1 #include <../src/mat/impls/baij/mpi/mpibaij.h> /*I "petscmat.h" I*/ 2 3 #include <petsc/private/hashseti.h> 4 #include <petscblaslapack.h> 5 #include <petscsf.h> 6 7 #if defined(PETSC_HAVE_HYPRE) 8 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 9 #endif 10 11 PetscErrorCode MatGetRowMaxAbs_MPIBAIJ(Mat A,Vec v,PetscInt idx[]) 12 { 13 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 14 PetscErrorCode ierr; 15 PetscInt i,*idxb = NULL,m = A->rmap->n,bs = A->cmap->bs; 16 PetscScalar *va,*vv; 17 Vec vB,vA; 18 const PetscScalar *vb; 19 20 PetscFunctionBegin; 21 ierr = VecCreateSeq(PETSC_COMM_SELF,m,&vA);CHKERRQ(ierr); 22 ierr = MatGetRowMaxAbs(a->A,vA,idx);CHKERRQ(ierr); 23 24 ierr = VecGetArrayWrite(vA,&va);CHKERRQ(ierr); 25 if (idx) { 26 for (i=0; i<m; i++) { 27 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 28 } 29 } 30 31 ierr = VecCreateSeq(PETSC_COMM_SELF,m,&vB);CHKERRQ(ierr); 32 ierr = PetscMalloc1(m,&idxb);CHKERRQ(ierr); 33 ierr = MatGetRowMaxAbs(a->B,vB,idxb);CHKERRQ(ierr); 34 35 ierr = VecGetArrayWrite(v,&vv);CHKERRQ(ierr); 36 ierr = VecGetArrayRead(vB,&vb);CHKERRQ(ierr); 37 for (i=0; i<m; i++) { 38 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 39 vv[i] = vb[i]; 40 if (idx) idx[i] = bs*a->garray[idxb[i]/bs] + (idxb[i] % bs); 41 } else { 42 vv[i] = va[i]; 43 if (idx && PetscAbsScalar(va[i]) == PetscAbsScalar(vb[i]) && idxb[i] != -1 && idx[i] > bs*a->garray[idxb[i]/bs] + (idxb[i] % bs)) 44 idx[i] = bs*a->garray[idxb[i]/bs] + (idxb[i] % bs); 45 } 46 } 47 ierr = VecRestoreArrayWrite(vA,&vv);CHKERRQ(ierr); 48 ierr = VecRestoreArrayWrite(vA,&va);CHKERRQ(ierr); 49 ierr = VecRestoreArrayRead(vB,&vb);CHKERRQ(ierr); 50 ierr = PetscFree(idxb);CHKERRQ(ierr); 51 ierr = VecDestroy(&vA);CHKERRQ(ierr); 52 ierr = VecDestroy(&vB);CHKERRQ(ierr); 53 PetscFunctionReturn(0); 54 } 55 56 PetscErrorCode MatStoreValues_MPIBAIJ(Mat mat) 57 { 58 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)mat->data; 59 PetscErrorCode ierr; 60 61 PetscFunctionBegin; 62 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 63 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 64 PetscFunctionReturn(0); 65 } 66 67 PetscErrorCode MatRetrieveValues_MPIBAIJ(Mat mat) 68 { 69 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)mat->data; 70 PetscErrorCode ierr; 71 72 PetscFunctionBegin; 73 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 74 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 75 PetscFunctionReturn(0); 76 } 77 78 /* 79 Local utility routine that creates a mapping from the global column 80 number to the local number in the off-diagonal part of the local 81 storage of the matrix. This is done in a non scalable way since the 82 length of colmap equals the global matrix length. 83 */ 84 PetscErrorCode MatCreateColmap_MPIBAIJ_Private(Mat mat) 85 { 86 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 87 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 88 PetscErrorCode ierr; 89 PetscInt nbs = B->nbs,i,bs=mat->rmap->bs; 90 91 PetscFunctionBegin; 92 #if defined(PETSC_USE_CTABLE) 93 ierr = PetscTableCreate(baij->nbs,baij->Nbs+1,&baij->colmap);CHKERRQ(ierr); 94 for (i=0; i<nbs; i++) { 95 ierr = PetscTableAdd(baij->colmap,baij->garray[i]+1,i*bs+1,INSERT_VALUES);CHKERRQ(ierr); 96 } 97 #else 98 ierr = PetscCalloc1(baij->Nbs+1,&baij->colmap);CHKERRQ(ierr); 99 ierr = PetscLogObjectMemory((PetscObject)mat,baij->Nbs*sizeof(PetscInt));CHKERRQ(ierr); 100 for (i=0; i<nbs; i++) baij->colmap[baij->garray[i]] = i*bs+1; 101 #endif 102 PetscFunctionReturn(0); 103 } 104 105 #define MatSetValues_SeqBAIJ_A_Private(row,col,value,addv,orow,ocol) \ 106 { \ 107 brow = row/bs; \ 108 rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; \ 109 rmax = aimax[brow]; nrow = ailen[brow]; \ 110 bcol = col/bs; \ 111 ridx = row % bs; cidx = col % bs; \ 112 low = 0; high = nrow; \ 113 while (high-low > 3) { \ 114 t = (low+high)/2; \ 115 if (rp[t] > bcol) high = t; \ 116 else low = t; \ 117 } \ 118 for (_i=low; _i<high; _i++) { \ 119 if (rp[_i] > bcol) break; \ 120 if (rp[_i] == bcol) { \ 121 bap = ap + bs2*_i + bs*cidx + ridx; \ 122 if (addv == ADD_VALUES) *bap += value; \ 123 else *bap = value; \ 124 goto a_noinsert; \ 125 } \ 126 } \ 127 if (a->nonew == 1) goto a_noinsert; \ 128 if (a->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 129 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,aimax,a->nonew,MatScalar); \ 130 N = nrow++ - 1; \ 131 /* shift up all the later entries in this row */ \ 132 ierr = PetscArraymove(rp+_i+1,rp+_i,N-_i+1);CHKERRQ(ierr);\ 133 ierr = PetscArraymove(ap+bs2*(_i+1),ap+bs2*_i,bs2*(N-_i+1));CHKERRQ(ierr); \ 134 ierr = PetscArrayzero(ap+bs2*_i,bs2);CHKERRQ(ierr); \ 135 rp[_i] = bcol; \ 136 ap[bs2*_i + bs*cidx + ridx] = value; \ 137 a_noinsert:; \ 138 ailen[brow] = nrow; \ 139 } 140 141 #define MatSetValues_SeqBAIJ_B_Private(row,col,value,addv,orow,ocol) \ 142 { \ 143 brow = row/bs; \ 144 rp = bj + bi[brow]; ap = ba + bs2*bi[brow]; \ 145 rmax = bimax[brow]; nrow = bilen[brow]; \ 146 bcol = col/bs; \ 147 ridx = row % bs; cidx = col % bs; \ 148 low = 0; high = nrow; \ 149 while (high-low > 3) { \ 150 t = (low+high)/2; \ 151 if (rp[t] > bcol) high = t; \ 152 else low = t; \ 153 } \ 154 for (_i=low; _i<high; _i++) { \ 155 if (rp[_i] > bcol) break; \ 156 if (rp[_i] == bcol) { \ 157 bap = ap + bs2*_i + bs*cidx + ridx; \ 158 if (addv == ADD_VALUES) *bap += value; \ 159 else *bap = value; \ 160 goto b_noinsert; \ 161 } \ 162 } \ 163 if (b->nonew == 1) goto b_noinsert; \ 164 if (b->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 165 MatSeqXAIJReallocateAIJ(B,b->mbs,bs2,nrow,brow,bcol,rmax,ba,bi,bj,rp,ap,bimax,b->nonew,MatScalar); \ 166 N = nrow++ - 1; \ 167 /* shift up all the later entries in this row */ \ 168 ierr = PetscArraymove(rp+_i+1,rp+_i,N-_i+1);CHKERRQ(ierr);\ 169 ierr = PetscArraymove(ap+bs2*(_i+1),ap+bs2*_i,bs2*(N-_i+1));CHKERRQ(ierr);\ 170 ierr = PetscArrayzero(ap+bs2*_i,bs2);CHKERRQ(ierr); \ 171 rp[_i] = bcol; \ 172 ap[bs2*_i + bs*cidx + ridx] = value; \ 173 b_noinsert:; \ 174 bilen[brow] = nrow; \ 175 } 176 177 PetscErrorCode MatSetValues_MPIBAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 178 { 179 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 180 MatScalar value; 181 PetscBool roworiented = baij->roworiented; 182 PetscErrorCode ierr; 183 PetscInt i,j,row,col; 184 PetscInt rstart_orig=mat->rmap->rstart; 185 PetscInt rend_orig =mat->rmap->rend,cstart_orig=mat->cmap->rstart; 186 PetscInt cend_orig =mat->cmap->rend,bs=mat->rmap->bs; 187 188 /* Some Variables required in the macro */ 189 Mat A = baij->A; 190 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)(A)->data; 191 PetscInt *aimax=a->imax,*ai=a->i,*ailen=a->ilen,*aj=a->j; 192 MatScalar *aa =a->a; 193 194 Mat B = baij->B; 195 Mat_SeqBAIJ *b = (Mat_SeqBAIJ*)(B)->data; 196 PetscInt *bimax=b->imax,*bi=b->i,*bilen=b->ilen,*bj=b->j; 197 MatScalar *ba =b->a; 198 199 PetscInt *rp,ii,nrow,_i,rmax,N,brow,bcol; 200 PetscInt low,high,t,ridx,cidx,bs2=a->bs2; 201 MatScalar *ap,*bap; 202 203 PetscFunctionBegin; 204 for (i=0; i<m; i++) { 205 if (im[i] < 0) continue; 206 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); 207 if (im[i] >= rstart_orig && im[i] < rend_orig) { 208 row = im[i] - rstart_orig; 209 for (j=0; j<n; j++) { 210 if (in[j] >= cstart_orig && in[j] < cend_orig) { 211 col = in[j] - cstart_orig; 212 if (roworiented) value = v[i*n+j]; 213 else value = v[i+j*m]; 214 MatSetValues_SeqBAIJ_A_Private(row,col,value,addv,im[i],in[j]); 215 } else if (in[j] < 0) continue; 216 else if (PetscUnlikely(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); 217 else { 218 if (mat->was_assembled) { 219 if (!baij->colmap) { 220 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 221 } 222 #if defined(PETSC_USE_CTABLE) 223 ierr = PetscTableFind(baij->colmap,in[j]/bs + 1,&col);CHKERRQ(ierr); 224 col = col - 1; 225 #else 226 col = baij->colmap[in[j]/bs] - 1; 227 #endif 228 if (col < 0 && !((Mat_SeqBAIJ*)(baij->B->data))->nonew) { 229 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 230 col = in[j]; 231 /* Reinitialize the variables required by MatSetValues_SeqBAIJ_B_Private() */ 232 B = baij->B; 233 b = (Mat_SeqBAIJ*)(B)->data; 234 bimax=b->imax;bi=b->i;bilen=b->ilen;bj=b->j; 235 ba =b->a; 236 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", im[i], in[j]); 237 else col += in[j]%bs; 238 } else col = in[j]; 239 if (roworiented) value = v[i*n+j]; 240 else value = v[i+j*m]; 241 MatSetValues_SeqBAIJ_B_Private(row,col,value,addv,im[i],in[j]); 242 /* ierr = MatSetValues_SeqBAIJ(baij->B,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ 243 } 244 } 245 } else { 246 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]); 247 if (!baij->donotstash) { 248 mat->assembled = PETSC_FALSE; 249 if (roworiented) { 250 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 251 } else { 252 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 253 } 254 } 255 } 256 } 257 PetscFunctionReturn(0); 258 } 259 260 PETSC_STATIC_INLINE PetscErrorCode MatSetValuesBlocked_SeqBAIJ_Inlined(Mat A,PetscInt row,PetscInt col,const PetscScalar v[],InsertMode is,PetscInt orow,PetscInt ocol) 261 { 262 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data; 263 PetscInt *rp,low,high,t,ii,jj,nrow,i,rmax,N; 264 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 265 PetscErrorCode ierr; 266 PetscInt *aj =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs; 267 PetscBool roworiented=a->roworiented; 268 const PetscScalar *value = v; 269 MatScalar *ap,*aa = a->a,*bap; 270 271 PetscFunctionBegin; 272 rp = aj + ai[row]; 273 ap = aa + bs2*ai[row]; 274 rmax = imax[row]; 275 nrow = ailen[row]; 276 value = v; 277 low = 0; 278 high = nrow; 279 while (high-low > 7) { 280 t = (low+high)/2; 281 if (rp[t] > col) high = t; 282 else low = t; 283 } 284 for (i=low; i<high; i++) { 285 if (rp[i] > col) break; 286 if (rp[i] == col) { 287 bap = ap + bs2*i; 288 if (roworiented) { 289 if (is == ADD_VALUES) { 290 for (ii=0; ii<bs; ii++) { 291 for (jj=ii; jj<bs2; jj+=bs) { 292 bap[jj] += *value++; 293 } 294 } 295 } else { 296 for (ii=0; ii<bs; ii++) { 297 for (jj=ii; jj<bs2; jj+=bs) { 298 bap[jj] = *value++; 299 } 300 } 301 } 302 } else { 303 if (is == ADD_VALUES) { 304 for (ii=0; ii<bs; ii++,value+=bs) { 305 for (jj=0; jj<bs; jj++) { 306 bap[jj] += value[jj]; 307 } 308 bap += bs; 309 } 310 } else { 311 for (ii=0; ii<bs; ii++,value+=bs) { 312 for (jj=0; jj<bs; jj++) { 313 bap[jj] = value[jj]; 314 } 315 bap += bs; 316 } 317 } 318 } 319 goto noinsert2; 320 } 321 } 322 if (nonew == 1) goto noinsert2; 323 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new global block indexed nonzero block (%D, %D) in the matrix", orow, ocol); 324 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 325 N = nrow++ - 1; high++; 326 /* shift up all the later entries in this row */ 327 ierr = PetscArraymove(rp+i+1,rp+i,N-i+1);CHKERRQ(ierr); 328 ierr = PetscArraymove(ap+bs2*(i+1),ap+bs2*i,bs2*(N-i+1));CHKERRQ(ierr); 329 rp[i] = col; 330 bap = ap + bs2*i; 331 if (roworiented) { 332 for (ii=0; ii<bs; ii++) { 333 for (jj=ii; jj<bs2; jj+=bs) { 334 bap[jj] = *value++; 335 } 336 } 337 } else { 338 for (ii=0; ii<bs; ii++) { 339 for (jj=0; jj<bs; jj++) { 340 *bap++ = *value++; 341 } 342 } 343 } 344 noinsert2:; 345 ailen[row] = nrow; 346 PetscFunctionReturn(0); 347 } 348 349 /* 350 This routine should be optimized so that the block copy at ** Here a copy is required ** below is not needed 351 by passing additional stride information into the MatSetValuesBlocked_SeqBAIJ_Inlined() routine 352 */ 353 PetscErrorCode MatSetValuesBlocked_MPIBAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 354 { 355 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 356 const PetscScalar *value; 357 MatScalar *barray = baij->barray; 358 PetscBool roworiented = baij->roworiented; 359 PetscErrorCode ierr; 360 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 361 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 362 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 363 364 PetscFunctionBegin; 365 if (!barray) { 366 ierr = PetscMalloc1(bs2,&barray);CHKERRQ(ierr); 367 baij->barray = barray; 368 } 369 370 if (roworiented) stepval = (n-1)*bs; 371 else stepval = (m-1)*bs; 372 373 for (i=0; i<m; i++) { 374 if (im[i] < 0) continue; 375 if (PetscUnlikelyDebug(im[i] >= baij->Mbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block indexed row too large %D max %D",im[i],baij->Mbs-1); 376 if (im[i] >= rstart && im[i] < rend) { 377 row = im[i] - rstart; 378 for (j=0; j<n; j++) { 379 /* If NumCol = 1 then a copy is not required */ 380 if ((roworiented) && (n == 1)) { 381 barray = (MatScalar*)v + i*bs2; 382 } else if ((!roworiented) && (m == 1)) { 383 barray = (MatScalar*)v + j*bs2; 384 } else { /* Here a copy is required */ 385 if (roworiented) { 386 value = v + (i*(stepval+bs) + j)*bs; 387 } else { 388 value = v + (j*(stepval+bs) + i)*bs; 389 } 390 for (ii=0; ii<bs; ii++,value+=bs+stepval) { 391 for (jj=0; jj<bs; jj++) barray[jj] = value[jj]; 392 barray += bs; 393 } 394 barray -= bs2; 395 } 396 397 if (in[j] >= cstart && in[j] < cend) { 398 col = in[j] - cstart; 399 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->A,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 400 } else if (in[j] < 0) continue; 401 else if (PetscUnlikelyDebug(in[j] >= baij->Nbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Block indexed column too large %D max %D",in[j],baij->Nbs-1); 402 else { 403 if (mat->was_assembled) { 404 if (!baij->colmap) { 405 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 406 } 407 408 #if defined(PETSC_USE_DEBUG) 409 #if defined(PETSC_USE_CTABLE) 410 { PetscInt data; 411 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 412 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 413 } 414 #else 415 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 416 #endif 417 #endif 418 #if defined(PETSC_USE_CTABLE) 419 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 420 col = (col - 1)/bs; 421 #else 422 col = (baij->colmap[in[j]] - 1)/bs; 423 #endif 424 if (col < 0 && !((Mat_SeqBAIJ*)(baij->B->data))->nonew) { 425 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 426 col = in[j]; 427 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new blocked indexed nonzero block (%D, %D) into matrix",im[i],in[j]); 428 } else col = in[j]; 429 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->B,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 430 } 431 } 432 } else { 433 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process block indexed row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 434 if (!baij->donotstash) { 435 if (roworiented) { 436 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 437 } else { 438 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 439 } 440 } 441 } 442 } 443 PetscFunctionReturn(0); 444 } 445 446 #define HASH_KEY 0.6180339887 447 #define HASH(size,key,tmp) (tmp = (key)*HASH_KEY,(PetscInt)((size)*(tmp-(PetscInt)tmp))) 448 /* #define HASH(size,key) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 449 /* #define HASH(size,key,tmp) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 450 PetscErrorCode MatSetValues_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 451 { 452 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 453 PetscBool roworiented = baij->roworiented; 454 PetscErrorCode ierr; 455 PetscInt i,j,row,col; 456 PetscInt rstart_orig=mat->rmap->rstart; 457 PetscInt rend_orig =mat->rmap->rend,Nbs=baij->Nbs; 458 PetscInt h1,key,size=baij->ht_size,bs=mat->rmap->bs,*HT=baij->ht,idx; 459 PetscReal tmp; 460 MatScalar **HD = baij->hd,value; 461 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 462 463 PetscFunctionBegin; 464 for (i=0; i<m; i++) { 465 if (PetscDefined(USE_DEBUG)) { 466 if (im[i] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row"); 467 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); 468 } 469 row = im[i]; 470 if (row >= rstart_orig && row < rend_orig) { 471 for (j=0; j<n; j++) { 472 col = in[j]; 473 if (roworiented) value = v[i*n+j]; 474 else value = v[i+j*m]; 475 /* Look up PetscInto the Hash Table */ 476 key = (row/bs)*Nbs+(col/bs)+1; 477 h1 = HASH(size,key,tmp); 478 479 idx = h1; 480 if (PetscDefined(USE_DEBUG)) { 481 insert_ct++; 482 total_ct++; 483 if (HT[idx] != key) { 484 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++) ; 485 if (idx == size) { 486 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++) ; 487 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 488 } 489 } 490 } else if (HT[idx] != key) { 491 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++) ; 492 if (idx == size) { 493 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++) ; 494 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 495 } 496 } 497 /* A HASH table entry is found, so insert the values at the correct address */ 498 if (addv == ADD_VALUES) *(HD[idx]+ (col % bs)*bs + (row % bs)) += value; 499 else *(HD[idx]+ (col % bs)*bs + (row % bs)) = value; 500 } 501 } else if (!baij->donotstash) { 502 if (roworiented) { 503 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 504 } else { 505 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 506 } 507 } 508 } 509 if (PetscDefined(USE_DEBUG)) { 510 baij->ht_total_ct += total_ct; 511 baij->ht_insert_ct += insert_ct; 512 } 513 PetscFunctionReturn(0); 514 } 515 516 PetscErrorCode MatSetValuesBlocked_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 517 { 518 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 519 PetscBool roworiented = baij->roworiented; 520 PetscErrorCode ierr; 521 PetscInt i,j,ii,jj,row,col; 522 PetscInt rstart=baij->rstartbs; 523 PetscInt rend =mat->rmap->rend,stepval,bs=mat->rmap->bs,bs2=baij->bs2,nbs2=n*bs2; 524 PetscInt h1,key,size=baij->ht_size,idx,*HT=baij->ht,Nbs=baij->Nbs; 525 PetscReal tmp; 526 MatScalar **HD = baij->hd,*baij_a; 527 const PetscScalar *v_t,*value; 528 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 529 530 PetscFunctionBegin; 531 if (roworiented) stepval = (n-1)*bs; 532 else stepval = (m-1)*bs; 533 534 for (i=0; i<m; i++) { 535 if (PetscDefined(USE_DEBUG)) { 536 if (im[i] < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",im[i]); 537 if (im[i] >= baij->Mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],baij->Mbs-1); 538 } 539 row = im[i]; 540 v_t = v + i*nbs2; 541 if (row >= rstart && row < rend) { 542 for (j=0; j<n; j++) { 543 col = in[j]; 544 545 /* Look up into the Hash Table */ 546 key = row*Nbs+col+1; 547 h1 = HASH(size,key,tmp); 548 549 idx = h1; 550 if (PetscDefined(USE_DEBUG)) { 551 total_ct++; 552 insert_ct++; 553 if (HT[idx] != key) { 554 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++) ; 555 if (idx == size) { 556 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++) ; 557 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 558 } 559 } 560 } else if (HT[idx] != key) { 561 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++) ; 562 if (idx == size) { 563 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++) ; 564 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 565 } 566 } 567 baij_a = HD[idx]; 568 if (roworiented) { 569 /*value = v + i*(stepval+bs)*bs + j*bs;*/ 570 /* value = v + (i*(stepval+bs)+j)*bs; */ 571 value = v_t; 572 v_t += bs; 573 if (addv == ADD_VALUES) { 574 for (ii=0; ii<bs; ii++,value+=stepval) { 575 for (jj=ii; jj<bs2; jj+=bs) { 576 baij_a[jj] += *value++; 577 } 578 } 579 } else { 580 for (ii=0; ii<bs; ii++,value+=stepval) { 581 for (jj=ii; jj<bs2; jj+=bs) { 582 baij_a[jj] = *value++; 583 } 584 } 585 } 586 } else { 587 value = v + j*(stepval+bs)*bs + i*bs; 588 if (addv == ADD_VALUES) { 589 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 590 for (jj=0; jj<bs; jj++) { 591 baij_a[jj] += *value++; 592 } 593 } 594 } else { 595 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 596 for (jj=0; jj<bs; jj++) { 597 baij_a[jj] = *value++; 598 } 599 } 600 } 601 } 602 } 603 } else { 604 if (!baij->donotstash) { 605 if (roworiented) { 606 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 607 } else { 608 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 609 } 610 } 611 } 612 } 613 if (PetscDefined(USE_DEBUG)) { 614 baij->ht_total_ct += total_ct; 615 baij->ht_insert_ct += insert_ct; 616 } 617 PetscFunctionReturn(0); 618 } 619 620 PetscErrorCode MatGetValues_MPIBAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 621 { 622 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 623 PetscErrorCode ierr; 624 PetscInt bs = mat->rmap->bs,i,j,bsrstart = mat->rmap->rstart,bsrend = mat->rmap->rend; 625 PetscInt bscstart = mat->cmap->rstart,bscend = mat->cmap->rend,row,col,data; 626 627 PetscFunctionBegin; 628 for (i=0; i<m; i++) { 629 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 630 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); 631 if (idxm[i] >= bsrstart && idxm[i] < bsrend) { 632 row = idxm[i] - bsrstart; 633 for (j=0; j<n; j++) { 634 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 635 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); 636 if (idxn[j] >= bscstart && idxn[j] < bscend) { 637 col = idxn[j] - bscstart; 638 ierr = MatGetValues_SeqBAIJ(baij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 639 } else { 640 if (!baij->colmap) { 641 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 642 } 643 #if defined(PETSC_USE_CTABLE) 644 ierr = PetscTableFind(baij->colmap,idxn[j]/bs+1,&data);CHKERRQ(ierr); 645 data--; 646 #else 647 data = baij->colmap[idxn[j]/bs]-1; 648 #endif 649 if ((data < 0) || (baij->garray[data/bs] != idxn[j]/bs)) *(v+i*n+j) = 0.0; 650 else { 651 col = data + idxn[j]%bs; 652 ierr = MatGetValues_SeqBAIJ(baij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 653 } 654 } 655 } 656 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 657 } 658 PetscFunctionReturn(0); 659 } 660 661 PetscErrorCode MatNorm_MPIBAIJ(Mat mat,NormType type,PetscReal *nrm) 662 { 663 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 664 Mat_SeqBAIJ *amat = (Mat_SeqBAIJ*)baij->A->data,*bmat = (Mat_SeqBAIJ*)baij->B->data; 665 PetscErrorCode ierr; 666 PetscInt i,j,bs2=baij->bs2,bs=baij->A->rmap->bs,nz,row,col; 667 PetscReal sum = 0.0; 668 MatScalar *v; 669 670 PetscFunctionBegin; 671 if (baij->size == 1) { 672 ierr = MatNorm(baij->A,type,nrm);CHKERRQ(ierr); 673 } else { 674 if (type == NORM_FROBENIUS) { 675 v = amat->a; 676 nz = amat->nz*bs2; 677 for (i=0; i<nz; i++) { 678 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 679 } 680 v = bmat->a; 681 nz = bmat->nz*bs2; 682 for (i=0; i<nz; i++) { 683 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 684 } 685 ierr = MPIU_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 686 *nrm = PetscSqrtReal(*nrm); 687 } else if (type == NORM_1) { /* max column sum */ 688 PetscReal *tmp,*tmp2; 689 PetscInt *jj,*garray=baij->garray,cstart=baij->rstartbs; 690 ierr = PetscCalloc1(mat->cmap->N,&tmp);CHKERRQ(ierr); 691 ierr = PetscMalloc1(mat->cmap->N,&tmp2);CHKERRQ(ierr); 692 v = amat->a; jj = amat->j; 693 for (i=0; i<amat->nz; i++) { 694 for (j=0; j<bs; j++) { 695 col = bs*(cstart + *jj) + j; /* column index */ 696 for (row=0; row<bs; row++) { 697 tmp[col] += PetscAbsScalar(*v); v++; 698 } 699 } 700 jj++; 701 } 702 v = bmat->a; jj = bmat->j; 703 for (i=0; i<bmat->nz; i++) { 704 for (j=0; j<bs; j++) { 705 col = bs*garray[*jj] + j; 706 for (row=0; row<bs; row++) { 707 tmp[col] += PetscAbsScalar(*v); v++; 708 } 709 } 710 jj++; 711 } 712 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 713 *nrm = 0.0; 714 for (j=0; j<mat->cmap->N; j++) { 715 if (tmp2[j] > *nrm) *nrm = tmp2[j]; 716 } 717 ierr = PetscFree(tmp);CHKERRQ(ierr); 718 ierr = PetscFree(tmp2);CHKERRQ(ierr); 719 } else if (type == NORM_INFINITY) { /* max row sum */ 720 PetscReal *sums; 721 ierr = PetscMalloc1(bs,&sums);CHKERRQ(ierr); 722 sum = 0.0; 723 for (j=0; j<amat->mbs; j++) { 724 for (row=0; row<bs; row++) sums[row] = 0.0; 725 v = amat->a + bs2*amat->i[j]; 726 nz = amat->i[j+1]-amat->i[j]; 727 for (i=0; i<nz; i++) { 728 for (col=0; col<bs; col++) { 729 for (row=0; row<bs; row++) { 730 sums[row] += PetscAbsScalar(*v); v++; 731 } 732 } 733 } 734 v = bmat->a + bs2*bmat->i[j]; 735 nz = bmat->i[j+1]-bmat->i[j]; 736 for (i=0; i<nz; i++) { 737 for (col=0; col<bs; col++) { 738 for (row=0; row<bs; row++) { 739 sums[row] += PetscAbsScalar(*v); v++; 740 } 741 } 742 } 743 for (row=0; row<bs; row++) { 744 if (sums[row] > sum) sum = sums[row]; 745 } 746 } 747 ierr = MPIU_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 748 ierr = PetscFree(sums);CHKERRQ(ierr); 749 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for this norm yet"); 750 } 751 PetscFunctionReturn(0); 752 } 753 754 /* 755 Creates the hash table, and sets the table 756 This table is created only once. 757 If new entried need to be added to the matrix 758 then the hash table has to be destroyed and 759 recreated. 760 */ 761 PetscErrorCode MatCreateHashTable_MPIBAIJ_Private(Mat mat,PetscReal factor) 762 { 763 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 764 Mat A = baij->A,B=baij->B; 765 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b=(Mat_SeqBAIJ*)B->data; 766 PetscInt i,j,k,nz=a->nz+b->nz,h1,*ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j; 767 PetscErrorCode ierr; 768 PetscInt ht_size,bs2=baij->bs2,rstart=baij->rstartbs; 769 PetscInt cstart=baij->cstartbs,*garray=baij->garray,row,col,Nbs=baij->Nbs; 770 PetscInt *HT,key; 771 MatScalar **HD; 772 PetscReal tmp; 773 #if defined(PETSC_USE_INFO) 774 PetscInt ct=0,max=0; 775 #endif 776 777 PetscFunctionBegin; 778 if (baij->ht) PetscFunctionReturn(0); 779 780 baij->ht_size = (PetscInt)(factor*nz); 781 ht_size = baij->ht_size; 782 783 /* Allocate Memory for Hash Table */ 784 ierr = PetscCalloc2(ht_size,&baij->hd,ht_size,&baij->ht);CHKERRQ(ierr); 785 HD = baij->hd; 786 HT = baij->ht; 787 788 /* Loop Over A */ 789 for (i=0; i<a->mbs; i++) { 790 for (j=ai[i]; j<ai[i+1]; j++) { 791 row = i+rstart; 792 col = aj[j]+cstart; 793 794 key = row*Nbs + col + 1; 795 h1 = HASH(ht_size,key,tmp); 796 for (k=0; k<ht_size; k++) { 797 if (!HT[(h1+k)%ht_size]) { 798 HT[(h1+k)%ht_size] = key; 799 HD[(h1+k)%ht_size] = a->a + j*bs2; 800 break; 801 #if defined(PETSC_USE_INFO) 802 } else { 803 ct++; 804 #endif 805 } 806 } 807 #if defined(PETSC_USE_INFO) 808 if (k> max) max = k; 809 #endif 810 } 811 } 812 /* Loop Over B */ 813 for (i=0; i<b->mbs; i++) { 814 for (j=bi[i]; j<bi[i+1]; j++) { 815 row = i+rstart; 816 col = garray[bj[j]]; 817 key = row*Nbs + col + 1; 818 h1 = HASH(ht_size,key,tmp); 819 for (k=0; k<ht_size; k++) { 820 if (!HT[(h1+k)%ht_size]) { 821 HT[(h1+k)%ht_size] = key; 822 HD[(h1+k)%ht_size] = b->a + j*bs2; 823 break; 824 #if defined(PETSC_USE_INFO) 825 } else { 826 ct++; 827 #endif 828 } 829 } 830 #if defined(PETSC_USE_INFO) 831 if (k> max) max = k; 832 #endif 833 } 834 } 835 836 /* Print Summary */ 837 #if defined(PETSC_USE_INFO) 838 for (i=0,j=0; i<ht_size; i++) { 839 if (HT[i]) j++; 840 } 841 ierr = PetscInfo2(mat,"Average Search = %5.2f,max search = %D\n",(!j)? 0.0:((PetscReal)(ct+j))/j,max);CHKERRQ(ierr); 842 #endif 843 PetscFunctionReturn(0); 844 } 845 846 PetscErrorCode MatAssemblyBegin_MPIBAIJ(Mat mat,MatAssemblyType mode) 847 { 848 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 849 PetscErrorCode ierr; 850 PetscInt nstash,reallocs; 851 852 PetscFunctionBegin; 853 if (baij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 854 855 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 856 ierr = MatStashScatterBegin_Private(mat,&mat->bstash,baij->rangebs);CHKERRQ(ierr); 857 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 858 ierr = PetscInfo2(mat,"Stash has %D entries,uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 859 ierr = MatStashGetInfo_Private(&mat->bstash,&nstash,&reallocs);CHKERRQ(ierr); 860 ierr = PetscInfo2(mat,"Block-Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 861 PetscFunctionReturn(0); 862 } 863 864 PetscErrorCode MatAssemblyEnd_MPIBAIJ(Mat mat,MatAssemblyType mode) 865 { 866 Mat_MPIBAIJ *baij=(Mat_MPIBAIJ*)mat->data; 867 Mat_SeqBAIJ *a =(Mat_SeqBAIJ*)baij->A->data; 868 PetscErrorCode ierr; 869 PetscInt i,j,rstart,ncols,flg,bs2=baij->bs2; 870 PetscInt *row,*col; 871 PetscBool r1,r2,r3,other_disassembled; 872 MatScalar *val; 873 PetscMPIInt n; 874 875 PetscFunctionBegin; 876 /* do not use 'b=(Mat_SeqBAIJ*)baij->B->data' as B can be reset in disassembly */ 877 if (!baij->donotstash && !mat->nooffprocentries) { 878 while (1) { 879 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 880 if (!flg) break; 881 882 for (i=0; i<n;) { 883 /* Now identify the consecutive vals belonging to the same row */ 884 for (j=i,rstart=row[j]; j<n; j++) { 885 if (row[j] != rstart) break; 886 } 887 if (j < n) ncols = j-i; 888 else ncols = n-i; 889 /* Now assemble all these values with a single function call */ 890 ierr = MatSetValues_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 891 i = j; 892 } 893 } 894 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 895 /* Now process the block-stash. Since the values are stashed column-oriented, 896 set the roworiented flag to column oriented, and after MatSetValues() 897 restore the original flags */ 898 r1 = baij->roworiented; 899 r2 = a->roworiented; 900 r3 = ((Mat_SeqBAIJ*)baij->B->data)->roworiented; 901 902 baij->roworiented = PETSC_FALSE; 903 a->roworiented = PETSC_FALSE; 904 905 (((Mat_SeqBAIJ*)baij->B->data))->roworiented = PETSC_FALSE; /* b->roworiented */ 906 while (1) { 907 ierr = MatStashScatterGetMesg_Private(&mat->bstash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 908 if (!flg) break; 909 910 for (i=0; i<n;) { 911 /* Now identify the consecutive vals belonging to the same row */ 912 for (j=i,rstart=row[j]; j<n; j++) { 913 if (row[j] != rstart) break; 914 } 915 if (j < n) ncols = j-i; 916 else ncols = n-i; 917 ierr = MatSetValuesBlocked_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i*bs2,mat->insertmode);CHKERRQ(ierr); 918 i = j; 919 } 920 } 921 ierr = MatStashScatterEnd_Private(&mat->bstash);CHKERRQ(ierr); 922 923 baij->roworiented = r1; 924 a->roworiented = r2; 925 926 ((Mat_SeqBAIJ*)baij->B->data)->roworiented = r3; /* b->roworiented */ 927 } 928 929 ierr = MatAssemblyBegin(baij->A,mode);CHKERRQ(ierr); 930 ierr = MatAssemblyEnd(baij->A,mode);CHKERRQ(ierr); 931 932 /* determine if any processor has disassembled, if so we must 933 also disassemble ourselfs, in order that we may reassemble. */ 934 /* 935 if nonzero structure of submatrix B cannot change then we know that 936 no processor disassembled thus we can skip this stuff 937 */ 938 if (!((Mat_SeqBAIJ*)baij->B->data)->nonew) { 939 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 940 if (mat->was_assembled && !other_disassembled) { 941 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 942 } 943 } 944 945 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 946 ierr = MatSetUpMultiply_MPIBAIJ(mat);CHKERRQ(ierr); 947 } 948 ierr = MatAssemblyBegin(baij->B,mode);CHKERRQ(ierr); 949 ierr = MatAssemblyEnd(baij->B,mode);CHKERRQ(ierr); 950 951 #if defined(PETSC_USE_INFO) 952 if (baij->ht && mode== MAT_FINAL_ASSEMBLY) { 953 ierr = PetscInfo1(mat,"Average Hash Table Search in MatSetValues = %5.2f\n",(double)((PetscReal)baij->ht_total_ct)/baij->ht_insert_ct);CHKERRQ(ierr); 954 955 baij->ht_total_ct = 0; 956 baij->ht_insert_ct = 0; 957 } 958 #endif 959 if (baij->ht_flag && !baij->ht && mode == MAT_FINAL_ASSEMBLY) { 960 ierr = MatCreateHashTable_MPIBAIJ_Private(mat,baij->ht_fact);CHKERRQ(ierr); 961 962 mat->ops->setvalues = MatSetValues_MPIBAIJ_HT; 963 mat->ops->setvaluesblocked = MatSetValuesBlocked_MPIBAIJ_HT; 964 } 965 966 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 967 968 baij->rowvalues = NULL; 969 970 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 971 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 972 PetscObjectState state = baij->A->nonzerostate + baij->B->nonzerostate; 973 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 974 } 975 PetscFunctionReturn(0); 976 } 977 978 extern PetscErrorCode MatView_SeqBAIJ(Mat,PetscViewer); 979 #include <petscdraw.h> 980 static PetscErrorCode MatView_MPIBAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 981 { 982 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 983 PetscErrorCode ierr; 984 PetscMPIInt rank = baij->rank; 985 PetscInt bs = mat->rmap->bs; 986 PetscBool iascii,isdraw; 987 PetscViewer sviewer; 988 PetscViewerFormat format; 989 990 PetscFunctionBegin; 991 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 992 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 993 if (iascii) { 994 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 995 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 996 MatInfo info; 997 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRMPI(ierr); 998 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 999 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1000 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D bs %D mem %g\n", 1001 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,mat->rmap->bs,(double)info.memory);CHKERRQ(ierr); 1002 ierr = MatGetInfo(baij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1003 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1004 ierr = MatGetInfo(baij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1005 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1006 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1007 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1008 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1009 ierr = VecScatterView(baij->Mvctx,viewer);CHKERRQ(ierr); 1010 PetscFunctionReturn(0); 1011 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1012 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 1013 PetscFunctionReturn(0); 1014 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1015 PetscFunctionReturn(0); 1016 } 1017 } 1018 1019 if (isdraw) { 1020 PetscDraw draw; 1021 PetscBool isnull; 1022 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1023 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1024 if (isnull) PetscFunctionReturn(0); 1025 } 1026 1027 { 1028 /* assemble the entire matrix onto first processor. */ 1029 Mat A; 1030 Mat_SeqBAIJ *Aloc; 1031 PetscInt M = mat->rmap->N,N = mat->cmap->N,*ai,*aj,col,i,j,k,*rvals,mbs = baij->mbs; 1032 MatScalar *a; 1033 const char *matname; 1034 1035 /* Here we are creating a temporary matrix, so will assume MPIBAIJ is acceptable */ 1036 /* Perhaps this should be the type of mat? */ 1037 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1038 if (!rank) { 1039 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1040 } else { 1041 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1042 } 1043 ierr = MatSetType(A,MATMPIBAIJ);CHKERRQ(ierr); 1044 ierr = MatMPIBAIJSetPreallocation(A,mat->rmap->bs,0,NULL,0,NULL);CHKERRQ(ierr); 1045 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1046 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1047 1048 /* copy over the A part */ 1049 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1050 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1051 ierr = PetscMalloc1(bs,&rvals);CHKERRQ(ierr); 1052 1053 for (i=0; i<mbs; i++) { 1054 rvals[0] = bs*(baij->rstartbs + i); 1055 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1056 for (j=ai[i]; j<ai[i+1]; j++) { 1057 col = (baij->cstartbs+aj[j])*bs; 1058 for (k=0; k<bs; k++) { 1059 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1060 col++; a += bs; 1061 } 1062 } 1063 } 1064 /* copy over the B part */ 1065 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1066 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1067 for (i=0; i<mbs; i++) { 1068 rvals[0] = bs*(baij->rstartbs + i); 1069 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1070 for (j=ai[i]; j<ai[i+1]; j++) { 1071 col = baij->garray[aj[j]]*bs; 1072 for (k=0; k<bs; k++) { 1073 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1074 col++; a += bs; 1075 } 1076 } 1077 } 1078 ierr = PetscFree(rvals);CHKERRQ(ierr); 1079 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1080 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1081 /* 1082 Everyone has to call to draw the matrix since the graphics waits are 1083 synchronized across all processors that share the PetscDraw object 1084 */ 1085 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1086 ierr = PetscObjectGetName((PetscObject)mat,&matname);CHKERRQ(ierr); 1087 if (!rank) { 1088 ierr = PetscObjectSetName((PetscObject)((Mat_MPIBAIJ*)(A->data))->A,matname);CHKERRQ(ierr); 1089 ierr = MatView_SeqBAIJ(((Mat_MPIBAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1090 } 1091 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1092 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1093 ierr = MatDestroy(&A);CHKERRQ(ierr); 1094 } 1095 PetscFunctionReturn(0); 1096 } 1097 1098 /* Used for both MPIBAIJ and MPISBAIJ matrices */ 1099 PetscErrorCode MatView_MPIBAIJ_Binary(Mat mat,PetscViewer viewer) 1100 { 1101 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)mat->data; 1102 Mat_SeqBAIJ *A = (Mat_SeqBAIJ*)aij->A->data; 1103 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)aij->B->data; 1104 const PetscInt *garray = aij->garray; 1105 PetscInt header[4],M,N,m,rs,cs,bs,nz,cnt,i,j,ja,jb,k,l; 1106 PetscInt *rowlens,*colidxs; 1107 PetscScalar *matvals; 1108 PetscErrorCode ierr; 1109 1110 PetscFunctionBegin; 1111 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 1112 1113 M = mat->rmap->N; 1114 N = mat->cmap->N; 1115 m = mat->rmap->n; 1116 rs = mat->rmap->rstart; 1117 cs = mat->cmap->rstart; 1118 bs = mat->rmap->bs; 1119 nz = bs*bs*(A->nz + B->nz); 1120 1121 /* write matrix header */ 1122 header[0] = MAT_FILE_CLASSID; 1123 header[1] = M; header[2] = N; header[3] = nz; 1124 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRMPI(ierr); 1125 ierr = PetscViewerBinaryWrite(viewer,header,4,PETSC_INT);CHKERRQ(ierr); 1126 1127 /* fill in and store row lengths */ 1128 ierr = PetscMalloc1(m,&rowlens);CHKERRQ(ierr); 1129 for (cnt=0, i=0; i<A->mbs; i++) 1130 for (j=0; j<bs; j++) 1131 rowlens[cnt++] = bs*(A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]); 1132 ierr = PetscViewerBinaryWriteAll(viewer,rowlens,m,rs,M,PETSC_INT);CHKERRQ(ierr); 1133 ierr = PetscFree(rowlens);CHKERRQ(ierr); 1134 1135 /* fill in and store column indices */ 1136 ierr = PetscMalloc1(nz,&colidxs);CHKERRQ(ierr); 1137 for (cnt=0, i=0; i<A->mbs; i++) { 1138 for (k=0; k<bs; k++) { 1139 for (jb=B->i[i]; jb<B->i[i+1]; jb++) { 1140 if (garray[B->j[jb]] > cs/bs) break; 1141 for (l=0; l<bs; l++) 1142 colidxs[cnt++] = bs*garray[B->j[jb]] + l; 1143 } 1144 for (ja=A->i[i]; ja<A->i[i+1]; ja++) 1145 for (l=0; l<bs; l++) 1146 colidxs[cnt++] = bs*A->j[ja] + l + cs; 1147 for (; jb<B->i[i+1]; jb++) 1148 for (l=0; l<bs; l++) 1149 colidxs[cnt++] = bs*garray[B->j[jb]] + l; 1150 } 1151 } 1152 if (cnt != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,nz); 1153 ierr = PetscViewerBinaryWriteAll(viewer,colidxs,nz,PETSC_DECIDE,PETSC_DECIDE,PETSC_INT);CHKERRQ(ierr); 1154 ierr = PetscFree(colidxs);CHKERRQ(ierr); 1155 1156 /* fill in and store nonzero values */ 1157 ierr = PetscMalloc1(nz,&matvals);CHKERRQ(ierr); 1158 for (cnt=0, i=0; i<A->mbs; i++) { 1159 for (k=0; k<bs; k++) { 1160 for (jb=B->i[i]; jb<B->i[i+1]; jb++) { 1161 if (garray[B->j[jb]] > cs/bs) break; 1162 for (l=0; l<bs; l++) 1163 matvals[cnt++] = B->a[bs*(bs*jb + l) + k]; 1164 } 1165 for (ja=A->i[i]; ja<A->i[i+1]; ja++) 1166 for (l=0; l<bs; l++) 1167 matvals[cnt++] = A->a[bs*(bs*ja + l) + k]; 1168 for (; jb<B->i[i+1]; jb++) 1169 for (l=0; l<bs; l++) 1170 matvals[cnt++] = B->a[bs*(bs*jb + l) + k]; 1171 } 1172 } 1173 ierr = PetscViewerBinaryWriteAll(viewer,matvals,nz,PETSC_DECIDE,PETSC_DECIDE,PETSC_SCALAR);CHKERRQ(ierr); 1174 ierr = PetscFree(matvals);CHKERRQ(ierr); 1175 1176 /* write block size option to the viewer's .info file */ 1177 ierr = MatView_Binary_BlockSizes(mat,viewer);CHKERRQ(ierr); 1178 PetscFunctionReturn(0); 1179 } 1180 1181 PetscErrorCode MatView_MPIBAIJ(Mat mat,PetscViewer viewer) 1182 { 1183 PetscErrorCode ierr; 1184 PetscBool iascii,isdraw,issocket,isbinary; 1185 1186 PetscFunctionBegin; 1187 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1188 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1189 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1190 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1191 if (iascii || isdraw || issocket) { 1192 ierr = MatView_MPIBAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1193 } else if (isbinary) { 1194 ierr = MatView_MPIBAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1195 } 1196 PetscFunctionReturn(0); 1197 } 1198 1199 PetscErrorCode MatDestroy_MPIBAIJ(Mat mat) 1200 { 1201 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1202 PetscErrorCode ierr; 1203 1204 PetscFunctionBegin; 1205 #if defined(PETSC_USE_LOG) 1206 PetscLogObjectState((PetscObject)mat,"Rows=%D,Cols=%D",mat->rmap->N,mat->cmap->N); 1207 #endif 1208 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1209 ierr = MatStashDestroy_Private(&mat->bstash);CHKERRQ(ierr); 1210 ierr = MatDestroy(&baij->A);CHKERRQ(ierr); 1211 ierr = MatDestroy(&baij->B);CHKERRQ(ierr); 1212 #if defined(PETSC_USE_CTABLE) 1213 ierr = PetscTableDestroy(&baij->colmap);CHKERRQ(ierr); 1214 #else 1215 ierr = PetscFree(baij->colmap);CHKERRQ(ierr); 1216 #endif 1217 ierr = PetscFree(baij->garray);CHKERRQ(ierr); 1218 ierr = VecDestroy(&baij->lvec);CHKERRQ(ierr); 1219 ierr = VecScatterDestroy(&baij->Mvctx);CHKERRQ(ierr); 1220 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 1221 ierr = PetscFree(baij->barray);CHKERRQ(ierr); 1222 ierr = PetscFree2(baij->hd,baij->ht);CHKERRQ(ierr); 1223 ierr = PetscFree(baij->rangebs);CHKERRQ(ierr); 1224 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1225 1226 ierr = PetscObjectChangeTypeName((PetscObject)mat,NULL);CHKERRQ(ierr); 1227 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1228 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1229 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1230 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1231 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1232 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatSetHashTableFactor_C",NULL);CHKERRQ(ierr); 1233 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1234 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpibstrm_C",NULL);CHKERRQ(ierr); 1235 #if defined(PETSC_HAVE_HYPRE) 1236 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_hypre_C",NULL);CHKERRQ(ierr); 1237 #endif 1238 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_is_C",NULL);CHKERRQ(ierr); 1239 PetscFunctionReturn(0); 1240 } 1241 1242 PetscErrorCode MatMult_MPIBAIJ(Mat A,Vec xx,Vec yy) 1243 { 1244 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1245 PetscErrorCode ierr; 1246 PetscInt nt; 1247 1248 PetscFunctionBegin; 1249 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 1250 if (nt != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A and xx"); 1251 ierr = VecGetLocalSize(yy,&nt);CHKERRQ(ierr); 1252 if (nt != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible parition of A and yy"); 1253 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1254 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 1255 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1256 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 PetscErrorCode MatMultAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1261 { 1262 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1263 PetscErrorCode ierr; 1264 1265 PetscFunctionBegin; 1266 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1267 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1268 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1269 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 1270 PetscFunctionReturn(0); 1271 } 1272 1273 PetscErrorCode MatMultTranspose_MPIBAIJ(Mat A,Vec xx,Vec yy) 1274 { 1275 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1276 PetscErrorCode ierr; 1277 1278 PetscFunctionBegin; 1279 /* do nondiagonal part */ 1280 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1281 /* do local part */ 1282 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1283 /* add partial results together */ 1284 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1285 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1286 PetscFunctionReturn(0); 1287 } 1288 1289 PetscErrorCode MatMultTransposeAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1290 { 1291 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1292 PetscErrorCode ierr; 1293 1294 PetscFunctionBegin; 1295 /* do nondiagonal part */ 1296 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1297 /* do local part */ 1298 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1299 /* add partial results together */ 1300 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1301 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1302 PetscFunctionReturn(0); 1303 } 1304 1305 /* 1306 This only works correctly for square matrices where the subblock A->A is the 1307 diagonal block 1308 */ 1309 PetscErrorCode MatGetDiagonal_MPIBAIJ(Mat A,Vec v) 1310 { 1311 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1312 PetscErrorCode ierr; 1313 1314 PetscFunctionBegin; 1315 if (A->rmap->N != A->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1316 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1317 PetscFunctionReturn(0); 1318 } 1319 1320 PetscErrorCode MatScale_MPIBAIJ(Mat A,PetscScalar aa) 1321 { 1322 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1323 PetscErrorCode ierr; 1324 1325 PetscFunctionBegin; 1326 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1327 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1328 PetscFunctionReturn(0); 1329 } 1330 1331 PetscErrorCode MatGetRow_MPIBAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1332 { 1333 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 1334 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1335 PetscErrorCode ierr; 1336 PetscInt bs = matin->rmap->bs,bs2 = mat->bs2,i,*cworkA,*cworkB,**pcA,**pcB; 1337 PetscInt nztot,nzA,nzB,lrow,brstart = matin->rmap->rstart,brend = matin->rmap->rend; 1338 PetscInt *cmap,*idx_p,cstart = mat->cstartbs; 1339 1340 PetscFunctionBegin; 1341 if (row < brstart || row >= brend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local rows"); 1342 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1343 mat->getrowactive = PETSC_TRUE; 1344 1345 if (!mat->rowvalues && (idx || v)) { 1346 /* 1347 allocate enough space to hold information from the longest row. 1348 */ 1349 Mat_SeqBAIJ *Aa = (Mat_SeqBAIJ*)mat->A->data,*Ba = (Mat_SeqBAIJ*)mat->B->data; 1350 PetscInt max = 1,mbs = mat->mbs,tmp; 1351 for (i=0; i<mbs; i++) { 1352 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1353 if (max < tmp) max = tmp; 1354 } 1355 ierr = PetscMalloc2(max*bs2,&mat->rowvalues,max*bs2,&mat->rowindices);CHKERRQ(ierr); 1356 } 1357 lrow = row - brstart; 1358 1359 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1360 if (!v) {pvA = NULL; pvB = NULL;} 1361 if (!idx) {pcA = NULL; if (!v) pcB = NULL;} 1362 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1363 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1364 nztot = nzA + nzB; 1365 1366 cmap = mat->garray; 1367 if (v || idx) { 1368 if (nztot) { 1369 /* Sort by increasing column numbers, assuming A and B already sorted */ 1370 PetscInt imark = -1; 1371 if (v) { 1372 *v = v_p = mat->rowvalues; 1373 for (i=0; i<nzB; i++) { 1374 if (cmap[cworkB[i]/bs] < cstart) v_p[i] = vworkB[i]; 1375 else break; 1376 } 1377 imark = i; 1378 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1379 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1380 } 1381 if (idx) { 1382 *idx = idx_p = mat->rowindices; 1383 if (imark > -1) { 1384 for (i=0; i<imark; i++) { 1385 idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs; 1386 } 1387 } else { 1388 for (i=0; i<nzB; i++) { 1389 if (cmap[cworkB[i]/bs] < cstart) idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs; 1390 else break; 1391 } 1392 imark = i; 1393 } 1394 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart*bs + cworkA[i]; 1395 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs ; 1396 } 1397 } else { 1398 if (idx) *idx = NULL; 1399 if (v) *v = NULL; 1400 } 1401 } 1402 *nz = nztot; 1403 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1404 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1405 PetscFunctionReturn(0); 1406 } 1407 1408 PetscErrorCode MatRestoreRow_MPIBAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1409 { 1410 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1411 1412 PetscFunctionBegin; 1413 if (!baij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow not called"); 1414 baij->getrowactive = PETSC_FALSE; 1415 PetscFunctionReturn(0); 1416 } 1417 1418 PetscErrorCode MatZeroEntries_MPIBAIJ(Mat A) 1419 { 1420 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1421 PetscErrorCode ierr; 1422 1423 PetscFunctionBegin; 1424 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 1425 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 1426 PetscFunctionReturn(0); 1427 } 1428 1429 PetscErrorCode MatGetInfo_MPIBAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1430 { 1431 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)matin->data; 1432 Mat A = a->A,B = a->B; 1433 PetscErrorCode ierr; 1434 PetscLogDouble isend[5],irecv[5]; 1435 1436 PetscFunctionBegin; 1437 info->block_size = (PetscReal)matin->rmap->bs; 1438 1439 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1440 1441 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1442 isend[3] = info->memory; isend[4] = info->mallocs; 1443 1444 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1445 1446 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1447 isend[3] += info->memory; isend[4] += info->mallocs; 1448 1449 if (flag == MAT_LOCAL) { 1450 info->nz_used = isend[0]; 1451 info->nz_allocated = isend[1]; 1452 info->nz_unneeded = isend[2]; 1453 info->memory = isend[3]; 1454 info->mallocs = isend[4]; 1455 } else if (flag == MAT_GLOBAL_MAX) { 1456 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_PETSCLOGDOUBLE,MPI_MAX,PetscObjectComm((PetscObject)matin));CHKERRMPI(ierr); 1457 1458 info->nz_used = irecv[0]; 1459 info->nz_allocated = irecv[1]; 1460 info->nz_unneeded = irecv[2]; 1461 info->memory = irecv[3]; 1462 info->mallocs = irecv[4]; 1463 } else if (flag == MAT_GLOBAL_SUM) { 1464 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_PETSCLOGDOUBLE,MPI_SUM,PetscObjectComm((PetscObject)matin));CHKERRMPI(ierr); 1465 1466 info->nz_used = irecv[0]; 1467 info->nz_allocated = irecv[1]; 1468 info->nz_unneeded = irecv[2]; 1469 info->memory = irecv[3]; 1470 info->mallocs = irecv[4]; 1471 } else SETERRQ1(PetscObjectComm((PetscObject)matin),PETSC_ERR_ARG_WRONG,"Unknown MatInfoType argument %d",(int)flag); 1472 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1473 info->fill_ratio_needed = 0; 1474 info->factor_mallocs = 0; 1475 PetscFunctionReturn(0); 1476 } 1477 1478 PetscErrorCode MatSetOption_MPIBAIJ(Mat A,MatOption op,PetscBool flg) 1479 { 1480 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1481 PetscErrorCode ierr; 1482 1483 PetscFunctionBegin; 1484 switch (op) { 1485 case MAT_NEW_NONZERO_LOCATIONS: 1486 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1487 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1488 case MAT_KEEP_NONZERO_PATTERN: 1489 case MAT_NEW_NONZERO_LOCATION_ERR: 1490 MatCheckPreallocated(A,1); 1491 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1492 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1493 break; 1494 case MAT_ROW_ORIENTED: 1495 MatCheckPreallocated(A,1); 1496 a->roworiented = flg; 1497 1498 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1499 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1500 break; 1501 case MAT_FORCE_DIAGONAL_ENTRIES: 1502 case MAT_SORTED_FULL: 1503 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1504 break; 1505 case MAT_IGNORE_OFF_PROC_ENTRIES: 1506 a->donotstash = flg; 1507 break; 1508 case MAT_USE_HASH_TABLE: 1509 a->ht_flag = flg; 1510 a->ht_fact = 1.39; 1511 break; 1512 case MAT_SYMMETRIC: 1513 case MAT_STRUCTURALLY_SYMMETRIC: 1514 case MAT_HERMITIAN: 1515 case MAT_SUBMAT_SINGLEIS: 1516 case MAT_SYMMETRY_ETERNAL: 1517 MatCheckPreallocated(A,1); 1518 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1519 break; 1520 default: 1521 SETERRQ1(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"unknown option %d",op); 1522 } 1523 PetscFunctionReturn(0); 1524 } 1525 1526 PetscErrorCode MatTranspose_MPIBAIJ(Mat A,MatReuse reuse,Mat *matout) 1527 { 1528 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data; 1529 Mat_SeqBAIJ *Aloc; 1530 Mat B; 1531 PetscErrorCode ierr; 1532 PetscInt M =A->rmap->N,N=A->cmap->N,*ai,*aj,i,*rvals,j,k,col; 1533 PetscInt bs=A->rmap->bs,mbs=baij->mbs; 1534 MatScalar *a; 1535 1536 PetscFunctionBegin; 1537 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_INPLACE_MATRIX) { 1538 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1539 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1540 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1541 /* Do not know preallocation information, but must set block size */ 1542 ierr = MatMPIBAIJSetPreallocation(B,A->rmap->bs,PETSC_DECIDE,NULL,PETSC_DECIDE,NULL);CHKERRQ(ierr); 1543 } else { 1544 B = *matout; 1545 } 1546 1547 /* copy over the A part */ 1548 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1549 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1550 ierr = PetscMalloc1(bs,&rvals);CHKERRQ(ierr); 1551 1552 for (i=0; i<mbs; i++) { 1553 rvals[0] = bs*(baij->rstartbs + i); 1554 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1555 for (j=ai[i]; j<ai[i+1]; j++) { 1556 col = (baij->cstartbs+aj[j])*bs; 1557 for (k=0; k<bs; k++) { 1558 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1559 1560 col++; a += bs; 1561 } 1562 } 1563 } 1564 /* copy over the B part */ 1565 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1566 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1567 for (i=0; i<mbs; i++) { 1568 rvals[0] = bs*(baij->rstartbs + i); 1569 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1570 for (j=ai[i]; j<ai[i+1]; j++) { 1571 col = baij->garray[aj[j]]*bs; 1572 for (k=0; k<bs; k++) { 1573 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1574 col++; 1575 a += bs; 1576 } 1577 } 1578 } 1579 ierr = PetscFree(rvals);CHKERRQ(ierr); 1580 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1581 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1582 1583 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) *matout = B; 1584 else { 1585 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1586 } 1587 PetscFunctionReturn(0); 1588 } 1589 1590 PetscErrorCode MatDiagonalScale_MPIBAIJ(Mat mat,Vec ll,Vec rr) 1591 { 1592 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1593 Mat a = baij->A,b = baij->B; 1594 PetscErrorCode ierr; 1595 PetscInt s1,s2,s3; 1596 1597 PetscFunctionBegin; 1598 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1599 if (rr) { 1600 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1601 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1602 /* Overlap communication with computation. */ 1603 ierr = VecScatterBegin(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1604 } 1605 if (ll) { 1606 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1607 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1608 ierr = (*b->ops->diagonalscale)(b,ll,NULL);CHKERRQ(ierr); 1609 } 1610 /* scale the diagonal block */ 1611 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 1612 1613 if (rr) { 1614 /* Do a scatter end and then right scale the off-diagonal block */ 1615 ierr = VecScatterEnd(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1616 ierr = (*b->ops->diagonalscale)(b,NULL,baij->lvec);CHKERRQ(ierr); 1617 } 1618 PetscFunctionReturn(0); 1619 } 1620 1621 PetscErrorCode MatZeroRows_MPIBAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1622 { 1623 Mat_MPIBAIJ *l = (Mat_MPIBAIJ *) A->data; 1624 PetscInt *lrows; 1625 PetscInt r, len; 1626 PetscBool cong; 1627 PetscErrorCode ierr; 1628 1629 PetscFunctionBegin; 1630 /* get locally owned rows */ 1631 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 1632 /* fix right hand side if needed */ 1633 if (x && b) { 1634 const PetscScalar *xx; 1635 PetscScalar *bb; 1636 1637 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1638 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1639 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 1640 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1641 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1642 } 1643 1644 /* actually zap the local rows */ 1645 /* 1646 Zero the required rows. If the "diagonal block" of the matrix 1647 is square and the user wishes to set the diagonal we use separate 1648 code so that MatSetValues() is not called for each diagonal allocating 1649 new memory, thus calling lots of mallocs and slowing things down. 1650 1651 */ 1652 /* must zero l->B before l->A because the (diag) case below may put values into l->B*/ 1653 ierr = MatZeroRows_SeqBAIJ(l->B,len,lrows,0.0,NULL,NULL);CHKERRQ(ierr); 1654 ierr = MatHasCongruentLayouts(A,&cong);CHKERRQ(ierr); 1655 if ((diag != 0.0) && cong) { 1656 ierr = MatZeroRows_SeqBAIJ(l->A,len,lrows,diag,NULL,NULL);CHKERRQ(ierr); 1657 } else if (diag != 0.0) { 1658 ierr = MatZeroRows_SeqBAIJ(l->A,len,lrows,0.0,NULL,NULL);CHKERRQ(ierr); 1659 if (((Mat_SeqBAIJ*)l->A->data)->nonew) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatZeroRows() on rectangular matrices cannot be used with the Mat options \n\ 1660 MAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 1661 for (r = 0; r < len; ++r) { 1662 const PetscInt row = lrows[r] + A->rmap->rstart; 1663 ierr = MatSetValues(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1664 } 1665 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1666 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1667 } else { 1668 ierr = MatZeroRows_SeqBAIJ(l->A,len,lrows,0.0,NULL,NULL);CHKERRQ(ierr); 1669 } 1670 ierr = PetscFree(lrows);CHKERRQ(ierr); 1671 1672 /* only change matrix nonzero state if pattern was allowed to be changed */ 1673 if (!((Mat_SeqBAIJ*)(l->A->data))->keepnonzeropattern) { 1674 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 1675 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 1676 } 1677 PetscFunctionReturn(0); 1678 } 1679 1680 PetscErrorCode MatZeroRowsColumns_MPIBAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1681 { 1682 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1683 PetscErrorCode ierr; 1684 PetscMPIInt n = A->rmap->n,p = 0; 1685 PetscInt i,j,k,r,len = 0,row,col,count; 1686 PetscInt *lrows,*owners = A->rmap->range; 1687 PetscSFNode *rrows; 1688 PetscSF sf; 1689 const PetscScalar *xx; 1690 PetscScalar *bb,*mask; 1691 Vec xmask,lmask; 1692 Mat_SeqBAIJ *baij = (Mat_SeqBAIJ*)l->B->data; 1693 PetscInt bs = A->rmap->bs, bs2 = baij->bs2; 1694 PetscScalar *aa; 1695 1696 PetscFunctionBegin; 1697 /* Create SF where leaves are input rows and roots are owned rows */ 1698 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 1699 for (r = 0; r < n; ++r) lrows[r] = -1; 1700 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 1701 for (r = 0; r < N; ++r) { 1702 const PetscInt idx = rows[r]; 1703 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 1704 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 1705 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 1706 } 1707 rrows[r].rank = p; 1708 rrows[r].index = rows[r] - owners[p]; 1709 } 1710 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 1711 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 1712 /* Collect flags for rows to be zeroed */ 1713 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 1714 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 1715 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1716 /* Compress and put in row numbers */ 1717 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 1718 /* zero diagonal part of matrix */ 1719 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 1720 /* handle off diagonal part of matrix */ 1721 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 1722 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 1723 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 1724 for (i=0; i<len; i++) bb[lrows[i]] = 1; 1725 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 1726 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1727 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1728 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 1729 if (x) { 1730 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1731 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1732 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 1733 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1734 } 1735 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 1736 /* remove zeroed rows of off diagonal matrix */ 1737 for (i = 0; i < len; ++i) { 1738 row = lrows[i]; 1739 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1740 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1741 for (k = 0; k < count; ++k) { 1742 aa[0] = 0.0; 1743 aa += bs; 1744 } 1745 } 1746 /* loop over all elements of off process part of matrix zeroing removed columns*/ 1747 for (i = 0; i < l->B->rmap->N; ++i) { 1748 row = i/bs; 1749 for (j = baij->i[row]; j < baij->i[row+1]; ++j) { 1750 for (k = 0; k < bs; ++k) { 1751 col = bs*baij->j[j] + k; 1752 if (PetscAbsScalar(mask[col])) { 1753 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1754 if (x) bb[i] -= aa[0]*xx[col]; 1755 aa[0] = 0.0; 1756 } 1757 } 1758 } 1759 } 1760 if (x) { 1761 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1762 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 1763 } 1764 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 1765 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 1766 ierr = PetscFree(lrows);CHKERRQ(ierr); 1767 1768 /* only change matrix nonzero state if pattern was allowed to be changed */ 1769 if (!((Mat_SeqBAIJ*)(l->A->data))->keepnonzeropattern) { 1770 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 1771 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 1772 } 1773 PetscFunctionReturn(0); 1774 } 1775 1776 PetscErrorCode MatSetUnfactored_MPIBAIJ(Mat A) 1777 { 1778 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1779 PetscErrorCode ierr; 1780 1781 PetscFunctionBegin; 1782 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 1783 PetscFunctionReturn(0); 1784 } 1785 1786 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat,MatDuplicateOption,Mat*); 1787 1788 PetscErrorCode MatEqual_MPIBAIJ(Mat A,Mat B,PetscBool *flag) 1789 { 1790 Mat_MPIBAIJ *matB = (Mat_MPIBAIJ*)B->data,*matA = (Mat_MPIBAIJ*)A->data; 1791 Mat a,b,c,d; 1792 PetscBool flg; 1793 PetscErrorCode ierr; 1794 1795 PetscFunctionBegin; 1796 a = matA->A; b = matA->B; 1797 c = matB->A; d = matB->B; 1798 1799 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 1800 if (flg) { 1801 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 1802 } 1803 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 1804 PetscFunctionReturn(0); 1805 } 1806 1807 PetscErrorCode MatCopy_MPIBAIJ(Mat A,Mat B,MatStructure str) 1808 { 1809 PetscErrorCode ierr; 1810 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1811 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 1812 1813 PetscFunctionBegin; 1814 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 1815 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 1816 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1817 } else { 1818 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 1819 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 1820 } 1821 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 1822 PetscFunctionReturn(0); 1823 } 1824 1825 PetscErrorCode MatSetUp_MPIBAIJ(Mat A) 1826 { 1827 PetscErrorCode ierr; 1828 1829 PetscFunctionBegin; 1830 ierr = MatMPIBAIJSetPreallocation(A,A->rmap->bs,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr); 1831 PetscFunctionReturn(0); 1832 } 1833 1834 PetscErrorCode MatAXPYGetPreallocation_MPIBAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 1835 { 1836 PetscErrorCode ierr; 1837 PetscInt bs = Y->rmap->bs,m = Y->rmap->N/bs; 1838 Mat_SeqBAIJ *x = (Mat_SeqBAIJ*)X->data; 1839 Mat_SeqBAIJ *y = (Mat_SeqBAIJ*)Y->data; 1840 1841 PetscFunctionBegin; 1842 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 1843 PetscFunctionReturn(0); 1844 } 1845 1846 PetscErrorCode MatAXPY_MPIBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1847 { 1848 PetscErrorCode ierr; 1849 Mat_MPIBAIJ *xx=(Mat_MPIBAIJ*)X->data,*yy=(Mat_MPIBAIJ*)Y->data; 1850 PetscBLASInt bnz,one=1; 1851 Mat_SeqBAIJ *x,*y; 1852 PetscInt bs2 = Y->rmap->bs*Y->rmap->bs; 1853 1854 PetscFunctionBegin; 1855 if (str == SAME_NONZERO_PATTERN) { 1856 PetscScalar alpha = a; 1857 x = (Mat_SeqBAIJ*)xx->A->data; 1858 y = (Mat_SeqBAIJ*)yy->A->data; 1859 ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); 1860 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1861 x = (Mat_SeqBAIJ*)xx->B->data; 1862 y = (Mat_SeqBAIJ*)yy->B->data; 1863 ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); 1864 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1865 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1866 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1867 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1868 } else { 1869 Mat B; 1870 PetscInt *nnz_d,*nnz_o,bs=Y->rmap->bs; 1871 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 1872 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 1873 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 1874 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 1875 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 1876 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 1877 ierr = MatSetType(B,MATMPIBAIJ);CHKERRQ(ierr); 1878 ierr = MatAXPYGetPreallocation_SeqBAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 1879 ierr = MatAXPYGetPreallocation_MPIBAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 1880 ierr = MatMPIBAIJSetPreallocation(B,bs,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 1881 /* MatAXPY_BasicWithPreallocation() for BAIJ matrix is much slower than AIJ, even for bs=1 ! */ 1882 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 1883 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 1884 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 1885 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatConjugate_MPIBAIJ(Mat mat) 1891 { 1892 #if defined(PETSC_USE_COMPLEX) 1893 PetscErrorCode ierr; 1894 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)mat->data; 1895 1896 PetscFunctionBegin; 1897 ierr = MatConjugate_SeqBAIJ(a->A);CHKERRQ(ierr); 1898 ierr = MatConjugate_SeqBAIJ(a->B);CHKERRQ(ierr); 1899 #else 1900 PetscFunctionBegin; 1901 #endif 1902 PetscFunctionReturn(0); 1903 } 1904 1905 PetscErrorCode MatRealPart_MPIBAIJ(Mat A) 1906 { 1907 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1908 PetscErrorCode ierr; 1909 1910 PetscFunctionBegin; 1911 ierr = MatRealPart(a->A);CHKERRQ(ierr); 1912 ierr = MatRealPart(a->B);CHKERRQ(ierr); 1913 PetscFunctionReturn(0); 1914 } 1915 1916 PetscErrorCode MatImaginaryPart_MPIBAIJ(Mat A) 1917 { 1918 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1919 PetscErrorCode ierr; 1920 1921 PetscFunctionBegin; 1922 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 1923 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 1924 PetscFunctionReturn(0); 1925 } 1926 1927 PetscErrorCode MatCreateSubMatrix_MPIBAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 1928 { 1929 PetscErrorCode ierr; 1930 IS iscol_local; 1931 PetscInt csize; 1932 1933 PetscFunctionBegin; 1934 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 1935 if (call == MAT_REUSE_MATRIX) { 1936 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 1937 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 1938 } else { 1939 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 1940 } 1941 ierr = MatCreateSubMatrix_MPIBAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 1942 if (call == MAT_INITIAL_MATRIX) { 1943 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 1944 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 1945 } 1946 PetscFunctionReturn(0); 1947 } 1948 1949 /* 1950 Not great since it makes two copies of the submatrix, first an SeqBAIJ 1951 in local and then by concatenating the local matrices the end result. 1952 Writing it directly would be much like MatCreateSubMatrices_MPIBAIJ(). 1953 This routine is used for BAIJ and SBAIJ matrices (unfortunate dependency). 1954 */ 1955 PetscErrorCode MatCreateSubMatrix_MPIBAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 1956 { 1957 PetscErrorCode ierr; 1958 PetscMPIInt rank,size; 1959 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs; 1960 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 1961 Mat M,Mreuse; 1962 MatScalar *vwork,*aa; 1963 MPI_Comm comm; 1964 IS isrow_new, iscol_new; 1965 Mat_SeqBAIJ *aij; 1966 1967 PetscFunctionBegin; 1968 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 1969 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 1970 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1971 /* The compression and expansion should be avoided. Doesn't point 1972 out errors, might change the indices, hence buggey */ 1973 ierr = ISCompressIndicesGeneral(mat->rmap->N,mat->rmap->n,mat->rmap->bs,1,&isrow,&isrow_new);CHKERRQ(ierr); 1974 ierr = ISCompressIndicesGeneral(mat->cmap->N,mat->cmap->n,mat->cmap->bs,1,&iscol,&iscol_new);CHKERRQ(ierr); 1975 1976 if (call == MAT_REUSE_MATRIX) { 1977 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 1978 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 1979 ierr = MatCreateSubMatrices_MPIBAIJ_local(mat,1,&isrow_new,&iscol_new,MAT_REUSE_MATRIX,&Mreuse);CHKERRQ(ierr); 1980 } else { 1981 ierr = MatCreateSubMatrices_MPIBAIJ_local(mat,1,&isrow_new,&iscol_new,MAT_INITIAL_MATRIX,&Mreuse);CHKERRQ(ierr); 1982 } 1983 ierr = ISDestroy(&isrow_new);CHKERRQ(ierr); 1984 ierr = ISDestroy(&iscol_new);CHKERRQ(ierr); 1985 /* 1986 m - number of local rows 1987 n - number of columns (same on all processors) 1988 rstart - first row in new global matrix generated 1989 */ 1990 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1991 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 1992 m = m/bs; 1993 n = n/bs; 1994 1995 if (call == MAT_INITIAL_MATRIX) { 1996 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 1997 ii = aij->i; 1998 jj = aij->j; 1999 2000 /* 2001 Determine the number of non-zeros in the diagonal and off-diagonal 2002 portions of the matrix in order to do correct preallocation 2003 */ 2004 2005 /* first get start and end of "diagonal" columns */ 2006 if (csize == PETSC_DECIDE) { 2007 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 2008 if (mglobal == n*bs) { /* square matrix */ 2009 nlocal = m; 2010 } else { 2011 nlocal = n/size + ((n % size) > rank); 2012 } 2013 } else { 2014 nlocal = csize/bs; 2015 } 2016 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRMPI(ierr); 2017 rstart = rend - nlocal; 2018 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); 2019 2020 /* next, compute all the lengths */ 2021 ierr = PetscMalloc2(m+1,&dlens,m+1,&olens);CHKERRQ(ierr); 2022 for (i=0; i<m; i++) { 2023 jend = ii[i+1] - ii[i]; 2024 olen = 0; 2025 dlen = 0; 2026 for (j=0; j<jend; j++) { 2027 if (*jj < rstart || *jj >= rend) olen++; 2028 else dlen++; 2029 jj++; 2030 } 2031 olens[i] = olen; 2032 dlens[i] = dlen; 2033 } 2034 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 2035 ierr = MatSetSizes(M,bs*m,bs*nlocal,PETSC_DECIDE,bs*n);CHKERRQ(ierr); 2036 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 2037 ierr = MatMPIBAIJSetPreallocation(M,bs,0,dlens,0,olens);CHKERRQ(ierr); 2038 ierr = MatMPISBAIJSetPreallocation(M,bs,0,dlens,0,olens);CHKERRQ(ierr); 2039 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 2040 } else { 2041 PetscInt ml,nl; 2042 2043 M = *newmat; 2044 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 2045 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 2046 ierr = MatZeroEntries(M);CHKERRQ(ierr); 2047 /* 2048 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 2049 rather than the slower MatSetValues(). 2050 */ 2051 M->was_assembled = PETSC_TRUE; 2052 M->assembled = PETSC_FALSE; 2053 } 2054 ierr = MatSetOption(M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 2055 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 2056 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 2057 ii = aij->i; 2058 jj = aij->j; 2059 aa = aij->a; 2060 for (i=0; i<m; i++) { 2061 row = rstart/bs + i; 2062 nz = ii[i+1] - ii[i]; 2063 cwork = jj; jj += nz; 2064 vwork = aa; aa += nz*bs*bs; 2065 ierr = MatSetValuesBlocked_MPIBAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 2066 } 2067 2068 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2069 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2070 *newmat = M; 2071 2072 /* save submatrix used in processor for next request */ 2073 if (call == MAT_INITIAL_MATRIX) { 2074 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 2075 ierr = PetscObjectDereference((PetscObject)Mreuse);CHKERRQ(ierr); 2076 } 2077 PetscFunctionReturn(0); 2078 } 2079 2080 PetscErrorCode MatPermute_MPIBAIJ(Mat A,IS rowp,IS colp,Mat *B) 2081 { 2082 MPI_Comm comm,pcomm; 2083 PetscInt clocal_size,nrows; 2084 const PetscInt *rows; 2085 PetscMPIInt size; 2086 IS crowp,lcolp; 2087 PetscErrorCode ierr; 2088 2089 PetscFunctionBegin; 2090 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 2091 /* make a collective version of 'rowp' */ 2092 ierr = PetscObjectGetComm((PetscObject)rowp,&pcomm);CHKERRQ(ierr); 2093 if (pcomm==comm) { 2094 crowp = rowp; 2095 } else { 2096 ierr = ISGetSize(rowp,&nrows);CHKERRQ(ierr); 2097 ierr = ISGetIndices(rowp,&rows);CHKERRQ(ierr); 2098 ierr = ISCreateGeneral(comm,nrows,rows,PETSC_COPY_VALUES,&crowp);CHKERRQ(ierr); 2099 ierr = ISRestoreIndices(rowp,&rows);CHKERRQ(ierr); 2100 } 2101 ierr = ISSetPermutation(crowp);CHKERRQ(ierr); 2102 /* make a local version of 'colp' */ 2103 ierr = PetscObjectGetComm((PetscObject)colp,&pcomm);CHKERRQ(ierr); 2104 ierr = MPI_Comm_size(pcomm,&size);CHKERRMPI(ierr); 2105 if (size==1) { 2106 lcolp = colp; 2107 } else { 2108 ierr = ISAllGather(colp,&lcolp);CHKERRQ(ierr); 2109 } 2110 ierr = ISSetPermutation(lcolp);CHKERRQ(ierr); 2111 /* now we just get the submatrix */ 2112 ierr = MatGetLocalSize(A,NULL,&clocal_size);CHKERRQ(ierr); 2113 ierr = MatCreateSubMatrix_MPIBAIJ_Private(A,crowp,lcolp,clocal_size,MAT_INITIAL_MATRIX,B);CHKERRQ(ierr); 2114 /* clean up */ 2115 if (pcomm!=comm) { 2116 ierr = ISDestroy(&crowp);CHKERRQ(ierr); 2117 } 2118 if (size>1) { 2119 ierr = ISDestroy(&lcolp);CHKERRQ(ierr); 2120 } 2121 PetscFunctionReturn(0); 2122 } 2123 2124 PetscErrorCode MatGetGhosts_MPIBAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 2125 { 2126 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*) mat->data; 2127 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 2128 2129 PetscFunctionBegin; 2130 if (nghosts) *nghosts = B->nbs; 2131 if (ghosts) *ghosts = baij->garray; 2132 PetscFunctionReturn(0); 2133 } 2134 2135 PetscErrorCode MatGetSeqNonzeroStructure_MPIBAIJ(Mat A,Mat *newmat) 2136 { 2137 Mat B; 2138 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2139 Mat_SeqBAIJ *ad = (Mat_SeqBAIJ*)a->A->data,*bd = (Mat_SeqBAIJ*)a->B->data; 2140 Mat_SeqAIJ *b; 2141 PetscErrorCode ierr; 2142 PetscMPIInt size,rank,*recvcounts = NULL,*displs = NULL; 2143 PetscInt sendcount,i,*rstarts = A->rmap->range,n,cnt,j,bs = A->rmap->bs; 2144 PetscInt m,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf; 2145 2146 PetscFunctionBegin; 2147 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);CHKERRMPI(ierr); 2148 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRMPI(ierr); 2149 2150 /* ---------------------------------------------------------------- 2151 Tell every processor the number of nonzeros per row 2152 */ 2153 ierr = PetscMalloc1(A->rmap->N/bs,&lens);CHKERRQ(ierr); 2154 for (i=A->rmap->rstart/bs; i<A->rmap->rend/bs; i++) { 2155 lens[i] = ad->i[i-A->rmap->rstart/bs+1] - ad->i[i-A->rmap->rstart/bs] + bd->i[i-A->rmap->rstart/bs+1] - bd->i[i-A->rmap->rstart/bs]; 2156 } 2157 ierr = PetscMalloc1(2*size,&recvcounts);CHKERRQ(ierr); 2158 displs = recvcounts + size; 2159 for (i=0; i<size; i++) { 2160 recvcounts[i] = A->rmap->range[i+1]/bs - A->rmap->range[i]/bs; 2161 displs[i] = A->rmap->range[i]/bs; 2162 } 2163 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2164 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2165 #else 2166 sendcount = A->rmap->rend/bs - A->rmap->rstart/bs; 2167 ierr = MPI_Allgatherv(lens+A->rmap->rstart/bs,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2168 #endif 2169 /* --------------------------------------------------------------- 2170 Create the sequential matrix of the same type as the local block diagonal 2171 */ 2172 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 2173 ierr = MatSetSizes(B,A->rmap->N/bs,A->cmap->N/bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2174 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 2175 ierr = MatSeqAIJSetPreallocation(B,0,lens);CHKERRQ(ierr); 2176 b = (Mat_SeqAIJ*)B->data; 2177 2178 /*-------------------------------------------------------------------- 2179 Copy my part of matrix column indices over 2180 */ 2181 sendcount = ad->nz + bd->nz; 2182 jsendbuf = b->j + b->i[rstarts[rank]/bs]; 2183 a_jsendbuf = ad->j; 2184 b_jsendbuf = bd->j; 2185 n = A->rmap->rend/bs - A->rmap->rstart/bs; 2186 cnt = 0; 2187 for (i=0; i<n; i++) { 2188 2189 /* put in lower diagonal portion */ 2190 m = bd->i[i+1] - bd->i[i]; 2191 while (m > 0) { 2192 /* is it above diagonal (in bd (compressed) numbering) */ 2193 if (garray[*b_jsendbuf] > A->rmap->rstart/bs + i) break; 2194 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2195 m--; 2196 } 2197 2198 /* put in diagonal portion */ 2199 for (j=ad->i[i]; j<ad->i[i+1]; j++) { 2200 jsendbuf[cnt++] = A->rmap->rstart/bs + *a_jsendbuf++; 2201 } 2202 2203 /* put in upper diagonal portion */ 2204 while (m-- > 0) { 2205 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2206 } 2207 } 2208 if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt); 2209 2210 /*-------------------------------------------------------------------- 2211 Gather all column indices to all processors 2212 */ 2213 for (i=0; i<size; i++) { 2214 recvcounts[i] = 0; 2215 for (j=A->rmap->range[i]/bs; j<A->rmap->range[i+1]/bs; j++) { 2216 recvcounts[i] += lens[j]; 2217 } 2218 } 2219 displs[0] = 0; 2220 for (i=1; i<size; i++) { 2221 displs[i] = displs[i-1] + recvcounts[i-1]; 2222 } 2223 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2224 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2225 #else 2226 ierr = MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2227 #endif 2228 /*-------------------------------------------------------------------- 2229 Assemble the matrix into useable form (note numerical values not yet set) 2230 */ 2231 /* set the b->ilen (length of each row) values */ 2232 ierr = PetscArraycpy(b->ilen,lens,A->rmap->N/bs);CHKERRQ(ierr); 2233 /* set the b->i indices */ 2234 b->i[0] = 0; 2235 for (i=1; i<=A->rmap->N/bs; i++) { 2236 b->i[i] = b->i[i-1] + lens[i-1]; 2237 } 2238 ierr = PetscFree(lens);CHKERRQ(ierr); 2239 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2240 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2241 ierr = PetscFree(recvcounts);CHKERRQ(ierr); 2242 2243 if (A->symmetric) { 2244 ierr = MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2245 } else if (A->hermitian) { 2246 ierr = MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr); 2247 } else if (A->structurally_symmetric) { 2248 ierr = MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2249 } 2250 *newmat = B; 2251 PetscFunctionReturn(0); 2252 } 2253 2254 PetscErrorCode MatSOR_MPIBAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 2255 { 2256 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 2257 PetscErrorCode ierr; 2258 Vec bb1 = NULL; 2259 2260 PetscFunctionBegin; 2261 if (flag == SOR_APPLY_UPPER) { 2262 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2263 PetscFunctionReturn(0); 2264 } 2265 2266 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS) { 2267 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 2268 } 2269 2270 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 2271 if (flag & SOR_ZERO_INITIAL_GUESS) { 2272 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2273 its--; 2274 } 2275 2276 while (its--) { 2277 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2278 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2279 2280 /* update rhs: bb1 = bb - B*x */ 2281 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2282 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2283 2284 /* local sweep */ 2285 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2286 } 2287 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 2288 if (flag & SOR_ZERO_INITIAL_GUESS) { 2289 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2290 its--; 2291 } 2292 while (its--) { 2293 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2294 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2295 2296 /* update rhs: bb1 = bb - B*x */ 2297 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2298 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2299 2300 /* local sweep */ 2301 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2302 } 2303 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 2304 if (flag & SOR_ZERO_INITIAL_GUESS) { 2305 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2306 its--; 2307 } 2308 while (its--) { 2309 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2310 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2311 2312 /* update rhs: bb1 = bb - B*x */ 2313 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2314 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2315 2316 /* local sweep */ 2317 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2318 } 2319 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel version of SOR requested not supported"); 2320 2321 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 2322 PetscFunctionReturn(0); 2323 } 2324 2325 PetscErrorCode MatGetColumnNorms_MPIBAIJ(Mat A,NormType type,PetscReal *norms) 2326 { 2327 PetscErrorCode ierr; 2328 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)A->data; 2329 PetscInt N,i,*garray = aij->garray; 2330 PetscInt ib,jb,bs = A->rmap->bs; 2331 Mat_SeqBAIJ *a_aij = (Mat_SeqBAIJ*) aij->A->data; 2332 MatScalar *a_val = a_aij->a; 2333 Mat_SeqBAIJ *b_aij = (Mat_SeqBAIJ*) aij->B->data; 2334 MatScalar *b_val = b_aij->a; 2335 PetscReal *work; 2336 2337 PetscFunctionBegin; 2338 ierr = MatGetSize(A,NULL,&N);CHKERRQ(ierr); 2339 ierr = PetscCalloc1(N,&work);CHKERRQ(ierr); 2340 if (type == NORM_2) { 2341 for (i=a_aij->i[0]; i<a_aij->i[aij->A->rmap->n/bs]; i++) { 2342 for (jb=0; jb<bs; jb++) { 2343 for (ib=0; ib<bs; ib++) { 2344 work[A->cmap->rstart + a_aij->j[i] * bs + jb] += PetscAbsScalar(*a_val * *a_val); 2345 a_val++; 2346 } 2347 } 2348 } 2349 for (i=b_aij->i[0]; i<b_aij->i[aij->B->rmap->n/bs]; i++) { 2350 for (jb=0; jb<bs; jb++) { 2351 for (ib=0; ib<bs; ib++) { 2352 work[garray[b_aij->j[i]] * bs + jb] += PetscAbsScalar(*b_val * *b_val); 2353 b_val++; 2354 } 2355 } 2356 } 2357 } else if (type == NORM_1) { 2358 for (i=a_aij->i[0]; i<a_aij->i[aij->A->rmap->n/bs]; i++) { 2359 for (jb=0; jb<bs; jb++) { 2360 for (ib=0; ib<bs; ib++) { 2361 work[A->cmap->rstart + a_aij->j[i] * bs + jb] += PetscAbsScalar(*a_val); 2362 a_val++; 2363 } 2364 } 2365 } 2366 for (i=b_aij->i[0]; i<b_aij->i[aij->B->rmap->n/bs]; i++) { 2367 for (jb=0; jb<bs; jb++) { 2368 for (ib=0; ib<bs; ib++) { 2369 work[garray[b_aij->j[i]] * bs + jb] += PetscAbsScalar(*b_val); 2370 b_val++; 2371 } 2372 } 2373 } 2374 } else if (type == NORM_INFINITY) { 2375 for (i=a_aij->i[0]; i<a_aij->i[aij->A->rmap->n/bs]; i++) { 2376 for (jb=0; jb<bs; jb++) { 2377 for (ib=0; ib<bs; ib++) { 2378 int col = A->cmap->rstart + a_aij->j[i] * bs + jb; 2379 work[col] = PetscMax(PetscAbsScalar(*a_val), work[col]); 2380 a_val++; 2381 } 2382 } 2383 } 2384 for (i=b_aij->i[0]; i<b_aij->i[aij->B->rmap->n/bs]; i++) { 2385 for (jb=0; jb<bs; jb++) { 2386 for (ib=0; ib<bs; ib++) { 2387 int col = garray[b_aij->j[i]] * bs + jb; 2388 work[col] = PetscMax(PetscAbsScalar(*b_val), work[col]); 2389 b_val++; 2390 } 2391 } 2392 } 2393 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 2394 if (type == NORM_INFINITY) { 2395 ierr = MPIU_Allreduce(work,norms,N,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2396 } else { 2397 ierr = MPIU_Allreduce(work,norms,N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2398 } 2399 ierr = PetscFree(work);CHKERRQ(ierr); 2400 if (type == NORM_2) { 2401 for (i=0; i<N; i++) norms[i] = PetscSqrtReal(norms[i]); 2402 } 2403 PetscFunctionReturn(0); 2404 } 2405 2406 PetscErrorCode MatInvertBlockDiagonal_MPIBAIJ(Mat A,const PetscScalar **values) 2407 { 2408 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; 2409 PetscErrorCode ierr; 2410 2411 PetscFunctionBegin; 2412 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2413 A->factorerrortype = a->A->factorerrortype; 2414 A->factorerror_zeropivot_value = a->A->factorerror_zeropivot_value; 2415 A->factorerror_zeropivot_row = a->A->factorerror_zeropivot_row; 2416 PetscFunctionReturn(0); 2417 } 2418 2419 PetscErrorCode MatShift_MPIBAIJ(Mat Y,PetscScalar a) 2420 { 2421 PetscErrorCode ierr; 2422 Mat_MPIBAIJ *maij = (Mat_MPIBAIJ*)Y->data; 2423 Mat_SeqBAIJ *aij = (Mat_SeqBAIJ*)maij->A->data; 2424 2425 PetscFunctionBegin; 2426 if (!Y->preallocated) { 2427 ierr = MatMPIBAIJSetPreallocation(Y,Y->rmap->bs,1,NULL,0,NULL);CHKERRQ(ierr); 2428 } else if (!aij->nz) { 2429 PetscInt nonew = aij->nonew; 2430 ierr = MatSeqBAIJSetPreallocation(maij->A,Y->rmap->bs,1,NULL);CHKERRQ(ierr); 2431 aij->nonew = nonew; 2432 } 2433 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2434 PetscFunctionReturn(0); 2435 } 2436 2437 PetscErrorCode MatMissingDiagonal_MPIBAIJ(Mat A,PetscBool *missing,PetscInt *d) 2438 { 2439 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2440 PetscErrorCode ierr; 2441 2442 PetscFunctionBegin; 2443 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2444 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2445 if (d) { 2446 PetscInt rstart; 2447 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2448 *d += rstart/A->rmap->bs; 2449 2450 } 2451 PetscFunctionReturn(0); 2452 } 2453 2454 PetscErrorCode MatGetDiagonalBlock_MPIBAIJ(Mat A,Mat *a) 2455 { 2456 PetscFunctionBegin; 2457 *a = ((Mat_MPIBAIJ*)A->data)->A; 2458 PetscFunctionReturn(0); 2459 } 2460 2461 /* -------------------------------------------------------------------*/ 2462 static struct _MatOps MatOps_Values = {MatSetValues_MPIBAIJ, 2463 MatGetRow_MPIBAIJ, 2464 MatRestoreRow_MPIBAIJ, 2465 MatMult_MPIBAIJ, 2466 /* 4*/ MatMultAdd_MPIBAIJ, 2467 MatMultTranspose_MPIBAIJ, 2468 MatMultTransposeAdd_MPIBAIJ, 2469 NULL, 2470 NULL, 2471 NULL, 2472 /*10*/ NULL, 2473 NULL, 2474 NULL, 2475 MatSOR_MPIBAIJ, 2476 MatTranspose_MPIBAIJ, 2477 /*15*/ MatGetInfo_MPIBAIJ, 2478 MatEqual_MPIBAIJ, 2479 MatGetDiagonal_MPIBAIJ, 2480 MatDiagonalScale_MPIBAIJ, 2481 MatNorm_MPIBAIJ, 2482 /*20*/ MatAssemblyBegin_MPIBAIJ, 2483 MatAssemblyEnd_MPIBAIJ, 2484 MatSetOption_MPIBAIJ, 2485 MatZeroEntries_MPIBAIJ, 2486 /*24*/ MatZeroRows_MPIBAIJ, 2487 NULL, 2488 NULL, 2489 NULL, 2490 NULL, 2491 /*29*/ MatSetUp_MPIBAIJ, 2492 NULL, 2493 NULL, 2494 MatGetDiagonalBlock_MPIBAIJ, 2495 NULL, 2496 /*34*/ MatDuplicate_MPIBAIJ, 2497 NULL, 2498 NULL, 2499 NULL, 2500 NULL, 2501 /*39*/ MatAXPY_MPIBAIJ, 2502 MatCreateSubMatrices_MPIBAIJ, 2503 MatIncreaseOverlap_MPIBAIJ, 2504 MatGetValues_MPIBAIJ, 2505 MatCopy_MPIBAIJ, 2506 /*44*/ NULL, 2507 MatScale_MPIBAIJ, 2508 MatShift_MPIBAIJ, 2509 NULL, 2510 MatZeroRowsColumns_MPIBAIJ, 2511 /*49*/ NULL, 2512 NULL, 2513 NULL, 2514 NULL, 2515 NULL, 2516 /*54*/ MatFDColoringCreate_MPIXAIJ, 2517 NULL, 2518 MatSetUnfactored_MPIBAIJ, 2519 MatPermute_MPIBAIJ, 2520 MatSetValuesBlocked_MPIBAIJ, 2521 /*59*/ MatCreateSubMatrix_MPIBAIJ, 2522 MatDestroy_MPIBAIJ, 2523 MatView_MPIBAIJ, 2524 NULL, 2525 NULL, 2526 /*64*/ NULL, 2527 NULL, 2528 NULL, 2529 NULL, 2530 NULL, 2531 /*69*/ MatGetRowMaxAbs_MPIBAIJ, 2532 NULL, 2533 NULL, 2534 NULL, 2535 NULL, 2536 /*74*/ NULL, 2537 MatFDColoringApply_BAIJ, 2538 NULL, 2539 NULL, 2540 NULL, 2541 /*79*/ NULL, 2542 NULL, 2543 NULL, 2544 NULL, 2545 MatLoad_MPIBAIJ, 2546 /*84*/ NULL, 2547 NULL, 2548 NULL, 2549 NULL, 2550 NULL, 2551 /*89*/ NULL, 2552 NULL, 2553 NULL, 2554 NULL, 2555 NULL, 2556 /*94*/ NULL, 2557 NULL, 2558 NULL, 2559 NULL, 2560 NULL, 2561 /*99*/ NULL, 2562 NULL, 2563 NULL, 2564 MatConjugate_MPIBAIJ, 2565 NULL, 2566 /*104*/NULL, 2567 MatRealPart_MPIBAIJ, 2568 MatImaginaryPart_MPIBAIJ, 2569 NULL, 2570 NULL, 2571 /*109*/NULL, 2572 NULL, 2573 NULL, 2574 NULL, 2575 MatMissingDiagonal_MPIBAIJ, 2576 /*114*/MatGetSeqNonzeroStructure_MPIBAIJ, 2577 NULL, 2578 MatGetGhosts_MPIBAIJ, 2579 NULL, 2580 NULL, 2581 /*119*/NULL, 2582 NULL, 2583 NULL, 2584 NULL, 2585 MatGetMultiProcBlock_MPIBAIJ, 2586 /*124*/NULL, 2587 MatGetColumnNorms_MPIBAIJ, 2588 MatInvertBlockDiagonal_MPIBAIJ, 2589 NULL, 2590 NULL, 2591 /*129*/ NULL, 2592 NULL, 2593 NULL, 2594 NULL, 2595 NULL, 2596 /*134*/ NULL, 2597 NULL, 2598 NULL, 2599 NULL, 2600 NULL, 2601 /*139*/ MatSetBlockSizes_Default, 2602 NULL, 2603 NULL, 2604 MatFDColoringSetUp_MPIXAIJ, 2605 NULL, 2606 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIBAIJ 2607 }; 2608 2609 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 2610 PETSC_INTERN PetscErrorCode MatConvert_XAIJ_IS(Mat,MatType,MatReuse,Mat*); 2611 2612 PetscErrorCode MatMPIBAIJSetPreallocationCSR_MPIBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[],const PetscScalar V[]) 2613 { 2614 PetscInt m,rstart,cstart,cend; 2615 PetscInt i,j,dlen,olen,nz,nz_max=0,*d_nnz=NULL,*o_nnz=NULL; 2616 const PetscInt *JJ =NULL; 2617 PetscScalar *values=NULL; 2618 PetscBool roworiented = ((Mat_MPIBAIJ*)B->data)->roworiented; 2619 PetscErrorCode ierr; 2620 PetscBool nooffprocentries; 2621 2622 PetscFunctionBegin; 2623 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 2624 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 2625 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2626 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2627 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2628 m = B->rmap->n/bs; 2629 rstart = B->rmap->rstart/bs; 2630 cstart = B->cmap->rstart/bs; 2631 cend = B->cmap->rend/bs; 2632 2633 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 2634 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 2635 for (i=0; i<m; i++) { 2636 nz = ii[i+1] - ii[i]; 2637 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative number of columns %D",i,nz); 2638 nz_max = PetscMax(nz_max,nz); 2639 dlen = 0; 2640 olen = 0; 2641 JJ = jj + ii[i]; 2642 for (j=0; j<nz; j++) { 2643 if (*JJ < cstart || *JJ >= cend) olen++; 2644 else dlen++; 2645 JJ++; 2646 } 2647 d_nnz[i] = dlen; 2648 o_nnz[i] = olen; 2649 } 2650 ierr = MatMPIBAIJSetPreallocation(B,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 2651 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 2652 2653 values = (PetscScalar*)V; 2654 if (!values) { 2655 ierr = PetscCalloc1(bs*bs*nz_max,&values);CHKERRQ(ierr); 2656 } 2657 for (i=0; i<m; i++) { 2658 PetscInt row = i + rstart; 2659 PetscInt ncols = ii[i+1] - ii[i]; 2660 const PetscInt *icols = jj + ii[i]; 2661 if (bs == 1 || !roworiented) { /* block ordering matches the non-nested layout of MatSetValues so we can insert entire rows */ 2662 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 2663 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 2664 } else { /* block ordering does not match so we can only insert one block at a time. */ 2665 PetscInt j; 2666 for (j=0; j<ncols; j++) { 2667 const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0); 2668 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,1,&icols[j],svals,INSERT_VALUES);CHKERRQ(ierr); 2669 } 2670 } 2671 } 2672 2673 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 2674 nooffprocentries = B->nooffprocentries; 2675 B->nooffprocentries = PETSC_TRUE; 2676 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2677 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2678 B->nooffprocentries = nooffprocentries; 2679 2680 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2681 PetscFunctionReturn(0); 2682 } 2683 2684 /*@C 2685 MatMPIBAIJSetPreallocationCSR - Creates a sparse parallel matrix in BAIJ format using the given nonzero structure and (optional) numerical values 2686 2687 Collective 2688 2689 Input Parameters: 2690 + B - the matrix 2691 . bs - the block size 2692 . i - the indices into j for the start of each local row (starts with zero) 2693 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2694 - v - optional values in the matrix 2695 2696 Level: advanced 2697 2698 Notes: 2699 The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs 2700 may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is 2701 over rows within a block and the last index is over columns within a block row. Fortran programs will likely set 2702 MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a 2703 block column and the second index is over columns within a block. 2704 2705 Though this routine has Preallocation() in the name it also sets the exact nonzero locations of the matrix entries and usually the numerical values as well 2706 2707 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIBAIJSetPreallocation(), MatCreateAIJ(), MPIAIJ, MatCreateMPIBAIJWithArrays(), MPIBAIJ 2708 @*/ 2709 PetscErrorCode MatMPIBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2710 { 2711 PetscErrorCode ierr; 2712 2713 PetscFunctionBegin; 2714 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2715 PetscValidType(B,1); 2716 PetscValidLogicalCollectiveInt(B,bs,2); 2717 ierr = PetscTryMethod(B,"MatMPIBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2718 PetscFunctionReturn(0); 2719 } 2720 2721 PetscErrorCode MatMPIBAIJSetPreallocation_MPIBAIJ(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt *d_nnz,PetscInt o_nz,const PetscInt *o_nnz) 2722 { 2723 Mat_MPIBAIJ *b; 2724 PetscErrorCode ierr; 2725 PetscInt i; 2726 PetscMPIInt size; 2727 2728 PetscFunctionBegin; 2729 ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); 2730 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2731 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2732 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2733 2734 if (d_nnz) { 2735 for (i=0; i<B->rmap->n/bs; i++) { 2736 if (d_nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"d_nnz cannot be less than -1: local row %D value %D",i,d_nnz[i]); 2737 } 2738 } 2739 if (o_nnz) { 2740 for (i=0; i<B->rmap->n/bs; i++) { 2741 if (o_nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"o_nnz cannot be less than -1: local row %D value %D",i,o_nnz[i]); 2742 } 2743 } 2744 2745 b = (Mat_MPIBAIJ*)B->data; 2746 b->bs2 = bs*bs; 2747 b->mbs = B->rmap->n/bs; 2748 b->nbs = B->cmap->n/bs; 2749 b->Mbs = B->rmap->N/bs; 2750 b->Nbs = B->cmap->N/bs; 2751 2752 for (i=0; i<=b->size; i++) { 2753 b->rangebs[i] = B->rmap->range[i]/bs; 2754 } 2755 b->rstartbs = B->rmap->rstart/bs; 2756 b->rendbs = B->rmap->rend/bs; 2757 b->cstartbs = B->cmap->rstart/bs; 2758 b->cendbs = B->cmap->rend/bs; 2759 2760 #if defined(PETSC_USE_CTABLE) 2761 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2762 #else 2763 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2764 #endif 2765 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2766 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2767 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2768 2769 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2770 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRMPI(ierr); 2771 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2772 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2773 ierr = MatSetSizes(b->B,B->rmap->n,size > 1 ? B->cmap->N : 0,B->rmap->n,size > 1 ? B->cmap->N : 0);CHKERRQ(ierr); 2774 ierr = MatSetType(b->B,MATSEQBAIJ);CHKERRQ(ierr); 2775 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2776 2777 if (!B->preallocated) { 2778 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2779 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2780 ierr = MatSetType(b->A,MATSEQBAIJ);CHKERRQ(ierr); 2781 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2782 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),bs,&B->bstash);CHKERRQ(ierr); 2783 } 2784 2785 ierr = MatSeqBAIJSetPreallocation(b->A,bs,d_nz,d_nnz);CHKERRQ(ierr); 2786 ierr = MatSeqBAIJSetPreallocation(b->B,bs,o_nz,o_nnz);CHKERRQ(ierr); 2787 B->preallocated = PETSC_TRUE; 2788 B->was_assembled = PETSC_FALSE; 2789 B->assembled = PETSC_FALSE; 2790 PetscFunctionReturn(0); 2791 } 2792 2793 extern PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat,Vec); 2794 extern PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat,PetscReal); 2795 2796 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAdj(Mat B, MatType newtype,MatReuse reuse,Mat *adj) 2797 { 2798 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 2799 PetscErrorCode ierr; 2800 Mat_SeqBAIJ *d = (Mat_SeqBAIJ*) b->A->data,*o = (Mat_SeqBAIJ*) b->B->data; 2801 PetscInt M = B->rmap->n/B->rmap->bs,i,*ii,*jj,cnt,j,k,rstart = B->rmap->rstart/B->rmap->bs; 2802 const PetscInt *id = d->i, *jd = d->j, *io = o->i, *jo = o->j, *garray = b->garray; 2803 2804 PetscFunctionBegin; 2805 ierr = PetscMalloc1(M+1,&ii);CHKERRQ(ierr); 2806 ii[0] = 0; 2807 for (i=0; i<M; i++) { 2808 if ((id[i+1] - id[i]) < 0) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Indices wrong %D %D %D",i,id[i],id[i+1]); 2809 if ((io[i+1] - io[i]) < 0) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Indices wrong %D %D %D",i,io[i],io[i+1]); 2810 ii[i+1] = ii[i] + id[i+1] - id[i] + io[i+1] - io[i]; 2811 /* remove one from count of matrix has diagonal */ 2812 for (j=id[i]; j<id[i+1]; j++) { 2813 if (jd[j] == i) {ii[i+1]--;break;} 2814 } 2815 } 2816 ierr = PetscMalloc1(ii[M],&jj);CHKERRQ(ierr); 2817 cnt = 0; 2818 for (i=0; i<M; i++) { 2819 for (j=io[i]; j<io[i+1]; j++) { 2820 if (garray[jo[j]] > rstart) break; 2821 jj[cnt++] = garray[jo[j]]; 2822 } 2823 for (k=id[i]; k<id[i+1]; k++) { 2824 if (jd[k] != i) { 2825 jj[cnt++] = rstart + jd[k]; 2826 } 2827 } 2828 for (; j<io[i+1]; j++) { 2829 jj[cnt++] = garray[jo[j]]; 2830 } 2831 } 2832 ierr = MatCreateMPIAdj(PetscObjectComm((PetscObject)B),M,B->cmap->N/B->rmap->bs,ii,jj,NULL,adj);CHKERRQ(ierr); 2833 PetscFunctionReturn(0); 2834 } 2835 2836 #include <../src/mat/impls/aij/mpi/mpiaij.h> 2837 2838 PETSC_INTERN PetscErrorCode MatConvert_SeqBAIJ_SeqAIJ(Mat,MatType,MatReuse,Mat*); 2839 2840 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat) 2841 { 2842 PetscErrorCode ierr; 2843 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2844 Mat B; 2845 Mat_MPIAIJ *b; 2846 2847 PetscFunctionBegin; 2848 if (!A->assembled) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Matrix must be assembled"); 2849 2850 if (reuse == MAT_REUSE_MATRIX) { 2851 B = *newmat; 2852 } else { 2853 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 2854 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2855 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 2856 ierr = MatSetBlockSizes(B,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 2857 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 2858 ierr = MatMPIAIJSetPreallocation(B,0,NULL,0,NULL);CHKERRQ(ierr); 2859 } 2860 b = (Mat_MPIAIJ*) B->data; 2861 2862 if (reuse == MAT_REUSE_MATRIX) { 2863 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_REUSE_MATRIX, &b->A);CHKERRQ(ierr); 2864 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_REUSE_MATRIX, &b->B);CHKERRQ(ierr); 2865 } else { 2866 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 2867 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2868 ierr = MatDisAssemble_MPIBAIJ(A);CHKERRQ(ierr); 2869 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->A);CHKERRQ(ierr); 2870 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->B);CHKERRQ(ierr); 2871 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2872 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2873 } 2874 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2875 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2876 2877 if (reuse == MAT_INPLACE_MATRIX) { 2878 ierr = MatHeaderReplace(A,&B);CHKERRQ(ierr); 2879 } else { 2880 *newmat = B; 2881 } 2882 PetscFunctionReturn(0); 2883 } 2884 2885 /*MC 2886 MATMPIBAIJ - MATMPIBAIJ = "mpibaij" - A matrix type to be used for distributed block sparse matrices. 2887 2888 Options Database Keys: 2889 + -mat_type mpibaij - sets the matrix type to "mpibaij" during a call to MatSetFromOptions() 2890 . -mat_block_size <bs> - set the blocksize used to store the matrix 2891 . -mat_baij_mult_version version - indicate the version of the matrix-vector product to use (0 often indicates using BLAS) 2892 - -mat_use_hash_table <fact> 2893 2894 Level: beginner 2895 2896 Notes: 2897 MatSetOptions(,MAT_STRUCTURE_ONLY,PETSC_TRUE) may be called for this matrix type. In this no 2898 space is allocated for the nonzero entries and any entries passed with MatSetValues() are ignored 2899 2900 .seealso: MatCreateBAIJ 2901 M*/ 2902 2903 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIBSTRM(Mat,MatType,MatReuse,Mat*); 2904 2905 PETSC_EXTERN PetscErrorCode MatCreate_MPIBAIJ(Mat B) 2906 { 2907 Mat_MPIBAIJ *b; 2908 PetscErrorCode ierr; 2909 PetscBool flg = PETSC_FALSE; 2910 2911 PetscFunctionBegin; 2912 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 2913 B->data = (void*)b; 2914 2915 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 2916 B->assembled = PETSC_FALSE; 2917 2918 B->insertmode = NOT_SET_VALUES; 2919 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRMPI(ierr); 2920 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&b->size);CHKERRMPI(ierr); 2921 2922 /* build local table of row and column ownerships */ 2923 ierr = PetscMalloc1(b->size+1,&b->rangebs);CHKERRQ(ierr); 2924 2925 /* build cache for off array entries formed */ 2926 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 2927 2928 b->donotstash = PETSC_FALSE; 2929 b->colmap = NULL; 2930 b->garray = NULL; 2931 b->roworiented = PETSC_TRUE; 2932 2933 /* stuff used in block assembly */ 2934 b->barray = NULL; 2935 2936 /* stuff used for matrix vector multiply */ 2937 b->lvec = NULL; 2938 b->Mvctx = NULL; 2939 2940 /* stuff for MatGetRow() */ 2941 b->rowindices = NULL; 2942 b->rowvalues = NULL; 2943 b->getrowactive = PETSC_FALSE; 2944 2945 /* hash table stuff */ 2946 b->ht = NULL; 2947 b->hd = NULL; 2948 b->ht_size = 0; 2949 b->ht_flag = PETSC_FALSE; 2950 b->ht_fact = 0; 2951 b->ht_total_ct = 0; 2952 b->ht_insert_ct = 0; 2953 2954 /* stuff for MatCreateSubMatrices_MPIBAIJ_local() */ 2955 b->ijonly = PETSC_FALSE; 2956 2957 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiadj_C",MatConvert_MPIBAIJ_MPIAdj);CHKERRQ(ierr); 2958 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiaij_C",MatConvert_MPIBAIJ_MPIAIJ);CHKERRQ(ierr); 2959 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpisbaij_C",MatConvert_MPIBAIJ_MPISBAIJ);CHKERRQ(ierr); 2960 #if defined(PETSC_HAVE_HYPRE) 2961 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 2962 #endif 2963 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIBAIJ);CHKERRQ(ierr); 2964 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIBAIJ);CHKERRQ(ierr); 2965 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocation_C",MatMPIBAIJSetPreallocation_MPIBAIJ);CHKERRQ(ierr); 2966 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocationCSR_C",MatMPIBAIJSetPreallocationCSR_MPIBAIJ);CHKERRQ(ierr); 2967 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIBAIJ);CHKERRQ(ierr); 2968 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSetHashTableFactor_C",MatSetHashTableFactor_MPIBAIJ);CHKERRQ(ierr); 2969 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_is_C",MatConvert_XAIJ_IS);CHKERRQ(ierr); 2970 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIBAIJ);CHKERRQ(ierr); 2971 2972 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),NULL,"Options for loading MPIBAIJ matrix 1","Mat");CHKERRQ(ierr); 2973 ierr = PetscOptionsName("-mat_use_hash_table","Use hash table to save time in constructing matrix","MatSetOption",&flg);CHKERRQ(ierr); 2974 if (flg) { 2975 PetscReal fact = 1.39; 2976 ierr = MatSetOption(B,MAT_USE_HASH_TABLE,PETSC_TRUE);CHKERRQ(ierr); 2977 ierr = PetscOptionsReal("-mat_use_hash_table","Use hash table factor","MatMPIBAIJSetHashTableFactor",fact,&fact,NULL);CHKERRQ(ierr); 2978 if (fact <= 1.0) fact = 1.39; 2979 ierr = MatMPIBAIJSetHashTableFactor(B,fact);CHKERRQ(ierr); 2980 ierr = PetscInfo1(B,"Hash table Factor used %5.2f\n",fact);CHKERRQ(ierr); 2981 } 2982 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2983 PetscFunctionReturn(0); 2984 } 2985 2986 /*MC 2987 MATBAIJ - MATBAIJ = "baij" - A matrix type to be used for block sparse matrices. 2988 2989 This matrix type is identical to MATSEQBAIJ when constructed with a single process communicator, 2990 and MATMPIBAIJ otherwise. 2991 2992 Options Database Keys: 2993 . -mat_type baij - sets the matrix type to "baij" during a call to MatSetFromOptions() 2994 2995 Level: beginner 2996 2997 .seealso: MatCreateBAIJ(),MATSEQBAIJ,MATMPIBAIJ, MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 2998 M*/ 2999 3000 /*@C 3001 MatMPIBAIJSetPreallocation - Allocates memory for a sparse parallel matrix in block AIJ format 3002 (block compressed row). For good matrix assembly performance 3003 the user should preallocate the matrix storage by setting the parameters 3004 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3005 performance can be increased by more than a factor of 50. 3006 3007 Collective on Mat 3008 3009 Input Parameters: 3010 + B - the matrix 3011 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 3012 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 3013 . d_nz - number of block nonzeros per block row in diagonal portion of local 3014 submatrix (same for all local rows) 3015 . d_nnz - array containing the number of block nonzeros in the various block rows 3016 of the in diagonal portion of the local (possibly different for each block 3017 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry and 3018 set it even if it is zero. 3019 . o_nz - number of block nonzeros per block row in the off-diagonal portion of local 3020 submatrix (same for all local rows). 3021 - o_nnz - array containing the number of nonzeros in the various block rows of the 3022 off-diagonal portion of the local submatrix (possibly different for 3023 each block row) or NULL. 3024 3025 If the *_nnz parameter is given then the *_nz parameter is ignored 3026 3027 Options Database Keys: 3028 + -mat_block_size - size of the blocks to use 3029 - -mat_use_hash_table <fact> 3030 3031 Notes: 3032 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3033 than it must be used on all processors that share the object for that argument. 3034 3035 Storage Information: 3036 For a square global matrix we define each processor's diagonal portion 3037 to be its local rows and the corresponding columns (a square submatrix); 3038 each processor's off-diagonal portion encompasses the remainder of the 3039 local matrix (a rectangular submatrix). 3040 3041 The user can specify preallocated storage for the diagonal part of 3042 the local submatrix with either d_nz or d_nnz (not both). Set 3043 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3044 memory allocation. Likewise, specify preallocated storage for the 3045 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3046 3047 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3048 the figure below we depict these three local rows and all columns (0-11). 3049 3050 .vb 3051 0 1 2 3 4 5 6 7 8 9 10 11 3052 -------------------------- 3053 row 3 |o o o d d d o o o o o o 3054 row 4 |o o o d d d o o o o o o 3055 row 5 |o o o d d d o o o o o o 3056 -------------------------- 3057 .ve 3058 3059 Thus, any entries in the d locations are stored in the d (diagonal) 3060 submatrix, and any entries in the o locations are stored in the 3061 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3062 stored simply in the MATSEQBAIJ format for compressed row storage. 3063 3064 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3065 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3066 In general, for PDE problems in which most nonzeros are near the diagonal, 3067 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3068 or you will get TERRIBLE performance; see the users' manual chapter on 3069 matrices. 3070 3071 You can call MatGetInfo() to get information on how effective the preallocation was; 3072 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3073 You can also run with the option -info and look for messages with the string 3074 malloc in them to see if additional memory allocation was needed. 3075 3076 Level: intermediate 3077 3078 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocationCSR(), PetscSplitOwnership() 3079 @*/ 3080 PetscErrorCode MatMPIBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3081 { 3082 PetscErrorCode ierr; 3083 3084 PetscFunctionBegin; 3085 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3086 PetscValidType(B,1); 3087 PetscValidLogicalCollectiveInt(B,bs,2); 3088 ierr = PetscTryMethod(B,"MatMPIBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,bs,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3089 PetscFunctionReturn(0); 3090 } 3091 3092 /*@C 3093 MatCreateBAIJ - Creates a sparse parallel matrix in block AIJ format 3094 (block compressed row). For good matrix assembly performance 3095 the user should preallocate the matrix storage by setting the parameters 3096 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3097 performance can be increased by more than a factor of 50. 3098 3099 Collective 3100 3101 Input Parameters: 3102 + comm - MPI communicator 3103 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 3104 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 3105 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3106 This value should be the same as the local size used in creating the 3107 y vector for the matrix-vector product y = Ax. 3108 . n - number of local columns (or PETSC_DECIDE to have calculated if N is given) 3109 This value should be the same as the local size used in creating the 3110 x vector for the matrix-vector product y = Ax. 3111 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3112 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3113 . d_nz - number of nonzero blocks per block row in diagonal portion of local 3114 submatrix (same for all local rows) 3115 . d_nnz - array containing the number of nonzero blocks in the various block rows 3116 of the in diagonal portion of the local (possibly different for each block 3117 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry 3118 and set it even if it is zero. 3119 . o_nz - number of nonzero blocks per block row in the off-diagonal portion of local 3120 submatrix (same for all local rows). 3121 - o_nnz - array containing the number of nonzero blocks in the various block rows of the 3122 off-diagonal portion of the local submatrix (possibly different for 3123 each block row) or NULL. 3124 3125 Output Parameter: 3126 . A - the matrix 3127 3128 Options Database Keys: 3129 + -mat_block_size - size of the blocks to use 3130 - -mat_use_hash_table <fact> 3131 3132 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3133 MatXXXXSetPreallocation() paradigm instead of this routine directly. 3134 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3135 3136 Notes: 3137 If the *_nnz parameter is given then the *_nz parameter is ignored 3138 3139 A nonzero block is any block that as 1 or more nonzeros in it 3140 3141 The user MUST specify either the local or global matrix dimensions 3142 (possibly both). 3143 3144 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3145 than it must be used on all processors that share the object for that argument. 3146 3147 Storage Information: 3148 For a square global matrix we define each processor's diagonal portion 3149 to be its local rows and the corresponding columns (a square submatrix); 3150 each processor's off-diagonal portion encompasses the remainder of the 3151 local matrix (a rectangular submatrix). 3152 3153 The user can specify preallocated storage for the diagonal part of 3154 the local submatrix with either d_nz or d_nnz (not both). Set 3155 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3156 memory allocation. Likewise, specify preallocated storage for the 3157 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3158 3159 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3160 the figure below we depict these three local rows and all columns (0-11). 3161 3162 .vb 3163 0 1 2 3 4 5 6 7 8 9 10 11 3164 -------------------------- 3165 row 3 |o o o d d d o o o o o o 3166 row 4 |o o o d d d o o o o o o 3167 row 5 |o o o d d d o o o o o o 3168 -------------------------- 3169 .ve 3170 3171 Thus, any entries in the d locations are stored in the d (diagonal) 3172 submatrix, and any entries in the o locations are stored in the 3173 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3174 stored simply in the MATSEQBAIJ format for compressed row storage. 3175 3176 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3177 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3178 In general, for PDE problems in which most nonzeros are near the diagonal, 3179 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3180 or you will get TERRIBLE performance; see the users' manual chapter on 3181 matrices. 3182 3183 Level: intermediate 3184 3185 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3186 @*/ 3187 PetscErrorCode MatCreateBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat *A) 3188 { 3189 PetscErrorCode ierr; 3190 PetscMPIInt size; 3191 3192 PetscFunctionBegin; 3193 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3194 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 3195 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 3196 if (size > 1) { 3197 ierr = MatSetType(*A,MATMPIBAIJ);CHKERRQ(ierr); 3198 ierr = MatMPIBAIJSetPreallocation(*A,bs,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 3199 } else { 3200 ierr = MatSetType(*A,MATSEQBAIJ);CHKERRQ(ierr); 3201 ierr = MatSeqBAIJSetPreallocation(*A,bs,d_nz,d_nnz);CHKERRQ(ierr); 3202 } 3203 PetscFunctionReturn(0); 3204 } 3205 3206 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 3207 { 3208 Mat mat; 3209 Mat_MPIBAIJ *a,*oldmat = (Mat_MPIBAIJ*)matin->data; 3210 PetscErrorCode ierr; 3211 PetscInt len=0; 3212 3213 PetscFunctionBegin; 3214 *newmat = NULL; 3215 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 3216 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 3217 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 3218 3219 mat->factortype = matin->factortype; 3220 mat->preallocated = PETSC_TRUE; 3221 mat->assembled = PETSC_TRUE; 3222 mat->insertmode = NOT_SET_VALUES; 3223 3224 a = (Mat_MPIBAIJ*)mat->data; 3225 mat->rmap->bs = matin->rmap->bs; 3226 a->bs2 = oldmat->bs2; 3227 a->mbs = oldmat->mbs; 3228 a->nbs = oldmat->nbs; 3229 a->Mbs = oldmat->Mbs; 3230 a->Nbs = oldmat->Nbs; 3231 3232 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 3233 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 3234 3235 a->size = oldmat->size; 3236 a->rank = oldmat->rank; 3237 a->donotstash = oldmat->donotstash; 3238 a->roworiented = oldmat->roworiented; 3239 a->rowindices = NULL; 3240 a->rowvalues = NULL; 3241 a->getrowactive = PETSC_FALSE; 3242 a->barray = NULL; 3243 a->rstartbs = oldmat->rstartbs; 3244 a->rendbs = oldmat->rendbs; 3245 a->cstartbs = oldmat->cstartbs; 3246 a->cendbs = oldmat->cendbs; 3247 3248 /* hash table stuff */ 3249 a->ht = NULL; 3250 a->hd = NULL; 3251 a->ht_size = 0; 3252 a->ht_flag = oldmat->ht_flag; 3253 a->ht_fact = oldmat->ht_fact; 3254 a->ht_total_ct = 0; 3255 a->ht_insert_ct = 0; 3256 3257 ierr = PetscArraycpy(a->rangebs,oldmat->rangebs,a->size+1);CHKERRQ(ierr); 3258 if (oldmat->colmap) { 3259 #if defined(PETSC_USE_CTABLE) 3260 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 3261 #else 3262 ierr = PetscMalloc1(a->Nbs,&a->colmap);CHKERRQ(ierr); 3263 ierr = PetscLogObjectMemory((PetscObject)mat,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3264 ierr = PetscArraycpy(a->colmap,oldmat->colmap,a->Nbs);CHKERRQ(ierr); 3265 #endif 3266 } else a->colmap = NULL; 3267 3268 if (oldmat->garray && (len = ((Mat_SeqBAIJ*)(oldmat->B->data))->nbs)) { 3269 ierr = PetscMalloc1(len,&a->garray);CHKERRQ(ierr); 3270 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 3271 ierr = PetscArraycpy(a->garray,oldmat->garray,len);CHKERRQ(ierr); 3272 } else a->garray = NULL; 3273 3274 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)matin),matin->rmap->bs,&mat->bstash);CHKERRQ(ierr); 3275 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 3276 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 3277 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 3278 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 3279 3280 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 3281 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 3282 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 3283 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 3284 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 3285 *newmat = mat; 3286 PetscFunctionReturn(0); 3287 } 3288 3289 /* Used for both MPIBAIJ and MPISBAIJ matrices */ 3290 PetscErrorCode MatLoad_MPIBAIJ_Binary(Mat mat,PetscViewer viewer) 3291 { 3292 PetscInt header[4],M,N,nz,bs,m,n,mbs,nbs,rows,cols,sum,i,j,k; 3293 PetscInt *rowidxs,*colidxs,rs,cs,ce; 3294 PetscScalar *matvals; 3295 PetscErrorCode ierr; 3296 3297 PetscFunctionBegin; 3298 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 3299 3300 /* read in matrix header */ 3301 ierr = PetscViewerBinaryRead(viewer,header,4,NULL,PETSC_INT);CHKERRQ(ierr); 3302 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Not a matrix object in file"); 3303 M = header[1]; N = header[2]; nz = header[3]; 3304 if (M < 0) SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Matrix row size (%D) in file is negative",M); 3305 if (N < 0) SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Matrix column size (%D) in file is negative",N); 3306 if (nz < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk, cannot load as MPIBAIJ"); 3307 3308 /* set block sizes from the viewer's .info file */ 3309 ierr = MatLoad_Binary_BlockSizes(mat,viewer);CHKERRQ(ierr); 3310 /* set local sizes if not set already */ 3311 if (mat->rmap->n < 0 && M == N) mat->rmap->n = mat->cmap->n; 3312 if (mat->cmap->n < 0 && M == N) mat->cmap->n = mat->rmap->n; 3313 /* set global sizes if not set already */ 3314 if (mat->rmap->N < 0) mat->rmap->N = M; 3315 if (mat->cmap->N < 0) mat->cmap->N = N; 3316 ierr = PetscLayoutSetUp(mat->rmap);CHKERRQ(ierr); 3317 ierr = PetscLayoutSetUp(mat->cmap);CHKERRQ(ierr); 3318 3319 /* check if the matrix sizes are correct */ 3320 ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr); 3321 if (M != rows || N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Matrix in file of different sizes (%D, %D) than the input matrix (%D, %D)",M,N,rows,cols); 3322 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 3323 ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr); 3324 ierr = PetscLayoutGetRange(mat->rmap,&rs,NULL);CHKERRQ(ierr); 3325 ierr = PetscLayoutGetRange(mat->cmap,&cs,&ce);CHKERRQ(ierr); 3326 mbs = m/bs; nbs = n/bs; 3327 3328 /* read in row lengths and build row indices */ 3329 ierr = PetscMalloc1(m+1,&rowidxs);CHKERRQ(ierr); 3330 ierr = PetscViewerBinaryReadAll(viewer,rowidxs+1,m,PETSC_DECIDE,M,PETSC_INT);CHKERRQ(ierr); 3331 rowidxs[0] = 0; for (i=0; i<m; i++) rowidxs[i+1] += rowidxs[i]; 3332 ierr = MPIU_Allreduce(&rowidxs[m],&sum,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)viewer));CHKERRMPI(ierr); 3333 if (sum != nz) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Inconsistent matrix data in file: nonzeros = %D, sum-row-lengths = %D\n",nz,sum); 3334 3335 /* read in column indices and matrix values */ 3336 ierr = PetscMalloc2(rowidxs[m],&colidxs,rowidxs[m],&matvals);CHKERRQ(ierr); 3337 ierr = PetscViewerBinaryReadAll(viewer,colidxs,rowidxs[m],PETSC_DETERMINE,PETSC_DETERMINE,PETSC_INT);CHKERRQ(ierr); 3338 ierr = PetscViewerBinaryReadAll(viewer,matvals,rowidxs[m],PETSC_DETERMINE,PETSC_DETERMINE,PETSC_SCALAR);CHKERRQ(ierr); 3339 3340 { /* preallocate matrix storage */ 3341 PetscBT bt; /* helper bit set to count diagonal nonzeros */ 3342 PetscHSetI ht; /* helper hash set to count off-diagonal nonzeros */ 3343 PetscBool sbaij,done; 3344 PetscInt *d_nnz,*o_nnz; 3345 3346 ierr = PetscBTCreate(nbs,&bt);CHKERRQ(ierr); 3347 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 3348 ierr = PetscCalloc2(mbs,&d_nnz,mbs,&o_nnz);CHKERRQ(ierr); 3349 ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPISBAIJ,&sbaij);CHKERRQ(ierr); 3350 for (i=0; i<mbs; i++) { 3351 ierr = PetscBTMemzero(nbs,bt);CHKERRQ(ierr); 3352 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 3353 for (k=0; k<bs; k++) { 3354 PetscInt row = bs*i + k; 3355 for (j=rowidxs[row]; j<rowidxs[row+1]; j++) { 3356 PetscInt col = colidxs[j]; 3357 if (!sbaij || col >= row) { 3358 if (col >= cs && col < ce) { 3359 if (!PetscBTLookupSet(bt,(col-cs)/bs)) d_nnz[i]++; 3360 } else { 3361 ierr = PetscHSetIQueryAdd(ht,col/bs,&done);CHKERRQ(ierr); 3362 if (done) o_nnz[i]++; 3363 } 3364 } 3365 } 3366 } 3367 } 3368 ierr = PetscBTDestroy(&bt);CHKERRQ(ierr); 3369 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 3370 ierr = MatMPIBAIJSetPreallocation(mat,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3371 ierr = MatMPISBAIJSetPreallocation(mat,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3372 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3373 } 3374 3375 /* store matrix values */ 3376 for (i=0; i<m; i++) { 3377 PetscInt row = rs + i, s = rowidxs[i], e = rowidxs[i+1]; 3378 ierr = (*mat->ops->setvalues)(mat,1,&row,e-s,colidxs+s,matvals+s,INSERT_VALUES);CHKERRQ(ierr); 3379 } 3380 3381 ierr = PetscFree(rowidxs);CHKERRQ(ierr); 3382 ierr = PetscFree2(colidxs,matvals);CHKERRQ(ierr); 3383 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3384 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3385 PetscFunctionReturn(0); 3386 } 3387 3388 PetscErrorCode MatLoad_MPIBAIJ(Mat mat,PetscViewer viewer) 3389 { 3390 PetscErrorCode ierr; 3391 PetscBool isbinary; 3392 3393 PetscFunctionBegin; 3394 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 3395 if (!isbinary) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Viewer type %s not yet supported for reading %s matrices",((PetscObject)viewer)->type_name,((PetscObject)mat)->type_name); 3396 ierr = MatLoad_MPIBAIJ_Binary(mat,viewer);CHKERRQ(ierr); 3397 PetscFunctionReturn(0); 3398 } 3399 3400 /*@ 3401 MatMPIBAIJSetHashTableFactor - Sets the factor required to compute the size of the HashTable. 3402 3403 Input Parameters: 3404 + mat - the matrix 3405 - fact - factor 3406 3407 Not Collective, each process can use a different factor 3408 3409 Level: advanced 3410 3411 Notes: 3412 This can also be set by the command line option: -mat_use_hash_table <fact> 3413 3414 .seealso: MatSetOption() 3415 @*/ 3416 PetscErrorCode MatMPIBAIJSetHashTableFactor(Mat mat,PetscReal fact) 3417 { 3418 PetscErrorCode ierr; 3419 3420 PetscFunctionBegin; 3421 ierr = PetscTryMethod(mat,"MatSetHashTableFactor_C",(Mat,PetscReal),(mat,fact));CHKERRQ(ierr); 3422 PetscFunctionReturn(0); 3423 } 3424 3425 PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat mat,PetscReal fact) 3426 { 3427 Mat_MPIBAIJ *baij; 3428 3429 PetscFunctionBegin; 3430 baij = (Mat_MPIBAIJ*)mat->data; 3431 baij->ht_fact = fact; 3432 PetscFunctionReturn(0); 3433 } 3434 3435 PetscErrorCode MatMPIBAIJGetSeqBAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 3436 { 3437 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 3438 PetscBool flg; 3439 PetscErrorCode ierr; 3440 3441 PetscFunctionBegin; 3442 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIBAIJ,&flg);CHKERRQ(ierr); 3443 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIBAIJ matrix as input"); 3444 if (Ad) *Ad = a->A; 3445 if (Ao) *Ao = a->B; 3446 if (colmap) *colmap = a->garray; 3447 PetscFunctionReturn(0); 3448 } 3449 3450 /* 3451 Special version for direct calls from Fortran (to eliminate two function call overheads 3452 */ 3453 #if defined(PETSC_HAVE_FORTRAN_CAPS) 3454 #define matmpibaijsetvaluesblocked_ MATMPIBAIJSETVALUESBLOCKED 3455 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 3456 #define matmpibaijsetvaluesblocked_ matmpibaijsetvaluesblocked 3457 #endif 3458 3459 /*@C 3460 MatMPIBAIJSetValuesBlocked - Direct Fortran call to replace call to MatSetValuesBlocked() 3461 3462 Collective on Mat 3463 3464 Input Parameters: 3465 + mat - the matrix 3466 . min - number of input rows 3467 . im - input rows 3468 . nin - number of input columns 3469 . in - input columns 3470 . v - numerical values input 3471 - addvin - INSERT_VALUES or ADD_VALUES 3472 3473 Notes: 3474 This has a complete copy of MatSetValuesBlocked_MPIBAIJ() which is terrible code un-reuse. 3475 3476 Level: advanced 3477 3478 .seealso: MatSetValuesBlocked() 3479 @*/ 3480 PetscErrorCode matmpibaijsetvaluesblocked_(Mat *matin,PetscInt *min,const PetscInt im[],PetscInt *nin,const PetscInt in[],const MatScalar v[],InsertMode *addvin) 3481 { 3482 /* convert input arguments to C version */ 3483 Mat mat = *matin; 3484 PetscInt m = *min, n = *nin; 3485 InsertMode addv = *addvin; 3486 3487 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 3488 const MatScalar *value; 3489 MatScalar *barray = baij->barray; 3490 PetscBool roworiented = baij->roworiented; 3491 PetscErrorCode ierr; 3492 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 3493 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 3494 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 3495 3496 PetscFunctionBegin; 3497 /* tasks normally handled by MatSetValuesBlocked() */ 3498 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 3499 else if (PetscUnlikely(mat->insertmode != addv)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 3500 if (PetscUnlikely(mat->factortype)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 3501 if (mat->assembled) { 3502 mat->was_assembled = PETSC_TRUE; 3503 mat->assembled = PETSC_FALSE; 3504 } 3505 ierr = PetscLogEventBegin(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3506 3507 if (!barray) { 3508 ierr = PetscMalloc1(bs2,&barray);CHKERRQ(ierr); 3509 baij->barray = barray; 3510 } 3511 3512 if (roworiented) stepval = (n-1)*bs; 3513 else stepval = (m-1)*bs; 3514 3515 for (i=0; i<m; i++) { 3516 if (im[i] < 0) continue; 3517 if (PetscUnlikelyDebug(im[i] >= baij->Mbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large, row %D max %D",im[i],baij->Mbs-1); 3518 if (im[i] >= rstart && im[i] < rend) { 3519 row = im[i] - rstart; 3520 for (j=0; j<n; j++) { 3521 /* If NumCol = 1 then a copy is not required */ 3522 if ((roworiented) && (n == 1)) { 3523 barray = (MatScalar*)v + i*bs2; 3524 } else if ((!roworiented) && (m == 1)) { 3525 barray = (MatScalar*)v + j*bs2; 3526 } else { /* Here a copy is required */ 3527 if (roworiented) { 3528 value = v + i*(stepval+bs)*bs + j*bs; 3529 } else { 3530 value = v + j*(stepval+bs)*bs + i*bs; 3531 } 3532 for (ii=0; ii<bs; ii++,value+=stepval) { 3533 for (jj=0; jj<bs; jj++) { 3534 *barray++ = *value++; 3535 } 3536 } 3537 barray -=bs2; 3538 } 3539 3540 if (in[j] >= cstart && in[j] < cend) { 3541 col = in[j] - cstart; 3542 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->A,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 3543 } else if (in[j] < 0) continue; 3544 else if (PetscUnlikelyDebug(in[j] >= baij->Nbs)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large, col %D max %D",in[j],baij->Nbs-1); 3545 else { 3546 if (mat->was_assembled) { 3547 if (!baij->colmap) { 3548 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 3549 } 3550 3551 #if defined(PETSC_USE_DEBUG) 3552 #if defined(PETSC_USE_CTABLE) 3553 { PetscInt data; 3554 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 3555 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3556 } 3557 #else 3558 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3559 #endif 3560 #endif 3561 #if defined(PETSC_USE_CTABLE) 3562 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 3563 col = (col - 1)/bs; 3564 #else 3565 col = (baij->colmap[in[j]] - 1)/bs; 3566 #endif 3567 if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 3568 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 3569 col = in[j]; 3570 } 3571 } else col = in[j]; 3572 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->B,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 3573 } 3574 } 3575 } else { 3576 if (!baij->donotstash) { 3577 if (roworiented) { 3578 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3579 } else { 3580 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3581 } 3582 } 3583 } 3584 } 3585 3586 /* task normally handled by MatSetValuesBlocked() */ 3587 ierr = PetscLogEventEnd(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3588 PetscFunctionReturn(0); 3589 } 3590 3591 /*@ 3592 MatCreateMPIBAIJWithArrays - creates a MPI BAIJ matrix using arrays that contain in standard block 3593 CSR format the local rows. 3594 3595 Collective 3596 3597 Input Parameters: 3598 + comm - MPI communicator 3599 . bs - the block size, only a block size of 1 is supported 3600 . m - number of local rows (Cannot be PETSC_DECIDE) 3601 . n - This value should be the same as the local size used in creating the 3602 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3603 calculated if N is given) For square matrices n is almost always m. 3604 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3605 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3606 . i - row indices; that is i[0] = 0, i[row] = i[row-1] + number of block elements in that rowth block row of the matrix 3607 . j - column indices 3608 - a - matrix values 3609 3610 Output Parameter: 3611 . mat - the matrix 3612 3613 Level: intermediate 3614 3615 Notes: 3616 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3617 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3618 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3619 3620 The order of the entries in values is the same as the block compressed sparse row storage format; that is, it is 3621 the same as a three dimensional array in Fortran values(bs,bs,nnz) that contains the first column of the first 3622 block, followed by the second column of the first block etc etc. That is, the blocks are contiguous in memory 3623 with column-major ordering within blocks. 3624 3625 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3626 3627 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3628 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3629 @*/ 3630 PetscErrorCode MatCreateMPIBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 3631 { 3632 PetscErrorCode ierr; 3633 3634 PetscFunctionBegin; 3635 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3636 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3637 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3638 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3639 ierr = MatSetType(*mat,MATMPIBAIJ);CHKERRQ(ierr); 3640 ierr = MatSetBlockSize(*mat,bs);CHKERRQ(ierr); 3641 ierr = MatSetUp(*mat);CHKERRQ(ierr); 3642 ierr = MatSetOption(*mat,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 3643 ierr = MatMPIBAIJSetPreallocationCSR(*mat,bs,i,j,a);CHKERRQ(ierr); 3644 ierr = MatSetOption(*mat,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr); 3645 PetscFunctionReturn(0); 3646 } 3647 3648 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIBAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 3649 { 3650 PetscErrorCode ierr; 3651 PetscInt m,N,i,rstart,nnz,Ii,bs,cbs; 3652 PetscInt *indx; 3653 PetscScalar *values; 3654 3655 PetscFunctionBegin; 3656 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 3657 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 3658 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)inmat->data; 3659 PetscInt *dnz,*onz,mbs,Nbs,nbs; 3660 PetscInt *bindx,rmax=a->rmax,j; 3661 PetscMPIInt rank,size; 3662 3663 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 3664 mbs = m/bs; Nbs = N/cbs; 3665 if (n == PETSC_DECIDE) { 3666 ierr = PetscSplitOwnershipBlock(comm,cbs,&n,&N);CHKERRQ(ierr); 3667 } 3668 nbs = n/cbs; 3669 3670 ierr = PetscMalloc1(rmax,&bindx);CHKERRQ(ierr); 3671 ierr = MatPreallocateInitialize(comm,mbs,nbs,dnz,onz);CHKERRQ(ierr); /* inline function, output __end and __rstart are used below */ 3672 3673 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 3674 ierr = MPI_Comm_rank(comm,&size);CHKERRMPI(ierr); 3675 if (rank == size-1) { 3676 /* Check sum(nbs) = Nbs */ 3677 if (__end != Nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local block columns %D != global block columns %D",__end,Nbs); 3678 } 3679 3680 rstart = __rstart; /* block rstart of *outmat; see inline function MatPreallocateInitialize */ 3681 for (i=0; i<mbs; i++) { 3682 ierr = MatGetRow_SeqBAIJ(inmat,i*bs,&nnz,&indx,NULL);CHKERRQ(ierr); /* non-blocked nnz and indx */ 3683 nnz = nnz/bs; 3684 for (j=0; j<nnz; j++) bindx[j] = indx[j*bs]/bs; 3685 ierr = MatPreallocateSet(i+rstart,nnz,bindx,dnz,onz);CHKERRQ(ierr); 3686 ierr = MatRestoreRow_SeqBAIJ(inmat,i*bs,&nnz,&indx,NULL);CHKERRQ(ierr); 3687 } 3688 ierr = PetscFree(bindx);CHKERRQ(ierr); 3689 3690 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 3691 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3692 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 3693 ierr = MatSetType(*outmat,MATBAIJ);CHKERRQ(ierr); 3694 ierr = MatSeqBAIJSetPreallocation(*outmat,bs,0,dnz);CHKERRQ(ierr); 3695 ierr = MatMPIBAIJSetPreallocation(*outmat,bs,0,dnz,0,onz);CHKERRQ(ierr); 3696 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 3697 ierr = MatSetOption(*outmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3698 } 3699 3700 /* numeric phase */ 3701 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 3702 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 3703 3704 for (i=0; i<m; i++) { 3705 ierr = MatGetRow_SeqBAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3706 Ii = i + rstart; 3707 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 3708 ierr = MatRestoreRow_SeqBAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3709 } 3710 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3711 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3712 PetscFunctionReturn(0); 3713 } 3714