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 MatGetColumnReductions_MPIBAIJ(Mat A,ReductionType type,PetscReal *reductions) 2326 { 2327 PetscErrorCode ierr; 2328 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)A->data; 2329 PetscInt m,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,&m,&N);CHKERRQ(ierr); 2339 ierr = PetscCalloc1(N,&work);CHKERRQ(ierr); 2340 if (type == REDUCTION_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 == REDUCTION_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 == REDUCTION_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 if (type == REDUCTION_SUM || REDUCTION_MEAN) { 2394 for (i=a_aij->i[0]; i<a_aij->i[aij->A->rmap->n/bs]; i++) { 2395 for (jb=0; jb<bs; jb++) { 2396 for (ib=0; ib<bs; ib++) { 2397 work[A->cmap->rstart + a_aij->j[i] * bs + jb] += *a_val; 2398 a_val++; 2399 } 2400 } 2401 } 2402 for (i=b_aij->i[0]; i<b_aij->i[aij->B->rmap->n/bs]; i++) { 2403 for (jb=0; jb<bs; jb++) { 2404 for (ib=0; ib<bs; ib++) { 2405 work[garray[b_aij->j[i]] * bs + jb] += *b_val; 2406 b_val++; 2407 } 2408 } 2409 } 2410 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown ReductionType"); 2411 if (type == REDUCTION_NORM_INFINITY) { 2412 ierr = MPIU_Allreduce(work,reductions,N,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2413 } else { 2414 ierr = MPIU_Allreduce(work,reductions,N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRMPI(ierr); 2415 } 2416 ierr = PetscFree(work);CHKERRQ(ierr); 2417 if (type == REDUCTION_NORM_2) { 2418 for (i=0; i<N; i++) reductions[i] = PetscSqrtReal(reductions[i]); 2419 } else if (type == REDUCTION_MEAN) { 2420 for (i=0; i<N; i++) reductions[i] /= m; 2421 } 2422 PetscFunctionReturn(0); 2423 } 2424 2425 PetscErrorCode MatInvertBlockDiagonal_MPIBAIJ(Mat A,const PetscScalar **values) 2426 { 2427 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; 2428 PetscErrorCode ierr; 2429 2430 PetscFunctionBegin; 2431 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2432 A->factorerrortype = a->A->factorerrortype; 2433 A->factorerror_zeropivot_value = a->A->factorerror_zeropivot_value; 2434 A->factorerror_zeropivot_row = a->A->factorerror_zeropivot_row; 2435 PetscFunctionReturn(0); 2436 } 2437 2438 PetscErrorCode MatShift_MPIBAIJ(Mat Y,PetscScalar a) 2439 { 2440 PetscErrorCode ierr; 2441 Mat_MPIBAIJ *maij = (Mat_MPIBAIJ*)Y->data; 2442 Mat_SeqBAIJ *aij = (Mat_SeqBAIJ*)maij->A->data; 2443 2444 PetscFunctionBegin; 2445 if (!Y->preallocated) { 2446 ierr = MatMPIBAIJSetPreallocation(Y,Y->rmap->bs,1,NULL,0,NULL);CHKERRQ(ierr); 2447 } else if (!aij->nz) { 2448 PetscInt nonew = aij->nonew; 2449 ierr = MatSeqBAIJSetPreallocation(maij->A,Y->rmap->bs,1,NULL);CHKERRQ(ierr); 2450 aij->nonew = nonew; 2451 } 2452 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2453 PetscFunctionReturn(0); 2454 } 2455 2456 PetscErrorCode MatMissingDiagonal_MPIBAIJ(Mat A,PetscBool *missing,PetscInt *d) 2457 { 2458 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2459 PetscErrorCode ierr; 2460 2461 PetscFunctionBegin; 2462 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2463 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2464 if (d) { 2465 PetscInt rstart; 2466 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2467 *d += rstart/A->rmap->bs; 2468 2469 } 2470 PetscFunctionReturn(0); 2471 } 2472 2473 PetscErrorCode MatGetDiagonalBlock_MPIBAIJ(Mat A,Mat *a) 2474 { 2475 PetscFunctionBegin; 2476 *a = ((Mat_MPIBAIJ*)A->data)->A; 2477 PetscFunctionReturn(0); 2478 } 2479 2480 /* -------------------------------------------------------------------*/ 2481 static struct _MatOps MatOps_Values = {MatSetValues_MPIBAIJ, 2482 MatGetRow_MPIBAIJ, 2483 MatRestoreRow_MPIBAIJ, 2484 MatMult_MPIBAIJ, 2485 /* 4*/ MatMultAdd_MPIBAIJ, 2486 MatMultTranspose_MPIBAIJ, 2487 MatMultTransposeAdd_MPIBAIJ, 2488 NULL, 2489 NULL, 2490 NULL, 2491 /*10*/ NULL, 2492 NULL, 2493 NULL, 2494 MatSOR_MPIBAIJ, 2495 MatTranspose_MPIBAIJ, 2496 /*15*/ MatGetInfo_MPIBAIJ, 2497 MatEqual_MPIBAIJ, 2498 MatGetDiagonal_MPIBAIJ, 2499 MatDiagonalScale_MPIBAIJ, 2500 MatNorm_MPIBAIJ, 2501 /*20*/ MatAssemblyBegin_MPIBAIJ, 2502 MatAssemblyEnd_MPIBAIJ, 2503 MatSetOption_MPIBAIJ, 2504 MatZeroEntries_MPIBAIJ, 2505 /*24*/ MatZeroRows_MPIBAIJ, 2506 NULL, 2507 NULL, 2508 NULL, 2509 NULL, 2510 /*29*/ MatSetUp_MPIBAIJ, 2511 NULL, 2512 NULL, 2513 MatGetDiagonalBlock_MPIBAIJ, 2514 NULL, 2515 /*34*/ MatDuplicate_MPIBAIJ, 2516 NULL, 2517 NULL, 2518 NULL, 2519 NULL, 2520 /*39*/ MatAXPY_MPIBAIJ, 2521 MatCreateSubMatrices_MPIBAIJ, 2522 MatIncreaseOverlap_MPIBAIJ, 2523 MatGetValues_MPIBAIJ, 2524 MatCopy_MPIBAIJ, 2525 /*44*/ NULL, 2526 MatScale_MPIBAIJ, 2527 MatShift_MPIBAIJ, 2528 NULL, 2529 MatZeroRowsColumns_MPIBAIJ, 2530 /*49*/ NULL, 2531 NULL, 2532 NULL, 2533 NULL, 2534 NULL, 2535 /*54*/ MatFDColoringCreate_MPIXAIJ, 2536 NULL, 2537 MatSetUnfactored_MPIBAIJ, 2538 MatPermute_MPIBAIJ, 2539 MatSetValuesBlocked_MPIBAIJ, 2540 /*59*/ MatCreateSubMatrix_MPIBAIJ, 2541 MatDestroy_MPIBAIJ, 2542 MatView_MPIBAIJ, 2543 NULL, 2544 NULL, 2545 /*64*/ NULL, 2546 NULL, 2547 NULL, 2548 NULL, 2549 NULL, 2550 /*69*/ MatGetRowMaxAbs_MPIBAIJ, 2551 NULL, 2552 NULL, 2553 NULL, 2554 NULL, 2555 /*74*/ NULL, 2556 MatFDColoringApply_BAIJ, 2557 NULL, 2558 NULL, 2559 NULL, 2560 /*79*/ NULL, 2561 NULL, 2562 NULL, 2563 NULL, 2564 MatLoad_MPIBAIJ, 2565 /*84*/ NULL, 2566 NULL, 2567 NULL, 2568 NULL, 2569 NULL, 2570 /*89*/ NULL, 2571 NULL, 2572 NULL, 2573 NULL, 2574 NULL, 2575 /*94*/ NULL, 2576 NULL, 2577 NULL, 2578 NULL, 2579 NULL, 2580 /*99*/ NULL, 2581 NULL, 2582 NULL, 2583 MatConjugate_MPIBAIJ, 2584 NULL, 2585 /*104*/NULL, 2586 MatRealPart_MPIBAIJ, 2587 MatImaginaryPart_MPIBAIJ, 2588 NULL, 2589 NULL, 2590 /*109*/NULL, 2591 NULL, 2592 NULL, 2593 NULL, 2594 MatMissingDiagonal_MPIBAIJ, 2595 /*114*/MatGetSeqNonzeroStructure_MPIBAIJ, 2596 NULL, 2597 MatGetGhosts_MPIBAIJ, 2598 NULL, 2599 NULL, 2600 /*119*/NULL, 2601 NULL, 2602 NULL, 2603 NULL, 2604 MatGetMultiProcBlock_MPIBAIJ, 2605 /*124*/NULL, 2606 MatGetColumnReductions_MPIBAIJ, 2607 MatInvertBlockDiagonal_MPIBAIJ, 2608 NULL, 2609 NULL, 2610 /*129*/ NULL, 2611 NULL, 2612 NULL, 2613 NULL, 2614 NULL, 2615 /*134*/ NULL, 2616 NULL, 2617 NULL, 2618 NULL, 2619 NULL, 2620 /*139*/ MatSetBlockSizes_Default, 2621 NULL, 2622 NULL, 2623 MatFDColoringSetUp_MPIXAIJ, 2624 NULL, 2625 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIBAIJ 2626 }; 2627 2628 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 2629 PETSC_INTERN PetscErrorCode MatConvert_XAIJ_IS(Mat,MatType,MatReuse,Mat*); 2630 2631 PetscErrorCode MatMPIBAIJSetPreallocationCSR_MPIBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[],const PetscScalar V[]) 2632 { 2633 PetscInt m,rstart,cstart,cend; 2634 PetscInt i,j,dlen,olen,nz,nz_max=0,*d_nnz=NULL,*o_nnz=NULL; 2635 const PetscInt *JJ =NULL; 2636 PetscScalar *values=NULL; 2637 PetscBool roworiented = ((Mat_MPIBAIJ*)B->data)->roworiented; 2638 PetscErrorCode ierr; 2639 PetscBool nooffprocentries; 2640 2641 PetscFunctionBegin; 2642 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 2643 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 2644 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2645 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2646 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2647 m = B->rmap->n/bs; 2648 rstart = B->rmap->rstart/bs; 2649 cstart = B->cmap->rstart/bs; 2650 cend = B->cmap->rend/bs; 2651 2652 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 2653 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 2654 for (i=0; i<m; i++) { 2655 nz = ii[i+1] - ii[i]; 2656 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative number of columns %D",i,nz); 2657 nz_max = PetscMax(nz_max,nz); 2658 dlen = 0; 2659 olen = 0; 2660 JJ = jj + ii[i]; 2661 for (j=0; j<nz; j++) { 2662 if (*JJ < cstart || *JJ >= cend) olen++; 2663 else dlen++; 2664 JJ++; 2665 } 2666 d_nnz[i] = dlen; 2667 o_nnz[i] = olen; 2668 } 2669 ierr = MatMPIBAIJSetPreallocation(B,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 2670 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 2671 2672 values = (PetscScalar*)V; 2673 if (!values) { 2674 ierr = PetscCalloc1(bs*bs*nz_max,&values);CHKERRQ(ierr); 2675 } 2676 for (i=0; i<m; i++) { 2677 PetscInt row = i + rstart; 2678 PetscInt ncols = ii[i+1] - ii[i]; 2679 const PetscInt *icols = jj + ii[i]; 2680 if (bs == 1 || !roworiented) { /* block ordering matches the non-nested layout of MatSetValues so we can insert entire rows */ 2681 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 2682 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 2683 } else { /* block ordering does not match so we can only insert one block at a time. */ 2684 PetscInt j; 2685 for (j=0; j<ncols; j++) { 2686 const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0); 2687 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,1,&icols[j],svals,INSERT_VALUES);CHKERRQ(ierr); 2688 } 2689 } 2690 } 2691 2692 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 2693 nooffprocentries = B->nooffprocentries; 2694 B->nooffprocentries = PETSC_TRUE; 2695 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2696 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2697 B->nooffprocentries = nooffprocentries; 2698 2699 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2700 PetscFunctionReturn(0); 2701 } 2702 2703 /*@C 2704 MatMPIBAIJSetPreallocationCSR - Creates a sparse parallel matrix in BAIJ format using the given nonzero structure and (optional) numerical values 2705 2706 Collective 2707 2708 Input Parameters: 2709 + B - the matrix 2710 . bs - the block size 2711 . i - the indices into j for the start of each local row (starts with zero) 2712 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2713 - v - optional values in the matrix 2714 2715 Level: advanced 2716 2717 Notes: 2718 The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs 2719 may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is 2720 over rows within a block and the last index is over columns within a block row. Fortran programs will likely set 2721 MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a 2722 block column and the second index is over columns within a block. 2723 2724 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 2725 2726 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIBAIJSetPreallocation(), MatCreateAIJ(), MPIAIJ, MatCreateMPIBAIJWithArrays(), MPIBAIJ 2727 @*/ 2728 PetscErrorCode MatMPIBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2729 { 2730 PetscErrorCode ierr; 2731 2732 PetscFunctionBegin; 2733 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2734 PetscValidType(B,1); 2735 PetscValidLogicalCollectiveInt(B,bs,2); 2736 ierr = PetscTryMethod(B,"MatMPIBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2737 PetscFunctionReturn(0); 2738 } 2739 2740 PetscErrorCode MatMPIBAIJSetPreallocation_MPIBAIJ(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt *d_nnz,PetscInt o_nz,const PetscInt *o_nnz) 2741 { 2742 Mat_MPIBAIJ *b; 2743 PetscErrorCode ierr; 2744 PetscInt i; 2745 PetscMPIInt size; 2746 2747 PetscFunctionBegin; 2748 ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); 2749 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2750 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2751 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2752 2753 if (d_nnz) { 2754 for (i=0; i<B->rmap->n/bs; i++) { 2755 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]); 2756 } 2757 } 2758 if (o_nnz) { 2759 for (i=0; i<B->rmap->n/bs; i++) { 2760 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]); 2761 } 2762 } 2763 2764 b = (Mat_MPIBAIJ*)B->data; 2765 b->bs2 = bs*bs; 2766 b->mbs = B->rmap->n/bs; 2767 b->nbs = B->cmap->n/bs; 2768 b->Mbs = B->rmap->N/bs; 2769 b->Nbs = B->cmap->N/bs; 2770 2771 for (i=0; i<=b->size; i++) { 2772 b->rangebs[i] = B->rmap->range[i]/bs; 2773 } 2774 b->rstartbs = B->rmap->rstart/bs; 2775 b->rendbs = B->rmap->rend/bs; 2776 b->cstartbs = B->cmap->rstart/bs; 2777 b->cendbs = B->cmap->rend/bs; 2778 2779 #if defined(PETSC_USE_CTABLE) 2780 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2781 #else 2782 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2783 #endif 2784 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2785 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2786 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2787 2788 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2789 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRMPI(ierr); 2790 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2791 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2792 ierr = MatSetSizes(b->B,B->rmap->n,size > 1 ? B->cmap->N : 0,B->rmap->n,size > 1 ? B->cmap->N : 0);CHKERRQ(ierr); 2793 ierr = MatSetType(b->B,MATSEQBAIJ);CHKERRQ(ierr); 2794 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2795 2796 if (!B->preallocated) { 2797 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2798 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2799 ierr = MatSetType(b->A,MATSEQBAIJ);CHKERRQ(ierr); 2800 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2801 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),bs,&B->bstash);CHKERRQ(ierr); 2802 } 2803 2804 ierr = MatSeqBAIJSetPreallocation(b->A,bs,d_nz,d_nnz);CHKERRQ(ierr); 2805 ierr = MatSeqBAIJSetPreallocation(b->B,bs,o_nz,o_nnz);CHKERRQ(ierr); 2806 B->preallocated = PETSC_TRUE; 2807 B->was_assembled = PETSC_FALSE; 2808 B->assembled = PETSC_FALSE; 2809 PetscFunctionReturn(0); 2810 } 2811 2812 extern PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat,Vec); 2813 extern PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat,PetscReal); 2814 2815 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAdj(Mat B, MatType newtype,MatReuse reuse,Mat *adj) 2816 { 2817 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 2818 PetscErrorCode ierr; 2819 Mat_SeqBAIJ *d = (Mat_SeqBAIJ*) b->A->data,*o = (Mat_SeqBAIJ*) b->B->data; 2820 PetscInt M = B->rmap->n/B->rmap->bs,i,*ii,*jj,cnt,j,k,rstart = B->rmap->rstart/B->rmap->bs; 2821 const PetscInt *id = d->i, *jd = d->j, *io = o->i, *jo = o->j, *garray = b->garray; 2822 2823 PetscFunctionBegin; 2824 ierr = PetscMalloc1(M+1,&ii);CHKERRQ(ierr); 2825 ii[0] = 0; 2826 for (i=0; i<M; i++) { 2827 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]); 2828 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]); 2829 ii[i+1] = ii[i] + id[i+1] - id[i] + io[i+1] - io[i]; 2830 /* remove one from count of matrix has diagonal */ 2831 for (j=id[i]; j<id[i+1]; j++) { 2832 if (jd[j] == i) {ii[i+1]--;break;} 2833 } 2834 } 2835 ierr = PetscMalloc1(ii[M],&jj);CHKERRQ(ierr); 2836 cnt = 0; 2837 for (i=0; i<M; i++) { 2838 for (j=io[i]; j<io[i+1]; j++) { 2839 if (garray[jo[j]] > rstart) break; 2840 jj[cnt++] = garray[jo[j]]; 2841 } 2842 for (k=id[i]; k<id[i+1]; k++) { 2843 if (jd[k] != i) { 2844 jj[cnt++] = rstart + jd[k]; 2845 } 2846 } 2847 for (; j<io[i+1]; j++) { 2848 jj[cnt++] = garray[jo[j]]; 2849 } 2850 } 2851 ierr = MatCreateMPIAdj(PetscObjectComm((PetscObject)B),M,B->cmap->N/B->rmap->bs,ii,jj,NULL,adj);CHKERRQ(ierr); 2852 PetscFunctionReturn(0); 2853 } 2854 2855 #include <../src/mat/impls/aij/mpi/mpiaij.h> 2856 2857 PETSC_INTERN PetscErrorCode MatConvert_SeqBAIJ_SeqAIJ(Mat,MatType,MatReuse,Mat*); 2858 2859 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat) 2860 { 2861 PetscErrorCode ierr; 2862 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2863 Mat B; 2864 Mat_MPIAIJ *b; 2865 2866 PetscFunctionBegin; 2867 if (!A->assembled) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Matrix must be assembled"); 2868 2869 if (reuse == MAT_REUSE_MATRIX) { 2870 B = *newmat; 2871 } else { 2872 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 2873 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2874 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 2875 ierr = MatSetBlockSizes(B,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 2876 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 2877 ierr = MatMPIAIJSetPreallocation(B,0,NULL,0,NULL);CHKERRQ(ierr); 2878 } 2879 b = (Mat_MPIAIJ*) B->data; 2880 2881 if (reuse == MAT_REUSE_MATRIX) { 2882 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_REUSE_MATRIX, &b->A);CHKERRQ(ierr); 2883 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_REUSE_MATRIX, &b->B);CHKERRQ(ierr); 2884 } else { 2885 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 2886 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2887 ierr = MatDisAssemble_MPIBAIJ(A);CHKERRQ(ierr); 2888 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->A);CHKERRQ(ierr); 2889 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->B);CHKERRQ(ierr); 2890 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2891 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2892 } 2893 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2894 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2895 2896 if (reuse == MAT_INPLACE_MATRIX) { 2897 ierr = MatHeaderReplace(A,&B);CHKERRQ(ierr); 2898 } else { 2899 *newmat = B; 2900 } 2901 PetscFunctionReturn(0); 2902 } 2903 2904 /*MC 2905 MATMPIBAIJ - MATMPIBAIJ = "mpibaij" - A matrix type to be used for distributed block sparse matrices. 2906 2907 Options Database Keys: 2908 + -mat_type mpibaij - sets the matrix type to "mpibaij" during a call to MatSetFromOptions() 2909 . -mat_block_size <bs> - set the blocksize used to store the matrix 2910 . -mat_baij_mult_version version - indicate the version of the matrix-vector product to use (0 often indicates using BLAS) 2911 - -mat_use_hash_table <fact> 2912 2913 Level: beginner 2914 2915 Notes: 2916 MatSetOptions(,MAT_STRUCTURE_ONLY,PETSC_TRUE) may be called for this matrix type. In this no 2917 space is allocated for the nonzero entries and any entries passed with MatSetValues() are ignored 2918 2919 .seealso: MatCreateBAIJ 2920 M*/ 2921 2922 PETSC_INTERN PetscErrorCode MatConvert_MPIBAIJ_MPIBSTRM(Mat,MatType,MatReuse,Mat*); 2923 2924 PETSC_EXTERN PetscErrorCode MatCreate_MPIBAIJ(Mat B) 2925 { 2926 Mat_MPIBAIJ *b; 2927 PetscErrorCode ierr; 2928 PetscBool flg = PETSC_FALSE; 2929 2930 PetscFunctionBegin; 2931 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 2932 B->data = (void*)b; 2933 2934 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 2935 B->assembled = PETSC_FALSE; 2936 2937 B->insertmode = NOT_SET_VALUES; 2938 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRMPI(ierr); 2939 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&b->size);CHKERRMPI(ierr); 2940 2941 /* build local table of row and column ownerships */ 2942 ierr = PetscMalloc1(b->size+1,&b->rangebs);CHKERRQ(ierr); 2943 2944 /* build cache for off array entries formed */ 2945 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 2946 2947 b->donotstash = PETSC_FALSE; 2948 b->colmap = NULL; 2949 b->garray = NULL; 2950 b->roworiented = PETSC_TRUE; 2951 2952 /* stuff used in block assembly */ 2953 b->barray = NULL; 2954 2955 /* stuff used for matrix vector multiply */ 2956 b->lvec = NULL; 2957 b->Mvctx = NULL; 2958 2959 /* stuff for MatGetRow() */ 2960 b->rowindices = NULL; 2961 b->rowvalues = NULL; 2962 b->getrowactive = PETSC_FALSE; 2963 2964 /* hash table stuff */ 2965 b->ht = NULL; 2966 b->hd = NULL; 2967 b->ht_size = 0; 2968 b->ht_flag = PETSC_FALSE; 2969 b->ht_fact = 0; 2970 b->ht_total_ct = 0; 2971 b->ht_insert_ct = 0; 2972 2973 /* stuff for MatCreateSubMatrices_MPIBAIJ_local() */ 2974 b->ijonly = PETSC_FALSE; 2975 2976 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiadj_C",MatConvert_MPIBAIJ_MPIAdj);CHKERRQ(ierr); 2977 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiaij_C",MatConvert_MPIBAIJ_MPIAIJ);CHKERRQ(ierr); 2978 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpisbaij_C",MatConvert_MPIBAIJ_MPISBAIJ);CHKERRQ(ierr); 2979 #if defined(PETSC_HAVE_HYPRE) 2980 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 2981 #endif 2982 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIBAIJ);CHKERRQ(ierr); 2983 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIBAIJ);CHKERRQ(ierr); 2984 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocation_C",MatMPIBAIJSetPreallocation_MPIBAIJ);CHKERRQ(ierr); 2985 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocationCSR_C",MatMPIBAIJSetPreallocationCSR_MPIBAIJ);CHKERRQ(ierr); 2986 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIBAIJ);CHKERRQ(ierr); 2987 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSetHashTableFactor_C",MatSetHashTableFactor_MPIBAIJ);CHKERRQ(ierr); 2988 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_is_C",MatConvert_XAIJ_IS);CHKERRQ(ierr); 2989 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIBAIJ);CHKERRQ(ierr); 2990 2991 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),NULL,"Options for loading MPIBAIJ matrix 1","Mat");CHKERRQ(ierr); 2992 ierr = PetscOptionsName("-mat_use_hash_table","Use hash table to save time in constructing matrix","MatSetOption",&flg);CHKERRQ(ierr); 2993 if (flg) { 2994 PetscReal fact = 1.39; 2995 ierr = MatSetOption(B,MAT_USE_HASH_TABLE,PETSC_TRUE);CHKERRQ(ierr); 2996 ierr = PetscOptionsReal("-mat_use_hash_table","Use hash table factor","MatMPIBAIJSetHashTableFactor",fact,&fact,NULL);CHKERRQ(ierr); 2997 if (fact <= 1.0) fact = 1.39; 2998 ierr = MatMPIBAIJSetHashTableFactor(B,fact);CHKERRQ(ierr); 2999 ierr = PetscInfo1(B,"Hash table Factor used %5.2f\n",fact);CHKERRQ(ierr); 3000 } 3001 ierr = PetscOptionsEnd();CHKERRQ(ierr); 3002 PetscFunctionReturn(0); 3003 } 3004 3005 /*MC 3006 MATBAIJ - MATBAIJ = "baij" - A matrix type to be used for block sparse matrices. 3007 3008 This matrix type is identical to MATSEQBAIJ when constructed with a single process communicator, 3009 and MATMPIBAIJ otherwise. 3010 3011 Options Database Keys: 3012 . -mat_type baij - sets the matrix type to "baij" during a call to MatSetFromOptions() 3013 3014 Level: beginner 3015 3016 .seealso: MatCreateBAIJ(),MATSEQBAIJ,MATMPIBAIJ, MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3017 M*/ 3018 3019 /*@C 3020 MatMPIBAIJSetPreallocation - Allocates memory for a sparse parallel matrix in block AIJ format 3021 (block compressed row). For good matrix assembly performance 3022 the user should preallocate the matrix storage by setting the parameters 3023 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3024 performance can be increased by more than a factor of 50. 3025 3026 Collective on Mat 3027 3028 Input Parameters: 3029 + B - the matrix 3030 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 3031 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 3032 . d_nz - number of block nonzeros per block row in diagonal portion of local 3033 submatrix (same for all local rows) 3034 . d_nnz - array containing the number of block nonzeros in the various block rows 3035 of the in diagonal portion of the local (possibly different for each block 3036 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry and 3037 set it even if it is zero. 3038 . o_nz - number of block nonzeros per block row in the off-diagonal portion of local 3039 submatrix (same for all local rows). 3040 - o_nnz - array containing the number of nonzeros in the various block rows of the 3041 off-diagonal portion of the local submatrix (possibly different for 3042 each block row) or NULL. 3043 3044 If the *_nnz parameter is given then the *_nz parameter is ignored 3045 3046 Options Database Keys: 3047 + -mat_block_size - size of the blocks to use 3048 - -mat_use_hash_table <fact> 3049 3050 Notes: 3051 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3052 than it must be used on all processors that share the object for that argument. 3053 3054 Storage Information: 3055 For a square global matrix we define each processor's diagonal portion 3056 to be its local rows and the corresponding columns (a square submatrix); 3057 each processor's off-diagonal portion encompasses the remainder of the 3058 local matrix (a rectangular submatrix). 3059 3060 The user can specify preallocated storage for the diagonal part of 3061 the local submatrix with either d_nz or d_nnz (not both). Set 3062 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3063 memory allocation. Likewise, specify preallocated storage for the 3064 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3065 3066 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3067 the figure below we depict these three local rows and all columns (0-11). 3068 3069 .vb 3070 0 1 2 3 4 5 6 7 8 9 10 11 3071 -------------------------- 3072 row 3 |o o o d d d o o o o o o 3073 row 4 |o o o d d d o o o o o o 3074 row 5 |o o o d d d o o o o o o 3075 -------------------------- 3076 .ve 3077 3078 Thus, any entries in the d locations are stored in the d (diagonal) 3079 submatrix, and any entries in the o locations are stored in the 3080 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3081 stored simply in the MATSEQBAIJ format for compressed row storage. 3082 3083 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3084 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3085 In general, for PDE problems in which most nonzeros are near the diagonal, 3086 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3087 or you will get TERRIBLE performance; see the users' manual chapter on 3088 matrices. 3089 3090 You can call MatGetInfo() to get information on how effective the preallocation was; 3091 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3092 You can also run with the option -info and look for messages with the string 3093 malloc in them to see if additional memory allocation was needed. 3094 3095 Level: intermediate 3096 3097 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocationCSR(), PetscSplitOwnership() 3098 @*/ 3099 PetscErrorCode MatMPIBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3100 { 3101 PetscErrorCode ierr; 3102 3103 PetscFunctionBegin; 3104 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3105 PetscValidType(B,1); 3106 PetscValidLogicalCollectiveInt(B,bs,2); 3107 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); 3108 PetscFunctionReturn(0); 3109 } 3110 3111 /*@C 3112 MatCreateBAIJ - Creates a sparse parallel matrix in block AIJ format 3113 (block compressed row). For good matrix assembly performance 3114 the user should preallocate the matrix storage by setting the parameters 3115 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3116 performance can be increased by more than a factor of 50. 3117 3118 Collective 3119 3120 Input Parameters: 3121 + comm - MPI communicator 3122 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 3123 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 3124 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3125 This value should be the same as the local size used in creating the 3126 y vector for the matrix-vector product y = Ax. 3127 . n - number of local columns (or PETSC_DECIDE to have calculated if N is given) 3128 This value should be the same as the local size used in creating the 3129 x vector for the matrix-vector product y = Ax. 3130 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3131 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3132 . d_nz - number of nonzero blocks per block row in diagonal portion of local 3133 submatrix (same for all local rows) 3134 . d_nnz - array containing the number of nonzero blocks in the various block rows 3135 of the in diagonal portion of the local (possibly different for each block 3136 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry 3137 and set it even if it is zero. 3138 . o_nz - number of nonzero blocks per block row in the off-diagonal portion of local 3139 submatrix (same for all local rows). 3140 - o_nnz - array containing the number of nonzero blocks in the various block rows of the 3141 off-diagonal portion of the local submatrix (possibly different for 3142 each block row) or NULL. 3143 3144 Output Parameter: 3145 . A - the matrix 3146 3147 Options Database Keys: 3148 + -mat_block_size - size of the blocks to use 3149 - -mat_use_hash_table <fact> 3150 3151 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3152 MatXXXXSetPreallocation() paradigm instead of this routine directly. 3153 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3154 3155 Notes: 3156 If the *_nnz parameter is given then the *_nz parameter is ignored 3157 3158 A nonzero block is any block that as 1 or more nonzeros in it 3159 3160 The user MUST specify either the local or global matrix dimensions 3161 (possibly both). 3162 3163 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3164 than it must be used on all processors that share the object for that argument. 3165 3166 Storage Information: 3167 For a square global matrix we define each processor's diagonal portion 3168 to be its local rows and the corresponding columns (a square submatrix); 3169 each processor's off-diagonal portion encompasses the remainder of the 3170 local matrix (a rectangular submatrix). 3171 3172 The user can specify preallocated storage for the diagonal part of 3173 the local submatrix with either d_nz or d_nnz (not both). Set 3174 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3175 memory allocation. Likewise, specify preallocated storage for the 3176 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3177 3178 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3179 the figure below we depict these three local rows and all columns (0-11). 3180 3181 .vb 3182 0 1 2 3 4 5 6 7 8 9 10 11 3183 -------------------------- 3184 row 3 |o o o d d d o o o o o o 3185 row 4 |o o o d d d o o o o o o 3186 row 5 |o o o d d d o o o o o o 3187 -------------------------- 3188 .ve 3189 3190 Thus, any entries in the d locations are stored in the d (diagonal) 3191 submatrix, and any entries in the o locations are stored in the 3192 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3193 stored simply in the MATSEQBAIJ format for compressed row storage. 3194 3195 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3196 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3197 In general, for PDE problems in which most nonzeros are near the diagonal, 3198 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3199 or you will get TERRIBLE performance; see the users' manual chapter on 3200 matrices. 3201 3202 Level: intermediate 3203 3204 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3205 @*/ 3206 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) 3207 { 3208 PetscErrorCode ierr; 3209 PetscMPIInt size; 3210 3211 PetscFunctionBegin; 3212 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3213 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 3214 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 3215 if (size > 1) { 3216 ierr = MatSetType(*A,MATMPIBAIJ);CHKERRQ(ierr); 3217 ierr = MatMPIBAIJSetPreallocation(*A,bs,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 3218 } else { 3219 ierr = MatSetType(*A,MATSEQBAIJ);CHKERRQ(ierr); 3220 ierr = MatSeqBAIJSetPreallocation(*A,bs,d_nz,d_nnz);CHKERRQ(ierr); 3221 } 3222 PetscFunctionReturn(0); 3223 } 3224 3225 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 3226 { 3227 Mat mat; 3228 Mat_MPIBAIJ *a,*oldmat = (Mat_MPIBAIJ*)matin->data; 3229 PetscErrorCode ierr; 3230 PetscInt len=0; 3231 3232 PetscFunctionBegin; 3233 *newmat = NULL; 3234 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 3235 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 3236 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 3237 3238 mat->factortype = matin->factortype; 3239 mat->preallocated = PETSC_TRUE; 3240 mat->assembled = PETSC_TRUE; 3241 mat->insertmode = NOT_SET_VALUES; 3242 3243 a = (Mat_MPIBAIJ*)mat->data; 3244 mat->rmap->bs = matin->rmap->bs; 3245 a->bs2 = oldmat->bs2; 3246 a->mbs = oldmat->mbs; 3247 a->nbs = oldmat->nbs; 3248 a->Mbs = oldmat->Mbs; 3249 a->Nbs = oldmat->Nbs; 3250 3251 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 3252 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 3253 3254 a->size = oldmat->size; 3255 a->rank = oldmat->rank; 3256 a->donotstash = oldmat->donotstash; 3257 a->roworiented = oldmat->roworiented; 3258 a->rowindices = NULL; 3259 a->rowvalues = NULL; 3260 a->getrowactive = PETSC_FALSE; 3261 a->barray = NULL; 3262 a->rstartbs = oldmat->rstartbs; 3263 a->rendbs = oldmat->rendbs; 3264 a->cstartbs = oldmat->cstartbs; 3265 a->cendbs = oldmat->cendbs; 3266 3267 /* hash table stuff */ 3268 a->ht = NULL; 3269 a->hd = NULL; 3270 a->ht_size = 0; 3271 a->ht_flag = oldmat->ht_flag; 3272 a->ht_fact = oldmat->ht_fact; 3273 a->ht_total_ct = 0; 3274 a->ht_insert_ct = 0; 3275 3276 ierr = PetscArraycpy(a->rangebs,oldmat->rangebs,a->size+1);CHKERRQ(ierr); 3277 if (oldmat->colmap) { 3278 #if defined(PETSC_USE_CTABLE) 3279 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 3280 #else 3281 ierr = PetscMalloc1(a->Nbs,&a->colmap);CHKERRQ(ierr); 3282 ierr = PetscLogObjectMemory((PetscObject)mat,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3283 ierr = PetscArraycpy(a->colmap,oldmat->colmap,a->Nbs);CHKERRQ(ierr); 3284 #endif 3285 } else a->colmap = NULL; 3286 3287 if (oldmat->garray && (len = ((Mat_SeqBAIJ*)(oldmat->B->data))->nbs)) { 3288 ierr = PetscMalloc1(len,&a->garray);CHKERRQ(ierr); 3289 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 3290 ierr = PetscArraycpy(a->garray,oldmat->garray,len);CHKERRQ(ierr); 3291 } else a->garray = NULL; 3292 3293 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)matin),matin->rmap->bs,&mat->bstash);CHKERRQ(ierr); 3294 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 3295 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 3296 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 3297 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 3298 3299 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 3300 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 3301 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 3302 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 3303 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 3304 *newmat = mat; 3305 PetscFunctionReturn(0); 3306 } 3307 3308 /* Used for both MPIBAIJ and MPISBAIJ matrices */ 3309 PetscErrorCode MatLoad_MPIBAIJ_Binary(Mat mat,PetscViewer viewer) 3310 { 3311 PetscInt header[4],M,N,nz,bs,m,n,mbs,nbs,rows,cols,sum,i,j,k; 3312 PetscInt *rowidxs,*colidxs,rs,cs,ce; 3313 PetscScalar *matvals; 3314 PetscErrorCode ierr; 3315 3316 PetscFunctionBegin; 3317 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 3318 3319 /* read in matrix header */ 3320 ierr = PetscViewerBinaryRead(viewer,header,4,NULL,PETSC_INT);CHKERRQ(ierr); 3321 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Not a matrix object in file"); 3322 M = header[1]; N = header[2]; nz = header[3]; 3323 if (M < 0) SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Matrix row size (%D) in file is negative",M); 3324 if (N < 0) SETERRQ1(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Matrix column size (%D) in file is negative",N); 3325 if (nz < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk, cannot load as MPIBAIJ"); 3326 3327 /* set block sizes from the viewer's .info file */ 3328 ierr = MatLoad_Binary_BlockSizes(mat,viewer);CHKERRQ(ierr); 3329 /* set local sizes if not set already */ 3330 if (mat->rmap->n < 0 && M == N) mat->rmap->n = mat->cmap->n; 3331 if (mat->cmap->n < 0 && M == N) mat->cmap->n = mat->rmap->n; 3332 /* set global sizes if not set already */ 3333 if (mat->rmap->N < 0) mat->rmap->N = M; 3334 if (mat->cmap->N < 0) mat->cmap->N = N; 3335 ierr = PetscLayoutSetUp(mat->rmap);CHKERRQ(ierr); 3336 ierr = PetscLayoutSetUp(mat->cmap);CHKERRQ(ierr); 3337 3338 /* check if the matrix sizes are correct */ 3339 ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr); 3340 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); 3341 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 3342 ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr); 3343 ierr = PetscLayoutGetRange(mat->rmap,&rs,NULL);CHKERRQ(ierr); 3344 ierr = PetscLayoutGetRange(mat->cmap,&cs,&ce);CHKERRQ(ierr); 3345 mbs = m/bs; nbs = n/bs; 3346 3347 /* read in row lengths and build row indices */ 3348 ierr = PetscMalloc1(m+1,&rowidxs);CHKERRQ(ierr); 3349 ierr = PetscViewerBinaryReadAll(viewer,rowidxs+1,m,PETSC_DECIDE,M,PETSC_INT);CHKERRQ(ierr); 3350 rowidxs[0] = 0; for (i=0; i<m; i++) rowidxs[i+1] += rowidxs[i]; 3351 ierr = MPIU_Allreduce(&rowidxs[m],&sum,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)viewer));CHKERRMPI(ierr); 3352 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); 3353 3354 /* read in column indices and matrix values */ 3355 ierr = PetscMalloc2(rowidxs[m],&colidxs,rowidxs[m],&matvals);CHKERRQ(ierr); 3356 ierr = PetscViewerBinaryReadAll(viewer,colidxs,rowidxs[m],PETSC_DETERMINE,PETSC_DETERMINE,PETSC_INT);CHKERRQ(ierr); 3357 ierr = PetscViewerBinaryReadAll(viewer,matvals,rowidxs[m],PETSC_DETERMINE,PETSC_DETERMINE,PETSC_SCALAR);CHKERRQ(ierr); 3358 3359 { /* preallocate matrix storage */ 3360 PetscBT bt; /* helper bit set to count diagonal nonzeros */ 3361 PetscHSetI ht; /* helper hash set to count off-diagonal nonzeros */ 3362 PetscBool sbaij,done; 3363 PetscInt *d_nnz,*o_nnz; 3364 3365 ierr = PetscBTCreate(nbs,&bt);CHKERRQ(ierr); 3366 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 3367 ierr = PetscCalloc2(mbs,&d_nnz,mbs,&o_nnz);CHKERRQ(ierr); 3368 ierr = PetscObjectTypeCompare((PetscObject)mat,MATMPISBAIJ,&sbaij);CHKERRQ(ierr); 3369 for (i=0; i<mbs; i++) { 3370 ierr = PetscBTMemzero(nbs,bt);CHKERRQ(ierr); 3371 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 3372 for (k=0; k<bs; k++) { 3373 PetscInt row = bs*i + k; 3374 for (j=rowidxs[row]; j<rowidxs[row+1]; j++) { 3375 PetscInt col = colidxs[j]; 3376 if (!sbaij || col >= row) { 3377 if (col >= cs && col < ce) { 3378 if (!PetscBTLookupSet(bt,(col-cs)/bs)) d_nnz[i]++; 3379 } else { 3380 ierr = PetscHSetIQueryAdd(ht,col/bs,&done);CHKERRQ(ierr); 3381 if (done) o_nnz[i]++; 3382 } 3383 } 3384 } 3385 } 3386 } 3387 ierr = PetscBTDestroy(&bt);CHKERRQ(ierr); 3388 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 3389 ierr = MatMPIBAIJSetPreallocation(mat,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3390 ierr = MatMPISBAIJSetPreallocation(mat,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3391 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3392 } 3393 3394 /* store matrix values */ 3395 for (i=0; i<m; i++) { 3396 PetscInt row = rs + i, s = rowidxs[i], e = rowidxs[i+1]; 3397 ierr = (*mat->ops->setvalues)(mat,1,&row,e-s,colidxs+s,matvals+s,INSERT_VALUES);CHKERRQ(ierr); 3398 } 3399 3400 ierr = PetscFree(rowidxs);CHKERRQ(ierr); 3401 ierr = PetscFree2(colidxs,matvals);CHKERRQ(ierr); 3402 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3403 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3404 PetscFunctionReturn(0); 3405 } 3406 3407 PetscErrorCode MatLoad_MPIBAIJ(Mat mat,PetscViewer viewer) 3408 { 3409 PetscErrorCode ierr; 3410 PetscBool isbinary; 3411 3412 PetscFunctionBegin; 3413 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 3414 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); 3415 ierr = MatLoad_MPIBAIJ_Binary(mat,viewer);CHKERRQ(ierr); 3416 PetscFunctionReturn(0); 3417 } 3418 3419 /*@ 3420 MatMPIBAIJSetHashTableFactor - Sets the factor required to compute the size of the HashTable. 3421 3422 Input Parameters: 3423 + mat - the matrix 3424 - fact - factor 3425 3426 Not Collective, each process can use a different factor 3427 3428 Level: advanced 3429 3430 Notes: 3431 This can also be set by the command line option: -mat_use_hash_table <fact> 3432 3433 .seealso: MatSetOption() 3434 @*/ 3435 PetscErrorCode MatMPIBAIJSetHashTableFactor(Mat mat,PetscReal fact) 3436 { 3437 PetscErrorCode ierr; 3438 3439 PetscFunctionBegin; 3440 ierr = PetscTryMethod(mat,"MatSetHashTableFactor_C",(Mat,PetscReal),(mat,fact));CHKERRQ(ierr); 3441 PetscFunctionReturn(0); 3442 } 3443 3444 PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat mat,PetscReal fact) 3445 { 3446 Mat_MPIBAIJ *baij; 3447 3448 PetscFunctionBegin; 3449 baij = (Mat_MPIBAIJ*)mat->data; 3450 baij->ht_fact = fact; 3451 PetscFunctionReturn(0); 3452 } 3453 3454 PetscErrorCode MatMPIBAIJGetSeqBAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 3455 { 3456 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 3457 PetscBool flg; 3458 PetscErrorCode ierr; 3459 3460 PetscFunctionBegin; 3461 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIBAIJ,&flg);CHKERRQ(ierr); 3462 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIBAIJ matrix as input"); 3463 if (Ad) *Ad = a->A; 3464 if (Ao) *Ao = a->B; 3465 if (colmap) *colmap = a->garray; 3466 PetscFunctionReturn(0); 3467 } 3468 3469 /* 3470 Special version for direct calls from Fortran (to eliminate two function call overheads 3471 */ 3472 #if defined(PETSC_HAVE_FORTRAN_CAPS) 3473 #define matmpibaijsetvaluesblocked_ MATMPIBAIJSETVALUESBLOCKED 3474 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 3475 #define matmpibaijsetvaluesblocked_ matmpibaijsetvaluesblocked 3476 #endif 3477 3478 /*@C 3479 MatMPIBAIJSetValuesBlocked - Direct Fortran call to replace call to MatSetValuesBlocked() 3480 3481 Collective on Mat 3482 3483 Input Parameters: 3484 + mat - the matrix 3485 . min - number of input rows 3486 . im - input rows 3487 . nin - number of input columns 3488 . in - input columns 3489 . v - numerical values input 3490 - addvin - INSERT_VALUES or ADD_VALUES 3491 3492 Notes: 3493 This has a complete copy of MatSetValuesBlocked_MPIBAIJ() which is terrible code un-reuse. 3494 3495 Level: advanced 3496 3497 .seealso: MatSetValuesBlocked() 3498 @*/ 3499 PetscErrorCode matmpibaijsetvaluesblocked_(Mat *matin,PetscInt *min,const PetscInt im[],PetscInt *nin,const PetscInt in[],const MatScalar v[],InsertMode *addvin) 3500 { 3501 /* convert input arguments to C version */ 3502 Mat mat = *matin; 3503 PetscInt m = *min, n = *nin; 3504 InsertMode addv = *addvin; 3505 3506 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 3507 const MatScalar *value; 3508 MatScalar *barray = baij->barray; 3509 PetscBool roworiented = baij->roworiented; 3510 PetscErrorCode ierr; 3511 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 3512 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 3513 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 3514 3515 PetscFunctionBegin; 3516 /* tasks normally handled by MatSetValuesBlocked() */ 3517 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 3518 else if (PetscUnlikely(mat->insertmode != addv)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 3519 if (PetscUnlikely(mat->factortype)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 3520 if (mat->assembled) { 3521 mat->was_assembled = PETSC_TRUE; 3522 mat->assembled = PETSC_FALSE; 3523 } 3524 ierr = PetscLogEventBegin(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3525 3526 if (!barray) { 3527 ierr = PetscMalloc1(bs2,&barray);CHKERRQ(ierr); 3528 baij->barray = barray; 3529 } 3530 3531 if (roworiented) stepval = (n-1)*bs; 3532 else stepval = (m-1)*bs; 3533 3534 for (i=0; i<m; i++) { 3535 if (im[i] < 0) continue; 3536 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); 3537 if (im[i] >= rstart && im[i] < rend) { 3538 row = im[i] - rstart; 3539 for (j=0; j<n; j++) { 3540 /* If NumCol = 1 then a copy is not required */ 3541 if ((roworiented) && (n == 1)) { 3542 barray = (MatScalar*)v + i*bs2; 3543 } else if ((!roworiented) && (m == 1)) { 3544 barray = (MatScalar*)v + j*bs2; 3545 } else { /* Here a copy is required */ 3546 if (roworiented) { 3547 value = v + i*(stepval+bs)*bs + j*bs; 3548 } else { 3549 value = v + j*(stepval+bs)*bs + i*bs; 3550 } 3551 for (ii=0; ii<bs; ii++,value+=stepval) { 3552 for (jj=0; jj<bs; jj++) { 3553 *barray++ = *value++; 3554 } 3555 } 3556 barray -=bs2; 3557 } 3558 3559 if (in[j] >= cstart && in[j] < cend) { 3560 col = in[j] - cstart; 3561 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->A,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 3562 } else if (in[j] < 0) continue; 3563 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); 3564 else { 3565 if (mat->was_assembled) { 3566 if (!baij->colmap) { 3567 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 3568 } 3569 3570 #if defined(PETSC_USE_DEBUG) 3571 #if defined(PETSC_USE_CTABLE) 3572 { PetscInt data; 3573 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 3574 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3575 } 3576 #else 3577 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3578 #endif 3579 #endif 3580 #if defined(PETSC_USE_CTABLE) 3581 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 3582 col = (col - 1)/bs; 3583 #else 3584 col = (baij->colmap[in[j]] - 1)/bs; 3585 #endif 3586 if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 3587 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 3588 col = in[j]; 3589 } 3590 } else col = in[j]; 3591 ierr = MatSetValuesBlocked_SeqBAIJ_Inlined(baij->B,row,col,barray,addv,im[i],in[j]);CHKERRQ(ierr); 3592 } 3593 } 3594 } else { 3595 if (!baij->donotstash) { 3596 if (roworiented) { 3597 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3598 } else { 3599 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3600 } 3601 } 3602 } 3603 } 3604 3605 /* task normally handled by MatSetValuesBlocked() */ 3606 ierr = PetscLogEventEnd(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3607 PetscFunctionReturn(0); 3608 } 3609 3610 /*@ 3611 MatCreateMPIBAIJWithArrays - creates a MPI BAIJ matrix using arrays that contain in standard block 3612 CSR format the local rows. 3613 3614 Collective 3615 3616 Input Parameters: 3617 + comm - MPI communicator 3618 . bs - the block size, only a block size of 1 is supported 3619 . m - number of local rows (Cannot be PETSC_DECIDE) 3620 . n - This value should be the same as the local size used in creating the 3621 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3622 calculated if N is given) For square matrices n is almost always m. 3623 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3624 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3625 . 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 3626 . j - column indices 3627 - a - matrix values 3628 3629 Output Parameter: 3630 . mat - the matrix 3631 3632 Level: intermediate 3633 3634 Notes: 3635 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3636 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3637 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3638 3639 The order of the entries in values is the same as the block compressed sparse row storage format; that is, it is 3640 the same as a three dimensional array in Fortran values(bs,bs,nnz) that contains the first column of the first 3641 block, followed by the second column of the first block etc etc. That is, the blocks are contiguous in memory 3642 with column-major ordering within blocks. 3643 3644 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3645 3646 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3647 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3648 @*/ 3649 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) 3650 { 3651 PetscErrorCode ierr; 3652 3653 PetscFunctionBegin; 3654 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3655 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3656 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3657 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3658 ierr = MatSetType(*mat,MATMPIBAIJ);CHKERRQ(ierr); 3659 ierr = MatSetBlockSize(*mat,bs);CHKERRQ(ierr); 3660 ierr = MatSetUp(*mat);CHKERRQ(ierr); 3661 ierr = MatSetOption(*mat,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 3662 ierr = MatMPIBAIJSetPreallocationCSR(*mat,bs,i,j,a);CHKERRQ(ierr); 3663 ierr = MatSetOption(*mat,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr); 3664 PetscFunctionReturn(0); 3665 } 3666 3667 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIBAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 3668 { 3669 PetscErrorCode ierr; 3670 PetscInt m,N,i,rstart,nnz,Ii,bs,cbs; 3671 PetscInt *indx; 3672 PetscScalar *values; 3673 3674 PetscFunctionBegin; 3675 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 3676 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 3677 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)inmat->data; 3678 PetscInt *dnz,*onz,mbs,Nbs,nbs; 3679 PetscInt *bindx,rmax=a->rmax,j; 3680 PetscMPIInt rank,size; 3681 3682 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 3683 mbs = m/bs; Nbs = N/cbs; 3684 if (n == PETSC_DECIDE) { 3685 ierr = PetscSplitOwnershipBlock(comm,cbs,&n,&N);CHKERRQ(ierr); 3686 } 3687 nbs = n/cbs; 3688 3689 ierr = PetscMalloc1(rmax,&bindx);CHKERRQ(ierr); 3690 ierr = MatPreallocateInitialize(comm,mbs,nbs,dnz,onz);CHKERRQ(ierr); /* inline function, output __end and __rstart are used below */ 3691 3692 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 3693 ierr = MPI_Comm_rank(comm,&size);CHKERRMPI(ierr); 3694 if (rank == size-1) { 3695 /* Check sum(nbs) = Nbs */ 3696 if (__end != Nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local block columns %D != global block columns %D",__end,Nbs); 3697 } 3698 3699 rstart = __rstart; /* block rstart of *outmat; see inline function MatPreallocateInitialize */ 3700 for (i=0; i<mbs; i++) { 3701 ierr = MatGetRow_SeqBAIJ(inmat,i*bs,&nnz,&indx,NULL);CHKERRQ(ierr); /* non-blocked nnz and indx */ 3702 nnz = nnz/bs; 3703 for (j=0; j<nnz; j++) bindx[j] = indx[j*bs]/bs; 3704 ierr = MatPreallocateSet(i+rstart,nnz,bindx,dnz,onz);CHKERRQ(ierr); 3705 ierr = MatRestoreRow_SeqBAIJ(inmat,i*bs,&nnz,&indx,NULL);CHKERRQ(ierr); 3706 } 3707 ierr = PetscFree(bindx);CHKERRQ(ierr); 3708 3709 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 3710 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3711 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 3712 ierr = MatSetType(*outmat,MATBAIJ);CHKERRQ(ierr); 3713 ierr = MatSeqBAIJSetPreallocation(*outmat,bs,0,dnz);CHKERRQ(ierr); 3714 ierr = MatMPIBAIJSetPreallocation(*outmat,bs,0,dnz,0,onz);CHKERRQ(ierr); 3715 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 3716 ierr = MatSetOption(*outmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3717 } 3718 3719 /* numeric phase */ 3720 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 3721 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 3722 3723 for (i=0; i<m; i++) { 3724 ierr = MatGetRow_SeqBAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3725 Ii = i + rstart; 3726 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 3727 ierr = MatRestoreRow_SeqBAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3728 } 3729 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3730 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3731 PetscFunctionReturn(0); 3732 } 3733