = idxm[i] - rstart; 605 for (j=0; j<n; j++) { 606 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 607 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 608 if (idxn[j] >= cstart && idxn[j] < cend) { 609 col = idxn[j] - cstart; 610 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 611 } else { 612 if (!aij->colmap) { 613 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 614 } 615 #if defined(PETSC_USE_CTABLE) 616 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 617 col--; 618 #else 619 col = aij->colmap[idxn[j]] - 1; 620 #endif 621 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 622 else { 623 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 624 } 625 } 626 } 627 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 628 } 629 PetscFunctionReturn(0); 630 } 631 632 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 633 634 #undef __FUNCT__ 635 #define __FUNCT__ "MatAssemblyBegin_MPIAIJ" 636 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 637 { 638 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 639 PetscErrorCode ierr; 640 PetscInt nstash,reallocs; 641 InsertMode addv; 642 643 PetscFunctionBegin; 644 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 645 646 /* make sure all processors are either in INSERTMODE or ADDMODE */ 647 ierr = MPI_Allreduce((PetscEnum*)&mat->insertmode,(PetscEnum*)&addv,1,MPIU_ENUM,MPI_BOR,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 648 if (addv == (ADD_VALUES|INSERT_VALUES)) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_WRONGSTATE,"Some processors inserted others added"); 649 mat->insertmode = addv; /* in case this processor had no cache */ 650 651 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 652 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 653 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 654 PetscFunctionReturn(0); 655 } 656 657 #undef __FUNCT__ 658 #define __FUNCT__ "MatAssemblyEnd_MPIAIJ" 659 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 660 { 661 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 662 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 663 PetscErrorCode ierr; 664 PetscMPIInt n; 665 PetscInt i,j,rstart,ncols,flg; 666 PetscInt *row,*col; 667 PetscBool other_disassembled; 668 PetscScalar *val; 669 InsertMode addv = mat->insertmode; 670 671 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 672 673 PetscFunctionBegin; 674 if (!aij->donotstash && !mat->nooffprocentries) { 675 while (1) { 676 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 677 if (!flg) break; 678 679 for (i=0; i<n; ) { 680 /* Now identify the consecutive vals belonging to the same row */ 681 for (j=i,rstart=row[j]; j<n; j++) { 682 if (row[j] != rstart) break; 683 } 684 if (j < n) ncols = j-i; 685 else ncols = n-i; 686 /* Now assemble all these values with a single function call */ 687 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,addv);CHKERRQ(ierr); 688 689 i = j; 690 } 691 } 692 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 693 } 694 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 695 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 696 697 /* determine if any processor has disassembled, if so we must 698 also disassemble ourselfs, in order that we may reassemble. */ 699 /* 700 if nonzero structure of submatrix B cannot change then we know that 701 no processor disassembled thus we can skip this stuff 702 */ 703 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 704 ierr = MPI_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 705 if (mat->was_assembled && !other_disassembled) { 706 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 707 } 708 } 709 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 710 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 711 } 712 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 713 ierr = MatSetOption(aij->B,MAT_CHECK_COMPRESSED_ROW,PETSC_FALSE);CHKERRQ(ierr); 714 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 715 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 716 717 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 718 719 aij->rowvalues = 0; 720 721 /* used by MatAXPY() */ 722 a->xtoy = 0; ((Mat_SeqAIJ*)aij->B->data)->xtoy = 0; /* b->xtoy = 0 */ 723 a->XtoY = 0; ((Mat_SeqAIJ*)aij->B->data)->XtoY = 0; /* b->XtoY = 0 */ 724 725 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 726 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 727 PetscFunctionReturn(0); 728 } 729 730 #undef __FUNCT__ 731 #define __FUNCT__ "MatZeroEntries_MPIAIJ" 732 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 733 { 734 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 735 PetscErrorCode ierr; 736 737 PetscFunctionBegin; 738 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 739 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 740 PetscFunctionReturn(0); 741 } 742 743 #undef __FUNCT__ 744 #define __FUNCT__ "MatZeroRows_MPIAIJ" 745 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 746 { 747 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 748 PetscErrorCode ierr; 749 PetscMPIInt size = l->size,imdex,n,rank = l->rank,tag = ((PetscObject)A)->tag,lastidx = -1; 750 PetscInt i,*owners = A->rmap->range; 751 PetscInt *nprocs,j,idx,nsends,row; 752 PetscInt nmax,*svalues,*starts,*owner,nrecvs; 753 PetscInt *rvalues,count,base,slen,*source; 754 PetscInt *lens,*lrows,*values,rstart=A->rmap->rstart; 755 MPI_Comm comm; 756 MPI_Request *send_waits,*recv_waits; 757 MPI_Status recv_status,*send_status; 758 const PetscScalar *xx; 759 PetscScalar *bb; 760 #if defined(PETSC_DEBUG) 761 PetscBool found = PETSC_FALSE; 762 #endif 763 764 PetscFunctionBegin; 765 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 766 /* first count number of contributors to each processor */ 767 ierr = PetscMalloc(2*size*sizeof(PetscInt),&nprocs);CHKERRQ(ierr); 768 ierr = PetscMemzero(nprocs,2*size*sizeof(PetscInt));CHKERRQ(ierr); 769 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&owner);CHKERRQ(ierr); /* see note*/ 770 j = 0; 771 for (i=0; i<N; i++) { 772 if (lastidx > (idx = rows[i])) j = 0; 773 lastidx = idx; 774 for (; j<size; j++) { 775 if (idx >= owners[j] && idx < owners[j+1]) { 776 nprocs[2*j]++; 777 nprocs[2*j+1] = 1; 778 owner[i] = j; 779 #if defined(PETSC_DEBUG) 780 found = PETSC_TRUE; 781 #endif 782 break; 783 } 784 } 785 #if defined(PETSC_DEBUG) 786 if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index out of range"); 787 found = PETSC_FALSE; 788 #endif 789 } 790 nsends = 0; 791 for (i=0; i<size; i++) nsends += nprocs[2*i+1]; 792 793 if (A->nooffproczerorows) { 794 if (nsends > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"You called MatSetOption(,MAT_NO_OFF_PROC_ZERO_ROWS,PETSC_TRUE) but set an off process zero row"); 795 nrecvs = nsends; 796 nmax = N; 797 } else { 798 /* inform other processors of number of messages and max length*/ 799 ierr = PetscMaxSum(comm,nprocs,&nmax,&nrecvs);CHKERRQ(ierr); 800 } 801 802 /* post receives: */ 803 ierr = PetscMalloc((nrecvs+1)*(nmax+1)*sizeof(PetscInt),&rvalues);CHKERRQ(ierr); 804 ierr = PetscMalloc((nrecvs+1)*sizeof(MPI_Request),&recv_waits);CHKERRQ(ierr); 805 for (i=0; i<nrecvs; i++) { 806 ierr = MPI_Irecv(rvalues+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag,comm,recv_waits+i);CHKERRQ(ierr); 807 } 808 809 /* do sends: 810 1) starts[i] gives the starting index in svalues for stuff going to 811 the ith processor 812 */ 813 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&svalues);CHKERRQ(ierr); 814 ierr = PetscMalloc((nsends+1)*sizeof(MPI_Request),&send_waits);CHKERRQ(ierr); 815 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&starts);CHKERRQ(ierr); 816 817 starts[0] = 0; 818 for (i=1; i<size; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 819 for (i=0; i<N; i++) svalues[starts[owner[i]]++] = rows[i]; 820 821 starts[0] = 0; 822 for (i=1; i<size+1; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 823 count = 0; 824 for (i=0; i<size; i++) { 825 if (nprocs[2*i+1]) { 826 ierr = MPI_Isend(svalues+starts[i],nprocs[2*i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr); 827 } 828 } 829 ierr = PetscFree(starts);CHKERRQ(ierr); 830 831 base = owners[rank]; 832 833 /* wait on receives */ 834 ierr = PetscMalloc2(nrecvs,PetscInt,&lens,nrecvs,PetscInt,&source);CHKERRQ(ierr); 835 count = nrecvs; slen = 0; 836 while (count) { 837 ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr); 838 /* unpack receives into our local space */ 839 ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr); 840 841 source[imdex] = recv_status.MPI_SOURCE; 842 lens[imdex] = n; 843 slen += n; 844 count--; 845 } 846 ierr = PetscFree(recv_waits);CHKERRQ(ierr); 847 848 /* move the data into the send scatter */ 849 ierr = PetscMalloc((slen+1)*sizeof(PetscInt),&lrows);CHKERRQ(ierr); 850 count = 0; 851 for (i=0; i<nrecvs; i++) { 852 values = rvalues + i*nmax; 853 for (j=0; j<lens[i]; j++) lrows[count++] = values[j] - base; 854 } 855 ierr = PetscFree(rvalues);CHKERRQ(ierr); 856 ierr = PetscFree2(lens,source);CHKERRQ(ierr); 857 ierr = PetscFree(owner);CHKERRQ(ierr); 858 ierr = PetscFree(nprocs);CHKERRQ(ierr); 859 860 /* fix right hand side if needed */ 861 if (x && b) { 862 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 863 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 864 for (i=0; i<slen; i++) bb[lrows[i]] = diag*xx[lrows[i]]; 865 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 866 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 867 } 868 /* 869 Zero the required rows. If the "diagonal block" of the matrix 870 is square and the user wishes to set the diagonal we use separate 871 code so that MatSetValues() is not called for each diagonal allocating 872 new memory, thus calling lots of mallocs and slowing things down. 873 874 */ 875 /* must zero l->B before l->A because the (diag) case below may put values into l->B*/ 876 ierr = MatZeroRows(l->B,slen,lrows,0.0,0,0);CHKERRQ(ierr); 877 if ((diag != 0.0) && (l->A->rmap->N == l->A->cmap->N)) { 878 ierr = MatZeroRows(l->A,slen,lrows,diag,0,0);CHKERRQ(ierr); 879 } else if (diag != 0.0) { 880 ierr = MatZeroRows(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 881 if (((Mat_SeqAIJ*)l->A->data)->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 882 for (i = 0; i < slen; i++) { 883 row = lrows[i] + rstart; 884 ierr = MatSetValues(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 885 } 886 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 887 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 888 } else { 889 ierr = MatZeroRows(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 890 } 891 ierr = PetscFree(lrows);CHKERRQ(ierr); 892 893 /* wait on sends */ 894 if (nsends) { 895 ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr); 896 ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr); 897 ierr = PetscFree(send_status);CHKERRQ(ierr); 898 } 899 ierr = PetscFree(send_waits);CHKERRQ(ierr); 900 ierr = PetscFree(svalues);CHKERRQ(ierr); 901 PetscFunctionReturn(0); 902 } 903 904 #undef __FUNCT__ 905 #define __FUNCT__ "MatZeroRowsColumns_MPIAIJ" 906 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 907 { 908 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 909 PetscErrorCode ierr; 910 PetscMPIInt size = l->size,imdex,n,rank = l->rank,tag = ((PetscObject)A)->tag,lastidx = -1; 911 PetscInt i,*owners = A->rmap->range; 912 PetscInt *nprocs,j,idx,nsends; 913 PetscInt nmax,*svalues,*starts,*owner,nrecvs; 914 PetscInt *rvalues,count,base,slen,*source; 915 PetscInt *lens,*lrows,*values,m; 916 MPI_Comm comm; 917 MPI_Request *send_waits,*recv_waits; 918 MPI_Status recv_status,*send_status; 919 const PetscScalar *xx; 920 PetscScalar *bb,*mask; 921 Vec xmask,lmask; 922 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 923 const PetscInt *aj, *ii,*ridx; 924 PetscScalar *aa; 925 #if defined(PETSC_DEBUG) 926 PetscBool found = PETSC_FALSE; 927 #endif 928 929 PetscFunctionBegin; 930 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 931 /* first count number of contributors to each processor */ 932 ierr = PetscMalloc(2*size*sizeof(PetscInt),&nprocs);CHKERRQ(ierr); 933 ierr = PetscMemzero(nprocs,2*size*sizeof(PetscInt));CHKERRQ(ierr); 934 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&owner);CHKERRQ(ierr); /* see note*/ 935 j = 0; 936 for (i=0; i<N; i++) { 937 if (lastidx > (idx = rows[i])) j = 0; 938 lastidx = idx; 939 for (; j<size; j++) { 940 if (idx >= owners[j] && idx < owners[j+1]) { 941 nprocs[2*j]++; 942 nprocs[2*j+1] = 1; 943 owner[i] = j; 944 #if defined(PETSC_DEBUG) 945 found = PETSC_TRUE; 946 #endif 947 break; 948 } 949 } 950 #if defined(PETSC_DEBUG) 951 if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index out of range"); 952 found = PETSC_FALSE; 953 #endif 954 } 955 nsends = 0; for (i=0; i<size; i++) nsends += nprocs[2*i+1]; 956 957 /* inform other processors of number of messages and max length*/ 958 ierr = PetscMaxSum(comm,nprocs,&nmax,&nrecvs);CHKERRQ(ierr); 959 960 /* post receives: */ 961 ierr = PetscMalloc((nrecvs+1)*(nmax+1)*sizeof(PetscInt),&rvalues);CHKERRQ(ierr); 962 ierr = PetscMalloc((nrecvs+1)*sizeof(MPI_Request),&recv_waits);CHKERRQ(ierr); 963 for (i=0; i<nrecvs; i++) { 964 ierr = MPI_Irecv(rvalues+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag,comm,recv_waits+i);CHKERRQ(ierr); 965 } 966 967 /* do sends: 968 1) starts[i] gives the starting index in svalues for stuff going to 969 the ith processor 970 */ 971 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&svalues);CHKERRQ(ierr); 972 ierr = PetscMalloc((nsends+1)*sizeof(MPI_Request),&send_waits);CHKERRQ(ierr); 973 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&starts);CHKERRQ(ierr); 974 975 starts[0] = 0; 976 for (i=1; i<size; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 977 for (i=0; i<N; i++) svalues[starts[owner[i]]++] = rows[i]; 978 979 starts[0] = 0; 980 for (i=1; i<size+1; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 981 count = 0; 982 for (i=0; i<size; i++) { 983 if (nprocs[2*i+1]) { 984 ierr = MPI_Isend(svalues+starts[i],nprocs[2*i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr); 985 } 986 } 987 ierr = PetscFree(starts);CHKERRQ(ierr); 988 989 base = owners[rank]; 990 991 /* wait on receives */ 992 ierr = PetscMalloc2(nrecvs,PetscInt,&lens,nrecvs,PetscInt,&source);CHKERRQ(ierr); 993 count = nrecvs; slen = 0; 994 while (count) { 995 ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr); 996 /* unpack receives into our local space */ 997 ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr); 998 999 source[imdex] = recv_status.MPI_SOURCE; 1000 lens[imdex] = n; 1001 slen += n; 1002 count--; 1003 } 1004 ierr = PetscFree(recv_waits);CHKERRQ(ierr); 1005 1006 /* move the data into the send scatter */ 1007 ierr = PetscMalloc((slen+1)*sizeof(PetscInt),&lrows);CHKERRQ(ierr); 1008 count = 0; 1009 for (i=0; i<nrecvs; i++) { 1010 values = rvalues + i*nmax; 1011 for (j=0; j<lens[i]; j++) lrows[count++] = values[j] - base; 1012 } 1013 ierr = PetscFree(rvalues);CHKERRQ(ierr); 1014 ierr = PetscFree2(lens,source);CHKERRQ(ierr); 1015 ierr = PetscFree(owner);CHKERRQ(ierr); 1016 ierr = PetscFree(nprocs);CHKERRQ(ierr); 1017 /* lrows are the local rows to be zeroed, slen is the number of local rows */ 1018 1019 /* zero diagonal part of matrix */ 1020 ierr = MatZeroRowsColumns(l->A,slen,lrows,diag,x,b);CHKERRQ(ierr); 1021 1022 /* handle off diagonal part of matrix */ 1023 ierr = MatGetVecs(A,&xmask,NULL);CHKERRQ(ierr); 1024 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 1025 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 1026 for (i=0; i<slen; i++) bb[lrows[i]] = 1; 1027 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 1028 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1029 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1030 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 1031 if (x) { 1032 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1033 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1034 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 1035 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1036 } 1037 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 1038 1039 /* remove zeroed rows of off diagonal matrix */ 1040 ii = aij->i; 1041 for (i=0; i<slen; i++) { 1042 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 1043 } 1044 1045 /* loop over all elements of off process part of matrix zeroing removed columns*/ 1046 if (aij->compressedrow.use) { 1047 m = aij->compressedrow.nrows; 1048 ii = aij->compressedrow.i; 1049 ridx = aij->compressedrow.rindex; 1050 for (i=0; i<m; i++) { 1051 n = ii[i+1] - ii[i]; 1052 aj = aij->j + ii[i]; 1053 aa = aij->a + ii[i]; 1054 1055 for (j=0; j<n; j++) { 1056 if (PetscAbsScalar(mask[*aj])) { 1057 if (b) bb[*ridx] -= *aa*xx[*aj]; 1058 *aa = 0.0; 1059 } 1060 aa++; 1061 aj++; 1062 } 1063 ridx++; 1064 } 1065 } else { /* do not use compressed row format */ 1066 m = l->B->rmap->n; 1067 for (i=0; i<m; i++) { 1068 n = ii[i+1] - ii[i]; 1069 aj = aij->j + ii[i]; 1070 aa = aij->a + ii[i]; 1071 for (j=0; j<n; j++) { 1072 if (PetscAbsScalar(mask[*aj])) { 1073 if (b) bb[i] -= *aa*xx[*aj]; 1074 *aa = 0.0; 1075 } 1076 aa++; 1077 aj++; 1078 } 1079 } 1080 } 1081 if (x) { 1082 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1083 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 1084 } 1085 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 1086 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 1087 ierr = PetscFree(lrows);CHKERRQ(ierr); 1088 1089 /* wait on sends */ 1090 if (nsends) { 1091 ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr); 1092 ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr); 1093 ierr = PetscFree(send_status);CHKERRQ(ierr); 1094 } 1095 ierr = PetscFree(send_waits);CHKERRQ(ierr); 1096 ierr = PetscFree(svalues);CHKERRQ(ierr); 1097 PetscFunctionReturn(0); 1098 } 1099 1100 #undef __FUNCT__ 1101 #define __FUNCT__ "MatMult_MPIAIJ" 1102 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 1103 { 1104 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1105 PetscErrorCode ierr; 1106 PetscInt nt; 1107 1108 PetscFunctionBegin; 1109 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 1110 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 1111 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1112 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 1113 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1114 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 1115 PetscFunctionReturn(0); 1116 } 1117 1118 #undef __FUNCT__ 1119 #define __FUNCT__ "MatMultDiagonalBlock_MPIAIJ" 1120 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 1121 { 1122 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1123 PetscErrorCode ierr; 1124 1125 PetscFunctionBegin; 1126 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 1127 PetscFunctionReturn(0); 1128 } 1129 1130 #undef __FUNCT__ 1131 #define __FUNCT__ "MatMultAdd_MPIAIJ" 1132 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1133 { 1134 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1135 PetscErrorCode ierr; 1136 1137 PetscFunctionBegin; 1138 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1139 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1140 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1141 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 1142 PetscFunctionReturn(0); 1143 } 1144 1145 #undef __FUNCT__ 1146 #define __FUNCT__ "MatMultTranspose_MPIAIJ" 1147 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 1148 { 1149 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1150 PetscErrorCode ierr; 1151 PetscBool merged; 1152 1153 PetscFunctionBegin; 1154 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 1155 /* do nondiagonal part */ 1156 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1157 if (!merged) { 1158 /* send it on its way */ 1159 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1160 /* do local part */ 1161 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1162 /* receive remote parts: note this assumes the values are not actually */ 1163 /* added in yy until the next line, */ 1164 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1165 } else { 1166 /* do local part */ 1167 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1168 /* send it on its way */ 1169 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1170 /* values actually were received in the Begin() but we need to call this nop */ 1171 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1172 } 1173 PetscFunctionReturn(0); 1174 } 1175 1176 #undef __FUNCT__ 1177 #define __FUNCT__ "MatIsTranspose_MPIAIJ" 1178 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1179 { 1180 MPI_Comm comm; 1181 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1182 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1183 IS Me,Notme; 1184 PetscErrorCode ierr; 1185 PetscInt M,N,first,last,*notme,i; 1186 PetscMPIInt size; 1187 1188 PetscFunctionBegin; 1189 /* Easy test: symmetric diagonal block */ 1190 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1191 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1192 if (!*f) PetscFunctionReturn(0); 1193 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1194 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1195 if (size == 1) PetscFunctionReturn(0); 1196 1197 /* Hard test: off-diagonal block. This takes a MatGetSubMatrix. */ 1198 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1199 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1200 ierr = PetscMalloc((N-last+first)*sizeof(PetscInt),¬me);CHKERRQ(ierr); 1201 for (i=0; i<first; i++) notme[i] = i; 1202 for (i=last; i<M; i++) notme[i-last+first] = i; 1203 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1204 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1205 ierr = MatGetSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1206 Aoff = Aoffs[0]; 1207 ierr = MatGetSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1208 Boff = Boffs[0]; 1209 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1210 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1211 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1212 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1213 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1214 ierr = PetscFree(notme);CHKERRQ(ierr); 1215 PetscFunctionReturn(0); 1216 } 1217 1218 #undef __FUNCT__ 1219 #define __FUNCT__ "MatMultTransposeAdd_MPIAIJ" 1220 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1221 { 1222 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1223 PetscErrorCode ierr; 1224 1225 PetscFunctionBegin; 1226 /* do nondiagonal part */ 1227 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1228 /* send it on its way */ 1229 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1230 /* do local part */ 1231 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1232 /* receive remote parts */ 1233 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1234 PetscFunctionReturn(0); 1235 } 1236 1237 /* 1238 This only works correctly for square matrices where the subblock A->A is the 1239 diagonal block 1240 */ 1241 #undef __FUNCT__ 1242 #define __FUNCT__ "MatGetDiagonal_MPIAIJ" 1243 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1244 { 1245 PetscErrorCode ierr; 1246 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1247 1248 PetscFunctionBegin; 1249 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1250 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1251 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1252 PetscFunctionReturn(0); 1253 } 1254 1255 #undef __FUNCT__ 1256 #define __FUNCT__ "MatScale_MPIAIJ" 1257 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1258 { 1259 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1260 PetscErrorCode ierr; 1261 1262 PetscFunctionBegin; 1263 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1264 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1265 PetscFunctionReturn(0); 1266 } 1267 1268 #undef __FUNCT__ 1269 #define __FUNCT__ "MatDestroy_MPIAIJ" 1270 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1271 { 1272 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1273 PetscErrorCode ierr; 1274 1275 PetscFunctionBegin; 1276 #if defined(PETSC_USE_LOG) 1277 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1278 #endif 1279 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1280 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1281 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1282 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1283 #if defined(PETSC_USE_CTABLE) 1284 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1285 #else 1286 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1287 #endif 1288 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1289 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1290 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1291 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1292 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1293 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1294 1295 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1296 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1297 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1298 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatGetDiagonalBlock_C",NULL);CHKERRQ(ierr); 1299 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1300 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1301 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1302 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1303 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1304 PetscFunctionReturn(0); 1305 } 1306 1307 #undef __FUNCT__ 1308 #define __FUNCT__ "MatView_MPIAIJ_Binary" 1309 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1310 { 1311 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1312 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1313 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1314 PetscErrorCode ierr; 1315 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1316 int fd; 1317 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1318 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz; 1319 PetscScalar *column_values; 1320 PetscInt message_count,flowcontrolcount; 1321 FILE *file; 1322 1323 PetscFunctionBegin; 1324 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1325 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1326 nz = A->nz + B->nz; 1327 if (!rank) { 1328 header[0] = MAT_FILE_CLASSID; 1329 header[1] = mat->rmap->N; 1330 header[2] = mat->cmap->N; 1331 1332 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1333 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1334 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1335 /* get largest number of rows any processor has */ 1336 rlen = mat->rmap->n; 1337 range = mat->rmap->range; 1338 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1339 } else { 1340 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1341 rlen = mat->rmap->n; 1342 } 1343 1344 /* load up the local row counts */ 1345 ierr = PetscMalloc((rlen+1)*sizeof(PetscInt),&row_lengths);CHKERRQ(ierr); 1346 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1347 1348 /* store the row lengths to the file */ 1349 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1350 if (!rank) { 1351 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1352 for (i=1; i<size; i++) { 1353 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1354 rlen = range[i+1] - range[i]; 1355 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1356 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1357 } 1358 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1359 } else { 1360 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1361 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1362 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1363 } 1364 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1365 1366 /* load up the local column indices */ 1367 nzmax = nz; /* th processor needs space a largest processor needs */ 1368 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1369 ierr = PetscMalloc((nzmax+1)*sizeof(PetscInt),&column_indices);CHKERRQ(ierr); 1370 cnt = 0; 1371 for (i=0; i<mat->rmap->n; i++) { 1372 for (j=B->i[i]; j<B->i[i+1]; j++) { 1373 if ((col = garray[B->j[j]]) > cstart) break; 1374 column_indices[cnt++] = col; 1375 } 1376 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1377 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1378 } 1379 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1380 1381 /* store the column indices to the file */ 1382 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1383 if (!rank) { 1384 MPI_Status status; 1385 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1386 for (i=1; i<size; i++) { 1387 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1388 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1389 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1390 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1391 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1392 } 1393 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1394 } else { 1395 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1396 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1397 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1398 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1399 } 1400 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1401 1402 /* load up the local column values */ 1403 ierr = PetscMalloc((nzmax+1)*sizeof(PetscScalar),&column_values);CHKERRQ(ierr); 1404 cnt = 0; 1405 for (i=0; i<mat->rmap->n; i++) { 1406 for (j=B->i[i]; j<B->i[i+1]; j++) { 1407 if (garray[B->j[j]] > cstart) break; 1408 column_values[cnt++] = B->a[j]; 1409 } 1410 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1411 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1412 } 1413 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1414 1415 /* store the column values to the file */ 1416 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1417 if (!rank) { 1418 MPI_Status status; 1419 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1420 for (i=1; i<size; i++) { 1421 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1422 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1423 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1424 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1425 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1426 } 1427 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1428 } else { 1429 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1430 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1431 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1432 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1433 } 1434 ierr = PetscFree(column_values);CHKERRQ(ierr); 1435 1436 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1437 if (file) fprintf(file,"-matload_block_size %d\n",(int)mat->rmap->bs); 1438 PetscFunctionReturn(0); 1439 } 1440 1441 #include <petscdraw.h> 1442 #undef __FUNCT__ 1443 #define __FUNCT__ "MatView_MPIAIJ_ASCIIorDraworSocket" 1444 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1445 { 1446 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1447 PetscErrorCode ierr; 1448 PetscMPIInt rank = aij->rank,size = aij->size; 1449 PetscBool isdraw,iascii,isbinary; 1450 PetscViewer sviewer; 1451 PetscViewerFormat format; 1452 1453 PetscFunctionBegin; 1454 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1455 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1456 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1457 if (iascii) { 1458 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1459 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1460 MatInfo info; 1461 PetscBool inodes; 1462 1463 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1464 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1465 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1466 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 1467 if (!inodes) { 1468 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1469 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1470 } else { 1471 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1472 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1473 } 1474 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1475 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1476 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1477 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1478 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1479 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr); 1480 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1481 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1482 PetscFunctionReturn(0); 1483 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1484 PetscInt inodecount,inodelimit,*inodes; 1485 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1486 if (inodes) { 1487 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1488 } else { 1489 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1490 } 1491 PetscFunctionReturn(0); 1492 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1493 PetscFunctionReturn(0); 1494 } 1495 } else if (isbinary) { 1496 if (size == 1) { 1497 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1498 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1499 } else { 1500 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1501 } 1502 PetscFunctionReturn(0); 1503 } else if (isdraw) { 1504 PetscDraw draw; 1505 PetscBool isnull; 1506 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1507 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 1508 } 1509 1510 if (size == 1) { 1511 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1512 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1513 } else { 1514 /* assemble the entire matrix onto first processor. */ 1515 Mat A; 1516 Mat_SeqAIJ *Aloc; 1517 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1518 MatScalar *a; 1519 1520 if (mat->rmap->N > 1024) { 1521 PetscBool flg = PETSC_FALSE; 1522 1523 ierr = PetscOptionsGetBool(((PetscObject) mat)->prefix, "-mat_ascii_output_large", &flg,NULL);CHKERRQ(ierr); 1524 if (!flg) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_OUTOFRANGE,"ASCII matrix output not allowed for matrices with more than 1024 rows, use binary format instead.\nYou can override this restriction using -mat_ascii_output_large."); 1525 } 1526 1527 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1528 if (!rank) { 1529 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1530 } else { 1531 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1532 } 1533 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1534 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1535 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1536 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1537 ierr = PetscLogObjectParent(mat,A);CHKERRQ(ierr); 1538 1539 /* copy over the A part */ 1540 Aloc = (Mat_SeqAIJ*)aij->A->data; 1541 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1542 row = mat->rmap->rstart; 1543 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1544 for (i=0; i<m; i++) { 1545 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1546 row++; 1547 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1548 } 1549 aj = Aloc->j; 1550 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1551 1552 /* copy over the B part */ 1553 Aloc = (Mat_SeqAIJ*)aij->B->data; 1554 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1555 row = mat->rmap->rstart; 1556 ierr = PetscMalloc((ai[m]+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 1557 ct = cols; 1558 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1559 for (i=0; i<m; i++) { 1560 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1561 row++; 1562 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1563 } 1564 ierr = PetscFree(ct);CHKERRQ(ierr); 1565 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1566 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1567 /* 1568 Everyone has to call to draw the matrix since the graphics waits are 1569 synchronized across all processors that share the PetscDraw object 1570 */ 1571 ierr = PetscViewerGetSingleton(viewer,&sviewer);CHKERRQ(ierr); 1572 if (!rank) { 1573 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1574 /* Set the type name to MATMPIAIJ so that the correct type can be printed out by PetscObjectPrintClassNamePrefixType() in MatView_SeqAIJ_ASCII()*/ 1575 PetscStrcpy(((PetscObject)((Mat_MPIAIJ*)(A->data))->A)->type_name,MATMPIAIJ); 1576 ierr = MatView(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1577 } 1578 ierr = PetscViewerRestoreSingleton(viewer,&sviewer);CHKERRQ(ierr); 1579 ierr = MatDestroy(&A);CHKERRQ(ierr); 1580 } 1581 PetscFunctionReturn(0); 1582 } 1583 1584 #undef __FUNCT__ 1585 #define __FUNCT__ "MatView_MPIAIJ" 1586 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1587 { 1588 PetscErrorCode ierr; 1589 PetscBool iascii,isdraw,issocket,isbinary; 1590 1591 PetscFunctionBegin; 1592 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1593 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1594 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1595 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1596 if (iascii || isdraw || isbinary || issocket) { 1597 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1598 } 1599 PetscFunctionReturn(0); 1600 } 1601 1602 #undef __FUNCT__ 1603 #define __FUNCT__ "MatSOR_MPIAIJ" 1604 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1605 { 1606 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1607 PetscErrorCode ierr; 1608 Vec bb1 = 0; 1609 PetscBool hasop; 1610 1611 PetscFunctionBegin; 1612 if (flag == SOR_APPLY_UPPER) { 1613 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1614 PetscFunctionReturn(0); 1615 } 1616 1617 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1618 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1619 } 1620 1621 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1622 if (flag & SOR_ZERO_INITIAL_GUESS) { 1623 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1624 its--; 1625 } 1626 1627 while (its--) { 1628 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1629 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1630 1631 /* update rhs: bb1 = bb - B*x */ 1632 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1633 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1634 1635 /* local sweep */ 1636 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1637 } 1638 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1639 if (flag & SOR_ZERO_INITIAL_GUESS) { 1640 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1641 its--; 1642 } 1643 while (its--) { 1644 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1645 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1646 1647 /* update rhs: bb1 = bb - B*x */ 1648 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1649 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1650 1651 /* local sweep */ 1652 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1653 } 1654 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1655 if (flag & SOR_ZERO_INITIAL_GUESS) { 1656 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1657 its--; 1658 } 1659 while (its--) { 1660 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1661 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1662 1663 /* update rhs: bb1 = bb - B*x */ 1664 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1665 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1666 1667 /* local sweep */ 1668 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1669 } 1670 } else if (flag & SOR_EISENSTAT) { 1671 Vec xx1; 1672 1673 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1674 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1675 1676 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1677 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1678 if (!mat->diag) { 1679 ierr = MatGetVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1680 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1681 } 1682 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1683 if (hasop) { 1684 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1685 } else { 1686 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1687 } 1688 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1689 1690 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1691 1692 /* local sweep */ 1693 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1694 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1695 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1696 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1697 1698 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1699 PetscFunctionReturn(0); 1700 } 1701 1702 #undef __FUNCT__ 1703 #define __FUNCT__ "MatPermute_MPIAIJ" 1704 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1705 { 1706 Mat aA,aB,Aperm; 1707 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1708 PetscScalar *aa,*ba; 1709 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1710 PetscSF rowsf,sf; 1711 IS parcolp = NULL; 1712 PetscBool done; 1713 PetscErrorCode ierr; 1714 1715 PetscFunctionBegin; 1716 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1717 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1718 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1719 ierr = PetscMalloc3(PetscMax(m,n),PetscInt,&work,m,PetscInt,&rdest,n,PetscInt,&cdest);CHKERRQ(ierr); 1720 1721 /* Invert row permutation to find out where my rows should go */ 1722 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1723 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1724 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1725 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1726 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1727 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1728 1729 /* Invert column permutation to find out where my columns should go */ 1730 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1731 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1732 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1733 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1734 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1735 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1736 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1737 1738 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1739 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1740 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1741 1742 /* Find out where my gcols should go */ 1743 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1744 ierr = PetscMalloc(ng*sizeof(PetscInt),&gcdest);CHKERRQ(ierr); 1745 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1746 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1747 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1748 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1749 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1750 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1751 1752 ierr = PetscMalloc4(m,PetscInt,&dnnz,m,PetscInt,&onnz,m,PetscInt,&tdnnz,m,PetscInt,&tonnz);CHKERRQ(ierr); 1753 ierr = PetscMemzero(dnnz,m*sizeof(PetscInt));CHKERRQ(ierr); 1754 ierr = PetscMemzero(onnz,m*sizeof(PetscInt));CHKERRQ(ierr); 1755 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1756 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1757 for (i=0; i<m; i++) { 1758 PetscInt row = rdest[i],rowner; 1759 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1760 for (j=ai[i]; j<ai[i+1]; j++) { 1761 PetscInt cowner,col = cdest[aj[j]]; 1762 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1763 if (rowner == cowner) dnnz[i]++; 1764 else onnz[i]++; 1765 } 1766 for (j=bi[i]; j<bi[i+1]; j++) { 1767 PetscInt cowner,col = gcdest[bj[j]]; 1768 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1769 if (rowner == cowner) dnnz[i]++; 1770 else onnz[i]++; 1771 } 1772 } 1773 ierr = PetscMemzero(tdnnz,m*sizeof(PetscInt));CHKERRQ(ierr); 1774 ierr = PetscMemzero(tonnz,m*sizeof(PetscInt));CHKERRQ(ierr); 1775 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1776 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1777 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1778 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1779 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1780 1781 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1782 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1783 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1784 for (i=0; i<m; i++) { 1785 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1786 PetscInt rowlen; 1787 rowlen = ai[i+1] - ai[i]; 1788 for (j=0; j<rowlen; j++) acols[j] = cdest[aj[ai[i]+j]]; 1789 ierr = MatSetValues(Aperm,1,&rdest[i],rowlen,acols,aa+ai[i],INSERT_VALUES);CHKERRQ(ierr); 1790 rowlen = bi[i+1] - bi[i]; 1791 for (j=0; j<rowlen; j++) bcols[j] = gcdest[bj[bi[i]+j]]; 1792 ierr = MatSetValues(Aperm,1,&rdest[i],rowlen,bcols,ba+bi[i],INSERT_VALUES);CHKERRQ(ierr); 1793 } 1794 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1795 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1796 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1797 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1798 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1799 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1800 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1801 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1802 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1803 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1804 *B = Aperm; 1805 PetscFunctionReturn(0); 1806 } 1807 1808 #undef __FUNCT__ 1809 #define __FUNCT__ "MatGetInfo_MPIAIJ" 1810 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1811 { 1812 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1813 Mat A = mat->A,B = mat->B; 1814 PetscErrorCode ierr; 1815 PetscReal isend[5],irecv[5]; 1816 1817 PetscFunctionBegin; 1818 info->block_size = 1.0; 1819 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1820 1821 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1822 isend[3] = info->memory; isend[4] = info->mallocs; 1823 1824 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1825 1826 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1827 isend[3] += info->memory; isend[4] += info->mallocs; 1828 if (flag == MAT_LOCAL) { 1829 info->nz_used = isend[0]; 1830 info->nz_allocated = isend[1]; 1831 info->nz_unneeded = isend[2]; 1832 info->memory = isend[3]; 1833 info->mallocs = isend[4]; 1834 } else if (flag == MAT_GLOBAL_MAX) { 1835 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1836 1837 info->nz_used = irecv[0]; 1838 info->nz_allocated = irecv[1]; 1839 info->nz_unneeded = irecv[2]; 1840 info->memory = irecv[3]; 1841 info->mallocs = irecv[4]; 1842 } else if (flag == MAT_GLOBAL_SUM) { 1843 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1844 1845 info->nz_used = irecv[0]; 1846 info->nz_allocated = irecv[1]; 1847 info->nz_unneeded = irecv[2]; 1848 info->memory = irecv[3]; 1849 info->mallocs = irecv[4]; 1850 } 1851 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1852 info->fill_ratio_needed = 0; 1853 info->factor_mallocs = 0; 1854 PetscFunctionReturn(0); 1855 } 1856 1857 #undef __FUNCT__ 1858 #define __FUNCT__ "MatSetOption_MPIAIJ" 1859 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1860 { 1861 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1862 PetscErrorCode ierr; 1863 1864 PetscFunctionBegin; 1865 switch (op) { 1866 case MAT_NEW_NONZERO_LOCATIONS: 1867 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1868 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1869 case MAT_KEEP_NONZERO_PATTERN: 1870 case MAT_NEW_NONZERO_LOCATION_ERR: 1871 case MAT_USE_INODES: 1872 case MAT_IGNORE_ZERO_ENTRIES: 1873 MatCheckPreallocated(A,1); 1874 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1875 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1876 break; 1877 case MAT_ROW_ORIENTED: 1878 a->roworiented = flg; 1879 1880 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1881 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1882 break; 1883 case MAT_NEW_DIAGONALS: 1884 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1885 break; 1886 case MAT_IGNORE_OFF_PROC_ENTRIES: 1887 a->donotstash = flg; 1888 break; 1889 case MAT_SPD: 1890 A->spd_set = PETSC_TRUE; 1891 A->spd = flg; 1892 if (flg) { 1893 A->symmetric = PETSC_TRUE; 1894 A->structurally_symmetric = PETSC_TRUE; 1895 A->symmetric_set = PETSC_TRUE; 1896 A->structurally_symmetric_set = PETSC_TRUE; 1897 } 1898 break; 1899 case MAT_SYMMETRIC: 1900 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1901 break; 1902 case MAT_STRUCTURALLY_SYMMETRIC: 1903 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1904 break; 1905 case MAT_HERMITIAN: 1906 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1907 break; 1908 case MAT_SYMMETRY_ETERNAL: 1909 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1910 break; 1911 default: 1912 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1913 } 1914 PetscFunctionReturn(0); 1915 } 1916 1917 #undef __FUNCT__ 1918 #define __FUNCT__ "MatGetRow_MPIAIJ" 1919 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1920 { 1921 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1922 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1923 PetscErrorCode ierr; 1924 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1925 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1926 PetscInt *cmap,*idx_p; 1927 1928 PetscFunctionBegin; 1929 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1930 mat->getrowactive = PETSC_TRUE; 1931 1932 if (!mat->rowvalues && (idx || v)) { 1933 /* 1934 allocate enough space to hold information from the longest row. 1935 */ 1936 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1937 PetscInt max = 1,tmp; 1938 for (i=0; i<matin->rmap->n; i++) { 1939 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1940 if (max < tmp) max = tmp; 1941 } 1942 ierr = PetscMalloc2(max,PetscScalar,&mat->rowvalues,max,PetscInt,&mat->rowindices);CHKERRQ(ierr); 1943 } 1944 1945 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1946 lrow = row - rstart; 1947 1948 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1949 if (!v) {pvA = 0; pvB = 0;} 1950 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1951 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1952 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1953 nztot = nzA + nzB; 1954 1955 cmap = mat->garray; 1956 if (v || idx) { 1957 if (nztot) { 1958 /* Sort by increasing column numbers, assuming A and B already sorted */ 1959 PetscInt imark = -1; 1960 if (v) { 1961 *v = v_p = mat->rowvalues; 1962 for (i=0; i<nzB; i++) { 1963 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1964 else break; 1965 } 1966 imark = i; 1967 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1968 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1969 } 1970 if (idx) { 1971 *idx = idx_p = mat->rowindices; 1972 if (imark > -1) { 1973 for (i=0; i<imark; i++) { 1974 idx_p[i] = cmap[cworkB[i]]; 1975 } 1976 } else { 1977 for (i=0; i<nzB; i++) { 1978 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1979 else break; 1980 } 1981 imark = i; 1982 } 1983 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1984 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1985 } 1986 } else { 1987 if (idx) *idx = 0; 1988 if (v) *v = 0; 1989 } 1990 } 1991 *nz = nztot; 1992 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1993 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1994 PetscFunctionReturn(0); 1995 } 1996 1997 #undef __FUNCT__ 1998 #define __FUNCT__ "MatRestoreRow_MPIAIJ" 1999 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 2000 { 2001 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2002 2003 PetscFunctionBegin; 2004 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 2005 aij->getrowactive = PETSC_FALSE; 2006 PetscFunctionReturn(0); 2007 } 2008 2009 #undef __FUNCT__ 2010 #define __FUNCT__ "MatNorm_MPIAIJ" 2011 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 2012 { 2013 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2014 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 2015 PetscErrorCode ierr; 2016 PetscInt i,j,cstart = mat->cmap->rstart; 2017 PetscReal sum = 0.0; 2018 MatScalar *v; 2019 2020 PetscFunctionBegin; 2021 if (aij->size == 1) { 2022 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 2023 } else { 2024 if (type == NORM_FROBENIUS) { 2025 v = amat->a; 2026 for (i=0; i<amat->nz; i++) { 2027 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 2028 } 2029 v = bmat->a; 2030 for (i=0; i<bmat->nz; i++) { 2031 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 2032 } 2033 ierr = MPI_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2034 *norm = PetscSqrtReal(*norm); 2035 } else if (type == NORM_1) { /* max column norm */ 2036 PetscReal *tmp,*tmp2; 2037 PetscInt *jj,*garray = aij->garray; 2038 ierr = PetscMalloc((mat->cmap->N+1)*sizeof(PetscReal),&tmp);CHKERRQ(ierr); 2039 ierr = PetscMalloc((mat->cmap->N+1)*sizeof(PetscReal),&tmp2);CHKERRQ(ierr); 2040 ierr = PetscMemzero(tmp,mat->cmap->N*sizeof(PetscReal));CHKERRQ(ierr); 2041 *norm = 0.0; 2042 v = amat->a; jj = amat->j; 2043 for (j=0; j<amat->nz; j++) { 2044 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 2045 } 2046 v = bmat->a; jj = bmat->j; 2047 for (j=0; j<bmat->nz; j++) { 2048 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 2049 } 2050 ierr = MPI_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2051 for (j=0; j<mat->cmap->N; j++) { 2052 if (tmp2[j] > *norm) *norm = tmp2[j]; 2053 } 2054 ierr = PetscFree(tmp);CHKERRQ(ierr); 2055 ierr = PetscFree(tmp2);CHKERRQ(ierr); 2056 } else if (type == NORM_INFINITY) { /* max row norm */ 2057 PetscReal ntemp = 0.0; 2058 for (j=0; j<aij->A->rmap->n; j++) { 2059 v = amat->a + amat->i[j]; 2060 sum = 0.0; 2061 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 2062 sum += PetscAbsScalar(*v); v++; 2063 } 2064 v = bmat->a + bmat->i[j]; 2065 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 2066 sum += PetscAbsScalar(*v); v++; 2067 } 2068 if (sum > ntemp) ntemp = sum; 2069 } 2070 ierr = MPI_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2071 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 2072 } 2073 PetscFunctionReturn(0); 2074 } 2075 2076 #undef __FUNCT__ 2077 #define __FUNCT__ "MatTranspose_MPIAIJ" 2078 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 2079 { 2080 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2081 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 2082 PetscErrorCode ierr; 2083 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 2084 PetscInt cstart = A->cmap->rstart,ncol; 2085 Mat B; 2086 MatScalar *array; 2087 2088 PetscFunctionBegin; 2089 if (reuse == MAT_REUSE_MATRIX && A == *matout && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 2090 2091 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 2092 ai = Aloc->i; aj = Aloc->j; 2093 bi = Bloc->i; bj = Bloc->j; 2094 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 2095 PetscInt *d_nnz,*g_nnz,*o_nnz; 2096 PetscSFNode *oloc; 2097 PETSC_UNUSED PetscSF sf; 2098 2099 ierr = PetscMalloc4(na,PetscInt,&d_nnz,na,PetscInt,&o_nnz,nb,PetscInt,&g_nnz,nb,PetscSFNode,&oloc);CHKERRQ(ierr); 2100 /* compute d_nnz for preallocation */ 2101 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 2102 for (i=0; i<ai[ma]; i++) { 2103 d_nnz[aj[i]]++; 2104 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 2105 } 2106 /* compute local off-diagonal contributions */ 2107 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 2108 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 2109 /* map those to global */ 2110 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 2111 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 2112 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 2113 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 2114 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 2115 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 2116 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 2117 2118 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 2119 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 2120 ierr = MatSetBlockSizes(B,A->cmap->bs,A->rmap->bs);CHKERRQ(ierr); 2121 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 2122 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 2123 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 2124 } else { 2125 B = *matout; 2126 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2127 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 2128 } 2129 2130 /* copy over the A part */ 2131 array = Aloc->a; 2132 row = A->rmap->rstart; 2133 for (i=0; i<ma; i++) { 2134 ncol = ai[i+1]-ai[i]; 2135 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 2136 row++; 2137 array += ncol; aj += ncol; 2138 } 2139 aj = Aloc->j; 2140 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 2141 2142 /* copy over the B part */ 2143 ierr = PetscMalloc(bi[mb]*sizeof(PetscInt),&cols);CHKERRQ(ierr); 2144 ierr = PetscMemzero(cols,bi[mb]*sizeof(PetscInt));CHKERRQ(ierr); 2145 array = Bloc->a; 2146 row = A->rmap->rstart; 2147 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 2148 cols_tmp = cols; 2149 for (i=0; i<mb; i++) { 2150 ncol = bi[i+1]-bi[i]; 2151 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 2152 row++; 2153 array += ncol; cols_tmp += ncol; 2154 } 2155 ierr = PetscFree(cols);CHKERRQ(ierr); 2156 2157 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2158 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2159 if (reuse == MAT_INITIAL_MATRIX || *matout != A) { 2160 *matout = B; 2161 } else { 2162 ierr = MatHeaderMerge(A,B);CHKERRQ(ierr); 2163 } 2164 PetscFunctionReturn(0); 2165 } 2166 2167 #undef __FUNCT__ 2168 #define __FUNCT__ "MatDiagonalScale_MPIAIJ" 2169 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 2170 { 2171 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2172 Mat a = aij->A,b = aij->B; 2173 PetscErrorCode ierr; 2174 PetscInt s1,s2,s3; 2175 2176 PetscFunctionBegin; 2177 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 2178 if (rr) { 2179 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 2180 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 2181 /* Overlap communication with computation. */ 2182 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2183 } 2184 if (ll) { 2185 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 2186 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 2187 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 2188 } 2189 /* scale the diagonal block */ 2190 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2191 2192 if (rr) { 2193 /* Do a scatter end and then right scale the off-diagonal block */ 2194 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2195 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2196 } 2197 PetscFunctionReturn(0); 2198 } 2199 2200 #undef __FUNCT__ 2201 #define __FUNCT__ "MatSetUnfactored_MPIAIJ" 2202 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2203 { 2204 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2205 PetscErrorCode ierr; 2206 2207 PetscFunctionBegin; 2208 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2209 PetscFunctionReturn(0); 2210 } 2211 2212 #undef __FUNCT__ 2213 #define __FUNCT__ "MatEqual_MPIAIJ" 2214 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2215 { 2216 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2217 Mat a,b,c,d; 2218 PetscBool flg; 2219 PetscErrorCode ierr; 2220 2221 PetscFunctionBegin; 2222 a = matA->A; b = matA->B; 2223 c = matB->A; d = matB->B; 2224 2225 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2226 if (flg) { 2227 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2228 } 2229 ierr = MPI_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2230 PetscFunctionReturn(0); 2231 } 2232 2233 #undef __FUNCT__ 2234 #define __FUNCT__ "MatCopy_MPIAIJ" 2235 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2236 { 2237 PetscErrorCode ierr; 2238 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2239 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2240 2241 PetscFunctionBegin; 2242 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2243 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2244 /* because of the column compression in the off-processor part of the matrix a->B, 2245 the number of columns in a->B and b->B may be different, hence we cannot call 2246 the MatCopy() directly on the two parts. If need be, we can provide a more 2247 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2248 then copying the submatrices */ 2249 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2250 } else { 2251 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2252 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2253 } 2254 PetscFunctionReturn(0); 2255 } 2256 2257 #undef __FUNCT__ 2258 #define __FUNCT__ "MatSetUp_MPIAIJ" 2259 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2260 { 2261 PetscErrorCode ierr; 2262 2263 PetscFunctionBegin; 2264 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2265 PetscFunctionReturn(0); 2266 } 2267 2268 #undef __FUNCT__ 2269 #define __FUNCT__ "MatAXPYGetPreallocation_MPIAIJ" 2270 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2271 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2272 { 2273 PetscInt i,m=Y->rmap->N; 2274 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2275 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2276 const PetscInt *xi = x->i,*yi = y->i; 2277 2278 PetscFunctionBegin; 2279 /* Set the number of nonzeros in the new matrix */ 2280 for (i=0; i<m; i++) { 2281 PetscInt j,k,nzx = xi[i+1] - xi[i],nzy = yi[i+1] - yi[i]; 2282 const PetscInt *xj = x->j+xi[i],*yj = y->j+yi[i]; 2283 nnz[i] = 0; 2284 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2285 for (; k<nzy && yltog[yj[k]]<xltog[xj[j]]; k++) nnz[i]++; /* Catch up to X */ 2286 if (k<nzy && yltog[yj[k]]==xltog[xj[j]]) k++; /* Skip duplicate */ 2287 nnz[i]++; 2288 } 2289 for (; k<nzy; k++) nnz[i]++; 2290 } 2291 PetscFunctionReturn(0); 2292 } 2293 2294 #undef __FUNCT__ 2295 #define __FUNCT__ "MatAXPY_MPIAIJ" 2296 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2297 { 2298 PetscErrorCode ierr; 2299 PetscInt i; 2300 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2301 PetscBLASInt bnz,one=1; 2302 Mat_SeqAIJ *x,*y; 2303 2304 PetscFunctionBegin; 2305 if (str == SAME_NONZERO_PATTERN) { 2306 PetscScalar alpha = a; 2307 x = (Mat_SeqAIJ*)xx->A->data; 2308 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2309 y = (Mat_SeqAIJ*)yy->A->data; 2310 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2311 x = (Mat_SeqAIJ*)xx->B->data; 2312 y = (Mat_SeqAIJ*)yy->B->data; 2313 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2314 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2315 } else if (str == SUBSET_NONZERO_PATTERN) { 2316 ierr = MatAXPY_SeqAIJ(yy->A,a,xx->A,str);CHKERRQ(ierr); 2317 2318 x = (Mat_SeqAIJ*)xx->B->data; 2319 y = (Mat_SeqAIJ*)yy->B->data; 2320 if (y->xtoy && y->XtoY != xx->B) { 2321 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 2322 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 2323 } 2324 if (!y->xtoy) { /* get xtoy */ 2325 ierr = MatAXPYGetxtoy_Private(xx->B->rmap->n,x->i,x->j,xx->garray,y->i,y->j,yy->garray,&y->xtoy);CHKERRQ(ierr); 2326 y->XtoY = xx->B; 2327 ierr = PetscObjectReference((PetscObject)xx->B);CHKERRQ(ierr); 2328 } 2329 for (i=0; i<x->nz; i++) y->a[y->xtoy[i]] += a*(x->a[i]); 2330 } else { 2331 Mat B; 2332 PetscInt *nnz_d,*nnz_o; 2333 ierr = PetscMalloc(yy->A->rmap->N*sizeof(PetscInt),&nnz_d);CHKERRQ(ierr); 2334 ierr = PetscMalloc(yy->B->rmap->N*sizeof(PetscInt),&nnz_o);CHKERRQ(ierr); 2335 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2336 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2337 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2338 ierr = MatSetBlockSizes(B,Y->rmap->bs,Y->cmap->bs);CHKERRQ(ierr); 2339 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2340 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2341 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2342 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2343 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2344 ierr = MatHeaderReplace(Y,B);CHKERRQ(ierr); 2345 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2346 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2347 } 2348 PetscFunctionReturn(0); 2349 } 2350 2351 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2352 2353 #undef __FUNCT__ 2354 #define __FUNCT__ "MatConjugate_MPIAIJ" 2355 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2356 { 2357 #if defined(PETSC_USE_COMPLEX) 2358 PetscErrorCode ierr; 2359 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2360 2361 PetscFunctionBegin; 2362 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2363 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2364 #else 2365 PetscFunctionBegin; 2366 #endif 2367 PetscFunctionReturn(0); 2368 } 2369 2370 #undef __FUNCT__ 2371 #define __FUNCT__ "MatRealPart_MPIAIJ" 2372 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2373 { 2374 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2375 PetscErrorCode ierr; 2376 2377 PetscFunctionBegin; 2378 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2379 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2380 PetscFunctionReturn(0); 2381 } 2382 2383 #undef __FUNCT__ 2384 #define __FUNCT__ "MatImaginaryPart_MPIAIJ" 2385 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2386 { 2387 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2388 PetscErrorCode ierr; 2389 2390 PetscFunctionBegin; 2391 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2392 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2393 PetscFunctionReturn(0); 2394 } 2395 2396 #if defined(PETSC_HAVE_PBGL) 2397 2398 #include <boost/parallel/mpi/bsp_process_group.hpp> 2399 #include <boost/graph/distributed/ilu_default_graph.hpp> 2400 #include <boost/graph/distributed/ilu_0_block.hpp> 2401 #include <boost/graph/distributed/ilu_preconditioner.hpp> 2402 #include <boost/graph/distributed/petsc/interface.hpp> 2403 #include <boost/multi_array.hpp> 2404 #include <boost/parallel/distributed_property_map->hpp> 2405 2406 #undef __FUNCT__ 2407 #define __FUNCT__ "MatILUFactorSymbolic_MPIAIJ" 2408 /* 2409 This uses the parallel ILU factorization of Peter Gottschling <pgottsch@osl.iu.edu> 2410 */ 2411 PetscErrorCode MatILUFactorSymbolic_MPIAIJ(Mat fact,Mat A, IS isrow, IS iscol, const MatFactorInfo *info) 2412 { 2413 namespace petsc = boost::distributed::petsc; 2414 2415 namespace graph_dist = boost::graph::distributed; 2416 using boost::graph::distributed::ilu_default::process_group_type; 2417 using boost::graph::ilu_permuted; 2418 2419 PetscBool row_identity, col_identity; 2420 PetscContainer c; 2421 PetscInt m, n, M, N; 2422 PetscErrorCode ierr; 2423 2424 PetscFunctionBegin; 2425 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels = 0 supported for parallel ilu"); 2426 ierr = ISIdentity(isrow, &row_identity);CHKERRQ(ierr); 2427 ierr = ISIdentity(iscol, &col_identity);CHKERRQ(ierr); 2428 if (!row_identity || !col_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Row and column permutations must be identity for parallel ILU"); 2429 2430 process_group_type pg; 2431 typedef graph_dist::ilu_default::ilu_level_graph_type lgraph_type; 2432 lgraph_type *lgraph_p = new lgraph_type(petsc::num_global_vertices(A), pg, petsc::matrix_distribution(A, pg)); 2433 lgraph_type& level_graph = *lgraph_p; 2434 graph_dist::ilu_default::graph_type& graph(level_graph.graph); 2435 2436 petsc::read_matrix(A, graph, get(boost::edge_weight, graph)); 2437 ilu_permuted(level_graph); 2438 2439 /* put together the new matrix */ 2440 ierr = MatCreate(PetscObjectComm((PetscObject)A), fact);CHKERRQ(ierr); 2441 ierr = MatGetLocalSize(A, &m, &n);CHKERRQ(ierr); 2442 ierr = MatGetSize(A, &M, &N);CHKERRQ(ierr); 2443 ierr = MatSetSizes(fact, m, n, M, N);CHKERRQ(ierr); 2444 ierr = MatSetBlockSizes(fact,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 2445 ierr = MatSetType(fact, ((PetscObject)A)->type_name);CHKERRQ(ierr); 2446 ierr = MatAssemblyBegin(fact, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2447 ierr = MatAssemblyEnd(fact, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2448 2449 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A), &c); 2450 ierr = PetscContainerSetPointer(c, lgraph_p); 2451 ierr = PetscObjectCompose((PetscObject) (fact), "graph", (PetscObject) c); 2452 ierr = PetscContainerDestroy(&c); 2453 PetscFunctionReturn(0); 2454 } 2455 2456 #undef __FUNCT__ 2457 #define __FUNCT__ "MatLUFactorNumeric_MPIAIJ" 2458 PetscErrorCode MatLUFactorNumeric_MPIAIJ(Mat B,Mat A, const MatFactorInfo *info) 2459 { 2460 PetscFunctionBegin; 2461 PetscFunctionReturn(0); 2462 } 2463 2464 #undef __FUNCT__ 2465 #define __FUNCT__ "MatSolve_MPIAIJ" 2466 /* 2467 This uses the parallel ILU factorization of Peter Gottschling <pgottsch@osl.iu.edu> 2468 */ 2469 PetscErrorCode MatSolve_MPIAIJ(Mat A, Vec b, Vec x) 2470 { 2471 namespace graph_dist = boost::graph::distributed; 2472 2473 typedef graph_dist::ilu_default::ilu_level_graph_type lgraph_type; 2474 lgraph_type *lgraph_p; 2475 PetscContainer c; 2476 PetscErrorCode ierr; 2477 2478 PetscFunctionBegin; 2479 ierr = PetscObjectQuery((PetscObject) A, "graph", (PetscObject*) &c);CHKERRQ(ierr); 2480 ierr = PetscContainerGetPointer(c, (void**) &lgraph_p);CHKERRQ(ierr); 2481 ierr = VecCopy(b, x);CHKERRQ(ierr); 2482 2483 PetscScalar *array_x; 2484 ierr = VecGetArray(x, &array_x);CHKERRQ(ierr); 2485 PetscInt sx; 2486 ierr = VecGetSize(x, &sx);CHKERRQ(ierr); 2487 2488 PetscScalar *array_b; 2489 ierr = VecGetArray(b, &array_b);CHKERRQ(ierr); 2490 PetscInt sb; 2491 ierr = VecGetSize(b, &sb);CHKERRQ(ierr); 2492 2493 lgraph_type& level_graph = *lgraph_p; 2494 graph_dist::ilu_default::graph_type& graph(level_graph.graph); 2495 2496 typedef boost::multi_array_ref<PetscScalar, 1> array_ref_type; 2497 array_ref_type ref_b(array_b, boost::extents[num_vertices(graph)]); 2498 array_ref_type ref_x(array_x, boost::extents[num_vertices(graph)]); 2499 2500 typedef boost::iterator_property_map<array_ref_type::iterator, 2501 boost::property_map<graph_dist::ilu_default::graph_type, boost::vertex_index_t>::type> gvector_type; 2502 gvector_type vector_b(ref_b.begin(), get(boost::vertex_index, graph)); 2503 gvector_type vector_x(ref_x.begin(), get(boost::vertex_index, graph)); 2504 2505 ilu_set_solve(*lgraph_p, vector_b, vector_x); 2506 PetscFunctionReturn(0); 2507 } 2508 #endif 2509 2510 #undef __FUNCT__ 2511 #define __FUNCT__ "MatDestroy_MatRedundant" 2512 PetscErrorCode MatDestroy_MatRedundant(Mat A) 2513 { 2514 PetscErrorCode ierr; 2515 Mat_Redundant *redund; 2516 PetscInt i; 2517 PetscMPIInt size; 2518 2519 PetscFunctionBegin; 2520 ierr = MPI_Comm_size(((PetscObject)A)->comm,&size);CHKERRQ(ierr); 2521 if (size == 1) { 2522 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 2523 redund = a->redundant; 2524 } else { 2525 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2526 redund = a->redundant; 2527 } 2528 if (redund){ 2529 ierr = PetscFree2(redund->send_rank,redund->recv_rank);CHKERRQ(ierr); 2530 ierr = PetscFree(redund->sbuf_j);CHKERRQ(ierr); 2531 ierr = PetscFree(redund->sbuf_a);CHKERRQ(ierr); 2532 for (i=0; i<redund->nrecvs; i++) { 2533 ierr = PetscFree(redund->rbuf_j[i]);CHKERRQ(ierr); 2534 ierr = PetscFree(redund->rbuf_a[i]);CHKERRQ(ierr); 2535 } 2536 ierr = PetscFree4(redund->sbuf_nz,redund->rbuf_nz,redund->rbuf_j,redund->rbuf_a);CHKERRQ(ierr); 2537 2538 if (redund->psubcomm) { 2539 ierr = PetscSubcommDestroy(&redund->psubcomm);CHKERRQ(ierr); 2540 } 2541 2542 ierr = redund->Destroy(A);CHKERRQ(ierr); 2543 ierr = PetscFree(redund);CHKERRQ(ierr); 2544 } 2545 PetscFunctionReturn(0); 2546 } 2547 2548 #undef __FUNCT__ 2549 #define __FUNCT__ "MatGetRedundantMatrix_MPIAIJ_psubcomm" 2550 PetscErrorCode MatGetRedundantMatrix_MPIAIJ_psubcomm(Mat mat,PetscInt nsubcomm,PetscSubcomm psubcomm,MatReuse reuse,Mat *matredundant) 2551 { 2552 PetscMPIInt rank,size; 2553 MPI_Comm comm,subcomm=psubcomm->comm; 2554 PetscErrorCode ierr; 2555 PetscInt nsends=0,nrecvs=0,i,rownz_max=0,M=mat->rmap->N,N=mat->cmap->N; 2556 PetscMPIInt *send_rank= NULL,*recv_rank=NULL,subrank,subsize; 2557 PetscInt *rowrange = mat->rmap->range; 2558 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2559 Mat A = aij->A,B=aij->B,C=*matredundant; 2560 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b=(Mat_SeqAIJ*)B->data; 2561 PetscScalar *sbuf_a; 2562 PetscInt nzlocal=a->nz+b->nz; 2563 PetscInt j,cstart=mat->cmap->rstart,cend=mat->cmap->rend,row,nzA,nzB,ncols,*cworkA,*cworkB; 2564 PetscInt rstart=mat->rmap->rstart,rend=mat->rmap->rend,*bmap=aij->garray; 2565 PetscInt *cols,ctmp,lwrite,*rptr,l,*sbuf_j; 2566 MatScalar *aworkA,*aworkB; 2567 PetscScalar *vals; 2568 PetscMPIInt tag1,tag2,tag3,imdex; 2569 MPI_Request *s_waits1=NULL,*s_waits2=NULL,*s_waits3=NULL; 2570 MPI_Request *r_waits1=NULL,*r_waits2=NULL,*r_waits3=NULL; 2571 MPI_Status recv_status,*send_status; 2572 PetscInt *sbuf_nz=NULL,*rbuf_nz=NULL,count; 2573 PetscInt **rbuf_j=NULL; 2574 PetscScalar **rbuf_a=NULL; 2575 Mat_Redundant *redund =NULL; 2576 PetscBool flg=PETSC_FALSE; 2577 2578 PetscFunctionBegin; 2579 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 2580 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2581 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2582 ierr = MPI_Comm_rank(subcomm,&subrank);CHKERRQ(ierr); 2583 ierr = MPI_Comm_size(subcomm,&subsize);CHKERRQ(ierr); 2584 2585 /* ---------- new imples: use MatGetSubMatrices() ------------*/ 2586 ierr = PetscOptionsGetBool(NULL,"-new",&flg,NULL);CHKERRQ(ierr); 2587 if (flg) { 2588 Mat *matseq; 2589 IS isrow,iscol; 2590 PetscInt mloc_sub,rstart,rend; 2591 2592 if (reuse == MAT_INITIAL_MATRIX) { 2593 /* create a local sequential matrix matseq[0] */ 2594 ierr = MatCreate(subcomm,&C);CHKERRQ(ierr); 2595 ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 2596 ierr = MatSetUp(C);CHKERRQ(ierr); 2597 ierr = MatSetFromOptions(C);CHKERRQ(ierr); 2598 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2599 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2600 2601 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2602 ierr = MatDestroy(&C);CHKERRQ(ierr); 2603 mloc_sub = rend - rstart; 2604 2605 printf("[%d] Use MatGetSubMatrices()...rows %d - %d, mloc_sub %d\n",rank,rstart,rend,mloc_sub); 2606 ierr = ISCreateStride(PETSC_COMM_SELF,mloc_sub,rstart,1,&isrow);CHKERRQ(ierr); 2607 ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&iscol);CHKERRQ(ierr); 2608 } else { /* reuse == MAT_REUSE_MATRIX */ 2609 if (subsize == 1) { 2610 Mat_SeqAIJ *c = (Mat_SeqAIJ*)C->data; 2611 redund = c->redundant; 2612 } else { 2613 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 2614 redund = c->redundant; 2615 } 2616 2617 isrow = redund->isrow; 2618 iscol = redund->iscol; 2619 matseq = redund->matseq; 2620 } 2621 2622 ierr = MatGetSubMatrices(mat,1,&isrow,&iscol,reuse,&matseq);CHKERRQ(ierr); 2623 if (rank==0) { 2624 printf("[%d] matsub:\n",rank); 2625 ierr = MatView(matseq[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 2626 } 2627 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 2628 2629 /* Create matredundant by concatenating matseq[0] from processors in this subcomm */ 2630 if (reuse == MAT_REUSE_MATRIX) { 2631 if (!rank) printf("matredundant:\n"); 2632 ierr = MatView(*matredundant,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2633 } 2634 ierr = MatCreateMPIAIJConcatenateSeqAIJ(subcomm,matseq[0],PETSC_DECIDE,reuse,matredundant);CHKERRQ(ierr); 2635 2636 if (nsubcomm == 1) { 2637 if (!rank) printf( "matredundant\n"); 2638 ierr = MatView(*matredundant,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2639 } 2640 /* 2641 ierr = MatDestroy(&matseq[0]);CHKERRQ(ierr); 2642 ierr = PetscFree(matseq);CHKERRQ(ierr); 2643 ierr = ISDestroy(&isrow);CHKERRQ(ierr); 2644 ierr = ISDestroy(&iscol);CHKERRQ(ierr); 2645 */ 2646 2647 if (reuse == MAT_INITIAL_MATRIX) { 2648 /* create a supporting struct and attach it to C for reuse */ 2649 ierr = PetscNewLog(*matredundant,Mat_Redundant,&redund);CHKERRQ(ierr); 2650 if (subsize == 1) { 2651 Mat_SeqAIJ *c = (Mat_SeqAIJ*)(*matredundant)->data; 2652 c->redundant = redund; 2653 } else { 2654 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*matredundant)->data; 2655 c->redundant = redund; 2656 } 2657 2658 redund->isrow = isrow; 2659 redund->iscol = iscol; 2660 redund->matseq = matseq; 2661 redund->psubcomm = NULL; 2662 2663 redund->Destroy = (*matredundant)->ops->destroy; 2664 (*matredundant)->ops->destroy = MatDestroy_MatRedundant; 2665 } 2666 PetscFunctionReturn(0); 2667 } 2668 /* ----------------------------------------------------*/ 2669 2670 if (reuse == MAT_REUSE_MATRIX) { 2671 if (M != mat->rmap->N || N != mat->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. Wrong global size"); 2672 if (subsize == 1) { 2673 Mat_SeqAIJ *c = (Mat_SeqAIJ*)C->data; 2674 redund = c->redundant; 2675 } else { 2676 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 2677 redund = c->redundant; 2678 } 2679 if (nzlocal != redund->nzlocal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. Wrong nzlocal"); 2680 2681 nsends = redund->nsends; 2682 nrecvs = redund->nrecvs; 2683 send_rank = redund->send_rank; 2684 recv_rank = redund->recv_rank; 2685 sbuf_nz = redund->sbuf_nz; 2686 rbuf_nz = redund->rbuf_nz; 2687 sbuf_j = redund->sbuf_j; 2688 sbuf_a = redund->sbuf_a; 2689 rbuf_j = redund->rbuf_j; 2690 rbuf_a = redund->rbuf_a; 2691 } 2692 2693 if (reuse == MAT_INITIAL_MATRIX) { 2694 PetscInt nleftover,np_subcomm; 2695 2696 /* get the destination processors' id send_rank, nsends and nrecvs */ 2697 ierr = PetscMalloc2(size,PetscMPIInt,&send_rank,size,PetscMPIInt,&recv_rank);CHKERRQ(ierr); 2698 2699 np_subcomm = size/nsubcomm; 2700 nleftover = size - nsubcomm*np_subcomm; 2701 2702 nsends = 0; nrecvs = 0; 2703 if (psubcomm->type == PETSC_SUBCOMM_INTERLACED) { 2704 /* -------------------------------------------*/ 2705 for (i=0; i<size; i++) { 2706 if (subrank == i/nsubcomm && i != rank) { /* my_subrank == other's subrank */ 2707 send_rank[nsends] = i; nsends++; 2708 recv_rank[nrecvs++] = i; 2709 /* printf("[%d] send to and recv from [%d]\n",rank,i); */ 2710 } 2711 } 2712 if (rank >= size - nleftover) { /* this proc is a leftover processor */ 2713 i = size-nleftover-1; 2714 j = 0; 2715 while (j < nsubcomm - nleftover) { 2716 send_rank[nsends++] = i; 2717 i--; j++; 2718 /* printf("[%d] send to [%d]\n",rank,i); */ 2719 } 2720 } 2721 2722 if (nleftover && subsize == size/nsubcomm && subrank==subsize-1) { /* this proc recvs from leftover processors */ 2723 for (i=0; i<nleftover; i++) { 2724 recv_rank[nrecvs++] = size-nleftover+i; 2725 /* printf("[%d] recv from [%d]\n",rank,i); */ 2726 } 2727 } 2728 } else if (psubcomm->type == PETSC_SUBCOMM_CONTIGUOUS) { 2729 /* --------------------------------------------------*/ 2730 /* ---------- new imples: use MatGetSubMatrices() ------------*/ 2731 PetscBool flg=PETSC_FALSE; 2732 ierr = PetscOptionsGetBool(NULL,"-new",&flg,NULL);CHKERRQ(ierr); 2733 if (flg) { 2734 Mat *matseq; 2735 IS isrow,iscol; 2736 PetscInt mloc_sub,rstart,rend; 2737 2738 /* create redundant matrix */ 2739 ierr = MatCreate(subcomm,&C);CHKERRQ(ierr); 2740 ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 2741 ierr = MatSetUp(C);CHKERRQ(ierr); 2742 ierr = MatSetFromOptions(C);CHKERRQ(ierr); 2743 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2744 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2745 2746 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2747 mloc_sub = rend - rstart; 2748 2749 printf("[%d] Use MatGetSubMatrices()...rows %d - %d, mloc_sub %d\n",rank,rstart,rend,mloc_sub); 2750 ierr = ISCreateStride(PETSC_COMM_SELF,mloc_sub,rstart,1,&isrow);CHKERRQ(ierr); 2751 ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&iscol);CHKERRQ(ierr); 2752 2753 ierr = MatGetSubMatrices(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&matseq);CHKERRQ(ierr); 2754 if (rank==1) { 2755 printf("[%d] matsub:\n",rank); 2756 ierr = MatView(matseq[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 2757 } 2758 2759 /* Create redundant matrix by concatenating local sequential 2760 matrices from processors in this subcomm */ 2761 ierr = MatDestroy(&C);CHKERRQ(ierr); 2762 2763 ierr = MatCreateMPIAIJConcatenateSeqAIJ(subcomm,matseq[0],PETSC_DECIDE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr); 2764 *matredundant = C; 2765 2766 if (nsubcomm == 1) { 2767 if (!rank) printf( "C\n"); 2768 ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2769 } 2770 2771 ierr = MatDestroy(&matseq[0]);CHKERRQ(ierr); 2772 ierr = PetscFree(matseq);CHKERRQ(ierr); 2773 ierr = ISDestroy(&isrow);CHKERRQ(ierr); 2774 ierr = ISDestroy(&iscol);CHKERRQ(ierr); 2775 //ierr = MPI_Barrier(comm);CHKERRQ(ierr); 2776 //SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No done yet"); 2777 PetscFunctionReturn(0); 2778 } 2779 2780 /*---------------------------------- */ 2781 PetscInt color,subcommstart; 2782 subcommstart=0; 2783 for (color=0; color<nsubcomm; color++) { 2784 if (psubcomm->color != color) { 2785 for (i=0; i<psubcomm->subsize[color]; i++) { 2786 if (subrank == i) { /* my_subrank == other's subrank */ 2787 send_rank[nsends++] = subcommstart+i; 2788 recv_rank[nrecvs++] = subcommstart+i; 2789 /* printf("[%d] send to and recv from [%d]\n",rank,subcommstart+i); */ 2790 } 2791 } 2792 } 2793 subcommstart += psubcomm->subsize[color]; 2794 } 2795 if (nleftover && subrank == size/nsubcomm) { /* this proc is a leftover proc, send to subcomm that does not have leftover proc */ 2796 subcommstart=0; 2797 for (color=0; color<nsubcomm; color++) { 2798 subcommstart += psubcomm->subsize[color]; 2799 if (psubcomm->color == color) continue; 2800 if (psubcomm->subsize[color] == size/nsubcomm) { /* subcomm does not have leftover proc */ 2801 send_rank[nsends++] = subcommstart -1; /* send to the last proc of subcomm[color] */ 2802 /* printf("[%d] leftover send to [%d] \n",rank,subcommstart -1); */ 2803 } 2804 } 2805 } 2806 2807 if (nleftover && subsize == size/nsubcomm && subrank==subsize-1) { /* this proc recvs from leftover processors */ 2808 subcommstart=0; 2809 for (color=0; color<nsubcomm; color++) { 2810 subcommstart += psubcomm->subsize[color]; 2811 if (psubcomm->subsize[color] > size/nsubcomm) { /* subcomm has leftover proc */ 2812 recv_rank[nrecvs++] = subcommstart -1; /* recv from the last proc of subcomm[color] */ 2813 /* printf("[%d] recv from [%d]\n",rank,subcommstart -1); */ 2814 } 2815 } 2816 } 2817 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for PetscSubcomm type %D",psubcomm->type); 2818 2819 /* allocate sbuf_j, sbuf_a */ 2820 i = nzlocal + rowrange[rank+1] - rowrange[rank] + 2; 2821 ierr = PetscMalloc(i*sizeof(PetscInt),&sbuf_j);CHKERRQ(ierr); 2822 ierr = PetscMalloc((nzlocal+1)*sizeof(PetscScalar),&sbuf_a);CHKERRQ(ierr); 2823 /* 2824 ierr = PetscSynchronizedPrintf(comm,"[%d] nsends %d, nrecvs %d\n",rank,nsends,nrecvs);CHKERRQ(ierr); 2825 ierr = PetscSynchronizedFlush(comm);CHKERRQ(ierr); 2826 */ 2827 } /* endof if (reuse == MAT_INITIAL_MATRIX) */ 2828 2829 /* copy mat's local entries into the buffers */ 2830 if (reuse == MAT_INITIAL_MATRIX) { 2831 rownz_max = 0; 2832 rptr = sbuf_j; 2833 cols = sbuf_j + rend-rstart + 1; 2834 vals = sbuf_a; 2835 rptr[0] = 0; 2836 for (i=0; i<rend-rstart; i++) { 2837 row = i + rstart; 2838 nzA = a->i[i+1] - a->i[i]; nzB = b->i[i+1] - b->i[i]; 2839 ncols = nzA + nzB; 2840 cworkA = a->j + a->i[i]; cworkB = b->j + b->i[i]; 2841 aworkA = a->a + a->i[i]; aworkB = b->a + b->i[i]; 2842 /* load the column indices for this row into cols */ 2843 lwrite = 0; 2844 for (l=0; l<nzB; l++) { 2845 if ((ctmp = bmap[cworkB[l]]) < cstart) { 2846 vals[lwrite] = aworkB[l]; 2847 cols[lwrite++] = ctmp; 2848 } 2849 } 2850 for (l=0; l<nzA; l++) { 2851 vals[lwrite] = aworkA[l]; 2852 cols[lwrite++] = cstart + cworkA[l]; 2853 } 2854 for (l=0; l<nzB; l++) { 2855 if ((ctmp = bmap[cworkB[l]]) >= cend) { 2856 vals[lwrite] = aworkB[l]; 2857 cols[lwrite++] = ctmp; 2858 } 2859 } 2860 vals += ncols; 2861 cols += ncols; 2862 rptr[i+1] = rptr[i] + ncols; 2863 if (rownz_max < ncols) rownz_max = ncols; 2864 } 2865 if (rptr[rend-rstart] != a->nz + b->nz) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB, "rptr[%d] %d != %d + %d",rend-rstart,rptr[rend-rstart+1],a->nz,b->nz); 2866 } else { /* only copy matrix values into sbuf_a */ 2867 rptr = sbuf_j; 2868 vals = sbuf_a; 2869 rptr[0] = 0; 2870 for (i=0; i<rend-rstart; i++) { 2871 row = i + rstart; 2872 nzA = a->i[i+1] - a->i[i]; nzB = b->i[i+1] - b->i[i]; 2873 ncols = nzA + nzB; 2874 cworkB = b->j + b->i[i]; 2875 aworkA = a->a + a->i[i]; 2876 aworkB = b->a + b->i[i]; 2877 lwrite = 0; 2878 for (l=0; l<nzB; l++) { 2879 if ((ctmp = bmap[cworkB[l]]) < cstart) vals[lwrite++] = aworkB[l]; 2880 } 2881 for (l=0; l<nzA; l++) vals[lwrite++] = aworkA[l]; 2882 for (l=0; l<nzB; l++) { 2883 if ((ctmp = bmap[cworkB[l]]) >= cend) vals[lwrite++] = aworkB[l]; 2884 } 2885 vals += ncols; 2886 rptr[i+1] = rptr[i] + ncols; 2887 } 2888 } /* endof if (reuse == MAT_INITIAL_MATRIX) */ 2889 2890 /* send nzlocal to others, and recv other's nzlocal */ 2891 /*--------------------------------------------------*/ 2892 if (reuse == MAT_INITIAL_MATRIX) { 2893 ierr = PetscMalloc2(3*(nsends + nrecvs)+1,MPI_Request,&s_waits3,nsends+1,MPI_Status,&send_status);CHKERRQ(ierr); 2894 2895 s_waits2 = s_waits3 + nsends; 2896 s_waits1 = s_waits2 + nsends; 2897 r_waits1 = s_waits1 + nsends; 2898 r_waits2 = r_waits1 + nrecvs; 2899 r_waits3 = r_waits2 + nrecvs; 2900 } else { 2901 ierr = PetscMalloc2(nsends + nrecvs +1,MPI_Request,&s_waits3,nsends+1,MPI_Status,&send_status);CHKERRQ(ierr); 2902 2903 r_waits3 = s_waits3 + nsends; 2904 } 2905 2906 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag3);CHKERRQ(ierr); 2907 if (reuse == MAT_INITIAL_MATRIX) { 2908 /* get new tags to keep the communication clean */ 2909 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag1);CHKERRQ(ierr); 2910 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag2);CHKERRQ(ierr); 2911 ierr = PetscMalloc4(nsends,PetscInt,&sbuf_nz,nrecvs,PetscInt,&rbuf_nz,nrecvs,PetscInt*,&rbuf_j,nrecvs,PetscScalar*,&rbuf_a);CHKERRQ(ierr); 2912 2913 /* post receives of other's nzlocal */ 2914 for (i=0; i<nrecvs; i++) { 2915 ierr = MPI_Irecv(rbuf_nz+i,1,MPIU_INT,MPI_ANY_SOURCE,tag1,comm,r_waits1+i);CHKERRQ(ierr); 2916 } 2917 /* send nzlocal to others */ 2918 for (i=0; i<nsends; i++) { 2919 sbuf_nz[i] = nzlocal; 2920 ierr = MPI_Isend(sbuf_nz+i,1,MPIU_INT,send_rank[i],tag1,comm,s_waits1+i);CHKERRQ(ierr); 2921 } 2922 /* wait on receives of nzlocal; allocate space for rbuf_j, rbuf_a */ 2923 count = nrecvs; 2924 while (count) { 2925 ierr = MPI_Waitany(nrecvs,r_waits1,&imdex,&recv_status);CHKERRQ(ierr); 2926 2927 recv_rank[imdex] = recv_status.MPI_SOURCE; 2928 /* allocate rbuf_a and rbuf_j; then post receives of rbuf_j */ 2929 ierr = PetscMalloc((rbuf_nz[imdex]+1)*sizeof(PetscScalar),&rbuf_a[imdex]);CHKERRQ(ierr); 2930 2931 i = rowrange[recv_status.MPI_SOURCE+1] - rowrange[recv_status.MPI_SOURCE]; /* number of expected mat->i */ 2932 2933 rbuf_nz[imdex] += i + 2; 2934 2935 ierr = PetscMalloc(rbuf_nz[imdex]*sizeof(PetscInt),&rbuf_j[imdex]);CHKERRQ(ierr); 2936 ierr = MPI_Irecv(rbuf_j[imdex],rbuf_nz[imdex],MPIU_INT,recv_status.MPI_SOURCE,tag2,comm,r_waits2+imdex);CHKERRQ(ierr); 2937 count--; 2938 } 2939 /* wait on sends of nzlocal */ 2940 if (nsends) {ierr = MPI_Waitall(nsends,s_waits1,send_status);CHKERRQ(ierr);} 2941 /* send mat->i,j to others, and recv from other's */ 2942 /*------------------------------------------------*/ 2943 for (i=0; i<nsends; i++) { 2944 j = nzlocal + rowrange[rank+1] - rowrange[rank] + 1; 2945 ierr = MPI_Isend(sbuf_j,j,MPIU_INT,send_rank[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 2946 } 2947 /* wait on receives of mat->i,j */ 2948 /*------------------------------*/ 2949 count = nrecvs; 2950 while (count) { 2951 ierr = MPI_Waitany(nrecvs,r_waits2,&imdex,&recv_status);CHKERRQ(ierr); 2952 if (recv_rank[imdex] != recv_status.MPI_SOURCE) SETERRQ2(PETSC_COMM_SELF,1, "recv_rank %d != MPI_SOURCE %d",recv_rank[imdex],recv_status.MPI_SOURCE); 2953 count--; 2954 } 2955 /* wait on sends of mat->i,j */ 2956 /*---------------------------*/ 2957 if (nsends) { 2958 ierr = MPI_Waitall(nsends,s_waits2,send_status);CHKERRQ(ierr); 2959 } 2960 } /* endof if (reuse == MAT_INITIAL_MATRIX) */ 2961 2962 /* post receives, send and receive mat->a */ 2963 /*----------------------------------------*/ 2964 for (imdex=0; imdex<nrecvs; imdex++) { 2965 ierr = MPI_Irecv(rbuf_a[imdex],rbuf_nz[imdex],MPIU_SCALAR,recv_rank[imdex],tag3,comm,r_waits3+imdex);CHKERRQ(ierr); 2966 } 2967 for (i=0; i<nsends; i++) { 2968 ierr = MPI_Isend(sbuf_a,nzlocal,MPIU_SCALAR,send_rank[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 2969 } 2970 count = nrecvs; 2971 while (count) { 2972 ierr = MPI_Waitany(nrecvs,r_waits3,&imdex,&recv_status);CHKERRQ(ierr); 2973 if (recv_rank[imdex] != recv_status.MPI_SOURCE) SETERRQ2(PETSC_COMM_SELF,1, "recv_rank %d != MPI_SOURCE %d",recv_rank[imdex],recv_status.MPI_SOURCE); 2974 count--; 2975 } 2976 if (nsends) { 2977 ierr = MPI_Waitall(nsends,s_waits3,send_status);CHKERRQ(ierr); 2978 } 2979 2980 ierr = PetscFree2(s_waits3,send_status);CHKERRQ(ierr); 2981 2982 /* create redundant matrix */ 2983 /*-------------------------*/ 2984 if (reuse == MAT_INITIAL_MATRIX) { 2985 const PetscInt *range; 2986 PetscInt rstart_sub,rend_sub,mloc_sub; 2987 2988 /* compute rownz_max for preallocation */ 2989 for (imdex=0; imdex<nrecvs; imdex++) { 2990 j = rowrange[recv_rank[imdex]+1] - rowrange[recv_rank[imdex]]; 2991 rptr = rbuf_j[imdex]; 2992 for (i=0; i<j; i++) { 2993 ncols = rptr[i+1] - rptr[i]; 2994 if (rownz_max < ncols) rownz_max = ncols; 2995 } 2996 } 2997 2998 ierr = MatCreate(subcomm,&C);CHKERRQ(ierr); 2999 3000 /* get local size of redundant matrix 3001 - mloc_sub is chosen for PETSC_SUBCOMM_INTERLACED, works for other types, but may not efficient! */ 3002 ierr = MatGetOwnershipRanges(mat,&range);CHKERRQ(ierr); 3003 rstart_sub = range[nsubcomm*subrank]; 3004 if (subrank+1 < subsize) { /* not the last proc in subcomm */ 3005 rend_sub = range[nsubcomm*(subrank+1)]; 3006 } else { 3007 rend_sub = mat->rmap->N; 3008 } 3009 mloc_sub = rend_sub - rstart_sub; 3010 3011 if (M == N) { 3012 ierr = MatSetSizes(C,mloc_sub,mloc_sub,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 3013 } else { /* non-square matrix */ 3014 ierr = MatSetSizes(C,mloc_sub,PETSC_DECIDE,PETSC_DECIDE,mat->cmap->N);CHKERRQ(ierr); 3015 } 3016 ierr = MatSetBlockSizes(C,mat->rmap->bs,mat->cmap->bs);CHKERRQ(ierr); 3017 ierr = MatSetFromOptions(C);CHKERRQ(ierr); 3018 ierr = MatSeqAIJSetPreallocation(C,rownz_max,NULL);CHKERRQ(ierr); 3019 ierr = MatMPIAIJSetPreallocation(C,rownz_max,NULL,rownz_max,NULL);CHKERRQ(ierr); 3020 } else { 3021 C = *matredundant; 3022 } 3023 3024 /* insert local matrix entries */ 3025 rptr = sbuf_j; 3026 cols = sbuf_j + rend-rstart + 1; 3027 vals = sbuf_a; 3028 for (i=0; i<rend-rstart; i++) { 3029 row = i + rstart; 3030 ncols = rptr[i+1] - rptr[i]; 3031 ierr = MatSetValues(C,1,&row,ncols,cols,vals,INSERT_VALUES);CHKERRQ(ierr); 3032 vals += ncols; 3033 cols += ncols; 3034 } 3035 /* insert received matrix entries */ 3036 for (imdex=0; imdex<nrecvs; imdex++) { 3037 rstart = rowrange[recv_rank[imdex]]; 3038 rend = rowrange[recv_rank[imdex]+1]; 3039 /* printf("[%d] insert rows %d - %d\n",rank,rstart,rend-1); */ 3040 rptr = rbuf_j[imdex]; 3041 cols = rbuf_j[imdex] + rend-rstart + 1; 3042 vals = rbuf_a[imdex]; 3043 for (i=0; i<rend-rstart; i++) { 3044 row = i + rstart; 3045 ncols = rptr[i+1] - rptr[i]; 3046 ierr = MatSetValues(C,1,&row,ncols,cols,vals,INSERT_VALUES);CHKERRQ(ierr); 3047 vals += ncols; 3048 cols += ncols; 3049 } 3050 } 3051 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3052 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3053 3054 if (reuse == MAT_INITIAL_MATRIX) { 3055 *matredundant = C; 3056 3057 /* create a supporting struct and attach it to C for reuse */ 3058 ierr = PetscNewLog(C,Mat_Redundant,&redund);CHKERRQ(ierr); 3059 if (subsize == 1) { 3060 Mat_SeqAIJ *c = (Mat_SeqAIJ*)C->data; 3061 c->redundant = redund; 3062 } else { 3063 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 3064 c->redundant = redund; 3065 } 3066 3067 redund->nzlocal = nzlocal; 3068 redund->nsends = nsends; 3069 redund->nrecvs = nrecvs; 3070 redund->send_rank = send_rank; 3071 redund->recv_rank = recv_rank; 3072 redund->sbuf_nz = sbuf_nz; 3073 redund->rbuf_nz = rbuf_nz; 3074 redund->sbuf_j = sbuf_j; 3075 redund->sbuf_a = sbuf_a; 3076 redund->rbuf_j = rbuf_j; 3077 redund->rbuf_a = rbuf_a; 3078 redund->psubcomm = NULL; 3079 3080 redund->Destroy = C->ops->destroy; 3081 C->ops->destroy = MatDestroy_MatRedundant; 3082 } 3083 PetscFunctionReturn(0); 3084 } 3085 3086 #undef __FUNCT__ 3087 #define __FUNCT__ "MatGetRedundantMatrix_MPIAIJ" 3088 PetscErrorCode MatGetRedundantMatrix_MPIAIJ(Mat mat,PetscInt nsubcomm,MPI_Comm subcomm,MatReuse reuse,Mat *matredundant) 3089 { 3090 PetscErrorCode ierr; 3091 3092 PetscFunctionBegin; 3093 if (subcomm == MPI_COMM_NULL || subcomm == PETSC_COMM_SELF) { /* create psubcomm */ 3094 MPI_Comm comm; 3095 PetscSubcomm psubcomm; 3096 PetscMPIInt size,subsize; 3097 3098 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3099 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3100 ierr = PetscSubcommCreate(comm,&psubcomm);CHKERRQ(ierr); 3101 ierr = PetscSubcommSetNumber(psubcomm,nsubcomm);CHKERRQ(ierr); 3102 ierr = PetscSubcommSetType(psubcomm,PETSC_SUBCOMM_INTERLACED);CHKERRQ(ierr); 3103 ierr = PetscSubcommSetFromOptions(psubcomm);CHKERRQ(ierr); 3104 3105 ierr = MatGetRedundantMatrix_MPIAIJ_psubcomm(mat,nsubcomm,psubcomm,reuse,matredundant);CHKERRQ(ierr); 3106 3107 /* free psubcomm in MatDestroy_MatRedundant() */ 3108 ierr = MPI_Comm_size(psubcomm->comm,&subsize);CHKERRQ(ierr); 3109 if (subsize == 1) { 3110 Mat_SeqAIJ *c = (Mat_SeqAIJ*)(*matredundant)->data; 3111 c->redundant->psubcomm = psubcomm; 3112 } else { 3113 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*matredundant)->data; 3114 c->redundant->psubcomm = psubcomm ; 3115 } 3116 } else { 3117 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support yet"); 3118 } 3119 PetscFunctionReturn(0); 3120 } 3121 3122 #undef __FUNCT__ 3123 #define __FUNCT__ "MatGetRowMaxAbs_MPIAIJ" 3124 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 3125 { 3126 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 3127 PetscErrorCode ierr; 3128 PetscInt i,*idxb = 0; 3129 PetscScalar *va,*vb; 3130 Vec vtmp; 3131 3132 PetscFunctionBegin; 3133 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 3134 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 3135 if (idx) { 3136 for (i=0; i<A->rmap->n; i++) { 3137 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 3138 } 3139 } 3140 3141 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 3142 if (idx) { 3143 ierr = PetscMalloc(A->rmap->n*sizeof(PetscInt),&idxb);CHKERRQ(ierr); 3144 } 3145 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 3146 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 3147 3148 for (i=0; i<A->rmap->n; i++) { 3149 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 3150 va[i] = vb[i]; 3151 if (idx) idx[i] = a->garray[idxb[i]]; 3152 } 3153 } 3154 3155 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 3156 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 3157 ierr = PetscFree(idxb);CHKERRQ(ierr); 3158 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 3159 PetscFunctionReturn(0); 3160 } 3161 3162 #undef __FUNCT__ 3163 #define __FUNCT__ "MatGetRowMinAbs_MPIAIJ" 3164 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 3165 { 3166 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 3167 PetscErrorCode ierr; 3168 PetscInt i,*idxb = 0; 3169 PetscScalar *va,*vb; 3170 Vec vtmp; 3171 3172 PetscFunctionBegin; 3173 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 3174 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 3175 if (idx) { 3176 for (i=0; i<A->cmap->n; i++) { 3177 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 3178 } 3179 } 3180 3181 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 3182 if (idx) { 3183 ierr = PetscMalloc(A->rmap->n*sizeof(PetscInt),&idxb);CHKERRQ(ierr); 3184 } 3185 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 3186 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 3187 3188 for (i=0; i<A->rmap->n; i++) { 3189 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 3190 va[i] = vb[i]; 3191 if (idx) idx[i] = a->garray[idxb[i]]; 3192 } 3193 } 3194 3195 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 3196 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 3197 ierr = PetscFree(idxb);CHKERRQ(ierr); 3198 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 3199 PetscFunctionReturn(0); 3200 } 3201 3202 #undef __FUNCT__ 3203 #define __FUNCT__ "MatGetRowMin_MPIAIJ" 3204 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 3205 { 3206 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 3207 PetscInt n = A->rmap->n; 3208 PetscInt cstart = A->cmap->rstart; 3209 PetscInt *cmap = mat->garray; 3210 PetscInt *diagIdx, *offdiagIdx; 3211 Vec diagV, offdiagV; 3212 PetscScalar *a, *diagA, *offdiagA; 3213 PetscInt r; 3214 PetscErrorCode ierr; 3215 3216 PetscFunctionBegin; 3217 ierr = PetscMalloc2(n,PetscInt,&diagIdx,n,PetscInt,&offdiagIdx);CHKERRQ(ierr); 3218 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 3219 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 3220 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 3221 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 3222 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 3223 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 3224 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 3225 for (r = 0; r < n; ++r) { 3226 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 3227 a[r] = diagA[r]; 3228 idx[r] = cstart + diagIdx[r]; 3229 } else { 3230 a[r] = offdiagA[r]; 3231 idx[r] = cmap[offdiagIdx[r]]; 3232 } 3233 } 3234 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 3235 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 3236 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 3237 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 3238 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 3239 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 3240 PetscFunctionReturn(0); 3241 } 3242 3243 #undef __FUNCT__ 3244 #define __FUNCT__ "MatGetRowMax_MPIAIJ" 3245 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 3246 { 3247 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 3248 PetscInt n = A->rmap->n; 3249 PetscInt cstart = A->cmap->rstart; 3250 PetscInt *cmap = mat->garray; 3251 PetscInt *diagIdx, *offdiagIdx; 3252 Vec diagV, offdiagV; 3253 PetscScalar *a, *diagA, *offdiagA; 3254 PetscInt r; 3255 PetscErrorCode ierr; 3256 3257 PetscFunctionBegin; 3258 ierr = PetscMalloc2(n,PetscInt,&diagIdx,n,PetscInt,&offdiagIdx);CHKERRQ(ierr); 3259 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 3260 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 3261 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 3262 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 3263 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 3264 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 3265 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 3266 for (r = 0; r < n; ++r) { 3267 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 3268 a[r] = diagA[r]; 3269 idx[r] = cstart + diagIdx[r]; 3270 } else { 3271 a[r] = offdiagA[r]; 3272 idx[r] = cmap[offdiagIdx[r]]; 3273 } 3274 } 3275 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 3276 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 3277 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 3278 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 3279 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 3280 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 3281 PetscFunctionReturn(0); 3282 } 3283 3284 #undef __FUNCT__ 3285 #define __FUNCT__ "MatGetSeqNonzeroStructure_MPIAIJ" 3286 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 3287 { 3288 PetscErrorCode ierr; 3289 Mat *dummy; 3290 3291 PetscFunctionBegin; 3292 ierr = MatGetSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 3293 *newmat = *dummy; 3294 ierr = PetscFree(dummy);CHKERRQ(ierr); 3295 PetscFunctionReturn(0); 3296 } 3297 3298 extern PetscErrorCode MatFDColoringApply_AIJ(Mat,MatFDColoring,Vec,MatStructure*,void*); 3299 3300 #undef __FUNCT__ 3301 #define __FUNCT__ "MatInvertBlockDiagonal_MPIAIJ" 3302 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 3303 { 3304 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 3305 PetscErrorCode ierr; 3306 3307 PetscFunctionBegin; 3308 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 3309 PetscFunctionReturn(0); 3310 } 3311 3312 #undef __FUNCT__ 3313 #define __FUNCT__ "MatSetRandom_MPIAIJ" 3314 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 3315 { 3316 PetscErrorCode ierr; 3317 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 3318 3319 PetscFunctionBegin; 3320 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 3321 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 3322 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3323 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3324 PetscFunctionReturn(0); 3325 } 3326 3327 /* -------------------------------------------------------------------*/ 3328 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 3329 MatGetRow_MPIAIJ, 3330 MatRestoreRow_MPIAIJ, 3331 MatMult_MPIAIJ, 3332 /* 4*/ MatMultAdd_MPIAIJ, 3333 MatMultTranspose_MPIAIJ, 3334 MatMultTransposeAdd_MPIAIJ, 3335 #if defined(PETSC_HAVE_PBGL) 3336 MatSolve_MPIAIJ, 3337 #else 3338 0, 3339 #endif 3340 0, 3341 0, 3342 /*10*/ 0, 3343 0, 3344 0, 3345 MatSOR_MPIAIJ, 3346 MatTranspose_MPIAIJ, 3347 /*15*/ MatGetInfo_MPIAIJ, 3348 MatEqual_MPIAIJ, 3349 MatGetDiagonal_MPIAIJ, 3350 MatDiagonalScale_MPIAIJ, 3351 MatNorm_MPIAIJ, 3352 /*20*/ MatAssemblyBegin_MPIAIJ, 3353 MatAssemblyEnd_MPIAIJ, 3354 MatSetOption_MPIAIJ, 3355 MatZeroEntries_MPIAIJ, 3356 /*24*/ MatZeroRows_MPIAIJ, 3357 0, 3358 #if defined(PETSC_HAVE_PBGL) 3359 0, 3360 #else 3361 0, 3362 #endif 3363 0, 3364 0, 3365 /*29*/ MatSetUp_MPIAIJ, 3366 #if defined(PETSC_HAVE_PBGL) 3367 0, 3368 #else 3369 0, 3370 #endif 3371 0, 3372 0, 3373 0, 3374 /*34*/ MatDuplicate_MPIAIJ, 3375 0, 3376 0, 3377 0, 3378 0, 3379 /*39*/ MatAXPY_MPIAIJ, 3380 MatGetSubMatrices_MPIAIJ, 3381 MatIncreaseOverlap_MPIAIJ, 3382 MatGetValues_MPIAIJ, 3383 MatCopy_MPIAIJ, 3384 /*44*/ MatGetRowMax_MPIAIJ, 3385 MatScale_MPIAIJ, 3386 0, 3387 0, 3388 MatZeroRowsColumns_MPIAIJ, 3389 /*49*/ MatSetRandom_MPIAIJ, 3390 0, 3391 0, 3392 0, 3393 0, 3394 /*54*/ MatFDColoringCreate_MPIAIJ, 3395 0, 3396 MatSetUnfactored_MPIAIJ, 3397 MatPermute_MPIAIJ, 3398 0, 3399 /*59*/ MatGetSubMatrix_MPIAIJ, 3400 MatDestroy_MPIAIJ, 3401 MatView_MPIAIJ, 3402 0, 3403 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 3404 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 3405 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 3406 0, 3407 0, 3408 0, 3409 /*69*/ MatGetRowMaxAbs_MPIAIJ, 3410 MatGetRowMinAbs_MPIAIJ, 3411 0, 3412 MatSetColoring_MPIAIJ, 3413 0, 3414 MatSetValuesAdifor_MPIAIJ, 3415 /*75*/ MatFDColoringApply_AIJ, 3416 0, 3417 0, 3418 0, 3419 MatFindZeroDiagonals_MPIAIJ, 3420 /*80*/ 0, 3421 0, 3422 0, 3423 /*83*/ MatLoad_MPIAIJ, 3424 0, 3425 0, 3426 0, 3427 0, 3428 0, 3429 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 3430 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 3431 MatMatMultNumeric_MPIAIJ_MPIAIJ, 3432 MatPtAP_MPIAIJ_MPIAIJ, 3433 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 3434 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 3435 0, 3436 0, 3437 0, 3438 0, 3439 /*99*/ 0, 3440 0, 3441 0, 3442 MatConjugate_MPIAIJ, 3443 0, 3444 /*104*/MatSetValuesRow_MPIAIJ, 3445 MatRealPart_MPIAIJ, 3446 MatImaginaryPart_MPIAIJ, 3447 0, 3448 0, 3449 /*109*/0, 3450 MatGetRedundantMatrix_MPIAIJ, 3451 MatGetRowMin_MPIAIJ, 3452 0, 3453 0, 3454 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 3455 0, 3456 0, 3457 0, 3458 0, 3459 /*119*/0, 3460 0, 3461 0, 3462 0, 3463 MatGetMultiProcBlock_MPIAIJ, 3464 /*124*/MatFindNonzeroRows_MPIAIJ, 3465 MatGetColumnNorms_MPIAIJ, 3466 MatInvertBlockDiagonal_MPIAIJ, 3467 0, 3468 MatGetSubMatricesParallel_MPIAIJ, 3469 /*129*/0, 3470 MatTransposeMatMult_MPIAIJ_MPIAIJ, 3471 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 3472 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 3473 0, 3474 /*134*/0, 3475 0, 3476 0, 3477 0, 3478 0, 3479 /*139*/0, 3480 0 3481 }; 3482 3483 /* ----------------------------------------------------------------------------------------*/ 3484 3485 #undef __FUNCT__ 3486 #define __FUNCT__ "MatStoreValues_MPIAIJ" 3487 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 3488 { 3489 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 3490 PetscErrorCode ierr; 3491 3492 PetscFunctionBegin; 3493 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 3494 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 3495 PetscFunctionReturn(0); 3496 } 3497 3498 #undef __FUNCT__ 3499 #define __FUNCT__ "MatRetrieveValues_MPIAIJ" 3500 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 3501 { 3502 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 3503 PetscErrorCode ierr; 3504 3505 PetscFunctionBegin; 3506 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 3507 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 3508 PetscFunctionReturn(0); 3509 } 3510 3511 #undef __FUNCT__ 3512 #define __FUNCT__ "MatMPIAIJSetPreallocation_MPIAIJ" 3513 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3514 { 3515 Mat_MPIAIJ *b; 3516 PetscErrorCode ierr; 3517 3518 PetscFunctionBegin; 3519 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3520 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3521 b = (Mat_MPIAIJ*)B->data; 3522 3523 if (!B->preallocated) { 3524 /* Explicitly create 2 MATSEQAIJ matrices. */ 3525 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 3526 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 3527 ierr = MatSetBlockSizes(b->A,B->rmap->bs,B->cmap->bs);CHKERRQ(ierr); 3528 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 3529 ierr = PetscLogObjectParent(B,b->A);CHKERRQ(ierr); 3530 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 3531 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 3532 ierr = MatSetBlockSizes(b->B,B->rmap->bs,B->cmap->bs);CHKERRQ(ierr); 3533 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 3534 ierr = PetscLogObjectParent(B,b->B);CHKERRQ(ierr); 3535 } 3536 3537 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 3538 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 3539 B->preallocated = PETSC_TRUE; 3540 PetscFunctionReturn(0); 3541 } 3542 3543 #undef __FUNCT__ 3544 #define __FUNCT__ "MatDuplicate_MPIAIJ" 3545 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 3546 { 3547 Mat mat; 3548 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 3549 PetscErrorCode ierr; 3550 3551 PetscFunctionBegin; 3552 *newmat = 0; 3553 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 3554 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 3555 ierr = MatSetBlockSizes(mat,matin->rmap->bs,matin->cmap->bs);CHKERRQ(ierr); 3556 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 3557 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 3558 a = (Mat_MPIAIJ*)mat->data; 3559 3560 mat->factortype = matin->factortype; 3561 mat->rmap->bs = matin->rmap->bs; 3562 mat->cmap->bs = matin->cmap->bs; 3563 mat->assembled = PETSC_TRUE; 3564 mat->insertmode = NOT_SET_VALUES; 3565 mat->preallocated = PETSC_TRUE; 3566 3567 a->size = oldmat->size; 3568 a->rank = oldmat->rank; 3569 a->donotstash = oldmat->donotstash; 3570 a->roworiented = oldmat->roworiented; 3571 a->rowindices = 0; 3572 a->rowvalues = 0; 3573 a->getrowactive = PETSC_FALSE; 3574 3575 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 3576 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 3577 3578 if (oldmat->colmap) { 3579 #if defined(PETSC_USE_CTABLE) 3580 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 3581 #else 3582 ierr = PetscMalloc((mat->cmap->N)*sizeof(PetscInt),&a->colmap);CHKERRQ(ierr); 3583 ierr = PetscLogObjectMemory(mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 3584 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 3585 #endif 3586 } else a->colmap = 0; 3587 if (oldmat->garray) { 3588 PetscInt len; 3589 len = oldmat->B->cmap->n; 3590 ierr = PetscMalloc((len+1)*sizeof(PetscInt),&a->garray);CHKERRQ(ierr); 3591 ierr = PetscLogObjectMemory(mat,len*sizeof(PetscInt));CHKERRQ(ierr); 3592 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 3593 } else a->garray = 0; 3594 3595 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 3596 ierr = PetscLogObjectParent(mat,a->lvec);CHKERRQ(ierr); 3597 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 3598 ierr = PetscLogObjectParent(mat,a->Mvctx);CHKERRQ(ierr); 3599 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 3600 ierr = PetscLogObjectParent(mat,a->A);CHKERRQ(ierr); 3601 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 3602 ierr = PetscLogObjectParent(mat,a->B);CHKERRQ(ierr); 3603 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 3604 *newmat = mat; 3605 PetscFunctionReturn(0); 3606 } 3607 3608 3609 3610 #undef __FUNCT__ 3611 #define __FUNCT__ "MatLoad_MPIAIJ" 3612 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 3613 { 3614 PetscScalar *vals,*svals; 3615 MPI_Comm comm; 3616 PetscErrorCode ierr; 3617 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 3618 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0,grows,gcols; 3619 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 3620 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 3621 PetscInt cend,cstart,n,*rowners,sizesset=1; 3622 int fd; 3623 PetscInt bs = 1; 3624 3625 PetscFunctionBegin; 3626 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 3627 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3628 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3629 if (!rank) { 3630 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 3631 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 3632 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 3633 } 3634 3635 ierr = PetscOptionsBegin(comm,NULL,"Options for loading SEQAIJ matrix","Mat");CHKERRQ(ierr); 3636 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 3637 ierr = PetscOptionsEnd();CHKERRQ(ierr); 3638 3639 if (newMat->rmap->n < 0 && newMat->rmap->N < 0 && newMat->cmap->n < 0 && newMat->cmap->N < 0) sizesset = 0; 3640 3641 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 3642 M = header[1]; N = header[2]; 3643 /* If global rows/cols are set to PETSC_DECIDE, set it to the sizes given in the file */ 3644 if (sizesset && newMat->rmap->N < 0) newMat->rmap->N = M; 3645 if (sizesset && newMat->cmap->N < 0) newMat->cmap->N = N; 3646 3647 /* If global sizes are set, check if they are consistent with that given in the file */ 3648 if (sizesset) { 3649 ierr = MatGetSize(newMat,&grows,&gcols);CHKERRQ(ierr); 3650 } 3651 if (sizesset && newMat->rmap->N != grows) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows:Matrix in file has (%d) and input matrix has (%d)",M,grows); 3652 if (sizesset && newMat->cmap->N != gcols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of cols:Matrix in file has (%d) and input matrix has (%d)",N,gcols); 3653 3654 /* determine ownership of all (block) rows */ 3655 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 3656 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 3657 else m = newMat->rmap->n; /* Set by user */ 3658 3659 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&rowners);CHKERRQ(ierr); 3660 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 3661 3662 /* First process needs enough room for process with most rows */ 3663 if (!rank) { 3664 mmax = rowners[1]; 3665 for (i=2; i<=size; i++) { 3666 mmax = PetscMax(mmax, rowners[i]); 3667 } 3668 } else mmax = -1; /* unused, but compilers complain */ 3669 3670 rowners[0] = 0; 3671 for (i=2; i<=size; i++) { 3672 rowners[i] += rowners[i-1]; 3673 } 3674 rstart = rowners[rank]; 3675 rend = rowners[rank+1]; 3676 3677 /* distribute row lengths to all processors */ 3678 ierr = PetscMalloc2(m,PetscInt,&ourlens,m,PetscInt,&offlens);CHKERRQ(ierr); 3679 if (!rank) { 3680 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 3681 ierr = PetscMalloc(mmax*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 3682 ierr = PetscMalloc(size*sizeof(PetscInt),&procsnz);CHKERRQ(ierr); 3683 ierr = PetscMemzero(procsnz,size*sizeof(PetscInt));CHKERRQ(ierr); 3684 for (j=0; j<m; j++) { 3685 procsnz[0] += ourlens[j]; 3686 } 3687 for (i=1; i<size; i++) { 3688 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 3689 /* calculate the number of nonzeros on each processor */ 3690 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 3691 procsnz[i] += rowlengths[j]; 3692 } 3693 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3694 } 3695 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 3696 } else { 3697 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 3698 } 3699 3700 if (!rank) { 3701 /* determine max buffer needed and allocate it */ 3702 maxnz = 0; 3703 for (i=0; i<size; i++) { 3704 maxnz = PetscMax(maxnz,procsnz[i]); 3705 } 3706 ierr = PetscMalloc(maxnz*sizeof(PetscInt),&cols);CHKERRQ(ierr); 3707 3708 /* read in my part of the matrix column indices */ 3709 nz = procsnz[0]; 3710 ierr = PetscMalloc(nz*sizeof(PetscInt),&mycols);CHKERRQ(ierr); 3711 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 3712 3713 /* read in every one elses and ship off */ 3714 for (i=1; i<size; i++) { 3715 nz = procsnz[i]; 3716 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 3717 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3718 } 3719 ierr = PetscFree(cols);CHKERRQ(ierr); 3720 } else { 3721 /* determine buffer space needed for message */ 3722 nz = 0; 3723 for (i=0; i<m; i++) { 3724 nz += ourlens[i]; 3725 } 3726 ierr = PetscMalloc(nz*sizeof(PetscInt),&mycols);CHKERRQ(ierr); 3727 3728 /* receive message of column indices*/ 3729 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 3730 } 3731 3732 /* determine column ownership if matrix is not square */ 3733 if (N != M) { 3734 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 3735 else n = newMat->cmap->n; 3736 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3737 cstart = cend - n; 3738 } else { 3739 cstart = rstart; 3740 cend = rend; 3741 n = cend - cstart; 3742 } 3743 3744 /* loop over local rows, determining number of off diagonal entries */ 3745 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 3746 jj = 0; 3747 for (i=0; i<m; i++) { 3748 for (j=0; j<ourlens[i]; j++) { 3749 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 3750 jj++; 3751 } 3752 } 3753 3754 for (i=0; i<m; i++) { 3755 ourlens[i] -= offlens[i]; 3756 } 3757 if (!sizesset) { 3758 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 3759 } 3760 3761 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 3762 3763 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 3764 3765 for (i=0; i<m; i++) { 3766 ourlens[i] += offlens[i]; 3767 } 3768 3769 if (!rank) { 3770 ierr = PetscMalloc((maxnz+1)*sizeof(PetscScalar),&vals);CHKERRQ(ierr); 3771 3772 /* read in my part of the matrix numerical values */ 3773 nz = procsnz[0]; 3774 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3775 3776 /* insert into matrix */ 3777 jj = rstart; 3778 smycols = mycols; 3779 svals = vals; 3780 for (i=0; i<m; i++) { 3781 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 3782 smycols += ourlens[i]; 3783 svals += ourlens[i]; 3784 jj++; 3785 } 3786 3787 /* read in other processors and ship out */ 3788 for (i=1; i<size; i++) { 3789 nz = procsnz[i]; 3790 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3791 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 3792 } 3793 ierr = PetscFree(procsnz);CHKERRQ(ierr); 3794 } else { 3795 /* receive numeric values */ 3796 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&vals);CHKERRQ(ierr); 3797 3798 /* receive message of values*/ 3799 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 3800 3801 /* insert into matrix */ 3802 jj = rstart; 3803 smycols = mycols; 3804 svals = vals; 3805 for (i=0; i<m; i++) { 3806 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 3807 smycols += ourlens[i]; 3808 svals += ourlens[i]; 3809 jj++; 3810 } 3811 } 3812 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 3813 ierr = PetscFree(vals);CHKERRQ(ierr); 3814 ierr = PetscFree(mycols);CHKERRQ(ierr); 3815 ierr = PetscFree(rowners);CHKERRQ(ierr); 3816 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3817 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3818 PetscFunctionReturn(0); 3819 } 3820 3821 #undef __FUNCT__ 3822 #define __FUNCT__ "MatGetSubMatrix_MPIAIJ" 3823 PetscErrorCode MatGetSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3824 { 3825 PetscErrorCode ierr; 3826 IS iscol_local; 3827 PetscInt csize; 3828 3829 PetscFunctionBegin; 3830 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3831 if (call == MAT_REUSE_MATRIX) { 3832 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3833 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3834 } else { 3835 PetscInt cbs; 3836 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3837 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 3838 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 3839 } 3840 ierr = MatGetSubMatrix_MPIAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3841 if (call == MAT_INITIAL_MATRIX) { 3842 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3843 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3844 } 3845 PetscFunctionReturn(0); 3846 } 3847 3848 extern PetscErrorCode MatGetSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool*,Mat*); 3849 #undef __FUNCT__ 3850 #define __FUNCT__ "MatGetSubMatrix_MPIAIJ_Private" 3851 /* 3852 Not great since it makes two copies of the submatrix, first an SeqAIJ 3853 in local and then by concatenating the local matrices the end result. 3854 Writing it directly would be much like MatGetSubMatrices_MPIAIJ() 3855 3856 Note: This requires a sequential iscol with all indices. 3857 */ 3858 PetscErrorCode MatGetSubMatrix_MPIAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3859 { 3860 PetscErrorCode ierr; 3861 PetscMPIInt rank,size; 3862 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3863 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal,ncol; 3864 PetscBool allcolumns, colflag; 3865 Mat M,Mreuse; 3866 MatScalar *vwork,*aa; 3867 MPI_Comm comm; 3868 Mat_SeqAIJ *aij; 3869 3870 PetscFunctionBegin; 3871 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3872 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3873 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3874 3875 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3876 ierr = ISGetLocalSize(iscol,&ncol);CHKERRQ(ierr); 3877 if (colflag && ncol == mat->cmap->N) { 3878 allcolumns = PETSC_TRUE; 3879 } else { 3880 allcolumns = PETSC_FALSE; 3881 } 3882 if (call == MAT_REUSE_MATRIX) { 3883 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3884 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3885 ierr = MatGetSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,&allcolumns,&Mreuse);CHKERRQ(ierr); 3886 } else { 3887 ierr = MatGetSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&allcolumns,&Mreuse);CHKERRQ(ierr); 3888 } 3889 3890 /* 3891 m - number of local rows 3892 n - number of columns (same on all processors) 3893 rstart - first row in new global matrix generated 3894 */ 3895 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3896 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3897 if (call == MAT_INITIAL_MATRIX) { 3898 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3899 ii = aij->i; 3900 jj = aij->j; 3901 3902 /* 3903 Determine the number of non-zeros in the diagonal and off-diagonal 3904 portions of the matrix in order to do correct preallocation 3905 */ 3906 3907 /* first get start and end of "diagonal" columns */ 3908 if (csize == PETSC_DECIDE) { 3909 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3910 if (mglobal == n) { /* square matrix */ 3911 nlocal = m; 3912 } else { 3913 nlocal = n/size + ((n % size) > rank); 3914 } 3915 } else { 3916 nlocal = csize; 3917 } 3918 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3919 rstart = rend - nlocal; 3920 if (rank == size - 1 && rend != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,n); 3921 3922 /* next, compute all the lengths */ 3923 ierr = PetscMalloc((2*m+1)*sizeof(PetscInt),&dlens);CHKERRQ(ierr); 3924 olens = dlens + m; 3925 for (i=0; i<m; i++) { 3926 jend = ii[i+1] - ii[i]; 3927 olen = 0; 3928 dlen = 0; 3929 for (j=0; j<jend; j++) { 3930 if (*jj < rstart || *jj >= rend) olen++; 3931 else dlen++; 3932 jj++; 3933 } 3934 olens[i] = olen; 3935 dlens[i] = dlen; 3936 } 3937 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3938 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3939 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3940 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3941 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3942 ierr = PetscFree(dlens);CHKERRQ(ierr); 3943 } else { 3944 PetscInt ml,nl; 3945 3946 M = *newmat; 3947 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3948 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3949 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3950 /* 3951 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3952 rather than the slower MatSetValues(). 3953 */ 3954 M->was_assembled = PETSC_TRUE; 3955 M->assembled = PETSC_FALSE; 3956 } 3957 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3958 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3959 ii = aij->i; 3960 jj = aij->j; 3961 aa = aij->a; 3962 for (i=0; i<m; i++) { 3963 row = rstart + i; 3964 nz = ii[i+1] - ii[i]; 3965 cwork = jj; jj += nz; 3966 vwork = aa; aa += nz; 3967 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3968 } 3969 3970 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3971 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3972 *newmat = M; 3973 3974 /* save submatrix used in processor for next request */ 3975 if (call == MAT_INITIAL_MATRIX) { 3976 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3977 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3978 } 3979 PetscFunctionReturn(0); 3980 } 3981 3982 #undef __FUNCT__ 3983 #define __FUNCT__ "MatMPIAIJSetPreallocationCSR_MPIAIJ" 3984 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3985 { 3986 PetscInt m,cstart, cend,j,nnz,i,d; 3987 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3988 const PetscInt *JJ; 3989 PetscScalar *values; 3990 PetscErrorCode ierr; 3991 3992 PetscFunctionBegin; 3993 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3994 3995 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3996 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3997 m = B->rmap->n; 3998 cstart = B->cmap->rstart; 3999 cend = B->cmap->rend; 4000 rstart = B->rmap->rstart; 4001 4002 ierr = PetscMalloc2(m,PetscInt,&d_nnz,m,PetscInt,&o_nnz);CHKERRQ(ierr); 4003 4004 #if defined(PETSC_USE_DEBUGGING) 4005 for (i=0; i<m; i++) { 4006 nnz = Ii[i+1]- Ii[i]; 4007 JJ = J + Ii[i]; 4008 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 4009 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 4010 if (nnz && (JJ[nnz-1] >= B->cmap->N) SETERRRQ3(PETSC_ERR_ARG_WRONGSTATE,"Row %D ends with too large a column index %D (max allowed %D)",i,JJ[nnz-1],B->cmap->N); 4011 } 4012 #endif 4013 4014 for (i=0; i<m; i++) { 4015 nnz = Ii[i+1]- Ii[i]; 4016 JJ = J + Ii[i]; 4017 nnz_max = PetscMax(nnz_max,nnz); 4018 d = 0; 4019 for (j=0; j<nnz; j++) { 4020 if (cstart <= JJ[j] && JJ[j] < cend) d++; 4021 } 4022 d_nnz[i] = d; 4023 o_nnz[i] = nnz - d; 4024 } 4025 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 4026 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 4027 4028 if (v) values = (PetscScalar*)v; 4029 else { 4030 ierr = PetscMalloc((nnz_max+1)*sizeof(PetscScalar),&values);CHKERRQ(ierr); 4031 ierr = PetscMemzero(values,nnz_max*sizeof(PetscScalar));CHKERRQ(ierr); 4032 } 4033 4034 for (i=0; i<m; i++) { 4035 ii = i + rstart; 4036 nnz = Ii[i+1]- Ii[i]; 4037 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 4038 } 4039 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4040 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4041 4042 if (!v) { 4043 ierr = PetscFree(values);CHKERRQ(ierr); 4044 } 4045 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 4046 PetscFunctionReturn(0); 4047 } 4048 4049 #undef __FUNCT__ 4050 #define __FUNCT__ "MatMPIAIJSetPreallocationCSR" 4051 /*@ 4052 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 4053 (the default parallel PETSc format). 4054 4055 Collective on MPI_Comm 4056 4057 Input Parameters: 4058 + B - the matrix 4059 . i - the indices into j for the start of each local row (starts with zero) 4060 . j - the column indices for each local row (starts with zero) 4061 - v - optional values in the matrix 4062 4063 Level: developer 4064 4065 Notes: 4066 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4067 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4068 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4069 4070 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4071 4072 The format which is used for the sparse matrix input, is equivalent to a 4073 row-major ordering.. i.e for the following matrix, the input data expected is 4074 as shown: 4075 4076 1 0 0 4077 2 0 3 P0 4078 ------- 4079 4 5 6 P1 4080 4081 Process0 [P0]: rows_owned=[0,1] 4082 i = {0,1,3} [size = nrow+1 = 2+1] 4083 j = {0,0,2} [size = nz = 6] 4084 v = {1,2,3} [size = nz = 6] 4085 4086 Process1 [P1]: rows_owned=[2] 4087 i = {0,3} [size = nrow+1 = 1+1] 4088 j = {0,1,2} [size = nz = 6] 4089 v = {4,5,6} [size = nz = 6] 4090 4091 .keywords: matrix, aij, compressed row, sparse, parallel 4092 4093 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MPIAIJ, 4094 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 4095 @*/ 4096 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 4097 { 4098 PetscErrorCode ierr; 4099 4100 PetscFunctionBegin; 4101 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 4102 PetscFunctionReturn(0); 4103 } 4104 4105 #undef __FUNCT__ 4106 #define __FUNCT__ "MatMPIAIJSetPreallocation" 4107 /*@C 4108 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 4109 (the default parallel PETSc format). For good matrix assembly performance 4110 the user should preallocate the matrix storage by setting the parameters 4111 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4112 performance can be increased by more than a factor of 50. 4113 4114 Collective on MPI_Comm 4115 4116 Input Parameters: 4117 + A - the matrix 4118 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4119 (same value is used for all local rows) 4120 . d_nnz - array containing the number of nonzeros in the various rows of the 4121 DIAGONAL portion of the local submatrix (possibly different for each row) 4122 or NULL, if d_nz is used to specify the nonzero structure. 4123 The size of this array is equal to the number of local rows, i.e 'm'. 4124 For matrices that will be factored, you must leave room for (and set) 4125 the diagonal entry even if it is zero. 4126 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4127 submatrix (same value is used for all local rows). 4128 - o_nnz - array containing the number of nonzeros in the various rows of the 4129 OFF-DIAGONAL portion of the local submatrix (possibly different for 4130 each row) or NULL, if o_nz is used to specify the nonzero 4131 structure. The size of this array is equal to the number 4132 of local rows, i.e 'm'. 4133 4134 If the *_nnz parameter is given then the *_nz parameter is ignored 4135 4136 The AIJ format (also called the Yale sparse matrix format or 4137 compressed row storage (CSR)), is fully compatible with standard Fortran 77 4138 storage. The stored row and column indices begin with zero. 4139 See the <A href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</A> for details. 4140 4141 The parallel matrix is partitioned such that the first m0 rows belong to 4142 process 0, the next m1 rows belong to process 1, the next m2 rows belong 4143 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 4144 4145 The DIAGONAL portion of the local submatrix of a processor can be defined 4146 as the submatrix which is obtained by extraction the part corresponding to 4147 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 4148 first row that belongs to the processor, r2 is the last row belonging to 4149 the this processor, and c1-c2 is range of indices of the local part of a 4150 vector suitable for applying the matrix to. This is an mxn matrix. In the 4151 common case of a square matrix, the row and column ranges are the same and 4152 the DIAGONAL part is also square. The remaining portion of the local 4153 submatrix (mxN) constitute the OFF-DIAGONAL portion. 4154 4155 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4156 4157 You can call MatGetInfo() to get information on how effective the preallocation was; 4158 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 4159 You can also run with the option -info and look for messages with the string 4160 malloc in them to see if additional memory allocation was needed. 4161 4162 Example usage: 4163 4164 Consider the following 8x8 matrix with 34 non-zero values, that is 4165 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4166 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4167 as follows: 4168 4169 .vb 4170 1 2 0 | 0 3 0 | 0 4 4171 Proc0 0 5 6 | 7 0 0 | 8 0 4172 9 0 10 | 11 0 0 | 12 0 4173 ------------------------------------- 4174 13 0 14 | 15 16 17 | 0 0 4175 Proc1 0 18 0 | 19 20 21 | 0 0 4176 0 0 0 | 22 23 0 | 24 0 4177 ------------------------------------- 4178 Proc2 25 26 27 | 0 0 28 | 29 0 4179 30 0 0 | 31 32 33 | 0 34 4180 .ve 4181 4182 This can be represented as a collection of submatrices as: 4183 4184 .vb 4185 A B C 4186 D E F 4187 G H I 4188 .ve 4189 4190 Where the submatrices A,B,C are owned by proc0, D,E,F are 4191 owned by proc1, G,H,I are owned by proc2. 4192 4193 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4194 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4195 The 'M','N' parameters are 8,8, and have the same values on all procs. 4196 4197 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4198 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4199 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4200 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4201 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4202 matrix, ans [DF] as another SeqAIJ matrix. 4203 4204 When d_nz, o_nz parameters are specified, d_nz storage elements are 4205 allocated for every row of the local diagonal submatrix, and o_nz 4206 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4207 One way to choose d_nz and o_nz is to use the max nonzerors per local 4208 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4209 In this case, the values of d_nz,o_nz are: 4210 .vb 4211 proc0 : dnz = 2, o_nz = 2 4212 proc1 : dnz = 3, o_nz = 2 4213 proc2 : dnz = 1, o_nz = 4 4214 .ve 4215 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4216 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4217 for proc3. i.e we are using 12+15+10=37 storage locations to store 4218 34 values. 4219 4220 When d_nnz, o_nnz parameters are specified, the storage is specified 4221 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4222 In the above case the values for d_nnz,o_nnz are: 4223 .vb 4224 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4225 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4226 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4227 .ve 4228 Here the space allocated is sum of all the above values i.e 34, and 4229 hence pre-allocation is perfect. 4230 4231 Level: intermediate 4232 4233 .keywords: matrix, aij, compressed row, sparse, parallel 4234 4235 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 4236 MPIAIJ, MatGetInfo(), PetscSplitOwnership() 4237 @*/ 4238 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 4239 { 4240 PetscErrorCode ierr; 4241 4242 PetscFunctionBegin; 4243 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 4244 PetscValidType(B,1); 4245 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 4246 PetscFunctionReturn(0); 4247 } 4248 4249 #undef __FUNCT__ 4250 #define __FUNCT__ "MatCreateMPIAIJWithArrays" 4251 /*@ 4252 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 4253 CSR format the local rows. 4254 4255 Collective on MPI_Comm 4256 4257 Input Parameters: 4258 + comm - MPI communicator 4259 . m - number of local rows (Cannot be PETSC_DECIDE) 4260 . n - This value should be the same as the local size used in creating the 4261 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4262 calculated if N is given) For square matrices n is almost always m. 4263 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4264 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4265 . i - row indices 4266 . j - column indices 4267 - a - matrix values 4268 4269 Output Parameter: 4270 . mat - the matrix 4271 4272 Level: intermediate 4273 4274 Notes: 4275 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4276 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4277 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4278 4279 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4280 4281 The format which is used for the sparse matrix input, is equivalent to a 4282 row-major ordering.. i.e for the following matrix, the input data expected is 4283 as shown: 4284 4285 1 0 0 4286 2 0 3 P0 4287 ------- 4288 4 5 6 P1 4289 4290 Process0 [P0]: rows_owned=[0,1] 4291 i = {0,1,3} [size = nrow+1 = 2+1] 4292 j = {0,0,2} [size = nz = 6] 4293 v = {1,2,3} [size = nz = 6] 4294 4295 Process1 [P1]: rows_owned=[2] 4296 i = {0,3} [size = nrow+1 = 1+1] 4297 j = {0,1,2} [size = nz = 6] 4298 v = {4,5,6} [size = nz = 6] 4299 4300 .keywords: matrix, aij, compressed row, sparse, parallel 4301 4302 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4303 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4304 @*/ 4305 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4306 { 4307 PetscErrorCode ierr; 4308 4309 PetscFunctionBegin; 4310 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4311 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4312 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4313 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4314 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4315 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4316 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4317 PetscFunctionReturn(0); 4318 } 4319 4320 #undef __FUNCT__ 4321 #define __FUNCT__ "MatCreateAIJ" 4322 /*@C 4323 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4324 (the default parallel PETSc format). For good matrix assembly performance 4325 the user should preallocate the matrix storage by setting the parameters 4326 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4327 performance can be increased by more than a factor of 50. 4328 4329 Collective on MPI_Comm 4330 4331 Input Parameters: 4332 + comm - MPI communicator 4333 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4334 This value should be the same as the local size used in creating the 4335 y vector for the matrix-vector product y = Ax. 4336 . n - This value should be the same as the local size used in creating the 4337 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4338 calculated if N is given) For square matrices n is almost always m. 4339 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4340 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4341 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4342 (same value is used for all local rows) 4343 . d_nnz - array containing the number of nonzeros in the various rows of the 4344 DIAGONAL portion of the local submatrix (possibly different for each row) 4345 or NULL, if d_nz is used to specify the nonzero structure. 4346 The size of this array is equal to the number of local rows, i.e 'm'. 4347 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4348 submatrix (same value is used for all local rows). 4349 - o_nnz - array containing the number of nonzeros in the various rows of the 4350 OFF-DIAGONAL portion of the local submatrix (possibly different for 4351 each row) or NULL, if o_nz is used to specify the nonzero 4352 structure. The size of this array is equal to the number 4353 of local rows, i.e 'm'. 4354 4355 Output Parameter: 4356 . A - the matrix 4357 4358 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4359 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4360 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4361 4362 Notes: 4363 If the *_nnz parameter is given then the *_nz parameter is ignored 4364 4365 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4366 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4367 storage requirements for this matrix. 4368 4369 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4370 processor than it must be used on all processors that share the object for 4371 that argument. 4372 4373 The user MUST specify either the local or global matrix dimensions 4374 (possibly both). 4375 4376 The parallel matrix is partitioned across processors such that the 4377 first m0 rows belong to process 0, the next m1 rows belong to 4378 process 1, the next m2 rows belong to process 2 etc.. where 4379 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4380 values corresponding to [m x N] submatrix. 4381 4382 The columns are logically partitioned with the n0 columns belonging 4383 to 0th partition, the next n1 columns belonging to the next 4384 partition etc.. where n0,n1,n2... are the the input parameter 'n'. 4385 4386 The DIAGONAL portion of the local submatrix on any given processor 4387 is the submatrix corresponding to the rows and columns m,n 4388 corresponding to the given processor. i.e diagonal matrix on 4389 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4390 etc. The remaining portion of the local submatrix [m x (N-n)] 4391 constitute the OFF-DIAGONAL portion. The example below better 4392 illustrates this concept. 4393 4394 For a square global matrix we define each processor's diagonal portion 4395 to be its local rows and the corresponding columns (a square submatrix); 4396 each processor's off-diagonal portion encompasses the remainder of the 4397 local matrix (a rectangular submatrix). 4398 4399 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4400 4401 When calling this routine with a single process communicator, a matrix of 4402 type SEQAIJ is returned. If a matrix of type MPIAIJ is desired for this 4403 type of communicator, use the construction mechanism: 4404 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4405 4406 By default, this format uses inodes (identical nodes) when possible. 4407 We search for consecutive rows with the same nonzero structure, thereby 4408 reusing matrix information to achieve increased efficiency. 4409 4410 Options Database Keys: 4411 + -mat_no_inode - Do not use inodes 4412 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4413 - -mat_aij_oneindex - Internally use indexing starting at 1 4414 rather than 0. Note that when calling MatSetValues(), 4415 the user still MUST index entries starting at 0! 4416 4417 4418 Example usage: 4419 4420 Consider the following 8x8 matrix with 34 non-zero values, that is 4421 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4422 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4423 as follows: 4424 4425 .vb 4426 1 2 0 | 0 3 0 | 0 4 4427 Proc0 0 5 6 | 7 0 0 | 8 0 4428 9 0 10 | 11 0 0 | 12 0 4429 ------------------------------------- 4430 13 0 14 | 15 16 17 | 0 0 4431 Proc1 0 18 0 | 19 20 21 | 0 0 4432 0 0 0 | 22 23 0 | 24 0 4433 ------------------------------------- 4434 Proc2 25 26 27 | 0 0 28 | 29 0 4435 30 0 0 | 31 32 33 | 0 34 4436 .ve 4437 4438 This can be represented as a collection of submatrices as: 4439 4440 .vb 4441 A B C 4442 D E F 4443 G H I 4444 .ve 4445 4446 Where the submatrices A,B,C are owned by proc0, D,E,F are 4447 owned by proc1, G,H,I are owned by proc2. 4448 4449 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4450 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4451 The 'M','N' parameters are 8,8, and have the same values on all procs. 4452 4453 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4454 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4455 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4456 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4457 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4458 matrix, ans [DF] as another SeqAIJ matrix. 4459 4460 When d_nz, o_nz parameters are specified, d_nz storage elements are 4461 allocated for every row of the local diagonal submatrix, and o_nz 4462 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4463 One way to choose d_nz and o_nz is to use the max nonzerors per local 4464 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4465 In this case, the values of d_nz,o_nz are: 4466 .vb 4467 proc0 : dnz = 2, o_nz = 2 4468 proc1 : dnz = 3, o_nz = 2 4469 proc2 : dnz = 1, o_nz = 4 4470 .ve 4471 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4472 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4473 for proc3. i.e we are using 12+15+10=37 storage locations to store 4474 34 values. 4475 4476 When d_nnz, o_nnz parameters are specified, the storage is specified 4477 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4478 In the above case the values for d_nnz,o_nnz are: 4479 .vb 4480 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4481 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4482 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4483 .ve 4484 Here the space allocated is sum of all the above values i.e 34, and 4485 hence pre-allocation is perfect. 4486 4487 Level: intermediate 4488 4489 .keywords: matrix, aij, compressed row, sparse, parallel 4490 4491 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4492 MPIAIJ, MatCreateMPIAIJWithArrays() 4493 @*/ 4494 PetscErrorCode MatCreateAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat *A) 4495 { 4496 PetscErrorCode ierr; 4497 PetscMPIInt size; 4498 4499 PetscFunctionBegin; 4500 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4501 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4502 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4503 if (size > 1) { 4504 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4505 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4506 } else { 4507 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4508 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4509 } 4510 PetscFunctionReturn(0); 4511 } 4512 4513 #undef __FUNCT__ 4514 #define __FUNCT__ "MatMPIAIJGetSeqAIJ" 4515 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4516 { 4517 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4518 4519 PetscFunctionBegin; 4520 *Ad = a->A; 4521 *Ao = a->B; 4522 *colmap = a->garray; 4523 PetscFunctionReturn(0); 4524 } 4525 4526 #undef __FUNCT__ 4527 #define __FUNCT__ "MatSetColoring_MPIAIJ" 4528 PetscErrorCode MatSetColoring_MPIAIJ(Mat A,ISColoring coloring) 4529 { 4530 PetscErrorCode ierr; 4531 PetscInt i; 4532 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4533 4534 PetscFunctionBegin; 4535 if (coloring->ctype == IS_COLORING_GLOBAL) { 4536 ISColoringValue *allcolors,*colors; 4537 ISColoring ocoloring; 4538 4539 /* set coloring for diagonal portion */ 4540 ierr = MatSetColoring_SeqAIJ(a->A,coloring);CHKERRQ(ierr); 4541 4542 /* set coloring for off-diagonal portion */ 4543 ierr = ISAllGatherColors(PetscObjectComm((PetscObject)A),coloring->n,coloring->colors,NULL,&allcolors);CHKERRQ(ierr); 4544 ierr = PetscMalloc((a->B->cmap->n+1)*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); 4545 for (i=0; i<a->B->cmap->n; i++) { 4546 colors[i] = allcolors[a->garray[i]]; 4547 } 4548 ierr = PetscFree(allcolors);CHKERRQ(ierr); 4549 ierr = ISColoringCreate(MPI_COMM_SELF,coloring->n,a->B->cmap->n,colors,&ocoloring);CHKERRQ(ierr); 4550 ierr = MatSetColoring_SeqAIJ(a->B,ocoloring);CHKERRQ(ierr); 4551 ierr = ISColoringDestroy(&ocoloring);CHKERRQ(ierr); 4552 } else if (coloring->ctype == IS_COLORING_GHOSTED) { 4553 ISColoringValue *colors; 4554 PetscInt *larray; 4555 ISColoring ocoloring; 4556 4557 /* set coloring for diagonal portion */ 4558 ierr = PetscMalloc((a->A->cmap->n+1)*sizeof(PetscInt),&larray);CHKERRQ(ierr); 4559 for (i=0; i<a->A->cmap->n; i++) { 4560 larray[i] = i + A->cmap->rstart; 4561 } 4562 ierr = ISGlobalToLocalMappingApply(A->cmap->mapping,IS_GTOLM_MASK,a->A->cmap->n,larray,NULL,larray);CHKERRQ(ierr); 4563 ierr = PetscMalloc((a->A->cmap->n+1)*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); 4564 for (i=0; i<a->A->cmap->n; i++) { 4565 colors[i] = coloring->colors[larray[i]]; 4566 } 4567 ierr = PetscFree(larray);CHKERRQ(ierr); 4568 ierr = ISColoringCreate(PETSC_COMM_SELF,coloring->n,a->A->cmap->n,colors,&ocoloring);CHKERRQ(ierr); 4569 ierr = MatSetColoring_SeqAIJ(a->A,ocoloring);CHKERRQ(ierr); 4570 ierr = ISColoringDestroy(&ocoloring);CHKERRQ(ierr); 4571 4572 /* set coloring for off-diagonal portion */ 4573 ierr = PetscMalloc((a->B->cmap->n+1)*sizeof(PetscInt),&larray);CHKERRQ(ierr); 4574 ierr = ISGlobalToLocalMappingApply(A->cmap->mapping,IS_GTOLM_MASK,a->B->cmap->n,a->garray,NULL,larray);CHKERRQ(ierr); 4575 ierr = PetscMalloc((a->B->cmap->n+1)*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); 4576 for (i=0; i<a->B->cmap->n; i++) { 4577 colors[i] = coloring->colors[larray[i]]; 4578 } 4579 ierr = PetscFree(larray);CHKERRQ(ierr); 4580 ierr = ISColoringCreate(MPI_COMM_SELF,coloring->n,a->B->cmap->n,colors,&ocoloring);CHKERRQ(ierr); 4581 ierr = MatSetColoring_SeqAIJ(a->B,ocoloring);CHKERRQ(ierr); 4582 ierr = ISColoringDestroy(&ocoloring);CHKERRQ(ierr); 4583 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support ISColoringType %d",(int)coloring->ctype); 4584 PetscFunctionReturn(0); 4585 } 4586 4587 #undef __FUNCT__ 4588 #define __FUNCT__ "MatSetValuesAdifor_MPIAIJ" 4589 PetscErrorCode MatSetValuesAdifor_MPIAIJ(Mat A,PetscInt nl,void *advalues) 4590 { 4591 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4592 PetscErrorCode ierr; 4593 4594 PetscFunctionBegin; 4595 ierr = MatSetValuesAdifor_SeqAIJ(a->A,nl,advalues);CHKERRQ(ierr); 4596 ierr = MatSetValuesAdifor_SeqAIJ(a->B,nl,advalues);CHKERRQ(ierr); 4597 PetscFunctionReturn(0); 4598 } 4599 4600 #undef __FUNCT__ 4601 #define __FUNCT__ "MatCreateMPIAIJConcatenateSeqAIJSymbolic" 4602 PetscErrorCode MatCreateMPIAIJConcatenateSeqAIJSymbolic(MPI_Comm comm,Mat inmat,PetscInt n,Mat *outmat) 4603 { 4604 PetscErrorCode ierr; 4605 PetscInt m,N,i,rstart,nnz,*dnz,*onz,sum,bs,cbs; 4606 PetscInt *indx; 4607 4608 PetscFunctionBegin; 4609 /* This routine will ONLY return MPIAIJ type matrix */ 4610 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4611 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4612 if (n == PETSC_DECIDE) { 4613 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4614 } 4615 /* Check sum(n) = N */ 4616 ierr = MPI_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4617 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4618 4619 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4620 rstart -= m; 4621 4622 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4623 for (i=0; i<m; i++) { 4624 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4625 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4626 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4627 } 4628 4629 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4630 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4631 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4632 ierr = MatSetType(*outmat,MATMPIAIJ);CHKERRQ(ierr); 4633 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4634 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4635 PetscFunctionReturn(0); 4636 } 4637 4638 #undef __FUNCT__ 4639 #define __FUNCT__ "MatCreateMPIAIJConcatenateSeqAIJNumeric" 4640 PetscErrorCode MatCreateMPIAIJConcatenateSeqAIJNumeric(MPI_Comm comm,Mat inmat,PetscInt n,Mat outmat) 4641 { 4642 PetscErrorCode ierr; 4643 PetscInt m,N,i,rstart,nnz,Ii; 4644 PetscInt *indx; 4645 PetscScalar *values; 4646 4647 PetscFunctionBegin; 4648 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4649 ierr = MatGetOwnershipRange(outmat,&rstart,NULL);CHKERRQ(ierr); 4650 for (i=0; i<m; i++) { 4651 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4652 Ii = i + rstart; 4653 ierr = MatSetValues(outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4654 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4655 } 4656 ierr = MatAssemblyBegin(outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4657 ierr = MatAssemblyEnd(outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4658 PetscFunctionReturn(0); 4659 } 4660 4661 #undef __FUNCT__ 4662 #define __FUNCT__ "MatCreateMPIAIJConcatenateSeqAIJ" 4663 /*@ 4664 MatCreateMPIAIJConcatenateSeqAIJ - Creates a single large PETSc matrix by concatenating sequential 4665 matrices from each processor 4666 4667 Collective on MPI_Comm 4668 4669 Input Parameters: 4670 + comm - the communicators the parallel matrix will live on 4671 . inmat - the input sequential matrices 4672 . n - number of local columns (or PETSC_DECIDE) 4673 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4674 4675 Output Parameter: 4676 . outmat - the parallel matrix generated 4677 4678 Level: advanced 4679 4680 Notes: The number of columns of the matrix in EACH processor MUST be the same. 4681 4682 @*/ 4683 PetscErrorCode MatCreateMPIAIJConcatenateSeqAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4684 { 4685 PetscErrorCode ierr; 4686 4687 PetscFunctionBegin; 4688 ierr = PetscLogEventBegin(MAT_Merge,inmat,0,0,0);CHKERRQ(ierr); 4689 if (scall == MAT_INITIAL_MATRIX) { 4690 ierr = MatCreateMPIAIJConcatenateSeqAIJSymbolic(comm,inmat,n,outmat);CHKERRQ(ierr); 4691 } 4692 ierr = MatCreateMPIAIJConcatenateSeqAIJNumeric(comm,inmat,n,*outmat);CHKERRQ(ierr); 4693 ierr = PetscLogEventEnd(MAT_Merge,inmat,0,0,0);CHKERRQ(ierr); 4694 PetscFunctionReturn(0); 4695 } 4696 4697 #undef __FUNCT__ 4698 #define __FUNCT__ "MatFileSplit" 4699 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4700 { 4701 PetscErrorCode ierr; 4702 PetscMPIInt rank; 4703 PetscInt m,N,i,rstart,nnz; 4704 size_t len; 4705 const PetscInt *indx; 4706 PetscViewer out; 4707 char *name; 4708 Mat B; 4709 const PetscScalar *values; 4710 4711 PetscFunctionBegin; 4712 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4713 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4714 /* Should this be the type of the diagonal block of A? */ 4715 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4716 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4717 ierr = MatSetBlockSizes(B,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 4718 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4719 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4720 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4721 for (i=0; i<m; i++) { 4722 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4723 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4724 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4725 } 4726 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4727 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4728 4729 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4730 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4731 ierr = PetscMalloc((len+5)*sizeof(char),&name);CHKERRQ(ierr); 4732 sprintf(name,"%s.%d",outfile,rank); 4733 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4734 ierr = PetscFree(name);CHKERRQ(ierr); 4735 ierr = MatView(B,out);CHKERRQ(ierr); 4736 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4737 ierr = MatDestroy(&B);CHKERRQ(ierr); 4738 PetscFunctionReturn(0); 4739 } 4740 4741 extern PetscErrorCode MatDestroy_MPIAIJ(Mat); 4742 #undef __FUNCT__ 4743 #define __FUNCT__ "MatDestroy_MPIAIJ_SeqsToMPI" 4744 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4745 { 4746 PetscErrorCode ierr; 4747 Mat_Merge_SeqsToMPI *merge; 4748 PetscContainer container; 4749 4750 PetscFunctionBegin; 4751 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4752 if (container) { 4753 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4754 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4755 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4756 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4757 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4758 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4759 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4760 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4761 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4762 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4763 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4764 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4765 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4766 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4767 ierr = PetscFree(merge);CHKERRQ(ierr); 4768 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4769 } 4770 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4771 PetscFunctionReturn(0); 4772 } 4773 4774 #include <../src/mat/utils/freespace.h> 4775 #include <petscbt.h> 4776 4777 #undef __FUNCT__ 4778 #define __FUNCT__ "MatCreateMPIAIJSumSeqAIJNumeric" 4779 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4780 { 4781 PetscErrorCode ierr; 4782 MPI_Comm comm; 4783 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4784 PetscMPIInt size,rank,taga,*len_s; 4785 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4786 PetscInt proc,m; 4787 PetscInt **buf_ri,**buf_rj; 4788 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4789 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4790 MPI_Request *s_waits,*r_waits; 4791 MPI_Status *status; 4792 MatScalar *aa=a->a; 4793 MatScalar **abuf_r,*ba_i; 4794 Mat_Merge_SeqsToMPI *merge; 4795 PetscContainer container; 4796 4797 PetscFunctionBegin; 4798 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4799 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4800 4801 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4802 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4803 4804 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4805 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4806 4807 bi = merge->bi; 4808 bj = merge->bj; 4809 buf_ri = merge->buf_ri; 4810 buf_rj = merge->buf_rj; 4811 4812 ierr = PetscMalloc(size*sizeof(MPI_Status),&status);CHKERRQ(ierr); 4813 owners = merge->rowmap->range; 4814 len_s = merge->len_s; 4815 4816 /* send and recv matrix values */ 4817 /*-----------------------------*/ 4818 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4819 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4820 4821 ierr = PetscMalloc((merge->nsend+1)*sizeof(MPI_Request),&s_waits);CHKERRQ(ierr); 4822 for (proc=0,k=0; proc<size; proc++) { 4823 if (!len_s[proc]) continue; 4824 i = owners[proc]; 4825 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4826 k++; 4827 } 4828 4829 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4830 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4831 ierr = PetscFree(status);CHKERRQ(ierr); 4832 4833 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4834 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4835 4836 /* insert mat values of mpimat */ 4837 /*----------------------------*/ 4838 ierr = PetscMalloc(N*sizeof(PetscScalar),&ba_i);CHKERRQ(ierr); 4839 ierr = PetscMalloc3(merge->nrecv,PetscInt*,&buf_ri_k,merge->nrecv,PetscInt*,&nextrow,merge->nrecv,PetscInt*,&nextai);CHKERRQ(ierr); 4840 4841 for (k=0; k<merge->nrecv; k++) { 4842 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4843 nrows = *(buf_ri_k[k]); 4844 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4845 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4846 } 4847 4848 /* set values of ba */ 4849 m = merge->rowmap->n; 4850 for (i=0; i<m; i++) { 4851 arow = owners[rank] + i; 4852 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4853 bnzi = bi[i+1] - bi[i]; 4854 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4855 4856 /* add local non-zero vals of this proc's seqmat into ba */ 4857 anzi = ai[arow+1] - ai[arow]; 4858 aj = a->j + ai[arow]; 4859 aa = a->a + ai[arow]; 4860 nextaj = 0; 4861 for (j=0; nextaj<anzi; j++) { 4862 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4863 ba_i[j] += aa[nextaj++]; 4864 } 4865 } 4866 4867 /* add received vals into ba */ 4868 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4869 /* i-th row */ 4870 if (i == *nextrow[k]) { 4871 anzi = *(nextai[k]+1) - *nextai[k]; 4872 aj = buf_rj[k] + *(nextai[k]); 4873 aa = abuf_r[k] + *(nextai[k]); 4874 nextaj = 0; 4875 for (j=0; nextaj<anzi; j++) { 4876 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4877 ba_i[j] += aa[nextaj++]; 4878 } 4879 } 4880 nextrow[k]++; nextai[k]++; 4881 } 4882 } 4883 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4884 } 4885 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4886 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4887 4888 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4889 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4890 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4891 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4892 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4893 PetscFunctionReturn(0); 4894 } 4895 4896 extern PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat); 4897 4898 #undef __FUNCT__ 4899 #define __FUNCT__ "MatCreateMPIAIJSumSeqAIJSymbolic" 4900 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4901 { 4902 PetscErrorCode ierr; 4903 Mat B_mpi; 4904 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4905 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4906 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4907 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4908 PetscInt len,proc,*dnz,*onz,bs,cbs; 4909 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4910 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4911 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4912 MPI_Status *status; 4913 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4914 PetscBT lnkbt; 4915 Mat_Merge_SeqsToMPI *merge; 4916 PetscContainer container; 4917 4918 PetscFunctionBegin; 4919 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4920 4921 /* make sure it is a PETSc comm */ 4922 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4923 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4924 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4925 4926 ierr = PetscNew(Mat_Merge_SeqsToMPI,&merge);CHKERRQ(ierr); 4927 ierr = PetscMalloc(size*sizeof(MPI_Status),&status);CHKERRQ(ierr); 4928 4929 /* determine row ownership */ 4930 /*---------------------------------------------------------*/ 4931 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4932 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4933 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4934 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4935 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4936 ierr = PetscMalloc(size*sizeof(PetscMPIInt),&len_si);CHKERRQ(ierr); 4937 ierr = PetscMalloc(size*sizeof(PetscMPIInt),&merge->len_s);CHKERRQ(ierr); 4938 4939 m = merge->rowmap->n; 4940 owners = merge->rowmap->range; 4941 4942 /* determine the number of messages to send, their lengths */ 4943 /*---------------------------------------------------------*/ 4944 len_s = merge->len_s; 4945 4946 len = 0; /* length of buf_si[] */ 4947 merge->nsend = 0; 4948 for (proc=0; proc<size; proc++) { 4949 len_si[proc] = 0; 4950 if (proc == rank) { 4951 len_s[proc] = 0; 4952 } else { 4953 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4954 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4955 } 4956 if (len_s[proc]) { 4957 merge->nsend++; 4958 nrows = 0; 4959 for (i=owners[proc]; i<owners[proc+1]; i++) { 4960 if (ai[i+1] > ai[i]) nrows++; 4961 } 4962 len_si[proc] = 2*(nrows+1); 4963 len += len_si[proc]; 4964 } 4965 } 4966 4967 /* determine the number and length of messages to receive for ij-structure */ 4968 /*-------------------------------------------------------------------------*/ 4969 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4970 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4971 4972 /* post the Irecv of j-structure */ 4973 /*-------------------------------*/ 4974 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4975 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4976 4977 /* post the Isend of j-structure */ 4978 /*--------------------------------*/ 4979 ierr = PetscMalloc2(merge->nsend,MPI_Request,&si_waits,merge->nsend,MPI_Request,&sj_waits);CHKERRQ(ierr); 4980 4981 for (proc=0, k=0; proc<size; proc++) { 4982 if (!len_s[proc]) continue; 4983 i = owners[proc]; 4984 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4985 k++; 4986 } 4987 4988 /* receives and sends of j-structure are complete */ 4989 /*------------------------------------------------*/ 4990 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4991 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4992 4993 /* send and recv i-structure */ 4994 /*---------------------------*/ 4995 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4996 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4997 4998 ierr = PetscMalloc((len+1)*sizeof(PetscInt),&buf_s);CHKERRQ(ierr); 4999 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 5000 for (proc=0,k=0; proc<size; proc++) { 5001 if (!len_s[proc]) continue; 5002 /* form outgoing message for i-structure: 5003 buf_si[0]: nrows to be sent 5004 [1:nrows]: row index (global) 5005 [nrows+1:2*nrows+1]: i-structure index 5006 */ 5007 /*-------------------------------------------*/ 5008 nrows = len_si[proc]/2 - 1; 5009 buf_si_i = buf_si + nrows+1; 5010 buf_si[0] = nrows; 5011 buf_si_i[0] = 0; 5012 nrows = 0; 5013 for (i=owners[proc]; i<owners[proc+1]; i++) { 5014 anzi = ai[i+1] - ai[i]; 5015 if (anzi) { 5016 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 5017 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 5018 nrows++; 5019 } 5020 } 5021 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 5022 k++; 5023 buf_si += len_si[proc]; 5024 } 5025 5026 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 5027 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 5028 5029 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 5030 for (i=0; i<merge->nrecv; i++) { 5031 ierr = PetscInfo3(seqmat,"recv len_ri=%D, len_rj=%D from [%D]\n",len_ri[i],merge->len_r[i],merge->id_r[i]);CHKERRQ(ierr); 5032 } 5033 5034 ierr = PetscFree(len_si);CHKERRQ(ierr); 5035 ierr = PetscFree(len_ri);CHKERRQ(ierr); 5036 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 5037 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 5038 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 5039 ierr = PetscFree(buf_s);CHKERRQ(ierr); 5040 ierr = PetscFree(status);CHKERRQ(ierr); 5041 5042 /* compute a local seq matrix in each processor */ 5043 /*----------------------------------------------*/ 5044 /* allocate bi array and free space for accumulating nonzero column info */ 5045 ierr = PetscMalloc((m+1)*sizeof(PetscInt),&bi);CHKERRQ(ierr); 5046 bi[0] = 0; 5047 5048 /* create and initialize a linked list */ 5049 nlnk = N+1; 5050 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 5051 5052 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 5053 len = ai[owners[rank+1]] - ai[owners[rank]]; 5054 ierr = PetscFreeSpaceGet((PetscInt)(2*len+1),&free_space);CHKERRQ(ierr); 5055 5056 current_space = free_space; 5057 5058 /* determine symbolic info for each local row */ 5059 ierr = PetscMalloc3(merge->nrecv,PetscInt*,&buf_ri_k,merge->nrecv,PetscInt*,&nextrow,merge->nrecv,PetscInt*,&nextai);CHKERRQ(ierr); 5060 5061 for (k=0; k<merge->nrecv; k++) { 5062 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 5063 nrows = *buf_ri_k[k]; 5064 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 5065 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 5066 } 5067 5068 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 5069 len = 0; 5070 for (i=0; i<m; i++) { 5071 bnzi = 0; 5072 /* add local non-zero cols of this proc's seqmat into lnk */ 5073 arow = owners[rank] + i; 5074 anzi = ai[arow+1] - ai[arow]; 5075 aj = a->j + ai[arow]; 5076 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 5077 bnzi += nlnk; 5078 /* add received col data into lnk */ 5079 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 5080 if (i == *nextrow[k]) { /* i-th row */ 5081 anzi = *(nextai[k]+1) - *nextai[k]; 5082 aj = buf_rj[k] + *nextai[k]; 5083 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 5084 bnzi += nlnk; 5085 nextrow[k]++; nextai[k]++; 5086 } 5087 } 5088 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 5089 5090 /* if free space is not available, make more free space */ 5091 if (current_space->local_remaining<bnzi) { 5092 ierr = PetscFreeSpaceGet(bnzi+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 5093 nspacedouble++; 5094 } 5095 /* copy data into free space, then initialize lnk */ 5096 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 5097 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 5098 5099 current_space->array += bnzi; 5100 current_space->local_used += bnzi; 5101 current_space->local_remaining -= bnzi; 5102 5103 bi[i+1] = bi[i] + bnzi; 5104 } 5105 5106 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 5107 5108 ierr = PetscMalloc((bi[m]+1)*sizeof(PetscInt),&bj);CHKERRQ(ierr); 5109 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 5110 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 5111 5112 /* create symbolic parallel matrix B_mpi */ 5113 /*---------------------------------------*/ 5114 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 5115 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 5116 if (n==PETSC_DECIDE) { 5117 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 5118 } else { 5119 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5120 } 5121 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 5122 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 5123 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 5124 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 5125 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 5126 5127 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 5128 B_mpi->assembled = PETSC_FALSE; 5129 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 5130 merge->bi = bi; 5131 merge->bj = bj; 5132 merge->buf_ri = buf_ri; 5133 merge->buf_rj = buf_rj; 5134 merge->coi = NULL; 5135 merge->coj = NULL; 5136 merge->owners_co = NULL; 5137 5138 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 5139 5140 /* attach the supporting struct to B_mpi for reuse */ 5141 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 5142 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 5143 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 5144 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 5145 *mpimat = B_mpi; 5146 5147 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 5148 PetscFunctionReturn(0); 5149 } 5150 5151 #undef __FUNCT__ 5152 #define __FUNCT__ "MatCreateMPIAIJSumSeqAIJ" 5153 /*@C 5154 MatCreateMPIAIJSumSeqAIJ - Creates a MPIAIJ matrix by adding sequential 5155 matrices from each processor 5156 5157 Collective on MPI_Comm 5158 5159 Input Parameters: 5160 + comm - the communicators the parallel matrix will live on 5161 . seqmat - the input sequential matrices 5162 . m - number of local rows (or PETSC_DECIDE) 5163 . n - number of local columns (or PETSC_DECIDE) 5164 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5165 5166 Output Parameter: 5167 . mpimat - the parallel matrix generated 5168 5169 Level: advanced 5170 5171 Notes: 5172 The dimensions of the sequential matrix in each processor MUST be the same. 5173 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 5174 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 5175 @*/ 5176 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 5177 { 5178 PetscErrorCode ierr; 5179 PetscMPIInt size; 5180 5181 PetscFunctionBegin; 5182 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5183 if (size == 1) { 5184 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 5185 if (scall == MAT_INITIAL_MATRIX) { 5186 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 5187 } else { 5188 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 5189 } 5190 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 5191 PetscFunctionReturn(0); 5192 } 5193 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 5194 if (scall == MAT_INITIAL_MATRIX) { 5195 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 5196 } 5197 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 5198 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 5199 PetscFunctionReturn(0); 5200 } 5201 5202 #undef __FUNCT__ 5203 #define __FUNCT__ "MatMPIAIJGetLocalMat" 5204 /*@ 5205 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 5206 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 5207 with MatGetSize() 5208 5209 Not Collective 5210 5211 Input Parameters: 5212 + A - the matrix 5213 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5214 5215 Output Parameter: 5216 . A_loc - the local sequential matrix generated 5217 5218 Level: developer 5219 5220 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 5221 5222 @*/ 5223 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 5224 { 5225 PetscErrorCode ierr; 5226 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 5227 Mat_SeqAIJ *mat,*a=(Mat_SeqAIJ*)(mpimat->A)->data,*b=(Mat_SeqAIJ*)(mpimat->B)->data; 5228 PetscInt *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,*cmap=mpimat->garray; 5229 MatScalar *aa=a->a,*ba=b->a,*cam; 5230 PetscScalar *ca; 5231 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 5232 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 5233 PetscBool match; 5234 5235 PetscFunctionBegin; 5236 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 5237 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MPIAIJ matrix as input"); 5238 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 5239 if (scall == MAT_INITIAL_MATRIX) { 5240 ierr = PetscMalloc((1+am)*sizeof(PetscInt),&ci);CHKERRQ(ierr); 5241 ci[0] = 0; 5242 for (i=0; i<am; i++) { 5243 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 5244 } 5245 ierr = PetscMalloc((1+ci[am])*sizeof(PetscInt),&cj);CHKERRQ(ierr); 5246 ierr = PetscMalloc((1+ci[am])*sizeof(PetscScalar),&ca);CHKERRQ(ierr); 5247 k = 0; 5248 for (i=0; i<am; i++) { 5249 ncols_o = bi[i+1] - bi[i]; 5250 ncols_d = ai[i+1] - ai[i]; 5251 /* off-diagonal portion of A */ 5252 for (jo=0; jo<ncols_o; jo++) { 5253 col = cmap[*bj]; 5254 if (col >= cstart) break; 5255 cj[k] = col; bj++; 5256 ca[k++] = *ba++; 5257 } 5258 /* diagonal portion of A */ 5259 for (j=0; j<ncols_d; j++) { 5260 cj[k] = cstart + *aj++; 5261 ca[k++] = *aa++; 5262 } 5263 /* off-diagonal portion of A */ 5264 for (j=jo; j<ncols_o; j++) { 5265 cj[k] = cmap[*bj++]; 5266 ca[k++] = *ba++; 5267 } 5268 } 5269 /* put together the new matrix */ 5270 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 5271 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5272 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5273 mat = (Mat_SeqAIJ*)(*A_loc)->data; 5274 mat->free_a = PETSC_TRUE; 5275 mat->free_ij = PETSC_TRUE; 5276 mat->nonew = 0; 5277 } else if (scall == MAT_REUSE_MATRIX) { 5278 mat=(Mat_SeqAIJ*)(*A_loc)->data; 5279 ci = mat->i; cj = mat->j; cam = mat->a; 5280 for (i=0; i<am; i++) { 5281 /* off-diagonal portion of A */ 5282 ncols_o = bi[i+1] - bi[i]; 5283 for (jo=0; jo<ncols_o; jo++) { 5284 col = cmap[*bj]; 5285 if (col >= cstart) break; 5286 *cam++ = *ba++; bj++; 5287 } 5288 /* diagonal portion of A */ 5289 ncols_d = ai[i+1] - ai[i]; 5290 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 5291 /* off-diagonal portion of A */ 5292 for (j=jo; j<ncols_o; j++) { 5293 *cam++ = *ba++; bj++; 5294 } 5295 } 5296 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 5297 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 5298 PetscFunctionReturn(0); 5299 } 5300 5301 #undef __FUNCT__ 5302 #define __FUNCT__ "MatMPIAIJGetLocalMatCondensed" 5303 /*@C 5304 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MPIAIJ matrix by taking all its local rows and NON-ZERO columns 5305 5306 Not Collective 5307 5308 Input Parameters: 5309 + A - the matrix 5310 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5311 - row, col - index sets of rows and columns to extract (or NULL) 5312 5313 Output Parameter: 5314 . A_loc - the local sequential matrix generated 5315 5316 Level: developer 5317 5318 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 5319 5320 @*/ 5321 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 5322 { 5323 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5324 PetscErrorCode ierr; 5325 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 5326 IS isrowa,iscola; 5327 Mat *aloc; 5328 PetscBool match; 5329 5330 PetscFunctionBegin; 5331 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 5332 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MPIAIJ matrix as input"); 5333 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5334 if (!row) { 5335 start = A->rmap->rstart; end = A->rmap->rend; 5336 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 5337 } else { 5338 isrowa = *row; 5339 } 5340 if (!col) { 5341 start = A->cmap->rstart; 5342 cmap = a->garray; 5343 nzA = a->A->cmap->n; 5344 nzB = a->B->cmap->n; 5345 ierr = PetscMalloc((nzA+nzB)*sizeof(PetscInt), &idx);CHKERRQ(ierr); 5346 ncols = 0; 5347 for (i=0; i<nzB; i++) { 5348 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5349 else break; 5350 } 5351 imark = i; 5352 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 5353 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 5354 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 5355 } else { 5356 iscola = *col; 5357 } 5358 if (scall != MAT_INITIAL_MATRIX) { 5359 ierr = PetscMalloc(sizeof(Mat),&aloc);CHKERRQ(ierr); 5360 aloc[0] = *A_loc; 5361 } 5362 ierr = MatGetSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 5363 *A_loc = aloc[0]; 5364 ierr = PetscFree(aloc);CHKERRQ(ierr); 5365 if (!row) { 5366 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 5367 } 5368 if (!col) { 5369 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 5370 } 5371 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5372 PetscFunctionReturn(0); 5373 } 5374 5375 #undef __FUNCT__ 5376 #define __FUNCT__ "MatGetBrowsOfAcols" 5377 /*@C 5378 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5379 5380 Collective on Mat 5381 5382 Input Parameters: 5383 + A,B - the matrices in mpiaij format 5384 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5385 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 5386 5387 Output Parameter: 5388 + rowb, colb - index sets of rows and columns of B to extract 5389 - B_seq - the sequential matrix generated 5390 5391 Level: developer 5392 5393 @*/ 5394 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5395 { 5396 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5397 PetscErrorCode ierr; 5398 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5399 IS isrowb,iscolb; 5400 Mat *bseq=NULL; 5401 5402 PetscFunctionBegin; 5403 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5404 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 5405 } 5406 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5407 5408 if (scall == MAT_INITIAL_MATRIX) { 5409 start = A->cmap->rstart; 5410 cmap = a->garray; 5411 nzA = a->A->cmap->n; 5412 nzB = a->B->cmap->n; 5413 ierr = PetscMalloc((nzA+nzB)*sizeof(PetscInt), &idx);CHKERRQ(ierr); 5414 ncols = 0; 5415 for (i=0; i<nzB; i++) { /* row < local row index */ 5416 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5417 else break; 5418 } 5419 imark = i; 5420 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5421 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5422 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5423 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5424 } else { 5425 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5426 isrowb = *rowb; iscolb = *colb; 5427 ierr = PetscMalloc(sizeof(Mat),&bseq);CHKERRQ(ierr); 5428 bseq[0] = *B_seq; 5429 } 5430 ierr = MatGetSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5431 *B_seq = bseq[0]; 5432 ierr = PetscFree(bseq);CHKERRQ(ierr); 5433 if (!rowb) { 5434 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5435 } else { 5436 *rowb = isrowb; 5437 } 5438 if (!colb) { 5439 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5440 } else { 5441 *colb = iscolb; 5442 } 5443 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5444 PetscFunctionReturn(0); 5445 } 5446 5447 #undef __FUNCT__ 5448 #define __FUNCT__ "MatGetBrowsOfAoCols_MPIAIJ" 5449 /* 5450 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5451 of the OFF-DIAGONAL portion of local A 5452 5453 Collective on Mat 5454 5455 Input Parameters: 5456 + A,B - the matrices in mpiaij format 5457 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5458 5459 Output Parameter: 5460 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5461 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5462 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5463 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5464 5465 Level: developer 5466 5467 */ 5468 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5469 { 5470 VecScatter_MPI_General *gen_to,*gen_from; 5471 PetscErrorCode ierr; 5472 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5473 Mat_SeqAIJ *b_oth; 5474 VecScatter ctx =a->Mvctx; 5475 MPI_Comm comm; 5476 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5477 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5478 PetscScalar *rvalues,*svalues; 5479 MatScalar *b_otha,*bufa,*bufA; 5480 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5481 MPI_Request *rwaits = NULL,*swaits = NULL; 5482 MPI_Status *sstatus,rstatus; 5483 PetscMPIInt jj; 5484 PetscInt *cols,sbs,rbs; 5485 PetscScalar *vals; 5486 5487 PetscFunctionBegin; 5488 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5489 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5490 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%d, %d) != (%d,%d)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 5491 } 5492 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5493 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5494 5495 gen_to = (VecScatter_MPI_General*)ctx->todata; 5496 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5497 rvalues = gen_from->values; /* holds the length of receiving row */ 5498 svalues = gen_to->values; /* holds the length of sending row */ 5499 nrecvs = gen_from->n; 5500 nsends = gen_to->n; 5501 5502 ierr = PetscMalloc2(nrecvs,MPI_Request,&rwaits,nsends,MPI_Request,&swaits);CHKERRQ(ierr); 5503 srow = gen_to->indices; /* local row index to be sent */ 5504 sstarts = gen_to->starts; 5505 sprocs = gen_to->procs; 5506 sstatus = gen_to->sstatus; 5507 sbs = gen_to->bs; 5508 rstarts = gen_from->starts; 5509 rprocs = gen_from->procs; 5510 rbs = gen_from->bs; 5511 5512 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5513 if (scall == MAT_INITIAL_MATRIX) { 5514 /* i-array */ 5515 /*---------*/ 5516 /* post receives */ 5517 for (i=0; i<nrecvs; i++) { 5518 rowlen = (PetscInt*)rvalues + rstarts[i]*rbs; 5519 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5520 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5521 } 5522 5523 /* pack the outgoing message */ 5524 ierr = PetscMalloc2(nsends+1,PetscInt,&sstartsj,nrecvs+1,PetscInt,&rstartsj);CHKERRQ(ierr); 5525 5526 sstartsj[0] = 0; 5527 rstartsj[0] = 0; 5528 len = 0; /* total length of j or a array to be sent */ 5529 k = 0; 5530 for (i=0; i<nsends; i++) { 5531 rowlen = (PetscInt*)svalues + sstarts[i]*sbs; 5532 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5533 for (j=0; j<nrows; j++) { 5534 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5535 for (l=0; l<sbs; l++) { 5536 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5537 5538 rowlen[j*sbs+l] = ncols; 5539 5540 len += ncols; 5541 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5542 } 5543 k++; 5544 } 5545 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5546 5547 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5548 } 5549 /* recvs and sends of i-array are completed */ 5550 i = nrecvs; 5551 while (i--) { 5552 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5553 } 5554 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5555 5556 /* allocate buffers for sending j and a arrays */ 5557 ierr = PetscMalloc((len+1)*sizeof(PetscInt),&bufj);CHKERRQ(ierr); 5558 ierr = PetscMalloc((len+1)*sizeof(PetscScalar),&bufa);CHKERRQ(ierr); 5559 5560 /* create i-array of B_oth */ 5561 ierr = PetscMalloc((aBn+2)*sizeof(PetscInt),&b_othi);CHKERRQ(ierr); 5562 5563 b_othi[0] = 0; 5564 len = 0; /* total length of j or a array to be received */ 5565 k = 0; 5566 for (i=0; i<nrecvs; i++) { 5567 rowlen = (PetscInt*)rvalues + rstarts[i]*rbs; 5568 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be recieved */ 5569 for (j=0; j<nrows; j++) { 5570 b_othi[k+1] = b_othi[k] + rowlen[j]; 5571 len += rowlen[j]; k++; 5572 } 5573 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5574 } 5575 5576 /* allocate space for j and a arrrays of B_oth */ 5577 ierr = PetscMalloc((b_othi[aBn]+1)*sizeof(PetscInt),&b_othj);CHKERRQ(ierr); 5578 ierr = PetscMalloc((b_othi[aBn]+1)*sizeof(MatScalar),&b_otha);CHKERRQ(ierr); 5579 5580 /* j-array */ 5581 /*---------*/ 5582 /* post receives of j-array */ 5583 for (i=0; i<nrecvs; i++) { 5584 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5585 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5586 } 5587 5588 /* pack the outgoing message j-array */ 5589 k = 0; 5590 for (i=0; i<nsends; i++) { 5591 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5592 bufJ = bufj+sstartsj[i]; 5593 for (j=0; j<nrows; j++) { 5594 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5595 for (ll=0; ll<sbs; ll++) { 5596 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5597 for (l=0; l<ncols; l++) { 5598 *bufJ++ = cols[l]; 5599 } 5600 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5601 } 5602 } 5603 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5604 } 5605 5606 /* recvs and sends of j-array are completed */ 5607 i = nrecvs; 5608 while (i--) { 5609 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5610 } 5611 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5612 } else if (scall == MAT_REUSE_MATRIX) { 5613 sstartsj = *startsj_s; 5614 rstartsj = *startsj_r; 5615 bufa = *bufa_ptr; 5616 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5617 b_otha = b_oth->a; 5618 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5619 5620 /* a-array */ 5621 /*---------*/ 5622 /* post receives of a-array */ 5623 for (i=0; i<nrecvs; i++) { 5624 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5625 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5626 } 5627 5628 /* pack the outgoing message a-array */ 5629 k = 0; 5630 for (i=0; i<nsends; i++) { 5631 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5632 bufA = bufa+sstartsj[i]; 5633 for (j=0; j<nrows; j++) { 5634 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5635 for (ll=0; ll<sbs; ll++) { 5636 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5637 for (l=0; l<ncols; l++) { 5638 *bufA++ = vals[l]; 5639 } 5640 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5641 } 5642 } 5643 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5644 } 5645 /* recvs and sends of a-array are completed */ 5646 i = nrecvs; 5647 while (i--) { 5648 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5649 } 5650 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5651 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5652 5653 if (scall == MAT_INITIAL_MATRIX) { 5654 /* put together the new matrix */ 5655 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5656 5657 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5658 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5659 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5660 b_oth->free_a = PETSC_TRUE; 5661 b_oth->free_ij = PETSC_TRUE; 5662 b_oth->nonew = 0; 5663 5664 ierr = PetscFree(bufj);CHKERRQ(ierr); 5665 if (!startsj_s || !bufa_ptr) { 5666 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5667 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5668 } else { 5669 *startsj_s = sstartsj; 5670 *startsj_r = rstartsj; 5671 *bufa_ptr = bufa; 5672 } 5673 } 5674 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5675 PetscFunctionReturn(0); 5676 } 5677 5678 #undef __FUNCT__ 5679 #define __FUNCT__ "MatGetCommunicationStructs" 5680 /*@C 5681 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5682 5683 Not Collective 5684 5685 Input Parameters: 5686 . A - The matrix in mpiaij format 5687 5688 Output Parameter: 5689 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5690 . colmap - A map from global column index to local index into lvec 5691 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5692 5693 Level: developer 5694 5695 @*/ 5696 #if defined(PETSC_USE_CTABLE) 5697 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5698 #else 5699 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5700 #endif 5701 { 5702 Mat_MPIAIJ *a; 5703 5704 PetscFunctionBegin; 5705 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5706 PetscValidPointer(lvec, 2); 5707 PetscValidPointer(colmap, 3); 5708 PetscValidPointer(multScatter, 4); 5709 a = (Mat_MPIAIJ*) A->data; 5710 if (lvec) *lvec = a->lvec; 5711 if (colmap) *colmap = a->colmap; 5712 if (multScatter) *multScatter = a->Mvctx; 5713 PetscFunctionReturn(0); 5714 } 5715 5716 PETSC_EXTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5717 PETSC_EXTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5718 PETSC_EXTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5719 5720 #undef __FUNCT__ 5721 #define __FUNCT__ "MatMatMultNumeric_MPIDense_MPIAIJ" 5722 /* 5723 Computes (B'*A')' since computing B*A directly is untenable 5724 5725 n p p 5726 ( ) ( ) ( ) 5727 m ( A ) * n ( B ) = m ( C ) 5728 ( ) ( ) ( ) 5729 5730 */ 5731 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5732 { 5733 PetscErrorCode ierr; 5734 Mat At,Bt,Ct; 5735 5736 PetscFunctionBegin; 5737 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5738 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5739 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5740 ierr = MatDestroy(&At);CHKERRQ(ierr); 5741 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5742 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5743 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5744 PetscFunctionReturn(0); 5745 } 5746 5747 #undef __FUNCT__ 5748 #define __FUNCT__ "MatMatMultSymbolic_MPIDense_MPIAIJ" 5749 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5750 { 5751 PetscErrorCode ierr; 5752 PetscInt m=A->rmap->n,n=B->cmap->n; 5753 Mat Cmat; 5754 5755 PetscFunctionBegin; 5756 if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"A->cmap->n %d != B->rmap->n %d\n",A->cmap->n,B->rmap->n); 5757 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5758 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5759 ierr = MatSetBlockSizes(Cmat,A->rmap->bs,B->cmap->bs);CHKERRQ(ierr); 5760 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5761 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5762 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5763 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5764 5765 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5766 5767 *C = Cmat; 5768 PetscFunctionReturn(0); 5769 } 5770 5771 /* ----------------------------------------------------------------*/ 5772 #undef __FUNCT__ 5773 #define __FUNCT__ "MatMatMult_MPIDense_MPIAIJ" 5774 PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5775 { 5776 PetscErrorCode ierr; 5777 5778 PetscFunctionBegin; 5779 if (scall == MAT_INITIAL_MATRIX) { 5780 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5781 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5782 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5783 } 5784 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5785 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5786 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5787 PetscFunctionReturn(0); 5788 } 5789 5790 #if defined(PETSC_HAVE_MUMPS) 5791 PETSC_EXTERN PetscErrorCode MatGetFactor_aij_mumps(Mat,MatFactorType,Mat*); 5792 #endif 5793 #if defined(PETSC_HAVE_PASTIX) 5794 PETSC_EXTERN PetscErrorCode MatGetFactor_mpiaij_pastix(Mat,MatFactorType,Mat*); 5795 #endif 5796 #if defined(PETSC_HAVE_SUPERLU_DIST) 5797 PETSC_EXTERN PetscErrorCode MatGetFactor_mpiaij_superlu_dist(Mat,MatFactorType,Mat*); 5798 #endif 5799 #if defined(PETSC_HAVE_CLIQUE) 5800 PETSC_EXTERN PetscErrorCode MatGetFactor_aij_clique(Mat,MatFactorType,Mat*); 5801 #endif 5802 5803 /*MC 5804 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5805 5806 Options Database Keys: 5807 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5808 5809 Level: beginner 5810 5811 .seealso: MatCreateAIJ() 5812 M*/ 5813 5814 #undef __FUNCT__ 5815 #define __FUNCT__ "MatCreate_MPIAIJ" 5816 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5817 { 5818 Mat_MPIAIJ *b; 5819 PetscErrorCode ierr; 5820 PetscMPIInt size; 5821 5822 PetscFunctionBegin; 5823 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5824 5825 ierr = PetscNewLog(B,Mat_MPIAIJ,&b);CHKERRQ(ierr); 5826 B->data = (void*)b; 5827 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5828 B->assembled = PETSC_FALSE; 5829 B->insertmode = NOT_SET_VALUES; 5830 b->size = size; 5831 5832 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5833 5834 /* build cache for off array entries formed */ 5835 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5836 5837 b->donotstash = PETSC_FALSE; 5838 b->colmap = 0; 5839 b->garray = 0; 5840 b->roworiented = PETSC_TRUE; 5841 5842 /* stuff used for matrix vector multiply */ 5843 b->lvec = NULL; 5844 b->Mvctx = NULL; 5845 5846 /* stuff for MatGetRow() */ 5847 b->rowindices = 0; 5848 b->rowvalues = 0; 5849 b->getrowactive = PETSC_FALSE; 5850 5851 /* flexible pointer used in CUSP/CUSPARSE classes */ 5852 b->spptr = NULL; 5853 5854 #if defined(PETSC_HAVE_MUMPS) 5855 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_aij_mumps);CHKERRQ(ierr); 5856 #endif 5857 #if defined(PETSC_HAVE_PASTIX) 5858 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_mpiaij_pastix);CHKERRQ(ierr); 5859 #endif 5860 #if defined(PETSC_HAVE_SUPERLU_DIST) 5861 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_superlu_dist_C",MatGetFactor_mpiaij_superlu_dist);CHKERRQ(ierr); 5862 #endif 5863 #if defined(PETSC_HAVE_CLIQUE) 5864 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_clique_C",MatGetFactor_aij_clique);CHKERRQ(ierr); 5865 #endif 5866 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5867 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5868 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetDiagonalBlock_C",MatGetDiagonalBlock_MPIAIJ);CHKERRQ(ierr); 5869 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5870 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5871 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5872 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5873 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5874 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5875 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5876 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5877 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5878 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5879 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5880 PetscFunctionReturn(0); 5881 } 5882 5883 #undef __FUNCT__ 5884 #define __FUNCT__ "MatCreateMPIAIJWithSplitArrays" 5885 /*@ 5886 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5887 and "off-diagonal" part of the matrix in CSR format. 5888 5889 Collective on MPI_Comm 5890 5891 Input Parameters: 5892 + comm - MPI communicator 5893 . m - number of local rows (Cannot be PETSC_DECIDE) 5894 . n - This value should be the same as the local size used in creating the 5895 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5896 calculated if N is given) For square matrices n is almost always m. 5897 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5898 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5899 . i - row indices for "diagonal" portion of matrix 5900 . j - column indices 5901 . a - matrix values 5902 . oi - row indices for "off-diagonal" portion of matrix 5903 . oj - column indices 5904 - oa - matrix values 5905 5906 Output Parameter: 5907 . mat - the matrix 5908 5909 Level: advanced 5910 5911 Notes: 5912 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5913 must free the arrays once the matrix has been destroyed and not before. 5914 5915 The i and j indices are 0 based 5916 5917 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5918 5919 This sets local rows and cannot be used to set off-processor values. 5920 5921 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5922 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5923 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5924 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5925 keep track of the underlying array. Use MatSetOption(A,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5926 communication if it is known that only local entries will be set. 5927 5928 .keywords: matrix, aij, compressed row, sparse, parallel 5929 5930 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5931 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5932 @*/ 5933 PetscErrorCode MatCreateMPIAIJWithSplitArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt i[],PetscInt j[],PetscScalar a[],PetscInt oi[], PetscInt oj[],PetscScalar oa[],Mat *mat) 5934 { 5935 PetscErrorCode ierr; 5936 Mat_MPIAIJ *maij; 5937 5938 PetscFunctionBegin; 5939 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5940 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5941 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5942 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5943 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5944 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5945 maij = (Mat_MPIAIJ*) (*mat)->data; 5946 5947 (*mat)->preallocated = PETSC_TRUE; 5948 5949 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5950 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5951 5952 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5953 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5954 5955 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5956 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5957 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5958 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5959 5960 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5961 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5962 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5963 PetscFunctionReturn(0); 5964 } 5965 5966 /* 5967 Special version for direct calls from Fortran 5968 */ 5969 #include <petsc-private/fortranimpl.h> 5970 5971 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5972 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5973 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5974 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5975 #endif 5976 5977 /* Change these macros so can be used in void function */ 5978 #undef CHKERRQ 5979 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5980 #undef SETERRQ2 5981 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5982 #undef SETERRQ3 5983 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5984 #undef SETERRQ 5985 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5986 5987 #undef __FUNCT__ 5988 #define __FUNCT__ "matsetvaluesmpiaij_" 5989 PETSC_EXTERN void PETSC_STDCALL matsetvaluesmpiaij_(Mat *mmat,PetscInt *mm,const PetscInt im[],PetscInt *mn,const PetscInt in[],const PetscScalar v[],InsertMode *maddv,PetscErrorCode *_ierr) 5990 { 5991 Mat mat = *mmat; 5992 PetscInt m = *mm, n = *mn; 5993 InsertMode addv = *maddv; 5994 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5995 PetscScalar value; 5996 PetscErrorCode ierr; 5997 5998 MatCheckPreallocated(mat,1); 5999 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 6000 6001 #if defined(PETSC_USE_DEBUG) 6002 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 6003 #endif 6004 { 6005 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 6006 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 6007 PetscBool roworiented = aij->roworiented; 6008 6009 /* Some Variables required in the macro */ 6010 Mat A = aij->A; 6011 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 6012 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 6013 MatScalar *aa = a->a; 6014 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 6015 Mat B = aij->B; 6016 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 6017 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 6018 MatScalar *ba = b->a; 6019 6020 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 6021 PetscInt nonew = a->nonew; 6022 MatScalar *ap1,*ap2; 6023 6024 PetscFunctionBegin; 6025 for (i=0; i<m; i++) { 6026 if (im[i] < 0) continue; 6027 #if defined(PETSC_USE_DEBUG) 6028 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 6029 #endif 6030 if (im[i] >= rstart && im[i] < rend) { 6031 row = im[i] - rstart; 6032 lastcol1 = -1; 6033 rp1 = aj + ai[row]; 6034 ap1 = aa + ai[row]; 6035 rmax1 = aimax[row]; 6036 nrow1 = ailen[row]; 6037 low1 = 0; 6038 high1 = nrow1; 6039 lastcol2 = -1; 6040 rp2 = bj + bi[row]; 6041 ap2 = ba + bi[row]; 6042 rmax2 = bimax[row]; 6043 nrow2 = bilen[row]; 6044 low2 = 0; 6045 high2 = nrow2; 6046 6047 for (j=0; j<n; j++) { 6048 if (roworiented) value = v[i*n+j]; 6049 else value = v[i+j*m]; 6050 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES)) continue; 6051 if (in[j] >= cstart && in[j] < cend) { 6052 col = in[j] - cstart; 6053 MatSetValues_SeqAIJ_A_Private(row,col,value,addv); 6054 } else if (in[j] < 0) continue; 6055 #if defined(PETSC_USE_DEBUG) 6056 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 6057 #endif 6058 else { 6059 if (mat->was_assembled) { 6060 if (!aij->colmap) { 6061 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 6062 } 6063 #if defined(PETSC_USE_CTABLE) 6064 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 6065 col--; 6066 #else 6067 col = aij->colmap[in[j]] - 1; 6068 #endif 6069 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 6070 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 6071 col = in[j]; 6072 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 6073 B = aij->B; 6074 b = (Mat_SeqAIJ*)B->data; 6075 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 6076 rp2 = bj + bi[row]; 6077 ap2 = ba + bi[row]; 6078 rmax2 = bimax[row]; 6079 nrow2 = bilen[row]; 6080 low2 = 0; 6081 high2 = nrow2; 6082 bm = aij->B->rmap->n; 6083 ba = b->a; 6084 } 6085 } else col = in[j]; 6086 MatSetValues_SeqAIJ_B_Private(row,col,value,addv); 6087 } 6088 } 6089 } else if (!aij->donotstash) { 6090 if (roworiented) { 6091 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 6092 } else { 6093 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 6094 } 6095 } 6096 } 6097 } 6098 PetscFunctionReturnVoid(); 6099 } 6100 6101