1 2 #include <../src/mat/impls/baij/mpi/mpibaij.h> /*I "petscmat.h" I*/ 3 #include <petscblaslapack.h> 4 5 extern PetscErrorCode MatSetUpMultiply_MPIBAIJ(Mat); 6 extern PetscErrorCode MatDisAssemble_MPIBAIJ(Mat); 7 extern PetscErrorCode MatGetValues_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt [],PetscScalar []); 8 extern PetscErrorCode MatSetValues_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt [],const PetscScalar [],InsertMode); 9 extern PetscErrorCode MatSetValuesBlocked_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode); 10 extern PetscErrorCode MatGetRow_SeqBAIJ(Mat,PetscInt,PetscInt*,PetscInt*[],PetscScalar*[]); 11 extern PetscErrorCode MatRestoreRow_SeqBAIJ(Mat,PetscInt,PetscInt*,PetscInt*[],PetscScalar*[]); 12 extern PetscErrorCode MatZeroRows_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscScalar,Vec,Vec); 13 14 #undef __FUNCT__ 15 #define __FUNCT__ "MatGetRowMaxAbs_MPIBAIJ" 16 PetscErrorCode MatGetRowMaxAbs_MPIBAIJ(Mat A,Vec v,PetscInt idx[]) 17 { 18 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 19 PetscErrorCode ierr; 20 PetscInt i,*idxb = 0; 21 PetscScalar *va,*vb; 22 Vec vtmp; 23 24 PetscFunctionBegin; 25 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 26 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 27 if (idx) { 28 for (i=0; i<A->rmap->n; i++) { 29 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 30 } 31 } 32 33 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 34 if (idx) {ierr = PetscMalloc(A->rmap->n*sizeof(PetscInt),&idxb);CHKERRQ(ierr);} 35 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 36 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 37 38 for (i=0; i<A->rmap->n; i++) { 39 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 40 va[i] = vb[i]; 41 if (idx) idx[i] = A->cmap->bs*a->garray[idxb[i]/A->cmap->bs] + (idxb[i] % A->cmap->bs); 42 } 43 } 44 45 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 46 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 47 ierr = PetscFree(idxb);CHKERRQ(ierr); 48 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 49 PetscFunctionReturn(0); 50 } 51 52 #undef __FUNCT__ 53 #define __FUNCT__ "MatStoreValues_MPIBAIJ" 54 PetscErrorCode MatStoreValues_MPIBAIJ(Mat mat) 55 { 56 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ*)mat->data; 57 PetscErrorCode ierr; 58 59 PetscFunctionBegin; 60 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 61 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 62 PetscFunctionReturn(0); 63 } 64 65 #undef __FUNCT__ 66 #define __FUNCT__ "MatRetrieveValues_MPIBAIJ" 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 #undef __FUNCT__ 85 #define __FUNCT__ "MatCreateColmap_MPIBAIJ_Private" 86 PetscErrorCode MatCreateColmap_MPIBAIJ_Private(Mat mat) 87 { 88 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 89 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 90 PetscErrorCode ierr; 91 PetscInt nbs = B->nbs,i,bs=mat->rmap->bs; 92 93 PetscFunctionBegin; 94 #if defined(PETSC_USE_CTABLE) 95 ierr = PetscTableCreate(baij->nbs,baij->Nbs+1,&baij->colmap);CHKERRQ(ierr); 96 for (i=0; i<nbs; i++) { 97 ierr = PetscTableAdd(baij->colmap,baij->garray[i]+1,i*bs+1,INSERT_VALUES);CHKERRQ(ierr); 98 } 99 #else 100 ierr = PetscMalloc((baij->Nbs+1)*sizeof(PetscInt),&baij->colmap);CHKERRQ(ierr); 101 ierr = PetscLogObjectMemory((PetscObject)mat,baij->Nbs*sizeof(PetscInt));CHKERRQ(ierr); 102 ierr = PetscMemzero(baij->colmap,baij->Nbs*sizeof(PetscInt));CHKERRQ(ierr); 103 for (i=0; i<nbs; i++) baij->colmap[baij->garray[i]] = i*bs+1; 104 #endif 105 PetscFunctionReturn(0); 106 } 107 108 #define MatSetValues_SeqBAIJ_A_Private(row,col,value,addv) \ 109 { \ 110 \ 111 brow = row/bs; \ 112 rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; \ 113 rmax = aimax[brow]; nrow = ailen[brow]; \ 114 bcol = col/bs; \ 115 ridx = row % bs; cidx = col % bs; \ 116 low = 0; high = nrow; \ 117 while (high-low > 3) { \ 118 t = (low+high)/2; \ 119 if (rp[t] > bcol) high = t; \ 120 else low = t; \ 121 } \ 122 for (_i=low; _i<high; _i++) { \ 123 if (rp[_i] > bcol) break; \ 124 if (rp[_i] == bcol) { \ 125 bap = ap + bs2*_i + bs*cidx + ridx; \ 126 if (addv == ADD_VALUES) *bap += value; \ 127 else *bap = value; \ 128 goto a_noinsert; \ 129 } \ 130 } \ 131 if (a->nonew == 1) goto a_noinsert; \ 132 if (a->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 133 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,aimax,a->nonew,MatScalar); \ 134 N = nrow++ - 1; \ 135 /* shift up all the later entries in this row */ \ 136 for (ii=N; ii>=_i; ii--) { \ 137 rp[ii+1] = rp[ii]; \ 138 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); \ 139 } \ 140 if (N>=_i) { ierr = PetscMemzero(ap+bs2*_i,bs2*sizeof(MatScalar));CHKERRQ(ierr); } \ 141 rp[_i] = bcol; \ 142 ap[bs2*_i + bs*cidx + ridx] = value; \ 143 a_noinsert:; \ 144 ailen[brow] = nrow; \ 145 } 146 147 #define MatSetValues_SeqBAIJ_B_Private(row,col,value,addv) \ 148 { \ 149 brow = row/bs; \ 150 rp = bj + bi[brow]; ap = ba + bs2*bi[brow]; \ 151 rmax = bimax[brow]; nrow = bilen[brow]; \ 152 bcol = col/bs; \ 153 ridx = row % bs; cidx = col % bs; \ 154 low = 0; high = nrow; \ 155 while (high-low > 3) { \ 156 t = (low+high)/2; \ 157 if (rp[t] > bcol) high = t; \ 158 else low = t; \ 159 } \ 160 for (_i=low; _i<high; _i++) { \ 161 if (rp[_i] > bcol) break; \ 162 if (rp[_i] == bcol) { \ 163 bap = ap + bs2*_i + bs*cidx + ridx; \ 164 if (addv == ADD_VALUES) *bap += value; \ 165 else *bap = value; \ 166 goto b_noinsert; \ 167 } \ 168 } \ 169 if (b->nonew == 1) goto b_noinsert; \ 170 if (b->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 171 MatSeqXAIJReallocateAIJ(B,b->mbs,bs2,nrow,brow,bcol,rmax,ba,bi,bj,rp,ap,bimax,b->nonew,MatScalar); \ 172 N = nrow++ - 1; \ 173 /* shift up all the later entries in this row */ \ 174 for (ii=N; ii>=_i; ii--) { \ 175 rp[ii+1] = rp[ii]; \ 176 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); \ 177 } \ 178 if (N>=_i) { ierr = PetscMemzero(ap+bs2*_i,bs2*sizeof(MatScalar));CHKERRQ(ierr);} \ 179 rp[_i] = bcol; \ 180 ap[bs2*_i + bs*cidx + ridx] = value; \ 181 b_noinsert:; \ 182 bilen[brow] = nrow; \ 183 } 184 185 #undef __FUNCT__ 186 #define __FUNCT__ "MatSetValues_MPIBAIJ" 187 PetscErrorCode MatSetValues_MPIBAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 188 { 189 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 190 MatScalar value; 191 PetscBool roworiented = baij->roworiented; 192 PetscErrorCode ierr; 193 PetscInt i,j,row,col; 194 PetscInt rstart_orig=mat->rmap->rstart; 195 PetscInt rend_orig =mat->rmap->rend,cstart_orig=mat->cmap->rstart; 196 PetscInt cend_orig =mat->cmap->rend,bs=mat->rmap->bs; 197 198 /* Some Variables required in the macro */ 199 Mat A = baij->A; 200 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)(A)->data; 201 PetscInt *aimax=a->imax,*ai=a->i,*ailen=a->ilen,*aj=a->j; 202 MatScalar *aa =a->a; 203 204 Mat B = baij->B; 205 Mat_SeqBAIJ *b = (Mat_SeqBAIJ*)(B)->data; 206 PetscInt *bimax=b->imax,*bi=b->i,*bilen=b->ilen,*bj=b->j; 207 MatScalar *ba =b->a; 208 209 PetscInt *rp,ii,nrow,_i,rmax,N,brow,bcol; 210 PetscInt low,high,t,ridx,cidx,bs2=a->bs2; 211 MatScalar *ap,*bap; 212 213 PetscFunctionBegin; 214 if (v) PetscValidScalarPointer(v,6); 215 for (i=0; i<m; i++) { 216 if (im[i] < 0) continue; 217 #if defined(PETSC_USE_DEBUG) 218 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); 219 #endif 220 if (im[i] >= rstart_orig && im[i] < rend_orig) { 221 row = im[i] - rstart_orig; 222 for (j=0; j<n; j++) { 223 if (in[j] >= cstart_orig && in[j] < cend_orig) { 224 col = in[j] - cstart_orig; 225 if (roworiented) value = v[i*n+j]; 226 else value = v[i+j*m]; 227 MatSetValues_SeqBAIJ_A_Private(row,col,value,addv); 228 /* ierr = MatSetValues_SeqBAIJ(baij->A,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ 229 } else if (in[j] < 0) continue; 230 #if defined(PETSC_USE_DEBUG) 231 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 232 #endif 233 else { 234 if (mat->was_assembled) { 235 if (!baij->colmap) { 236 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 237 } 238 #if defined(PETSC_USE_CTABLE) 239 ierr = PetscTableFind(baij->colmap,in[j]/bs + 1,&col);CHKERRQ(ierr); 240 col = col - 1; 241 #else 242 col = baij->colmap[in[j]/bs] - 1; 243 #endif 244 if (col < 0 && !((Mat_SeqBAIJ*)(baij->B->data))->nonew) { 245 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 246 col = in[j]; 247 /* Reinitialize the variables required by MatSetValues_SeqBAIJ_B_Private() */ 248 B = baij->B; 249 b = (Mat_SeqBAIJ*)(B)->data; 250 bimax=b->imax;bi=b->i;bilen=b->ilen;bj=b->j; 251 ba =b->a; 252 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", im[i], in[j]); 253 else col += in[j]%bs; 254 } else col = in[j]; 255 if (roworiented) value = v[i*n+j]; 256 else value = v[i+j*m]; 257 MatSetValues_SeqBAIJ_B_Private(row,col,value,addv); 258 /* ierr = MatSetValues_SeqBAIJ(baij->B,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ 259 } 260 } 261 } else { 262 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]); 263 if (!baij->donotstash) { 264 mat->assembled = PETSC_FALSE; 265 if (roworiented) { 266 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 267 } else { 268 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 269 } 270 } 271 } 272 } 273 PetscFunctionReturn(0); 274 } 275 276 #undef __FUNCT__ 277 #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ" 278 PetscErrorCode MatSetValuesBlocked_MPIBAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 279 { 280 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 281 const PetscScalar *value; 282 MatScalar *barray = baij->barray; 283 PetscBool roworiented = baij->roworiented; 284 PetscErrorCode ierr; 285 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 286 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 287 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 288 289 PetscFunctionBegin; 290 if (!barray) { 291 ierr = PetscMalloc(bs2*sizeof(MatScalar),&barray);CHKERRQ(ierr); 292 baij->barray = barray; 293 } 294 295 if (roworiented) stepval = (n-1)*bs; 296 else stepval = (m-1)*bs; 297 298 for (i=0; i<m; i++) { 299 if (im[i] < 0) continue; 300 #if defined(PETSC_USE_DEBUG) 301 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); 302 #endif 303 if (im[i] >= rstart && im[i] < rend) { 304 row = im[i] - rstart; 305 for (j=0; j<n; j++) { 306 /* If NumCol = 1 then a copy is not required */ 307 if ((roworiented) && (n == 1)) { 308 barray = (MatScalar*)v + i*bs2; 309 } else if ((!roworiented) && (m == 1)) { 310 barray = (MatScalar*)v + j*bs2; 311 } else { /* Here a copy is required */ 312 if (roworiented) { 313 value = v + (i*(stepval+bs) + j)*bs; 314 } else { 315 value = v + (j*(stepval+bs) + i)*bs; 316 } 317 for (ii=0; ii<bs; ii++,value+=bs+stepval) { 318 for (jj=0; jj<bs; jj++) barray[jj] = value[jj]; 319 barray += bs; 320 } 321 barray -= bs2; 322 } 323 324 if (in[j] >= cstart && in[j] < cend) { 325 col = in[j] - cstart; 326 ierr = MatSetValuesBlocked_SeqBAIJ(baij->A,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 327 } else if (in[j] < 0) continue; 328 #if defined(PETSC_USE_DEBUG) 329 else if (in[j] >= baij->Nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large, col %D max %D",in[j],baij->Nbs-1); 330 #endif 331 else { 332 if (mat->was_assembled) { 333 if (!baij->colmap) { 334 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 335 } 336 337 #if defined(PETSC_USE_DEBUG) 338 #if defined(PETSC_USE_CTABLE) 339 { PetscInt data; 340 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 341 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 342 } 343 #else 344 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 345 #endif 346 #endif 347 #if defined(PETSC_USE_CTABLE) 348 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 349 col = (col - 1)/bs; 350 #else 351 col = (baij->colmap[in[j]] - 1)/bs; 352 #endif 353 if (col < 0 && !((Mat_SeqBAIJ*)(baij->B->data))->nonew) { 354 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 355 col = in[j]; 356 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", bs*im[i], bs*in[j]); 357 } else col = in[j]; 358 ierr = MatSetValuesBlocked_SeqBAIJ(baij->B,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 359 } 360 } 361 } else { 362 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]); 363 if (!baij->donotstash) { 364 if (roworiented) { 365 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 366 } else { 367 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 368 } 369 } 370 } 371 } 372 PetscFunctionReturn(0); 373 } 374 375 #define HASH_KEY 0.6180339887 376 #define HASH(size,key,tmp) (tmp = (key)*HASH_KEY,(PetscInt)((size)*(tmp-(PetscInt)tmp))) 377 /* #define HASH(size,key) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 378 /* #define HASH(size,key,tmp) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 379 #undef __FUNCT__ 380 #define __FUNCT__ "MatSetValues_MPIBAIJ_HT" 381 PetscErrorCode MatSetValues_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 382 { 383 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 384 PetscBool roworiented = baij->roworiented; 385 PetscErrorCode ierr; 386 PetscInt i,j,row,col; 387 PetscInt rstart_orig=mat->rmap->rstart; 388 PetscInt rend_orig =mat->rmap->rend,Nbs=baij->Nbs; 389 PetscInt h1,key,size=baij->ht_size,bs=mat->rmap->bs,*HT=baij->ht,idx; 390 PetscReal tmp; 391 MatScalar **HD = baij->hd,value; 392 #if defined(PETSC_USE_DEBUG) 393 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 394 #endif 395 396 PetscFunctionBegin; 397 if (v) PetscValidScalarPointer(v,6); 398 for (i=0; i<m; i++) { 399 #if defined(PETSC_USE_DEBUG) 400 if (im[i] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row"); 401 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); 402 #endif 403 row = im[i]; 404 if (row >= rstart_orig && row < rend_orig) { 405 for (j=0; j<n; j++) { 406 col = in[j]; 407 if (roworiented) value = v[i*n+j]; 408 else value = v[i+j*m]; 409 /* Look up PetscInto the Hash Table */ 410 key = (row/bs)*Nbs+(col/bs)+1; 411 h1 = HASH(size,key,tmp); 412 413 414 idx = h1; 415 #if defined(PETSC_USE_DEBUG) 416 insert_ct++; 417 total_ct++; 418 if (HT[idx] != key) { 419 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++) ; 420 if (idx == size) { 421 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++) ; 422 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 423 } 424 } 425 #else 426 if (HT[idx] != key) { 427 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++) ; 428 if (idx == size) { 429 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++) ; 430 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 431 } 432 } 433 #endif 434 /* A HASH table entry is found, so insert the values at the correct address */ 435 if (addv == ADD_VALUES) *(HD[idx]+ (col % bs)*bs + (row % bs)) += value; 436 else *(HD[idx]+ (col % bs)*bs + (row % bs)) = value; 437 } 438 } else if (!baij->donotstash) { 439 if (roworiented) { 440 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 441 } else { 442 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 443 } 444 } 445 } 446 #if defined(PETSC_USE_DEBUG) 447 baij->ht_total_ct = total_ct; 448 baij->ht_insert_ct = insert_ct; 449 #endif 450 PetscFunctionReturn(0); 451 } 452 453 #undef __FUNCT__ 454 #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ_HT" 455 PetscErrorCode MatSetValuesBlocked_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 456 { 457 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 458 PetscBool roworiented = baij->roworiented; 459 PetscErrorCode ierr; 460 PetscInt i,j,ii,jj,row,col; 461 PetscInt rstart=baij->rstartbs; 462 PetscInt rend =mat->rmap->rend,stepval,bs=mat->rmap->bs,bs2=baij->bs2,nbs2=n*bs2; 463 PetscInt h1,key,size=baij->ht_size,idx,*HT=baij->ht,Nbs=baij->Nbs; 464 PetscReal tmp; 465 MatScalar **HD = baij->hd,*baij_a; 466 const PetscScalar *v_t,*value; 467 #if defined(PETSC_USE_DEBUG) 468 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 469 #endif 470 471 PetscFunctionBegin; 472 if (roworiented) stepval = (n-1)*bs; 473 else stepval = (m-1)*bs; 474 475 for (i=0; i<m; i++) { 476 #if defined(PETSC_USE_DEBUG) 477 if (im[i] < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",im[i]); 478 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); 479 #endif 480 row = im[i]; 481 v_t = v + i*nbs2; 482 if (row >= rstart && row < rend) { 483 for (j=0; j<n; j++) { 484 col = in[j]; 485 486 /* Look up into the Hash Table */ 487 key = row*Nbs+col+1; 488 h1 = HASH(size,key,tmp); 489 490 idx = h1; 491 #if defined(PETSC_USE_DEBUG) 492 total_ct++; 493 insert_ct++; 494 if (HT[idx] != key) { 495 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++) ; 496 if (idx == size) { 497 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++) ; 498 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 499 } 500 } 501 #else 502 if (HT[idx] != key) { 503 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++) ; 504 if (idx == size) { 505 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++) ; 506 if (idx == h1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 507 } 508 } 509 #endif 510 baij_a = HD[idx]; 511 if (roworiented) { 512 /*value = v + i*(stepval+bs)*bs + j*bs;*/ 513 /* value = v + (i*(stepval+bs)+j)*bs; */ 514 value = v_t; 515 v_t += bs; 516 if (addv == ADD_VALUES) { 517 for (ii=0; ii<bs; ii++,value+=stepval) { 518 for (jj=ii; jj<bs2; jj+=bs) { 519 baij_a[jj] += *value++; 520 } 521 } 522 } else { 523 for (ii=0; ii<bs; ii++,value+=stepval) { 524 for (jj=ii; jj<bs2; jj+=bs) { 525 baij_a[jj] = *value++; 526 } 527 } 528 } 529 } else { 530 value = v + j*(stepval+bs)*bs + i*bs; 531 if (addv == ADD_VALUES) { 532 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 533 for (jj=0; jj<bs; jj++) { 534 baij_a[jj] += *value++; 535 } 536 } 537 } else { 538 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 539 for (jj=0; jj<bs; jj++) { 540 baij_a[jj] = *value++; 541 } 542 } 543 } 544 } 545 } 546 } else { 547 if (!baij->donotstash) { 548 if (roworiented) { 549 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 550 } else { 551 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 552 } 553 } 554 } 555 } 556 #if defined(PETSC_USE_DEBUG) 557 baij->ht_total_ct = total_ct; 558 baij->ht_insert_ct = insert_ct; 559 #endif 560 PetscFunctionReturn(0); 561 } 562 563 #undef __FUNCT__ 564 #define __FUNCT__ "MatGetValues_MPIBAIJ" 565 PetscErrorCode MatGetValues_MPIBAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 566 { 567 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 568 PetscErrorCode ierr; 569 PetscInt bs = mat->rmap->bs,i,j,bsrstart = mat->rmap->rstart,bsrend = mat->rmap->rend; 570 PetscInt bscstart = mat->cmap->rstart,bscend = mat->cmap->rend,row,col,data; 571 572 PetscFunctionBegin; 573 for (i=0; i<m; i++) { 574 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 575 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); 576 if (idxm[i] >= bsrstart && idxm[i] < bsrend) { 577 row = idxm[i] - bsrstart; 578 for (j=0; j<n; j++) { 579 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 580 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); 581 if (idxn[j] >= bscstart && idxn[j] < bscend) { 582 col = idxn[j] - bscstart; 583 ierr = MatGetValues_SeqBAIJ(baij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 584 } else { 585 if (!baij->colmap) { 586 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 587 } 588 #if defined(PETSC_USE_CTABLE) 589 ierr = PetscTableFind(baij->colmap,idxn[j]/bs+1,&data);CHKERRQ(ierr); 590 data--; 591 #else 592 data = baij->colmap[idxn[j]/bs]-1; 593 #endif 594 if ((data < 0) || (baij->garray[data/bs] != idxn[j]/bs)) *(v+i*n+j) = 0.0; 595 else { 596 col = data + idxn[j]%bs; 597 ierr = MatGetValues_SeqBAIJ(baij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 598 } 599 } 600 } 601 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 602 } 603 PetscFunctionReturn(0); 604 } 605 606 #undef __FUNCT__ 607 #define __FUNCT__ "MatNorm_MPIBAIJ" 608 PetscErrorCode MatNorm_MPIBAIJ(Mat mat,NormType type,PetscReal *nrm) 609 { 610 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 611 Mat_SeqBAIJ *amat = (Mat_SeqBAIJ*)baij->A->data,*bmat = (Mat_SeqBAIJ*)baij->B->data; 612 PetscErrorCode ierr; 613 PetscInt i,j,bs2=baij->bs2,bs=baij->A->rmap->bs,nz,row,col; 614 PetscReal sum = 0.0; 615 MatScalar *v; 616 617 PetscFunctionBegin; 618 if (baij->size == 1) { 619 ierr = MatNorm(baij->A,type,nrm);CHKERRQ(ierr); 620 } else { 621 if (type == NORM_FROBENIUS) { 622 v = amat->a; 623 nz = amat->nz*bs2; 624 for (i=0; i<nz; i++) { 625 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 626 } 627 v = bmat->a; 628 nz = bmat->nz*bs2; 629 for (i=0; i<nz; i++) { 630 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 631 } 632 ierr = MPI_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 633 *nrm = PetscSqrtReal(*nrm); 634 } else if (type == NORM_1) { /* max column sum */ 635 PetscReal *tmp,*tmp2; 636 PetscInt *jj,*garray=baij->garray,cstart=baij->rstartbs; 637 ierr = PetscMalloc2(mat->cmap->N,PetscReal,&tmp,mat->cmap->N,PetscReal,&tmp2);CHKERRQ(ierr); 638 ierr = PetscMemzero(tmp,mat->cmap->N*sizeof(PetscReal));CHKERRQ(ierr); 639 v = amat->a; jj = amat->j; 640 for (i=0; i<amat->nz; i++) { 641 for (j=0; j<bs; j++) { 642 col = bs*(cstart + *jj) + j; /* column index */ 643 for (row=0; row<bs; row++) { 644 tmp[col] += PetscAbsScalar(*v); v++; 645 } 646 } 647 jj++; 648 } 649 v = bmat->a; jj = bmat->j; 650 for (i=0; i<bmat->nz; i++) { 651 for (j=0; j<bs; j++) { 652 col = bs*garray[*jj] + j; 653 for (row=0; row<bs; row++) { 654 tmp[col] += PetscAbsScalar(*v); v++; 655 } 656 } 657 jj++; 658 } 659 ierr = MPI_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 660 *nrm = 0.0; 661 for (j=0; j<mat->cmap->N; j++) { 662 if (tmp2[j] > *nrm) *nrm = tmp2[j]; 663 } 664 ierr = PetscFree2(tmp,tmp2);CHKERRQ(ierr); 665 } else if (type == NORM_INFINITY) { /* max row sum */ 666 PetscReal *sums; 667 ierr = PetscMalloc(bs*sizeof(PetscReal),&sums);CHKERRQ(ierr); 668 sum = 0.0; 669 for (j=0; j<amat->mbs; j++) { 670 for (row=0; row<bs; row++) sums[row] = 0.0; 671 v = amat->a + bs2*amat->i[j]; 672 nz = amat->i[j+1]-amat->i[j]; 673 for (i=0; i<nz; i++) { 674 for (col=0; col<bs; col++) { 675 for (row=0; row<bs; row++) { 676 sums[row] += PetscAbsScalar(*v); v++; 677 } 678 } 679 } 680 v = bmat->a + bs2*bmat->i[j]; 681 nz = bmat->i[j+1]-bmat->i[j]; 682 for (i=0; i<nz; i++) { 683 for (col=0; col<bs; col++) { 684 for (row=0; row<bs; row++) { 685 sums[row] += PetscAbsScalar(*v); v++; 686 } 687 } 688 } 689 for (row=0; row<bs; row++) { 690 if (sums[row] > sum) sum = sums[row]; 691 } 692 } 693 ierr = MPI_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 694 ierr = PetscFree(sums);CHKERRQ(ierr); 695 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for this norm yet"); 696 } 697 PetscFunctionReturn(0); 698 } 699 700 /* 701 Creates the hash table, and sets the table 702 This table is created only once. 703 If new entried need to be added to the matrix 704 then the hash table has to be destroyed and 705 recreated. 706 */ 707 #undef __FUNCT__ 708 #define __FUNCT__ "MatCreateHashTable_MPIBAIJ_Private" 709 PetscErrorCode MatCreateHashTable_MPIBAIJ_Private(Mat mat,PetscReal factor) 710 { 711 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 712 Mat A = baij->A,B=baij->B; 713 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b=(Mat_SeqBAIJ*)B->data; 714 PetscInt i,j,k,nz=a->nz+b->nz,h1,*ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j; 715 PetscErrorCode ierr; 716 PetscInt ht_size,bs2=baij->bs2,rstart=baij->rstartbs; 717 PetscInt cstart=baij->cstartbs,*garray=baij->garray,row,col,Nbs=baij->Nbs; 718 PetscInt *HT,key; 719 MatScalar **HD; 720 PetscReal tmp; 721 #if defined(PETSC_USE_INFO) 722 PetscInt ct=0,max=0; 723 #endif 724 725 PetscFunctionBegin; 726 if (baij->ht) PetscFunctionReturn(0); 727 728 baij->ht_size = (PetscInt)(factor*nz); 729 ht_size = baij->ht_size; 730 731 /* Allocate Memory for Hash Table */ 732 ierr = PetscMalloc2(ht_size,MatScalar*,&baij->hd,ht_size,PetscInt,&baij->ht);CHKERRQ(ierr); 733 ierr = PetscMemzero(baij->hd,ht_size*sizeof(MatScalar*));CHKERRQ(ierr); 734 ierr = PetscMemzero(baij->ht,ht_size*sizeof(PetscInt));CHKERRQ(ierr); 735 HD = baij->hd; 736 HT = baij->ht; 737 738 /* Loop Over A */ 739 for (i=0; i<a->mbs; i++) { 740 for (j=ai[i]; j<ai[i+1]; j++) { 741 row = i+rstart; 742 col = aj[j]+cstart; 743 744 key = row*Nbs + col + 1; 745 h1 = HASH(ht_size,key,tmp); 746 for (k=0; k<ht_size; k++) { 747 if (!HT[(h1+k)%ht_size]) { 748 HT[(h1+k)%ht_size] = key; 749 HD[(h1+k)%ht_size] = a->a + j*bs2; 750 break; 751 #if defined(PETSC_USE_INFO) 752 } else { 753 ct++; 754 #endif 755 } 756 } 757 #if defined(PETSC_USE_INFO) 758 if (k> max) max = k; 759 #endif 760 } 761 } 762 /* Loop Over B */ 763 for (i=0; i<b->mbs; i++) { 764 for (j=bi[i]; j<bi[i+1]; j++) { 765 row = i+rstart; 766 col = garray[bj[j]]; 767 key = row*Nbs + col + 1; 768 h1 = HASH(ht_size,key,tmp); 769 for (k=0; k<ht_size; k++) { 770 if (!HT[(h1+k)%ht_size]) { 771 HT[(h1+k)%ht_size] = key; 772 HD[(h1+k)%ht_size] = b->a + j*bs2; 773 break; 774 #if defined(PETSC_USE_INFO) 775 } else { 776 ct++; 777 #endif 778 } 779 } 780 #if defined(PETSC_USE_INFO) 781 if (k> max) max = k; 782 #endif 783 } 784 } 785 786 /* Print Summary */ 787 #if defined(PETSC_USE_INFO) 788 for (i=0,j=0; i<ht_size; i++) { 789 if (HT[i]) j++; 790 } 791 ierr = PetscInfo2(mat,"Average Search = %5.2f,max search = %D\n",(!j)? 0.0:((PetscReal)(ct+j))/j,max);CHKERRQ(ierr); 792 #endif 793 PetscFunctionReturn(0); 794 } 795 796 #undef __FUNCT__ 797 #define __FUNCT__ "MatAssemblyBegin_MPIBAIJ" 798 PetscErrorCode MatAssemblyBegin_MPIBAIJ(Mat mat,MatAssemblyType mode) 799 { 800 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 801 PetscErrorCode ierr; 802 PetscInt nstash,reallocs; 803 InsertMode addv; 804 805 PetscFunctionBegin; 806 if (baij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 807 808 /* make sure all processors are either in INSERTMODE or ADDMODE */ 809 ierr = MPI_Allreduce((PetscEnum*)&mat->insertmode,(PetscEnum*)&addv,1,MPIU_ENUM,MPI_BOR,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 810 if (addv == (ADD_VALUES|INSERT_VALUES)) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_WRONGSTATE,"Some processors inserted others added"); 811 mat->insertmode = addv; /* in case this processor had no cache */ 812 813 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 814 ierr = MatStashScatterBegin_Private(mat,&mat->bstash,baij->rangebs);CHKERRQ(ierr); 815 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 816 ierr = PetscInfo2(mat,"Stash has %D entries,uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 817 ierr = MatStashGetInfo_Private(&mat->bstash,&nstash,&reallocs);CHKERRQ(ierr); 818 ierr = PetscInfo2(mat,"Block-Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 819 PetscFunctionReturn(0); 820 } 821 822 #undef __FUNCT__ 823 #define __FUNCT__ "MatAssemblyEnd_MPIBAIJ" 824 PetscErrorCode MatAssemblyEnd_MPIBAIJ(Mat mat,MatAssemblyType mode) 825 { 826 Mat_MPIBAIJ *baij=(Mat_MPIBAIJ*)mat->data; 827 Mat_SeqBAIJ *a =(Mat_SeqBAIJ*)baij->A->data; 828 PetscErrorCode ierr; 829 PetscInt i,j,rstart,ncols,flg,bs2=baij->bs2; 830 PetscInt *row,*col; 831 PetscBool r1,r2,r3,other_disassembled; 832 MatScalar *val; 833 InsertMode addv = mat->insertmode; 834 PetscMPIInt n; 835 836 PetscFunctionBegin; 837 /* do not use 'b=(Mat_SeqBAIJ*)baij->B->data' as B can be reset in disassembly */ 838 if (!baij->donotstash && !mat->nooffprocentries) { 839 while (1) { 840 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 841 if (!flg) break; 842 843 for (i=0; i<n;) { 844 /* Now identify the consecutive vals belonging to the same row */ 845 for (j=i,rstart=row[j]; j<n; j++) { 846 if (row[j] != rstart) break; 847 } 848 if (j < n) ncols = j-i; 849 else ncols = n-i; 850 /* Now assemble all these values with a single function call */ 851 ierr = MatSetValues_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i,addv);CHKERRQ(ierr); 852 i = j; 853 } 854 } 855 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 856 /* Now process the block-stash. Since the values are stashed column-oriented, 857 set the roworiented flag to column oriented, and after MatSetValues() 858 restore the original flags */ 859 r1 = baij->roworiented; 860 r2 = a->roworiented; 861 r3 = ((Mat_SeqBAIJ*)baij->B->data)->roworiented; 862 863 baij->roworiented = PETSC_FALSE; 864 a->roworiented = PETSC_FALSE; 865 866 (((Mat_SeqBAIJ*)baij->B->data))->roworiented = PETSC_FALSE; /* b->roworiented */ 867 while (1) { 868 ierr = MatStashScatterGetMesg_Private(&mat->bstash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 869 if (!flg) break; 870 871 for (i=0; i<n;) { 872 /* Now identify the consecutive vals belonging to the same row */ 873 for (j=i,rstart=row[j]; j<n; j++) { 874 if (row[j] != rstart) break; 875 } 876 if (j < n) ncols = j-i; 877 else ncols = n-i; 878 ierr = MatSetValuesBlocked_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i*bs2,addv);CHKERRQ(ierr); 879 i = j; 880 } 881 } 882 ierr = MatStashScatterEnd_Private(&mat->bstash);CHKERRQ(ierr); 883 884 baij->roworiented = r1; 885 a->roworiented = r2; 886 887 ((Mat_SeqBAIJ*)baij->B->data)->roworiented = r3; /* b->roworiented */ 888 } 889 890 ierr = MatAssemblyBegin(baij->A,mode);CHKERRQ(ierr); 891 ierr = MatAssemblyEnd(baij->A,mode);CHKERRQ(ierr); 892 893 /* determine if any processor has disassembled, if so we must 894 also disassemble ourselfs, in order that we may reassemble. */ 895 /* 896 if nonzero structure of submatrix B cannot change then we know that 897 no processor disassembled thus we can skip this stuff 898 */ 899 if (!((Mat_SeqBAIJ*)baij->B->data)->nonew) { 900 ierr = MPI_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 901 if (mat->was_assembled && !other_disassembled) { 902 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 903 } 904 } 905 906 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 907 ierr = MatSetUpMultiply_MPIBAIJ(mat);CHKERRQ(ierr); 908 } 909 ierr = MatSetOption(baij->B,MAT_CHECK_COMPRESSED_ROW,PETSC_FALSE);CHKERRQ(ierr); 910 ierr = MatAssemblyBegin(baij->B,mode);CHKERRQ(ierr); 911 ierr = MatAssemblyEnd(baij->B,mode);CHKERRQ(ierr); 912 913 #if defined(PETSC_USE_INFO) 914 if (baij->ht && mode== MAT_FINAL_ASSEMBLY) { 915 ierr = PetscInfo1(mat,"Average Hash Table Search in MatSetValues = %5.2f\n",((PetscReal)baij->ht_total_ct)/baij->ht_insert_ct);CHKERRQ(ierr); 916 917 baij->ht_total_ct = 0; 918 baij->ht_insert_ct = 0; 919 } 920 #endif 921 if (baij->ht_flag && !baij->ht && mode == MAT_FINAL_ASSEMBLY) { 922 ierr = MatCreateHashTable_MPIBAIJ_Private(mat,baij->ht_fact);CHKERRQ(ierr); 923 924 mat->ops->setvalues = MatSetValues_MPIBAIJ_HT; 925 mat->ops->setvaluesblocked = MatSetValuesBlocked_MPIBAIJ_HT; 926 } 927 928 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 929 930 baij->rowvalues = 0; 931 PetscFunctionReturn(0); 932 } 933 934 #include <petscdraw.h> 935 #undef __FUNCT__ 936 #define __FUNCT__ "MatView_MPIBAIJ_ASCIIorDraworSocket" 937 static PetscErrorCode MatView_MPIBAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 938 { 939 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 940 PetscErrorCode ierr; 941 PetscMPIInt size = baij->size,rank = baij->rank; 942 PetscInt bs = mat->rmap->bs; 943 PetscBool iascii,isdraw; 944 PetscViewer sviewer; 945 PetscViewerFormat format; 946 947 PetscFunctionBegin; 948 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 949 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 950 if (iascii) { 951 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 952 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 953 MatInfo info; 954 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 955 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 956 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 957 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D bs %D mem %D\n", 958 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,mat->rmap->bs,(PetscInt)info.memory);CHKERRQ(ierr); 959 ierr = MatGetInfo(baij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 960 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 961 ierr = MatGetInfo(baij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 962 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 963 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 964 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr); 965 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 966 ierr = VecScatterView(baij->Mvctx,viewer);CHKERRQ(ierr); 967 PetscFunctionReturn(0); 968 } else if (format == PETSC_VIEWER_ASCII_INFO) { 969 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 970 PetscFunctionReturn(0); 971 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 972 PetscFunctionReturn(0); 973 } 974 } 975 976 if (isdraw) { 977 PetscDraw draw; 978 PetscBool isnull; 979 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 980 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 981 } 982 983 if (size == 1) { 984 ierr = PetscObjectSetName((PetscObject)baij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 985 ierr = MatView(baij->A,viewer);CHKERRQ(ierr); 986 } else { 987 /* assemble the entire matrix onto first processor. */ 988 Mat A; 989 Mat_SeqBAIJ *Aloc; 990 PetscInt M = mat->rmap->N,N = mat->cmap->N,*ai,*aj,col,i,j,k,*rvals,mbs = baij->mbs; 991 MatScalar *a; 992 993 /* Here we are creating a temporary matrix, so will assume MPIBAIJ is acceptable */ 994 /* Perhaps this should be the type of mat? */ 995 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 996 if (!rank) { 997 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 998 } else { 999 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1000 } 1001 ierr = MatSetType(A,MATMPIBAIJ);CHKERRQ(ierr); 1002 ierr = MatMPIBAIJSetPreallocation(A,mat->rmap->bs,0,NULL,0,NULL);CHKERRQ(ierr); 1003 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1004 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1005 1006 /* copy over the A part */ 1007 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1008 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1009 ierr = PetscMalloc(bs*sizeof(PetscInt),&rvals);CHKERRQ(ierr); 1010 1011 for (i=0; i<mbs; i++) { 1012 rvals[0] = bs*(baij->rstartbs + i); 1013 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1014 for (j=ai[i]; j<ai[i+1]; j++) { 1015 col = (baij->cstartbs+aj[j])*bs; 1016 for (k=0; k<bs; k++) { 1017 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1018 col++; a += bs; 1019 } 1020 } 1021 } 1022 /* copy over the B part */ 1023 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1024 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1025 for (i=0; i<mbs; i++) { 1026 rvals[0] = bs*(baij->rstartbs + i); 1027 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1028 for (j=ai[i]; j<ai[i+1]; j++) { 1029 col = baij->garray[aj[j]]*bs; 1030 for (k=0; k<bs; k++) { 1031 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1032 col++; a += bs; 1033 } 1034 } 1035 } 1036 ierr = PetscFree(rvals);CHKERRQ(ierr); 1037 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1038 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1039 /* 1040 Everyone has to call to draw the matrix since the graphics waits are 1041 synchronized across all processors that share the PetscDraw object 1042 */ 1043 ierr = PetscViewerGetSingleton(viewer,&sviewer);CHKERRQ(ierr); 1044 if (!rank) { 1045 ierr = PetscObjectSetName((PetscObject)((Mat_MPIBAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1046 /* Set the type name to MATMPIBAIJ so that the correct type can be printed out by PetscObjectPrintClassNamePrefixType() in MatView_SeqBAIJ_ASCII()*/ 1047 PetscStrcpy(((PetscObject)((Mat_MPIBAIJ*)(A->data))->A)->type_name,MATMPIBAIJ); 1048 ierr = MatView(((Mat_MPIBAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1049 } 1050 ierr = PetscViewerRestoreSingleton(viewer,&sviewer);CHKERRQ(ierr); 1051 ierr = MatDestroy(&A);CHKERRQ(ierr); 1052 } 1053 PetscFunctionReturn(0); 1054 } 1055 1056 #undef __FUNCT__ 1057 #define __FUNCT__ "MatView_MPIBAIJ_Binary" 1058 static PetscErrorCode MatView_MPIBAIJ_Binary(Mat mat,PetscViewer viewer) 1059 { 1060 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)mat->data; 1061 Mat_SeqBAIJ *A = (Mat_SeqBAIJ*)a->A->data; 1062 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)a->B->data; 1063 PetscErrorCode ierr; 1064 PetscInt i,*row_lens,*crow_lens,bs = mat->rmap->bs,j,k,bs2=a->bs2,header[4],nz,rlen; 1065 PetscInt *range=0,nzmax,*column_indices,cnt,col,*garray = a->garray,cstart = mat->cmap->rstart/bs,len,pcnt,l,ll; 1066 int fd; 1067 PetscScalar *column_values; 1068 FILE *file; 1069 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1070 PetscInt message_count,flowcontrolcount; 1071 1072 PetscFunctionBegin; 1073 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1074 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1075 nz = bs2*(A->nz + B->nz); 1076 rlen = mat->rmap->n; 1077 if (!rank) { 1078 header[0] = MAT_FILE_CLASSID; 1079 header[1] = mat->rmap->N; 1080 header[2] = mat->cmap->N; 1081 1082 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1083 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1084 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1085 /* get largest number of rows any processor has */ 1086 range = mat->rmap->range; 1087 for (i=1; i<size; i++) { 1088 rlen = PetscMax(rlen,range[i+1] - range[i]); 1089 } 1090 } else { 1091 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1092 } 1093 1094 ierr = PetscMalloc((rlen/bs)*sizeof(PetscInt),&crow_lens);CHKERRQ(ierr); 1095 /* compute lengths of each row */ 1096 for (i=0; i<a->mbs; i++) { 1097 crow_lens[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1098 } 1099 /* store the row lengths to the file */ 1100 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1101 if (!rank) { 1102 MPI_Status status; 1103 ierr = PetscMalloc(rlen*sizeof(PetscInt),&row_lens);CHKERRQ(ierr); 1104 rlen = (range[1] - range[0])/bs; 1105 for (i=0; i<rlen; i++) { 1106 for (j=0; j<bs; j++) { 1107 row_lens[i*bs+j] = bs*crow_lens[i]; 1108 } 1109 } 1110 ierr = PetscBinaryWrite(fd,row_lens,bs*rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1111 for (i=1; i<size; i++) { 1112 rlen = (range[i+1] - range[i])/bs; 1113 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1114 ierr = MPI_Recv(crow_lens,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1115 for (k=0; k<rlen; k++) { 1116 for (j=0; j<bs; j++) { 1117 row_lens[k*bs+j] = bs*crow_lens[k]; 1118 } 1119 } 1120 ierr = PetscBinaryWrite(fd,row_lens,bs*rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1121 } 1122 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1123 ierr = PetscFree(row_lens);CHKERRQ(ierr); 1124 } else { 1125 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1126 ierr = MPI_Send(crow_lens,mat->rmap->n/bs,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1127 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1128 } 1129 ierr = PetscFree(crow_lens);CHKERRQ(ierr); 1130 1131 /* load up the local column indices. Include for all rows not just one for each block row since process 0 does not have the 1132 information needed to make it for each row from a block row. This does require more communication but still not more than 1133 the communication needed for the nonzero values */ 1134 nzmax = nz; /* space a largest processor needs */ 1135 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1136 ierr = PetscMalloc(nzmax*sizeof(PetscInt),&column_indices);CHKERRQ(ierr); 1137 cnt = 0; 1138 for (i=0; i<a->mbs; i++) { 1139 pcnt = cnt; 1140 for (j=B->i[i]; j<B->i[i+1]; j++) { 1141 if ((col = garray[B->j[j]]) > cstart) break; 1142 for (l=0; l<bs; l++) { 1143 column_indices[cnt++] = bs*col+l; 1144 } 1145 } 1146 for (k=A->i[i]; k<A->i[i+1]; k++) { 1147 for (l=0; l<bs; l++) { 1148 column_indices[cnt++] = bs*(A->j[k] + cstart)+l; 1149 } 1150 } 1151 for (; j<B->i[i+1]; j++) { 1152 for (l=0; l<bs; l++) { 1153 column_indices[cnt++] = bs*garray[B->j[j]]+l; 1154 } 1155 } 1156 len = cnt - pcnt; 1157 for (k=1; k<bs; k++) { 1158 ierr = PetscMemcpy(&column_indices[cnt],&column_indices[pcnt],len*sizeof(PetscInt));CHKERRQ(ierr); 1159 cnt += len; 1160 } 1161 } 1162 if (cnt != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,nz); 1163 1164 /* store the columns to the file */ 1165 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1166 if (!rank) { 1167 MPI_Status status; 1168 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1169 for (i=1; i<size; i++) { 1170 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1171 ierr = MPI_Recv(&cnt,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1172 ierr = MPI_Recv(column_indices,cnt,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1173 ierr = PetscBinaryWrite(fd,column_indices,cnt,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1174 } 1175 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1176 } else { 1177 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1178 ierr = MPI_Send(&cnt,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1179 ierr = MPI_Send(column_indices,cnt,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1180 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1181 } 1182 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1183 1184 /* load up the numerical values */ 1185 ierr = PetscMalloc(nzmax*sizeof(PetscScalar),&column_values);CHKERRQ(ierr); 1186 cnt = 0; 1187 for (i=0; i<a->mbs; i++) { 1188 rlen = bs*(B->i[i+1] - B->i[i] + A->i[i+1] - A->i[i]); 1189 for (j=B->i[i]; j<B->i[i+1]; j++) { 1190 if (garray[B->j[j]] > cstart) break; 1191 for (l=0; l<bs; l++) { 1192 for (ll=0; ll<bs; ll++) { 1193 column_values[cnt + l*rlen + ll] = B->a[bs2*j+l+bs*ll]; 1194 } 1195 } 1196 cnt += bs; 1197 } 1198 for (k=A->i[i]; k<A->i[i+1]; k++) { 1199 for (l=0; l<bs; l++) { 1200 for (ll=0; ll<bs; ll++) { 1201 column_values[cnt + l*rlen + ll] = A->a[bs2*k+l+bs*ll]; 1202 } 1203 } 1204 cnt += bs; 1205 } 1206 for (; j<B->i[i+1]; j++) { 1207 for (l=0; l<bs; l++) { 1208 for (ll=0; ll<bs; ll++) { 1209 column_values[cnt + l*rlen + ll] = B->a[bs2*j+l+bs*ll]; 1210 } 1211 } 1212 cnt += bs; 1213 } 1214 cnt += (bs-1)*rlen; 1215 } 1216 if (cnt != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,nz); 1217 1218 /* store the column values to the file */ 1219 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1220 if (!rank) { 1221 MPI_Status status; 1222 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1223 for (i=1; i<size; i++) { 1224 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1225 ierr = MPI_Recv(&cnt,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1226 ierr = MPI_Recv(column_values,cnt,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1227 ierr = PetscBinaryWrite(fd,column_values,cnt,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1228 } 1229 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1230 } else { 1231 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1232 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1233 ierr = MPI_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1234 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1235 } 1236 ierr = PetscFree(column_values);CHKERRQ(ierr); 1237 1238 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1239 if (file) { 1240 fprintf(file,"-matload_block_size %d\n",(int)mat->rmap->bs); 1241 } 1242 PetscFunctionReturn(0); 1243 } 1244 1245 #undef __FUNCT__ 1246 #define __FUNCT__ "MatView_MPIBAIJ" 1247 PetscErrorCode MatView_MPIBAIJ(Mat mat,PetscViewer viewer) 1248 { 1249 PetscErrorCode ierr; 1250 PetscBool iascii,isdraw,issocket,isbinary; 1251 1252 PetscFunctionBegin; 1253 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1254 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1255 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1256 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1257 if (iascii || isdraw || issocket) { 1258 ierr = MatView_MPIBAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1259 } else if (isbinary) { 1260 ierr = MatView_MPIBAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1261 } 1262 PetscFunctionReturn(0); 1263 } 1264 1265 #undef __FUNCT__ 1266 #define __FUNCT__ "MatDestroy_MPIBAIJ" 1267 PetscErrorCode MatDestroy_MPIBAIJ(Mat mat) 1268 { 1269 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1270 PetscErrorCode ierr; 1271 1272 PetscFunctionBegin; 1273 #if defined(PETSC_USE_LOG) 1274 PetscLogObjectState((PetscObject)mat,"Rows=%D,Cols=%D",mat->rmap->N,mat->cmap->N); 1275 #endif 1276 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1277 ierr = MatStashDestroy_Private(&mat->bstash);CHKERRQ(ierr); 1278 ierr = MatDestroy(&baij->A);CHKERRQ(ierr); 1279 ierr = MatDestroy(&baij->B);CHKERRQ(ierr); 1280 #if defined(PETSC_USE_CTABLE) 1281 ierr = PetscTableDestroy(&baij->colmap);CHKERRQ(ierr); 1282 #else 1283 ierr = PetscFree(baij->colmap);CHKERRQ(ierr); 1284 #endif 1285 ierr = PetscFree(baij->garray);CHKERRQ(ierr); 1286 ierr = VecDestroy(&baij->lvec);CHKERRQ(ierr); 1287 ierr = VecScatterDestroy(&baij->Mvctx);CHKERRQ(ierr); 1288 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 1289 ierr = PetscFree(baij->barray);CHKERRQ(ierr); 1290 ierr = PetscFree2(baij->hd,baij->ht);CHKERRQ(ierr); 1291 ierr = PetscFree(baij->rangebs);CHKERRQ(ierr); 1292 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1293 1294 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1295 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1296 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1297 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatGetDiagonalBlock_C",NULL);CHKERRQ(ierr); 1298 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1299 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1300 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1301 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatSetHashTableFactor_C",NULL);CHKERRQ(ierr); 1302 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1303 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpibstrm_C",NULL);CHKERRQ(ierr); 1304 PetscFunctionReturn(0); 1305 } 1306 1307 #undef __FUNCT__ 1308 #define __FUNCT__ "MatMult_MPIBAIJ" 1309 PetscErrorCode MatMult_MPIBAIJ(Mat A,Vec xx,Vec yy) 1310 { 1311 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1312 PetscErrorCode ierr; 1313 PetscInt nt; 1314 1315 PetscFunctionBegin; 1316 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 1317 if (nt != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A and xx"); 1318 ierr = VecGetLocalSize(yy,&nt);CHKERRQ(ierr); 1319 if (nt != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible parition of A and yy"); 1320 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1321 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 1322 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1323 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 1324 PetscFunctionReturn(0); 1325 } 1326 1327 #undef __FUNCT__ 1328 #define __FUNCT__ "MatMultAdd_MPIBAIJ" 1329 PetscErrorCode MatMultAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1330 { 1331 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1332 PetscErrorCode ierr; 1333 1334 PetscFunctionBegin; 1335 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1336 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1337 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1338 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 1339 PetscFunctionReturn(0); 1340 } 1341 1342 #undef __FUNCT__ 1343 #define __FUNCT__ "MatMultTranspose_MPIBAIJ" 1344 PetscErrorCode MatMultTranspose_MPIBAIJ(Mat A,Vec xx,Vec yy) 1345 { 1346 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1347 PetscErrorCode ierr; 1348 PetscBool merged; 1349 1350 PetscFunctionBegin; 1351 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 1352 /* do nondiagonal part */ 1353 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1354 if (!merged) { 1355 /* send it on its way */ 1356 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1357 /* do local part */ 1358 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1359 /* receive remote parts: note this assumes the values are not actually */ 1360 /* inserted in yy until the next line */ 1361 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1362 } else { 1363 /* do local part */ 1364 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1365 /* send it on its way */ 1366 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1367 /* values actually were received in the Begin() but we need to call this nop */ 1368 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1369 } 1370 PetscFunctionReturn(0); 1371 } 1372 1373 #undef __FUNCT__ 1374 #define __FUNCT__ "MatMultTransposeAdd_MPIBAIJ" 1375 PetscErrorCode MatMultTransposeAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1376 { 1377 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1378 PetscErrorCode ierr; 1379 1380 PetscFunctionBegin; 1381 /* do nondiagonal part */ 1382 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1383 /* send it on its way */ 1384 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1385 /* do local part */ 1386 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1387 /* receive remote parts: note this assumes the values are not actually */ 1388 /* inserted in yy until the next line, which is true for my implementation*/ 1389 /* but is not perhaps always true. */ 1390 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1391 PetscFunctionReturn(0); 1392 } 1393 1394 /* 1395 This only works correctly for square matrices where the subblock A->A is the 1396 diagonal block 1397 */ 1398 #undef __FUNCT__ 1399 #define __FUNCT__ "MatGetDiagonal_MPIBAIJ" 1400 PetscErrorCode MatGetDiagonal_MPIBAIJ(Mat A,Vec v) 1401 { 1402 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1403 PetscErrorCode ierr; 1404 1405 PetscFunctionBegin; 1406 if (A->rmap->N != A->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1407 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1408 PetscFunctionReturn(0); 1409 } 1410 1411 #undef __FUNCT__ 1412 #define __FUNCT__ "MatScale_MPIBAIJ" 1413 PetscErrorCode MatScale_MPIBAIJ(Mat A,PetscScalar aa) 1414 { 1415 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1416 PetscErrorCode ierr; 1417 1418 PetscFunctionBegin; 1419 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1420 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1421 PetscFunctionReturn(0); 1422 } 1423 1424 #undef __FUNCT__ 1425 #define __FUNCT__ "MatGetRow_MPIBAIJ" 1426 PetscErrorCode MatGetRow_MPIBAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1427 { 1428 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 1429 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1430 PetscErrorCode ierr; 1431 PetscInt bs = matin->rmap->bs,bs2 = mat->bs2,i,*cworkA,*cworkB,**pcA,**pcB; 1432 PetscInt nztot,nzA,nzB,lrow,brstart = matin->rmap->rstart,brend = matin->rmap->rend; 1433 PetscInt *cmap,*idx_p,cstart = mat->cstartbs; 1434 1435 PetscFunctionBegin; 1436 if (row < brstart || row >= brend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local rows"); 1437 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1438 mat->getrowactive = PETSC_TRUE; 1439 1440 if (!mat->rowvalues && (idx || v)) { 1441 /* 1442 allocate enough space to hold information from the longest row. 1443 */ 1444 Mat_SeqBAIJ *Aa = (Mat_SeqBAIJ*)mat->A->data,*Ba = (Mat_SeqBAIJ*)mat->B->data; 1445 PetscInt max = 1,mbs = mat->mbs,tmp; 1446 for (i=0; i<mbs; i++) { 1447 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1448 if (max < tmp) max = tmp; 1449 } 1450 ierr = PetscMalloc2(max*bs2,PetscScalar,&mat->rowvalues,max*bs2,PetscInt,&mat->rowindices);CHKERRQ(ierr); 1451 } 1452 lrow = row - brstart; 1453 1454 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1455 if (!v) {pvA = 0; pvB = 0;} 1456 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1457 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1458 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1459 nztot = nzA + nzB; 1460 1461 cmap = mat->garray; 1462 if (v || idx) { 1463 if (nztot) { 1464 /* Sort by increasing column numbers, assuming A and B already sorted */ 1465 PetscInt imark = -1; 1466 if (v) { 1467 *v = v_p = mat->rowvalues; 1468 for (i=0; i<nzB; i++) { 1469 if (cmap[cworkB[i]/bs] < cstart) v_p[i] = vworkB[i]; 1470 else break; 1471 } 1472 imark = i; 1473 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1474 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1475 } 1476 if (idx) { 1477 *idx = idx_p = mat->rowindices; 1478 if (imark > -1) { 1479 for (i=0; i<imark; i++) { 1480 idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs; 1481 } 1482 } else { 1483 for (i=0; i<nzB; i++) { 1484 if (cmap[cworkB[i]/bs] < cstart) idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs; 1485 else break; 1486 } 1487 imark = i; 1488 } 1489 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart*bs + cworkA[i]; 1490 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs ; 1491 } 1492 } else { 1493 if (idx) *idx = 0; 1494 if (v) *v = 0; 1495 } 1496 } 1497 *nz = nztot; 1498 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1499 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1500 PetscFunctionReturn(0); 1501 } 1502 1503 #undef __FUNCT__ 1504 #define __FUNCT__ "MatRestoreRow_MPIBAIJ" 1505 PetscErrorCode MatRestoreRow_MPIBAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1506 { 1507 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1508 1509 PetscFunctionBegin; 1510 if (!baij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow not called"); 1511 baij->getrowactive = PETSC_FALSE; 1512 PetscFunctionReturn(0); 1513 } 1514 1515 #undef __FUNCT__ 1516 #define __FUNCT__ "MatZeroEntries_MPIBAIJ" 1517 PetscErrorCode MatZeroEntries_MPIBAIJ(Mat A) 1518 { 1519 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1520 PetscErrorCode ierr; 1521 1522 PetscFunctionBegin; 1523 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 1524 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 1525 PetscFunctionReturn(0); 1526 } 1527 1528 #undef __FUNCT__ 1529 #define __FUNCT__ "MatGetInfo_MPIBAIJ" 1530 PetscErrorCode MatGetInfo_MPIBAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1531 { 1532 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)matin->data; 1533 Mat A = a->A,B = a->B; 1534 PetscErrorCode ierr; 1535 PetscReal isend[5],irecv[5]; 1536 1537 PetscFunctionBegin; 1538 info->block_size = (PetscReal)matin->rmap->bs; 1539 1540 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1541 1542 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1543 isend[3] = info->memory; isend[4] = info->mallocs; 1544 1545 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1546 1547 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1548 isend[3] += info->memory; isend[4] += info->mallocs; 1549 1550 if (flag == MAT_LOCAL) { 1551 info->nz_used = isend[0]; 1552 info->nz_allocated = isend[1]; 1553 info->nz_unneeded = isend[2]; 1554 info->memory = isend[3]; 1555 info->mallocs = isend[4]; 1556 } else if (flag == MAT_GLOBAL_MAX) { 1557 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1558 1559 info->nz_used = irecv[0]; 1560 info->nz_allocated = irecv[1]; 1561 info->nz_unneeded = irecv[2]; 1562 info->memory = irecv[3]; 1563 info->mallocs = irecv[4]; 1564 } else if (flag == MAT_GLOBAL_SUM) { 1565 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1566 1567 info->nz_used = irecv[0]; 1568 info->nz_allocated = irecv[1]; 1569 info->nz_unneeded = irecv[2]; 1570 info->memory = irecv[3]; 1571 info->mallocs = irecv[4]; 1572 } else SETERRQ1(PetscObjectComm((PetscObject)matin),PETSC_ERR_ARG_WRONG,"Unknown MatInfoType argument %d",(int)flag); 1573 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1574 info->fill_ratio_needed = 0; 1575 info->factor_mallocs = 0; 1576 PetscFunctionReturn(0); 1577 } 1578 1579 #undef __FUNCT__ 1580 #define __FUNCT__ "MatSetOption_MPIBAIJ" 1581 PetscErrorCode MatSetOption_MPIBAIJ(Mat A,MatOption op,PetscBool flg) 1582 { 1583 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1584 PetscErrorCode ierr; 1585 1586 PetscFunctionBegin; 1587 switch (op) { 1588 case MAT_NEW_NONZERO_LOCATIONS: 1589 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1590 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1591 case MAT_KEEP_NONZERO_PATTERN: 1592 case MAT_NEW_NONZERO_LOCATION_ERR: 1593 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1594 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1595 break; 1596 case MAT_ROW_ORIENTED: 1597 a->roworiented = flg; 1598 1599 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1600 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1601 break; 1602 case MAT_NEW_DIAGONALS: 1603 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1604 break; 1605 case MAT_IGNORE_OFF_PROC_ENTRIES: 1606 a->donotstash = flg; 1607 break; 1608 case MAT_USE_HASH_TABLE: 1609 a->ht_flag = flg; 1610 break; 1611 case MAT_SYMMETRIC: 1612 case MAT_STRUCTURALLY_SYMMETRIC: 1613 case MAT_HERMITIAN: 1614 case MAT_SYMMETRY_ETERNAL: 1615 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1616 break; 1617 default: 1618 SETERRQ1(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"unknown option %d",op); 1619 } 1620 PetscFunctionReturn(0); 1621 } 1622 1623 #undef __FUNCT__ 1624 #define __FUNCT__ "MatTranspose_MPIBAIJ" 1625 PetscErrorCode MatTranspose_MPIBAIJ(Mat A,MatReuse reuse,Mat *matout) 1626 { 1627 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data; 1628 Mat_SeqBAIJ *Aloc; 1629 Mat B; 1630 PetscErrorCode ierr; 1631 PetscInt M =A->rmap->N,N=A->cmap->N,*ai,*aj,i,*rvals,j,k,col; 1632 PetscInt bs=A->rmap->bs,mbs=baij->mbs; 1633 MatScalar *a; 1634 1635 PetscFunctionBegin; 1636 if (reuse == MAT_REUSE_MATRIX && A == *matout && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1637 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1638 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1639 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1640 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1641 /* Do not know preallocation information, but must set block size */ 1642 ierr = MatMPIBAIJSetPreallocation(B,A->rmap->bs,PETSC_DECIDE,NULL,PETSC_DECIDE,NULL);CHKERRQ(ierr); 1643 } else { 1644 B = *matout; 1645 } 1646 1647 /* copy over the A part */ 1648 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1649 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1650 ierr = PetscMalloc(bs*sizeof(PetscInt),&rvals);CHKERRQ(ierr); 1651 1652 for (i=0; i<mbs; i++) { 1653 rvals[0] = bs*(baij->rstartbs + i); 1654 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1655 for (j=ai[i]; j<ai[i+1]; j++) { 1656 col = (baij->cstartbs+aj[j])*bs; 1657 for (k=0; k<bs; k++) { 1658 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1659 1660 col++; a += bs; 1661 } 1662 } 1663 } 1664 /* copy over the B part */ 1665 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1666 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1667 for (i=0; i<mbs; i++) { 1668 rvals[0] = bs*(baij->rstartbs + i); 1669 for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1; 1670 for (j=ai[i]; j<ai[i+1]; j++) { 1671 col = baij->garray[aj[j]]*bs; 1672 for (k=0; k<bs; k++) { 1673 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1674 col++; 1675 a += bs; 1676 } 1677 } 1678 } 1679 ierr = PetscFree(rvals);CHKERRQ(ierr); 1680 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1681 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1682 1683 if (reuse == MAT_INITIAL_MATRIX || *matout != A) *matout = B; 1684 else { 1685 ierr = MatHeaderMerge(A,B);CHKERRQ(ierr); 1686 } 1687 PetscFunctionReturn(0); 1688 } 1689 1690 #undef __FUNCT__ 1691 #define __FUNCT__ "MatDiagonalScale_MPIBAIJ" 1692 PetscErrorCode MatDiagonalScale_MPIBAIJ(Mat mat,Vec ll,Vec rr) 1693 { 1694 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1695 Mat a = baij->A,b = baij->B; 1696 PetscErrorCode ierr; 1697 PetscInt s1,s2,s3; 1698 1699 PetscFunctionBegin; 1700 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1701 if (rr) { 1702 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1703 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1704 /* Overlap communication with computation. */ 1705 ierr = VecScatterBegin(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1706 } 1707 if (ll) { 1708 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1709 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1710 ierr = (*b->ops->diagonalscale)(b,ll,NULL);CHKERRQ(ierr); 1711 } 1712 /* scale the diagonal block */ 1713 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 1714 1715 if (rr) { 1716 /* Do a scatter end and then right scale the off-diagonal block */ 1717 ierr = VecScatterEnd(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1718 ierr = (*b->ops->diagonalscale)(b,NULL,baij->lvec);CHKERRQ(ierr); 1719 } 1720 PetscFunctionReturn(0); 1721 } 1722 1723 #undef __FUNCT__ 1724 #define __FUNCT__ "MatZeroRows_MPIBAIJ" 1725 PetscErrorCode MatZeroRows_MPIBAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1726 { 1727 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1728 PetscErrorCode ierr; 1729 PetscMPIInt imdex,size = l->size,n,rank = l->rank; 1730 PetscInt i,*owners = A->rmap->range; 1731 PetscInt *nprocs,j,idx,nsends,row; 1732 PetscInt nmax,*svalues,*starts,*owner,nrecvs; 1733 PetscInt *rvalues,tag = ((PetscObject)A)->tag,count,base,slen,*source,lastidx = -1; 1734 PetscInt *lens,*lrows,*values,rstart_bs=A->rmap->rstart; 1735 MPI_Comm comm; 1736 MPI_Request *send_waits,*recv_waits; 1737 MPI_Status recv_status,*send_status; 1738 const PetscScalar *xx; 1739 PetscScalar *bb; 1740 #if defined(PETSC_DEBUG) 1741 PetscBool found = PETSC_FALSE; 1742 #endif 1743 1744 PetscFunctionBegin; 1745 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1746 /* first count number of contributors to each processor */ 1747 ierr = PetscMalloc(2*size*sizeof(PetscInt),&nprocs);CHKERRQ(ierr); 1748 ierr = PetscMemzero(nprocs,2*size*sizeof(PetscInt));CHKERRQ(ierr); 1749 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&owner);CHKERRQ(ierr); /* see note*/ 1750 j = 0; 1751 for (i=0; i<N; i++) { 1752 if (lastidx > (idx = rows[i])) j = 0; 1753 lastidx = idx; 1754 for (; j<size; j++) { 1755 if (idx >= owners[j] && idx < owners[j+1]) { 1756 nprocs[2*j]++; 1757 nprocs[2*j+1] = 1; 1758 owner[i] = j; 1759 #if defined(PETSC_DEBUG) 1760 found = PETSC_TRUE; 1761 #endif 1762 break; 1763 } 1764 } 1765 #if defined(PETSC_DEBUG) 1766 if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index out of range"); 1767 found = PETSC_FALSE; 1768 #endif 1769 } 1770 nsends = 0; for (i=0; i<size; i++) nsends += nprocs[2*i+1]; 1771 1772 if (A->nooffproczerorows) { 1773 if (nsends > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"You called MatSetOption(,MAT_NO_OFF_PROC_ZERO_ROWS,PETSC_TRUE) but set an off process zero row"); 1774 nrecvs = nsends; 1775 nmax = N; 1776 } else { 1777 /* inform other processors of number of messages and max length*/ 1778 ierr = PetscMaxSum(comm,nprocs,&nmax,&nrecvs);CHKERRQ(ierr); 1779 } 1780 1781 /* post receives: */ 1782 ierr = PetscMalloc((nrecvs+1)*(nmax+1)*sizeof(PetscInt),&rvalues);CHKERRQ(ierr); 1783 ierr = PetscMalloc((nrecvs+1)*sizeof(MPI_Request),&recv_waits);CHKERRQ(ierr); 1784 for (i=0; i<nrecvs; i++) { 1785 ierr = MPI_Irecv(rvalues+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag,comm,recv_waits+i);CHKERRQ(ierr); 1786 } 1787 1788 /* do sends: 1789 1) starts[i] gives the starting index in svalues for stuff going to 1790 the ith processor 1791 */ 1792 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&svalues);CHKERRQ(ierr); 1793 ierr = PetscMalloc((nsends+1)*sizeof(MPI_Request),&send_waits);CHKERRQ(ierr); 1794 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&starts);CHKERRQ(ierr); 1795 starts[0] = 0; 1796 for (i=1; i<size; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 1797 for (i=0; i<N; i++) { 1798 svalues[starts[owner[i]]++] = rows[i]; 1799 } 1800 1801 starts[0] = 0; 1802 for (i=1; i<size+1; i++) starts[i] = starts[i-1] + nprocs[2*i-2]; 1803 count = 0; 1804 for (i=0; i<size; i++) { 1805 if (nprocs[2*i+1]) { 1806 ierr = MPI_Isend(svalues+starts[i],nprocs[2*i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr); 1807 } 1808 } 1809 ierr = PetscFree(starts);CHKERRQ(ierr); 1810 1811 base = owners[rank]; 1812 1813 /* wait on receives */ 1814 ierr = PetscMalloc2(nrecvs+1,PetscInt,&lens,nrecvs+1,PetscInt,&source);CHKERRQ(ierr); 1815 count = nrecvs; 1816 slen = 0; 1817 while (count) { 1818 ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr); 1819 /* unpack receives into our local space */ 1820 ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr); 1821 1822 source[imdex] = recv_status.MPI_SOURCE; 1823 lens[imdex] = n; 1824 slen += n; 1825 count--; 1826 } 1827 ierr = PetscFree(recv_waits);CHKERRQ(ierr); 1828 1829 /* move the data into the send scatter */ 1830 ierr = PetscMalloc((slen+1)*sizeof(PetscInt),&lrows);CHKERRQ(ierr); 1831 count = 0; 1832 for (i=0; i<nrecvs; i++) { 1833 values = rvalues + i*nmax; 1834 for (j=0; j<lens[i]; j++) { 1835 lrows[count++] = values[j] - base; 1836 } 1837 } 1838 ierr = PetscFree(rvalues);CHKERRQ(ierr); 1839 ierr = PetscFree2(lens,source);CHKERRQ(ierr); 1840 ierr = PetscFree(owner);CHKERRQ(ierr); 1841 ierr = PetscFree(nprocs);CHKERRQ(ierr); 1842 1843 /* fix right hand side if needed */ 1844 if (x && b) { 1845 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1846 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1847 for (i=0; i<slen; i++) { 1848 bb[lrows[i]] = diag*xx[lrows[i]]; 1849 } 1850 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1851 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1852 } 1853 1854 /* actually zap the local rows */ 1855 /* 1856 Zero the required rows. If the "diagonal block" of the matrix 1857 is square and the user wishes to set the diagonal we use separate 1858 code so that MatSetValues() is not called for each diagonal allocating 1859 new memory, thus calling lots of mallocs and slowing things down. 1860 1861 */ 1862 /* must zero l->B before l->A because the (diag) case below may put values into l->B*/ 1863 ierr = MatZeroRows_SeqBAIJ(l->B,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1864 if ((diag != 0.0) && (l->A->rmap->N == l->A->cmap->N)) { 1865 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,diag,0,0);CHKERRQ(ierr); 1866 } else if (diag != 0.0) { 1867 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1868 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\ 1869 MAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 1870 for (i=0; i<slen; i++) { 1871 row = lrows[i] + rstart_bs; 1872 ierr = MatSetValues(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1873 } 1874 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1875 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1876 } else { 1877 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1878 } 1879 1880 ierr = PetscFree(lrows);CHKERRQ(ierr); 1881 1882 /* wait on sends */ 1883 if (nsends) { 1884 ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr); 1885 ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr); 1886 ierr = PetscFree(send_status);CHKERRQ(ierr); 1887 } 1888 ierr = PetscFree(send_waits);CHKERRQ(ierr); 1889 ierr = PetscFree(svalues);CHKERRQ(ierr); 1890 PetscFunctionReturn(0); 1891 } 1892 1893 #undef __FUNCT__ 1894 #define __FUNCT__ "MatSetUnfactored_MPIBAIJ" 1895 PetscErrorCode MatSetUnfactored_MPIBAIJ(Mat A) 1896 { 1897 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1898 PetscErrorCode ierr; 1899 1900 PetscFunctionBegin; 1901 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 1902 PetscFunctionReturn(0); 1903 } 1904 1905 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat,MatDuplicateOption,Mat*); 1906 1907 #undef __FUNCT__ 1908 #define __FUNCT__ "MatEqual_MPIBAIJ" 1909 PetscErrorCode MatEqual_MPIBAIJ(Mat A,Mat B,PetscBool *flag) 1910 { 1911 Mat_MPIBAIJ *matB = (Mat_MPIBAIJ*)B->data,*matA = (Mat_MPIBAIJ*)A->data; 1912 Mat a,b,c,d; 1913 PetscBool flg; 1914 PetscErrorCode ierr; 1915 1916 PetscFunctionBegin; 1917 a = matA->A; b = matA->B; 1918 c = matB->A; d = matB->B; 1919 1920 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 1921 if (flg) { 1922 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 1923 } 1924 ierr = MPI_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1925 PetscFunctionReturn(0); 1926 } 1927 1928 #undef __FUNCT__ 1929 #define __FUNCT__ "MatCopy_MPIBAIJ" 1930 PetscErrorCode MatCopy_MPIBAIJ(Mat A,Mat B,MatStructure str) 1931 { 1932 PetscErrorCode ierr; 1933 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1934 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 1935 1936 PetscFunctionBegin; 1937 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 1938 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 1939 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1940 } else { 1941 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 1942 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 1943 } 1944 PetscFunctionReturn(0); 1945 } 1946 1947 #undef __FUNCT__ 1948 #define __FUNCT__ "MatSetUp_MPIBAIJ" 1949 PetscErrorCode MatSetUp_MPIBAIJ(Mat A) 1950 { 1951 PetscErrorCode ierr; 1952 1953 PetscFunctionBegin; 1954 ierr = MatMPIBAIJSetPreallocation(A,A->rmap->bs,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 1955 PetscFunctionReturn(0); 1956 } 1957 1958 #undef __FUNCT__ 1959 #define __FUNCT__ "MatAXPY_MPIBAIJ" 1960 PetscErrorCode MatAXPY_MPIBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1961 { 1962 PetscErrorCode ierr; 1963 Mat_MPIBAIJ *xx=(Mat_MPIBAIJ*)X->data,*yy=(Mat_MPIBAIJ*)Y->data; 1964 PetscBLASInt bnz,one=1; 1965 Mat_SeqBAIJ *x,*y; 1966 1967 PetscFunctionBegin; 1968 if (str == SAME_NONZERO_PATTERN) { 1969 PetscScalar alpha = a; 1970 x = (Mat_SeqBAIJ*)xx->A->data; 1971 y = (Mat_SeqBAIJ*)yy->A->data; 1972 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 1973 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1974 x = (Mat_SeqBAIJ*)xx->B->data; 1975 y = (Mat_SeqBAIJ*)yy->B->data; 1976 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 1977 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1978 } else { 1979 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1980 } 1981 PetscFunctionReturn(0); 1982 } 1983 1984 #undef __FUNCT__ 1985 #define __FUNCT__ "MatRealPart_MPIBAIJ" 1986 PetscErrorCode MatRealPart_MPIBAIJ(Mat A) 1987 { 1988 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1989 PetscErrorCode ierr; 1990 1991 PetscFunctionBegin; 1992 ierr = MatRealPart(a->A);CHKERRQ(ierr); 1993 ierr = MatRealPart(a->B);CHKERRQ(ierr); 1994 PetscFunctionReturn(0); 1995 } 1996 1997 #undef __FUNCT__ 1998 #define __FUNCT__ "MatImaginaryPart_MPIBAIJ" 1999 PetscErrorCode MatImaginaryPart_MPIBAIJ(Mat A) 2000 { 2001 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2002 PetscErrorCode ierr; 2003 2004 PetscFunctionBegin; 2005 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2006 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2007 PetscFunctionReturn(0); 2008 } 2009 2010 #undef __FUNCT__ 2011 #define __FUNCT__ "MatGetSubMatrix_MPIBAIJ" 2012 PetscErrorCode MatGetSubMatrix_MPIBAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 2013 { 2014 PetscErrorCode ierr; 2015 IS iscol_local; 2016 PetscInt csize; 2017 2018 PetscFunctionBegin; 2019 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 2020 if (call == MAT_REUSE_MATRIX) { 2021 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 2022 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 2023 } else { 2024 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2025 } 2026 ierr = MatGetSubMatrix_MPIBAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 2027 if (call == MAT_INITIAL_MATRIX) { 2028 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 2029 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 2030 } 2031 PetscFunctionReturn(0); 2032 } 2033 extern PetscErrorCode MatGetSubMatrices_MPIBAIJ_local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool*,PetscBool*,Mat*); 2034 #undef __FUNCT__ 2035 #define __FUNCT__ "MatGetSubMatrix_MPIBAIJ_Private" 2036 /* 2037 Not great since it makes two copies of the submatrix, first an SeqBAIJ 2038 in local and then by concatenating the local matrices the end result. 2039 Writing it directly would be much like MatGetSubMatrices_MPIBAIJ() 2040 */ 2041 PetscErrorCode MatGetSubMatrix_MPIBAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 2042 { 2043 PetscErrorCode ierr; 2044 PetscMPIInt rank,size; 2045 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs; 2046 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal,ncol,nrow; 2047 Mat M,Mreuse; 2048 MatScalar *vwork,*aa; 2049 MPI_Comm comm; 2050 IS isrow_new, iscol_new; 2051 PetscBool idflag,allrows, allcols; 2052 Mat_SeqBAIJ *aij; 2053 2054 PetscFunctionBegin; 2055 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 2056 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2057 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2058 /* The compression and expansion should be avoided. Doesn't point 2059 out errors, might change the indices, hence buggey */ 2060 ierr = ISCompressIndicesGeneral(mat->rmap->N,mat->rmap->n,mat->rmap->bs,1,&isrow,&isrow_new);CHKERRQ(ierr); 2061 ierr = ISCompressIndicesGeneral(mat->cmap->N,mat->cmap->n,mat->cmap->bs,1,&iscol,&iscol_new);CHKERRQ(ierr); 2062 2063 /* Check for special case: each processor gets entire matrix columns */ 2064 ierr = ISIdentity(iscol,&idflag);CHKERRQ(ierr); 2065 ierr = ISGetLocalSize(iscol,&ncol);CHKERRQ(ierr); 2066 if (idflag && ncol == mat->cmap->N) allcols = PETSC_TRUE; 2067 else allcols = PETSC_FALSE; 2068 2069 ierr = ISIdentity(isrow,&idflag);CHKERRQ(ierr); 2070 ierr = ISGetLocalSize(isrow,&nrow);CHKERRQ(ierr); 2071 if (idflag && nrow == mat->rmap->N) allrows = PETSC_TRUE; 2072 else allrows = PETSC_FALSE; 2073 2074 if (call == MAT_REUSE_MATRIX) { 2075 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 2076 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 2077 ierr = MatGetSubMatrices_MPIBAIJ_local(mat,1,&isrow_new,&iscol_new,MAT_REUSE_MATRIX,&allrows,&allcols,&Mreuse);CHKERRQ(ierr); 2078 } else { 2079 ierr = MatGetSubMatrices_MPIBAIJ_local(mat,1,&isrow_new,&iscol_new,MAT_INITIAL_MATRIX,&allrows,&allcols,&Mreuse);CHKERRQ(ierr); 2080 } 2081 ierr = ISDestroy(&isrow_new);CHKERRQ(ierr); 2082 ierr = ISDestroy(&iscol_new);CHKERRQ(ierr); 2083 /* 2084 m - number of local rows 2085 n - number of columns (same on all processors) 2086 rstart - first row in new global matrix generated 2087 */ 2088 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 2089 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 2090 m = m/bs; 2091 n = n/bs; 2092 2093 if (call == MAT_INITIAL_MATRIX) { 2094 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 2095 ii = aij->i; 2096 jj = aij->j; 2097 2098 /* 2099 Determine the number of non-zeros in the diagonal and off-diagonal 2100 portions of the matrix in order to do correct preallocation 2101 */ 2102 2103 /* first get start and end of "diagonal" columns */ 2104 if (csize == PETSC_DECIDE) { 2105 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 2106 if (mglobal == n*bs) { /* square matrix */ 2107 nlocal = m; 2108 } else { 2109 nlocal = n/size + ((n % size) > rank); 2110 } 2111 } else { 2112 nlocal = csize/bs; 2113 } 2114 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2115 rstart = rend - nlocal; 2116 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); 2117 2118 /* next, compute all the lengths */ 2119 ierr = PetscMalloc2(m+1,PetscInt,&dlens,m+1,PetscInt,&olens);CHKERRQ(ierr); 2120 for (i=0; i<m; i++) { 2121 jend = ii[i+1] - ii[i]; 2122 olen = 0; 2123 dlen = 0; 2124 for (j=0; j<jend; j++) { 2125 if (*jj < rstart || *jj >= rend) olen++; 2126 else dlen++; 2127 jj++; 2128 } 2129 olens[i] = olen; 2130 dlens[i] = dlen; 2131 } 2132 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 2133 ierr = MatSetSizes(M,bs*m,bs*nlocal,PETSC_DECIDE,bs*n);CHKERRQ(ierr); 2134 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 2135 ierr = MatMPIBAIJSetPreallocation(M,bs,0,dlens,0,olens);CHKERRQ(ierr); 2136 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 2137 } else { 2138 PetscInt ml,nl; 2139 2140 M = *newmat; 2141 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 2142 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 2143 ierr = MatZeroEntries(M);CHKERRQ(ierr); 2144 /* 2145 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 2146 rather than the slower MatSetValues(). 2147 */ 2148 M->was_assembled = PETSC_TRUE; 2149 M->assembled = PETSC_FALSE; 2150 } 2151 ierr = MatSetOption(M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 2152 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 2153 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 2154 ii = aij->i; 2155 jj = aij->j; 2156 aa = aij->a; 2157 for (i=0; i<m; i++) { 2158 row = rstart/bs + i; 2159 nz = ii[i+1] - ii[i]; 2160 cwork = jj; jj += nz; 2161 vwork = aa; aa += nz*bs*bs; 2162 ierr = MatSetValuesBlocked_MPIBAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 2163 } 2164 2165 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2166 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2167 *newmat = M; 2168 2169 /* save submatrix used in processor for next request */ 2170 if (call == MAT_INITIAL_MATRIX) { 2171 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 2172 ierr = PetscObjectDereference((PetscObject)Mreuse);CHKERRQ(ierr); 2173 } 2174 PetscFunctionReturn(0); 2175 } 2176 2177 #undef __FUNCT__ 2178 #define __FUNCT__ "MatPermute_MPIBAIJ" 2179 PetscErrorCode MatPermute_MPIBAIJ(Mat A,IS rowp,IS colp,Mat *B) 2180 { 2181 MPI_Comm comm,pcomm; 2182 PetscInt first,rlocal_size,clocal_size,nrows; 2183 const PetscInt *rows; 2184 PetscMPIInt size; 2185 IS crowp,growp,irowp,lrowp,lcolp; 2186 PetscErrorCode ierr; 2187 2188 PetscFunctionBegin; 2189 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 2190 /* make a collective version of 'rowp' */ 2191 ierr = PetscObjectGetComm((PetscObject)rowp,&pcomm);CHKERRQ(ierr); 2192 if (pcomm==comm) { 2193 crowp = rowp; 2194 } else { 2195 ierr = ISGetSize(rowp,&nrows);CHKERRQ(ierr); 2196 ierr = ISGetIndices(rowp,&rows);CHKERRQ(ierr); 2197 ierr = ISCreateGeneral(comm,nrows,rows,PETSC_COPY_VALUES,&crowp);CHKERRQ(ierr); 2198 ierr = ISRestoreIndices(rowp,&rows);CHKERRQ(ierr); 2199 } 2200 /* collect the global row permutation and invert it */ 2201 ierr = ISAllGather(crowp,&growp);CHKERRQ(ierr); 2202 ierr = ISSetPermutation(growp);CHKERRQ(ierr); 2203 if (pcomm!=comm) { 2204 ierr = ISDestroy(&crowp);CHKERRQ(ierr); 2205 } 2206 ierr = ISInvertPermutation(growp,PETSC_DECIDE,&irowp);CHKERRQ(ierr); 2207 ierr = ISDestroy(&growp);CHKERRQ(ierr); 2208 /* get the local target indices */ 2209 ierr = MatGetOwnershipRange(A,&first,NULL);CHKERRQ(ierr); 2210 ierr = MatGetLocalSize(A,&rlocal_size,&clocal_size);CHKERRQ(ierr); 2211 ierr = ISGetIndices(irowp,&rows);CHKERRQ(ierr); 2212 ierr = ISCreateGeneral(MPI_COMM_SELF,rlocal_size,rows+first,PETSC_COPY_VALUES,&lrowp);CHKERRQ(ierr); 2213 ierr = ISRestoreIndices(irowp,&rows);CHKERRQ(ierr); 2214 ierr = ISDestroy(&irowp);CHKERRQ(ierr); 2215 /* the column permutation is so much easier; 2216 make a local version of 'colp' and invert it */ 2217 ierr = PetscObjectGetComm((PetscObject)colp,&pcomm);CHKERRQ(ierr); 2218 ierr = MPI_Comm_size(pcomm,&size);CHKERRQ(ierr); 2219 if (size==1) { 2220 lcolp = colp; 2221 } else { 2222 ierr = ISAllGather(colp,&lcolp);CHKERRQ(ierr); 2223 } 2224 ierr = ISSetPermutation(lcolp);CHKERRQ(ierr); 2225 /* now we just get the submatrix */ 2226 ierr = MatGetSubMatrix_MPIBAIJ_Private(A,lrowp,lcolp,clocal_size,MAT_INITIAL_MATRIX,B);CHKERRQ(ierr); 2227 if (size>1) { 2228 ierr = ISDestroy(&lcolp);CHKERRQ(ierr); 2229 } 2230 /* clean up */ 2231 ierr = ISDestroy(&lrowp);CHKERRQ(ierr); 2232 PetscFunctionReturn(0); 2233 } 2234 2235 #undef __FUNCT__ 2236 #define __FUNCT__ "MatGetGhosts_MPIBAIJ" 2237 PetscErrorCode MatGetGhosts_MPIBAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 2238 { 2239 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*) mat->data; 2240 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 2241 2242 PetscFunctionBegin; 2243 if (nghosts) *nghosts = B->nbs; 2244 if (ghosts) *ghosts = baij->garray; 2245 PetscFunctionReturn(0); 2246 } 2247 2248 #undef __FUNCT__ 2249 #define __FUNCT__ "MatGetSeqNonzeroStructure_MPIBAIJ" 2250 PetscErrorCode MatGetSeqNonzeroStructure_MPIBAIJ(Mat A,Mat *newmat) 2251 { 2252 Mat B; 2253 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2254 Mat_SeqBAIJ *ad = (Mat_SeqBAIJ*)a->A->data,*bd = (Mat_SeqBAIJ*)a->B->data; 2255 Mat_SeqAIJ *b; 2256 PetscErrorCode ierr; 2257 PetscMPIInt size,rank,*recvcounts = 0,*displs = 0; 2258 PetscInt sendcount,i,*rstarts = A->rmap->range,n,cnt,j,bs = A->rmap->bs; 2259 PetscInt m,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf; 2260 2261 PetscFunctionBegin; 2262 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);CHKERRQ(ierr); 2263 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 2264 2265 /* ---------------------------------------------------------------- 2266 Tell every processor the number of nonzeros per row 2267 */ 2268 ierr = PetscMalloc((A->rmap->N/bs)*sizeof(PetscInt),&lens);CHKERRQ(ierr); 2269 for (i=A->rmap->rstart/bs; i<A->rmap->rend/bs; i++) { 2270 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]; 2271 } 2272 sendcount = A->rmap->rend/bs - A->rmap->rstart/bs; 2273 ierr = PetscMalloc(2*size*sizeof(PetscMPIInt),&recvcounts);CHKERRQ(ierr); 2274 displs = recvcounts + size; 2275 for (i=0; i<size; i++) { 2276 recvcounts[i] = A->rmap->range[i+1]/bs - A->rmap->range[i]/bs; 2277 displs[i] = A->rmap->range[i]/bs; 2278 } 2279 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2280 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2281 #else 2282 ierr = MPI_Allgatherv(lens+A->rmap->rstart/bs,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2283 #endif 2284 /* --------------------------------------------------------------- 2285 Create the sequential matrix of the same type as the local block diagonal 2286 */ 2287 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 2288 ierr = MatSetSizes(B,A->rmap->N/bs,A->cmap->N/bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2289 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 2290 ierr = MatSeqAIJSetPreallocation(B,0,lens);CHKERRQ(ierr); 2291 b = (Mat_SeqAIJ*)B->data; 2292 2293 /*-------------------------------------------------------------------- 2294 Copy my part of matrix column indices over 2295 */ 2296 sendcount = ad->nz + bd->nz; 2297 jsendbuf = b->j + b->i[rstarts[rank]/bs]; 2298 a_jsendbuf = ad->j; 2299 b_jsendbuf = bd->j; 2300 n = A->rmap->rend/bs - A->rmap->rstart/bs; 2301 cnt = 0; 2302 for (i=0; i<n; i++) { 2303 2304 /* put in lower diagonal portion */ 2305 m = bd->i[i+1] - bd->i[i]; 2306 while (m > 0) { 2307 /* is it above diagonal (in bd (compressed) numbering) */ 2308 if (garray[*b_jsendbuf] > A->rmap->rstart/bs + i) break; 2309 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2310 m--; 2311 } 2312 2313 /* put in diagonal portion */ 2314 for (j=ad->i[i]; j<ad->i[i+1]; j++) { 2315 jsendbuf[cnt++] = A->rmap->rstart/bs + *a_jsendbuf++; 2316 } 2317 2318 /* put in upper diagonal portion */ 2319 while (m-- > 0) { 2320 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2321 } 2322 } 2323 if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt); 2324 2325 /*-------------------------------------------------------------------- 2326 Gather all column indices to all processors 2327 */ 2328 for (i=0; i<size; i++) { 2329 recvcounts[i] = 0; 2330 for (j=A->rmap->range[i]/bs; j<A->rmap->range[i+1]/bs; j++) { 2331 recvcounts[i] += lens[j]; 2332 } 2333 } 2334 displs[0] = 0; 2335 for (i=1; i<size; i++) { 2336 displs[i] = displs[i-1] + recvcounts[i-1]; 2337 } 2338 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2339 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2340 #else 2341 ierr = MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2342 #endif 2343 /*-------------------------------------------------------------------- 2344 Assemble the matrix into useable form (note numerical values not yet set) 2345 */ 2346 /* set the b->ilen (length of each row) values */ 2347 ierr = PetscMemcpy(b->ilen,lens,(A->rmap->N/bs)*sizeof(PetscInt));CHKERRQ(ierr); 2348 /* set the b->i indices */ 2349 b->i[0] = 0; 2350 for (i=1; i<=A->rmap->N/bs; i++) { 2351 b->i[i] = b->i[i-1] + lens[i-1]; 2352 } 2353 ierr = PetscFree(lens);CHKERRQ(ierr); 2354 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2355 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2356 ierr = PetscFree(recvcounts);CHKERRQ(ierr); 2357 2358 if (A->symmetric) { 2359 ierr = MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2360 } else if (A->hermitian) { 2361 ierr = MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr); 2362 } else if (A->structurally_symmetric) { 2363 ierr = MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2364 } 2365 *newmat = B; 2366 PetscFunctionReturn(0); 2367 } 2368 2369 #undef __FUNCT__ 2370 #define __FUNCT__ "MatSOR_MPIBAIJ" 2371 PetscErrorCode MatSOR_MPIBAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 2372 { 2373 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 2374 PetscErrorCode ierr; 2375 Vec bb1 = 0; 2376 2377 PetscFunctionBegin; 2378 if (flag == SOR_APPLY_UPPER) { 2379 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2380 PetscFunctionReturn(0); 2381 } 2382 2383 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS) { 2384 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 2385 } 2386 2387 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 2388 if (flag & SOR_ZERO_INITIAL_GUESS) { 2389 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2390 its--; 2391 } 2392 2393 while (its--) { 2394 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2395 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2396 2397 /* update rhs: bb1 = bb - B*x */ 2398 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2399 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2400 2401 /* local sweep */ 2402 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2403 } 2404 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 2405 if (flag & SOR_ZERO_INITIAL_GUESS) { 2406 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2407 its--; 2408 } 2409 while (its--) { 2410 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2411 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2412 2413 /* update rhs: bb1 = bb - B*x */ 2414 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2415 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2416 2417 /* local sweep */ 2418 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2419 } 2420 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 2421 if (flag & SOR_ZERO_INITIAL_GUESS) { 2422 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2423 its--; 2424 } 2425 while (its--) { 2426 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2427 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2428 2429 /* update rhs: bb1 = bb - B*x */ 2430 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2431 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2432 2433 /* local sweep */ 2434 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2435 } 2436 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel version of SOR requested not supported"); 2437 2438 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 #undef __FUNCT__ 2443 #define __FUNCT__ "MatInvertBlockDiagonal_MPIBAIJ" 2444 PetscErrorCode MatInvertBlockDiagonal_MPIBAIJ(Mat A,const PetscScalar **values) 2445 { 2446 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; 2447 PetscErrorCode ierr; 2448 2449 PetscFunctionBegin; 2450 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2451 PetscFunctionReturn(0); 2452 } 2453 2454 2455 /* -------------------------------------------------------------------*/ 2456 static struct _MatOps MatOps_Values = {MatSetValues_MPIBAIJ, 2457 MatGetRow_MPIBAIJ, 2458 MatRestoreRow_MPIBAIJ, 2459 MatMult_MPIBAIJ, 2460 /* 4*/ MatMultAdd_MPIBAIJ, 2461 MatMultTranspose_MPIBAIJ, 2462 MatMultTransposeAdd_MPIBAIJ, 2463 0, 2464 0, 2465 0, 2466 /*10*/ 0, 2467 0, 2468 0, 2469 MatSOR_MPIBAIJ, 2470 MatTranspose_MPIBAIJ, 2471 /*15*/ MatGetInfo_MPIBAIJ, 2472 MatEqual_MPIBAIJ, 2473 MatGetDiagonal_MPIBAIJ, 2474 MatDiagonalScale_MPIBAIJ, 2475 MatNorm_MPIBAIJ, 2476 /*20*/ MatAssemblyBegin_MPIBAIJ, 2477 MatAssemblyEnd_MPIBAIJ, 2478 MatSetOption_MPIBAIJ, 2479 MatZeroEntries_MPIBAIJ, 2480 /*24*/ MatZeroRows_MPIBAIJ, 2481 0, 2482 0, 2483 0, 2484 0, 2485 /*29*/ MatSetUp_MPIBAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*34*/ MatDuplicate_MPIBAIJ, 2491 0, 2492 0, 2493 0, 2494 0, 2495 /*39*/ MatAXPY_MPIBAIJ, 2496 MatGetSubMatrices_MPIBAIJ, 2497 MatIncreaseOverlap_MPIBAIJ, 2498 MatGetValues_MPIBAIJ, 2499 MatCopy_MPIBAIJ, 2500 /*44*/ 0, 2501 MatScale_MPIBAIJ, 2502 0, 2503 0, 2504 0, 2505 /*49*/ 0, 2506 0, 2507 0, 2508 0, 2509 0, 2510 /*54*/ 0, 2511 0, 2512 MatSetUnfactored_MPIBAIJ, 2513 MatPermute_MPIBAIJ, 2514 MatSetValuesBlocked_MPIBAIJ, 2515 /*59*/ MatGetSubMatrix_MPIBAIJ, 2516 MatDestroy_MPIBAIJ, 2517 MatView_MPIBAIJ, 2518 0, 2519 0, 2520 /*64*/ 0, 2521 0, 2522 0, 2523 0, 2524 0, 2525 /*69*/ MatGetRowMaxAbs_MPIBAIJ, 2526 0, 2527 0, 2528 0, 2529 0, 2530 /*74*/ 0, 2531 MatFDColoringApply_BAIJ, 2532 0, 2533 0, 2534 0, 2535 /*79*/ 0, 2536 0, 2537 0, 2538 0, 2539 MatLoad_MPIBAIJ, 2540 /*84*/ 0, 2541 0, 2542 0, 2543 0, 2544 0, 2545 /*89*/ 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*94*/ 0, 2551 0, 2552 0, 2553 0, 2554 0, 2555 /*99*/ 0, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*104*/0, 2561 MatRealPart_MPIBAIJ, 2562 MatImaginaryPart_MPIBAIJ, 2563 0, 2564 0, 2565 /*109*/0, 2566 0, 2567 0, 2568 0, 2569 0, 2570 /*114*/MatGetSeqNonzeroStructure_MPIBAIJ, 2571 0, 2572 MatGetGhosts_MPIBAIJ, 2573 0, 2574 0, 2575 /*119*/0, 2576 0, 2577 0, 2578 0, 2579 MatGetMultiProcBlock_MPIBAIJ, 2580 /*124*/0, 2581 0, 2582 MatInvertBlockDiagonal_MPIBAIJ, 2583 0, 2584 0, 2585 /*129*/ 0, 2586 0, 2587 0, 2588 0, 2589 0, 2590 /*134*/ 0, 2591 0, 2592 0, 2593 0, 2594 0, 2595 /*139*/ 0, 2596 0, 2597 MatFDColoringSetUp_MPIXAIJ 2598 }; 2599 2600 #undef __FUNCT__ 2601 #define __FUNCT__ "MatGetDiagonalBlock_MPIBAIJ" 2602 PetscErrorCode MatGetDiagonalBlock_MPIBAIJ(Mat A,Mat *a) 2603 { 2604 PetscFunctionBegin; 2605 *a = ((Mat_MPIBAIJ*)A->data)->A; 2606 PetscFunctionReturn(0); 2607 } 2608 2609 PETSC_EXTERN PetscErrorCode MatConvert_MPIBAIJ_MPISBAIJ(Mat, MatType,MatReuse,Mat*); 2610 2611 #undef __FUNCT__ 2612 #define __FUNCT__ "MatMPIBAIJSetPreallocationCSR_MPIBAIJ" 2613 PetscErrorCode MatMPIBAIJSetPreallocationCSR_MPIBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[],const PetscScalar V[]) 2614 { 2615 PetscInt m,rstart,cstart,cend; 2616 PetscInt i,j,d,nz,nz_max=0,*d_nnz=0,*o_nnz=0; 2617 const PetscInt *JJ =0; 2618 PetscScalar *values=0; 2619 PetscErrorCode ierr; 2620 2621 PetscFunctionBegin; 2622 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 2623 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 2624 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2625 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2626 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2627 m = B->rmap->n/bs; 2628 rstart = B->rmap->rstart/bs; 2629 cstart = B->cmap->rstart/bs; 2630 cend = B->cmap->rend/bs; 2631 2632 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 2633 ierr = PetscMalloc2(m,PetscInt,&d_nnz,m,PetscInt,&o_nnz);CHKERRQ(ierr); 2634 for (i=0; i<m; i++) { 2635 nz = ii[i+1] - ii[i]; 2636 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative number of columns %D",i,nz); 2637 nz_max = PetscMax(nz_max,nz); 2638 JJ = jj + ii[i]; 2639 for (j=0; j<nz; j++) { 2640 if (*JJ >= cstart) break; 2641 JJ++; 2642 } 2643 d = 0; 2644 for (; j<nz; j++) { 2645 if (*JJ++ >= cend) break; 2646 d++; 2647 } 2648 d_nnz[i] = d; 2649 o_nnz[i] = nz - d; 2650 } 2651 ierr = MatMPIBAIJSetPreallocation(B,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 2652 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 2653 2654 values = (PetscScalar*)V; 2655 if (!values) { 2656 ierr = PetscMalloc(bs*bs*nz_max*sizeof(PetscScalar),&values);CHKERRQ(ierr); 2657 ierr = PetscMemzero(values,bs*bs*nz_max*sizeof(PetscScalar));CHKERRQ(ierr); 2658 } 2659 for (i=0; i<m; i++) { 2660 PetscInt row = i + rstart; 2661 PetscInt ncols = ii[i+1] - ii[i]; 2662 const PetscInt *icols = jj + ii[i]; 2663 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 2664 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 2665 } 2666 2667 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 2668 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2669 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2670 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2671 PetscFunctionReturn(0); 2672 } 2673 2674 #undef __FUNCT__ 2675 #define __FUNCT__ "MatMPIBAIJSetPreallocationCSR" 2676 /*@C 2677 MatMPIBAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in BAIJ format 2678 (the default parallel PETSc format). 2679 2680 Collective on MPI_Comm 2681 2682 Input Parameters: 2683 + A - the matrix 2684 . bs - the block size 2685 . i - the indices into j for the start of each local row (starts with zero) 2686 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2687 - v - optional values in the matrix 2688 2689 Level: developer 2690 2691 .keywords: matrix, aij, compressed row, sparse, parallel 2692 2693 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIBAIJSetPreallocation(), MatCreateAIJ(), MPIAIJ 2694 @*/ 2695 PetscErrorCode MatMPIBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2696 { 2697 PetscErrorCode ierr; 2698 2699 PetscFunctionBegin; 2700 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2701 PetscValidType(B,1); 2702 PetscValidLogicalCollectiveInt(B,bs,2); 2703 ierr = PetscTryMethod(B,"MatMPIBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2704 PetscFunctionReturn(0); 2705 } 2706 2707 #undef __FUNCT__ 2708 #define __FUNCT__ "MatMPIBAIJSetPreallocation_MPIBAIJ" 2709 PetscErrorCode MatMPIBAIJSetPreallocation_MPIBAIJ(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt *d_nnz,PetscInt o_nz,const PetscInt *o_nnz) 2710 { 2711 Mat_MPIBAIJ *b; 2712 PetscErrorCode ierr; 2713 PetscInt i; 2714 2715 PetscFunctionBegin; 2716 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 2717 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 2718 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2719 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2720 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2721 2722 if (d_nnz) { 2723 for (i=0; i<B->rmap->n/bs; i++) { 2724 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]); 2725 } 2726 } 2727 if (o_nnz) { 2728 for (i=0; i<B->rmap->n/bs; i++) { 2729 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]); 2730 } 2731 } 2732 2733 b = (Mat_MPIBAIJ*)B->data; 2734 b->bs2 = bs*bs; 2735 b->mbs = B->rmap->n/bs; 2736 b->nbs = B->cmap->n/bs; 2737 b->Mbs = B->rmap->N/bs; 2738 b->Nbs = B->cmap->N/bs; 2739 2740 for (i=0; i<=b->size; i++) { 2741 b->rangebs[i] = B->rmap->range[i]/bs; 2742 } 2743 b->rstartbs = B->rmap->rstart/bs; 2744 b->rendbs = B->rmap->rend/bs; 2745 b->cstartbs = B->cmap->rstart/bs; 2746 b->cendbs = B->cmap->rend/bs; 2747 2748 if (!B->preallocated) { 2749 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2750 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2751 ierr = MatSetType(b->A,MATSEQBAIJ);CHKERRQ(ierr); 2752 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2753 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2754 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2755 ierr = MatSetType(b->B,MATSEQBAIJ);CHKERRQ(ierr); 2756 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2757 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),bs,&B->bstash);CHKERRQ(ierr); 2758 } 2759 2760 ierr = MatSeqBAIJSetPreallocation(b->A,bs,d_nz,d_nnz);CHKERRQ(ierr); 2761 ierr = MatSeqBAIJSetPreallocation(b->B,bs,o_nz,o_nnz);CHKERRQ(ierr); 2762 B->preallocated = PETSC_TRUE; 2763 PetscFunctionReturn(0); 2764 } 2765 2766 extern PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat,Vec); 2767 extern PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat,PetscReal); 2768 2769 #undef __FUNCT__ 2770 #define __FUNCT__ "MatConvert_MPIBAIJ_MPIAdj" 2771 PETSC_EXTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAdj(Mat B, MatType newtype,MatReuse reuse,Mat *adj) 2772 { 2773 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 2774 PetscErrorCode ierr; 2775 Mat_SeqBAIJ *d = (Mat_SeqBAIJ*) b->A->data,*o = (Mat_SeqBAIJ*) b->B->data; 2776 PetscInt M = B->rmap->n/B->rmap->bs,i,*ii,*jj,cnt,j,k,rstart = B->rmap->rstart/B->rmap->bs; 2777 const PetscInt *id = d->i, *jd = d->j, *io = o->i, *jo = o->j, *garray = b->garray; 2778 2779 PetscFunctionBegin; 2780 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&ii);CHKERRQ(ierr); 2781 ii[0] = 0; 2782 for (i=0; i<M; i++) { 2783 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]); 2784 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]); 2785 ii[i+1] = ii[i] + id[i+1] - id[i] + io[i+1] - io[i]; 2786 /* remove one from count of matrix has diagonal */ 2787 for (j=id[i]; j<id[i+1]; j++) { 2788 if (jd[j] == i) {ii[i+1]--;break;} 2789 } 2790 } 2791 ierr = PetscMalloc(ii[M]*sizeof(PetscInt),&jj);CHKERRQ(ierr); 2792 cnt = 0; 2793 for (i=0; i<M; i++) { 2794 for (j=io[i]; j<io[i+1]; j++) { 2795 if (garray[jo[j]] > rstart) break; 2796 jj[cnt++] = garray[jo[j]]; 2797 } 2798 for (k=id[i]; k<id[i+1]; k++) { 2799 if (jd[k] != i) { 2800 jj[cnt++] = rstart + jd[k]; 2801 } 2802 } 2803 for (; j<io[i+1]; j++) { 2804 jj[cnt++] = garray[jo[j]]; 2805 } 2806 } 2807 ierr = MatCreateMPIAdj(PetscObjectComm((PetscObject)B),M,B->cmap->N/B->rmap->bs,ii,jj,NULL,adj);CHKERRQ(ierr); 2808 PetscFunctionReturn(0); 2809 } 2810 2811 #include <../src/mat/impls/aij/mpi/mpiaij.h> 2812 2813 PETSC_EXTERN PetscErrorCode MatConvert_SeqBAIJ_SeqAIJ(Mat,MatType,MatReuse,Mat*); 2814 2815 #undef __FUNCT__ 2816 #define __FUNCT__ "MatConvert_MPIBAIJ_MPIAIJ" 2817 PETSC_EXTERN PetscErrorCode MatConvert_MPIBAIJ_MPIAIJ(Mat A,MatType newtype,MatReuse reuse,Mat *newmat) 2818 { 2819 PetscErrorCode ierr; 2820 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2821 Mat B; 2822 Mat_MPIAIJ *b; 2823 2824 PetscFunctionBegin; 2825 if (!A->assembled) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Matrix must be assembled"); 2826 2827 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 2828 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 2829 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2830 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 2831 ierr = MatMPIAIJSetPreallocation(B,0,NULL,0,NULL);CHKERRQ(ierr); 2832 b = (Mat_MPIAIJ*) B->data; 2833 2834 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 2835 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2836 ierr = MatDisAssemble_MPIBAIJ(A);CHKERRQ(ierr); 2837 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->A);CHKERRQ(ierr); 2838 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->B);CHKERRQ(ierr); 2839 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2840 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2841 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2842 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2843 if (reuse == MAT_REUSE_MATRIX) { 2844 ierr = MatHeaderReplace(A,B);CHKERRQ(ierr); 2845 } else { 2846 *newmat = B; 2847 } 2848 PetscFunctionReturn(0); 2849 } 2850 2851 #if defined(PETSC_HAVE_MUMPS) 2852 PETSC_EXTERN PetscErrorCode MatGetFactor_baij_mumps(Mat,MatFactorType,Mat*); 2853 #endif 2854 2855 /*MC 2856 MATMPIBAIJ - MATMPIBAIJ = "mpibaij" - A matrix type to be used for distributed block sparse matrices. 2857 2858 Options Database Keys: 2859 + -mat_type mpibaij - sets the matrix type to "mpibaij" during a call to MatSetFromOptions() 2860 . -mat_block_size <bs> - set the blocksize used to store the matrix 2861 - -mat_use_hash_table <fact> 2862 2863 Level: beginner 2864 2865 .seealso: MatCreateMPIBAIJ 2866 M*/ 2867 2868 PETSC_EXTERN PetscErrorCode MatConvert_MPIBAIJ_MPIBSTRM(Mat,MatType,MatReuse,Mat*); 2869 2870 #undef __FUNCT__ 2871 #define __FUNCT__ "MatCreate_MPIBAIJ" 2872 PETSC_EXTERN PetscErrorCode MatCreate_MPIBAIJ(Mat B) 2873 { 2874 Mat_MPIBAIJ *b; 2875 PetscErrorCode ierr; 2876 PetscBool flg; 2877 2878 PetscFunctionBegin; 2879 ierr = PetscNewLog(B,Mat_MPIBAIJ,&b);CHKERRQ(ierr); 2880 B->data = (void*)b; 2881 2882 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 2883 B->assembled = PETSC_FALSE; 2884 2885 B->insertmode = NOT_SET_VALUES; 2886 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 2887 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&b->size);CHKERRQ(ierr); 2888 2889 /* build local table of row and column ownerships */ 2890 ierr = PetscMalloc((b->size+1)*sizeof(PetscInt),&b->rangebs);CHKERRQ(ierr); 2891 2892 /* build cache for off array entries formed */ 2893 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 2894 2895 b->donotstash = PETSC_FALSE; 2896 b->colmap = NULL; 2897 b->garray = NULL; 2898 b->roworiented = PETSC_TRUE; 2899 2900 /* stuff used in block assembly */ 2901 b->barray = 0; 2902 2903 /* stuff used for matrix vector multiply */ 2904 b->lvec = 0; 2905 b->Mvctx = 0; 2906 2907 /* stuff for MatGetRow() */ 2908 b->rowindices = 0; 2909 b->rowvalues = 0; 2910 b->getrowactive = PETSC_FALSE; 2911 2912 /* hash table stuff */ 2913 b->ht = 0; 2914 b->hd = 0; 2915 b->ht_size = 0; 2916 b->ht_flag = PETSC_FALSE; 2917 b->ht_fact = 0; 2918 b->ht_total_ct = 0; 2919 b->ht_insert_ct = 0; 2920 2921 /* stuff for MatGetSubMatrices_MPIBAIJ_local() */ 2922 b->ijonly = PETSC_FALSE; 2923 2924 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),NULL,"Options for loading MPIBAIJ matrix 1","Mat");CHKERRQ(ierr); 2925 ierr = PetscOptionsBool("-mat_use_hash_table","Use hash table to save memory in constructing matrix","MatSetOption",PETSC_FALSE,&flg,NULL);CHKERRQ(ierr); 2926 if (flg) { 2927 PetscReal fact = 1.39; 2928 ierr = MatSetOption(B,MAT_USE_HASH_TABLE,PETSC_TRUE);CHKERRQ(ierr); 2929 ierr = PetscOptionsReal("-mat_use_hash_table","Use hash table factor","MatMPIBAIJSetHashTableFactor",fact,&fact,NULL);CHKERRQ(ierr); 2930 if (fact <= 1.0) fact = 1.39; 2931 ierr = MatMPIBAIJSetHashTableFactor(B,fact);CHKERRQ(ierr); 2932 ierr = PetscInfo1(B,"Hash table Factor used %5.2f\n",fact);CHKERRQ(ierr); 2933 } 2934 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2935 2936 #if defined(PETSC_HAVE_MUMPS) 2937 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_baij_mumps);CHKERRQ(ierr); 2938 #endif 2939 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiadj_C",MatConvert_MPIBAIJ_MPIAdj);CHKERRQ(ierr); 2940 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpiaij_C",MatConvert_MPIBAIJ_MPIAIJ);CHKERRQ(ierr); 2941 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpisbaij_C",MatConvert_MPIBAIJ_MPISBAIJ);CHKERRQ(ierr); 2942 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIBAIJ);CHKERRQ(ierr); 2943 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIBAIJ);CHKERRQ(ierr); 2944 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetDiagonalBlock_C",MatGetDiagonalBlock_MPIBAIJ);CHKERRQ(ierr); 2945 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocation_C",MatMPIBAIJSetPreallocation_MPIBAIJ);CHKERRQ(ierr); 2946 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIBAIJSetPreallocationCSR_C",MatMPIBAIJSetPreallocationCSR_MPIBAIJ);CHKERRQ(ierr); 2947 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIBAIJ);CHKERRQ(ierr); 2948 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSetHashTableFactor_C",MatSetHashTableFactor_MPIBAIJ);CHKERRQ(ierr); 2949 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpibaij_mpibstrm_C",MatConvert_MPIBAIJ_MPIBSTRM);CHKERRQ(ierr); 2950 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIBAIJ);CHKERRQ(ierr); 2951 PetscFunctionReturn(0); 2952 } 2953 2954 /*MC 2955 MATBAIJ - MATBAIJ = "baij" - A matrix type to be used for block sparse matrices. 2956 2957 This matrix type is identical to MATSEQBAIJ when constructed with a single process communicator, 2958 and MATMPIBAIJ otherwise. 2959 2960 Options Database Keys: 2961 . -mat_type baij - sets the matrix type to "baij" during a call to MatSetFromOptions() 2962 2963 Level: beginner 2964 2965 .seealso: MatCreateBAIJ(),MATSEQBAIJ,MATMPIBAIJ, MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 2966 M*/ 2967 2968 #undef __FUNCT__ 2969 #define __FUNCT__ "MatMPIBAIJSetPreallocation" 2970 /*@C 2971 MatMPIBAIJSetPreallocation - Allocates memory for a sparse parallel matrix in block AIJ format 2972 (block compressed row). For good matrix assembly performance 2973 the user should preallocate the matrix storage by setting the parameters 2974 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 2975 performance can be increased by more than a factor of 50. 2976 2977 Collective on Mat 2978 2979 Input Parameters: 2980 + A - the matrix 2981 . bs - size of block 2982 . d_nz - number of block nonzeros per block row in diagonal portion of local 2983 submatrix (same for all local rows) 2984 . d_nnz - array containing the number of block nonzeros in the various block rows 2985 of the in diagonal portion of the local (possibly different for each block 2986 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry and 2987 set it even if it is zero. 2988 . o_nz - number of block nonzeros per block row in the off-diagonal portion of local 2989 submatrix (same for all local rows). 2990 - o_nnz - array containing the number of nonzeros in the various block rows of the 2991 off-diagonal portion of the local submatrix (possibly different for 2992 each block row) or NULL. 2993 2994 If the *_nnz parameter is given then the *_nz parameter is ignored 2995 2996 Options Database Keys: 2997 + -mat_block_size - size of the blocks to use 2998 - -mat_use_hash_table <fact> 2999 3000 Notes: 3001 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3002 than it must be used on all processors that share the object for that argument. 3003 3004 Storage Information: 3005 For a square global matrix we define each processor's diagonal portion 3006 to be its local rows and the corresponding columns (a square submatrix); 3007 each processor's off-diagonal portion encompasses the remainder of the 3008 local matrix (a rectangular submatrix). 3009 3010 The user can specify preallocated storage for the diagonal part of 3011 the local submatrix with either d_nz or d_nnz (not both). Set 3012 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3013 memory allocation. Likewise, specify preallocated storage for the 3014 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3015 3016 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3017 the figure below we depict these three local rows and all columns (0-11). 3018 3019 .vb 3020 0 1 2 3 4 5 6 7 8 9 10 11 3021 -------------------------- 3022 row 3 |o o o d d d o o o o o o 3023 row 4 |o o o d d d o o o o o o 3024 row 5 |o o o d d d o o o o o o 3025 -------------------------- 3026 .ve 3027 3028 Thus, any entries in the d locations are stored in the d (diagonal) 3029 submatrix, and any entries in the o locations are stored in the 3030 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3031 stored simply in the MATSEQBAIJ format for compressed row storage. 3032 3033 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3034 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3035 In general, for PDE problems in which most nonzeros are near the diagonal, 3036 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3037 or you will get TERRIBLE performance; see the users' manual chapter on 3038 matrices. 3039 3040 You can call MatGetInfo() to get information on how effective the preallocation was; 3041 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3042 You can also run with the option -info and look for messages with the string 3043 malloc in them to see if additional memory allocation was needed. 3044 3045 Level: intermediate 3046 3047 .keywords: matrix, block, aij, compressed row, sparse, parallel 3048 3049 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocationCSR(), PetscSplitOwnership() 3050 @*/ 3051 PetscErrorCode MatMPIBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3052 { 3053 PetscErrorCode ierr; 3054 3055 PetscFunctionBegin; 3056 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3057 PetscValidType(B,1); 3058 PetscValidLogicalCollectiveInt(B,bs,2); 3059 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); 3060 PetscFunctionReturn(0); 3061 } 3062 3063 #undef __FUNCT__ 3064 #define __FUNCT__ "MatCreateBAIJ" 3065 /*@C 3066 MatCreateBAIJ - Creates a sparse parallel matrix in block AIJ format 3067 (block compressed row). For good matrix assembly performance 3068 the user should preallocate the matrix storage by setting the parameters 3069 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3070 performance can be increased by more than a factor of 50. 3071 3072 Collective on MPI_Comm 3073 3074 Input Parameters: 3075 + comm - MPI communicator 3076 . bs - size of blockk 3077 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3078 This value should be the same as the local size used in creating the 3079 y vector for the matrix-vector product y = Ax. 3080 . n - number of local columns (or PETSC_DECIDE to have calculated if N is given) 3081 This value should be the same as the local size used in creating the 3082 x vector for the matrix-vector product y = Ax. 3083 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3084 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3085 . d_nz - number of nonzero blocks per block row in diagonal portion of local 3086 submatrix (same for all local rows) 3087 . d_nnz - array containing the number of nonzero blocks in the various block rows 3088 of the in diagonal portion of the local (possibly different for each block 3089 row) or NULL. If you plan to factor the matrix you must leave room for the diagonal entry 3090 and set it even if it is zero. 3091 . o_nz - number of nonzero blocks per block row in the off-diagonal portion of local 3092 submatrix (same for all local rows). 3093 - o_nnz - array containing the number of nonzero blocks in the various block rows of the 3094 off-diagonal portion of the local submatrix (possibly different for 3095 each block row) or NULL. 3096 3097 Output Parameter: 3098 . A - the matrix 3099 3100 Options Database Keys: 3101 + -mat_block_size - size of the blocks to use 3102 - -mat_use_hash_table <fact> 3103 3104 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3105 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3106 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3107 3108 Notes: 3109 If the *_nnz parameter is given then the *_nz parameter is ignored 3110 3111 A nonzero block is any block that as 1 or more nonzeros in it 3112 3113 The user MUST specify either the local or global matrix dimensions 3114 (possibly both). 3115 3116 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3117 than it must be used on all processors that share the object for that argument. 3118 3119 Storage Information: 3120 For a square global matrix we define each processor's diagonal portion 3121 to be its local rows and the corresponding columns (a square submatrix); 3122 each processor's off-diagonal portion encompasses the remainder of the 3123 local matrix (a rectangular submatrix). 3124 3125 The user can specify preallocated storage for the diagonal part of 3126 the local submatrix with either d_nz or d_nnz (not both). Set 3127 d_nz=PETSC_DEFAULT and d_nnz=NULL for PETSc to control dynamic 3128 memory allocation. Likewise, specify preallocated storage for the 3129 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3130 3131 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3132 the figure below we depict these three local rows and all columns (0-11). 3133 3134 .vb 3135 0 1 2 3 4 5 6 7 8 9 10 11 3136 -------------------------- 3137 row 3 |o o o d d d o o o o o o 3138 row 4 |o o o d d d o o o o o o 3139 row 5 |o o o d d d o o o o o o 3140 -------------------------- 3141 .ve 3142 3143 Thus, any entries in the d locations are stored in the d (diagonal) 3144 submatrix, and any entries in the o locations are stored in the 3145 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3146 stored simply in the MATSEQBAIJ format for compressed row storage. 3147 3148 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3149 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3150 In general, for PDE problems in which most nonzeros are near the diagonal, 3151 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3152 or you will get TERRIBLE performance; see the users' manual chapter on 3153 matrices. 3154 3155 Level: intermediate 3156 3157 .keywords: matrix, block, aij, compressed row, sparse, parallel 3158 3159 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3160 @*/ 3161 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) 3162 { 3163 PetscErrorCode ierr; 3164 PetscMPIInt size; 3165 3166 PetscFunctionBegin; 3167 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3168 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 3169 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3170 if (size > 1) { 3171 ierr = MatSetType(*A,MATMPIBAIJ);CHKERRQ(ierr); 3172 ierr = MatMPIBAIJSetPreallocation(*A,bs,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 3173 } else { 3174 ierr = MatSetType(*A,MATSEQBAIJ);CHKERRQ(ierr); 3175 ierr = MatSeqBAIJSetPreallocation(*A,bs,d_nz,d_nnz);CHKERRQ(ierr); 3176 } 3177 PetscFunctionReturn(0); 3178 } 3179 3180 #undef __FUNCT__ 3181 #define __FUNCT__ "MatDuplicate_MPIBAIJ" 3182 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 3183 { 3184 Mat mat; 3185 Mat_MPIBAIJ *a,*oldmat = (Mat_MPIBAIJ*)matin->data; 3186 PetscErrorCode ierr; 3187 PetscInt len=0; 3188 3189 PetscFunctionBegin; 3190 *newmat = 0; 3191 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 3192 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 3193 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 3194 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 3195 3196 mat->factortype = matin->factortype; 3197 mat->preallocated = PETSC_TRUE; 3198 mat->assembled = PETSC_TRUE; 3199 mat->insertmode = NOT_SET_VALUES; 3200 3201 a = (Mat_MPIBAIJ*)mat->data; 3202 mat->rmap->bs = matin->rmap->bs; 3203 a->bs2 = oldmat->bs2; 3204 a->mbs = oldmat->mbs; 3205 a->nbs = oldmat->nbs; 3206 a->Mbs = oldmat->Mbs; 3207 a->Nbs = oldmat->Nbs; 3208 3209 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 3210 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 3211 3212 a->size = oldmat->size; 3213 a->rank = oldmat->rank; 3214 a->donotstash = oldmat->donotstash; 3215 a->roworiented = oldmat->roworiented; 3216 a->rowindices = 0; 3217 a->rowvalues = 0; 3218 a->getrowactive = PETSC_FALSE; 3219 a->barray = 0; 3220 a->rstartbs = oldmat->rstartbs; 3221 a->rendbs = oldmat->rendbs; 3222 a->cstartbs = oldmat->cstartbs; 3223 a->cendbs = oldmat->cendbs; 3224 3225 /* hash table stuff */ 3226 a->ht = 0; 3227 a->hd = 0; 3228 a->ht_size = 0; 3229 a->ht_flag = oldmat->ht_flag; 3230 a->ht_fact = oldmat->ht_fact; 3231 a->ht_total_ct = 0; 3232 a->ht_insert_ct = 0; 3233 3234 ierr = PetscMemcpy(a->rangebs,oldmat->rangebs,(a->size+1)*sizeof(PetscInt));CHKERRQ(ierr); 3235 if (oldmat->colmap) { 3236 #if defined(PETSC_USE_CTABLE) 3237 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 3238 #else 3239 ierr = PetscMalloc((a->Nbs)*sizeof(PetscInt),&a->colmap);CHKERRQ(ierr); 3240 ierr = PetscLogObjectMemory((PetscObject)mat,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3241 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3242 #endif 3243 } else a->colmap = 0; 3244 3245 if (oldmat->garray && (len = ((Mat_SeqBAIJ*)(oldmat->B->data))->nbs)) { 3246 ierr = PetscMalloc(len*sizeof(PetscInt),&a->garray);CHKERRQ(ierr); 3247 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 3248 ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); 3249 } else a->garray = 0; 3250 3251 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)matin),matin->rmap->bs,&mat->bstash);CHKERRQ(ierr); 3252 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 3253 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 3254 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 3255 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 3256 3257 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 3258 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 3259 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 3260 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 3261 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 3262 *newmat = mat; 3263 PetscFunctionReturn(0); 3264 } 3265 3266 #undef __FUNCT__ 3267 #define __FUNCT__ "MatLoad_MPIBAIJ" 3268 PetscErrorCode MatLoad_MPIBAIJ(Mat newmat,PetscViewer viewer) 3269 { 3270 PetscErrorCode ierr; 3271 int fd; 3272 PetscInt i,nz,j,rstart,rend; 3273 PetscScalar *vals,*buf; 3274 MPI_Comm comm; 3275 MPI_Status status; 3276 PetscMPIInt rank,size,maxnz; 3277 PetscInt header[4],*rowlengths = 0,M,N,m,*rowners,*cols; 3278 PetscInt *locrowlens = NULL,*procsnz = NULL,*browners = NULL; 3279 PetscInt jj,*mycols,*ibuf,bs=1,Mbs,mbs,extra_rows,mmax; 3280 PetscMPIInt tag = ((PetscObject)viewer)->tag; 3281 PetscInt *dlens = NULL,*odlens = NULL,*mask = NULL,*masked1 = NULL,*masked2 = NULL,rowcount,odcount; 3282 PetscInt dcount,kmax,k,nzcount,tmp,mend,sizesset=1,grows,gcols; 3283 3284 PetscFunctionBegin; 3285 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 3286 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MPIBAIJ matrix 2","Mat");CHKERRQ(ierr); 3287 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 3288 ierr = PetscOptionsEnd();CHKERRQ(ierr); 3289 3290 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3291 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3292 if (!rank) { 3293 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 3294 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 3295 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 3296 } 3297 3298 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) sizesset = 0; 3299 3300 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 3301 M = header[1]; N = header[2]; 3302 3303 /* If global rows/cols are set to PETSC_DECIDE, set it to the sizes given in the file */ 3304 if (sizesset && newmat->rmap->N < 0) newmat->rmap->N = M; 3305 if (sizesset && newmat->cmap->N < 0) newmat->cmap->N = N; 3306 3307 /* If global sizes are set, check if they are consistent with that given in the file */ 3308 if (sizesset) { 3309 ierr = MatGetSize(newmat,&grows,&gcols);CHKERRQ(ierr); 3310 } 3311 if (sizesset && newmat->rmap->N != grows) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows:Matrix in file has (%d) and input matrix has (%d)",M,grows); 3312 if (sizesset && newmat->cmap->N != gcols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of cols:Matrix in file has (%d) and input matrix has (%d)",N,gcols); 3313 3314 if (M != N) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Can only do square matrices"); 3315 3316 /* 3317 This code adds extra rows to make sure the number of rows is 3318 divisible by the blocksize 3319 */ 3320 Mbs = M/bs; 3321 extra_rows = bs - M + bs*Mbs; 3322 if (extra_rows == bs) extra_rows = 0; 3323 else Mbs++; 3324 if (extra_rows && !rank) { 3325 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 3326 } 3327 3328 /* determine ownership of all rows */ 3329 if (newmat->rmap->n < 0) { /* PETSC_DECIDE */ 3330 mbs = Mbs/size + ((Mbs % size) > rank); 3331 m = mbs*bs; 3332 } else { /* User set */ 3333 m = newmat->rmap->n; 3334 mbs = m/bs; 3335 } 3336 ierr = PetscMalloc2(size+1,PetscInt,&rowners,size+1,PetscInt,&browners);CHKERRQ(ierr); 3337 ierr = MPI_Allgather(&mbs,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 3338 3339 /* process 0 needs enough room for process with most rows */ 3340 if (!rank) { 3341 mmax = rowners[1]; 3342 for (i=2; i<=size; i++) { 3343 mmax = PetscMax(mmax,rowners[i]); 3344 } 3345 mmax*=bs; 3346 } else mmax = -1; /* unused, but compiler warns anyway */ 3347 3348 rowners[0] = 0; 3349 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 3350 for (i=0; i<=size; i++) browners[i] = rowners[i]*bs; 3351 rstart = rowners[rank]; 3352 rend = rowners[rank+1]; 3353 3354 /* distribute row lengths to all processors */ 3355 ierr = PetscMalloc(m*sizeof(PetscInt),&locrowlens);CHKERRQ(ierr); 3356 if (!rank) { 3357 mend = m; 3358 if (size == 1) mend = mend - extra_rows; 3359 ierr = PetscBinaryRead(fd,locrowlens,mend,PETSC_INT);CHKERRQ(ierr); 3360 for (j=mend; j<m; j++) locrowlens[j] = 1; 3361 ierr = PetscMalloc(mmax*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 3362 ierr = PetscMalloc(size*sizeof(PetscInt),&procsnz);CHKERRQ(ierr); 3363 ierr = PetscMemzero(procsnz,size*sizeof(PetscInt));CHKERRQ(ierr); 3364 for (j=0; j<m; j++) { 3365 procsnz[0] += locrowlens[j]; 3366 } 3367 for (i=1; i<size; i++) { 3368 mend = browners[i+1] - browners[i]; 3369 if (i == size-1) mend = mend - extra_rows; 3370 ierr = PetscBinaryRead(fd,rowlengths,mend,PETSC_INT);CHKERRQ(ierr); 3371 for (j=mend; j<browners[i+1] - browners[i]; j++) rowlengths[j] = 1; 3372 /* calculate the number of nonzeros on each processor */ 3373 for (j=0; j<browners[i+1]-browners[i]; j++) { 3374 procsnz[i] += rowlengths[j]; 3375 } 3376 ierr = MPI_Send(rowlengths,browners[i+1]-browners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3377 } 3378 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 3379 } else { 3380 ierr = MPI_Recv(locrowlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 3381 } 3382 3383 if (!rank) { 3384 /* determine max buffer needed and allocate it */ 3385 maxnz = procsnz[0]; 3386 for (i=1; i<size; i++) { 3387 maxnz = PetscMax(maxnz,procsnz[i]); 3388 } 3389 ierr = PetscMalloc(maxnz*sizeof(PetscInt),&cols);CHKERRQ(ierr); 3390 3391 /* read in my part of the matrix column indices */ 3392 nz = procsnz[0]; 3393 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&ibuf);CHKERRQ(ierr); 3394 mycols = ibuf; 3395 if (size == 1) nz -= extra_rows; 3396 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 3397 if (size == 1) { 3398 for (i=0; i< extra_rows; i++) mycols[nz+i] = M+i; 3399 } 3400 3401 /* read in every ones (except the last) and ship off */ 3402 for (i=1; i<size-1; i++) { 3403 nz = procsnz[i]; 3404 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 3405 ierr = MPI_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3406 } 3407 /* read in the stuff for the last proc */ 3408 if (size != 1) { 3409 nz = procsnz[size-1] - extra_rows; /* the extra rows are not on the disk */ 3410 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 3411 for (i=0; i<extra_rows; i++) cols[nz+i] = M+i; 3412 ierr = MPI_Send(cols,nz+extra_rows,MPIU_INT,size-1,tag,comm);CHKERRQ(ierr); 3413 } 3414 ierr = PetscFree(cols);CHKERRQ(ierr); 3415 } else { 3416 /* determine buffer space needed for message */ 3417 nz = 0; 3418 for (i=0; i<m; i++) { 3419 nz += locrowlens[i]; 3420 } 3421 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&ibuf);CHKERRQ(ierr); 3422 mycols = ibuf; 3423 /* receive message of column indices*/ 3424 ierr = MPI_Recv(mycols,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 3425 ierr = MPI_Get_count(&status,MPIU_INT,&maxnz);CHKERRQ(ierr); 3426 if (maxnz != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"something is wrong with file"); 3427 } 3428 3429 /* loop over local rows, determining number of off diagonal entries */ 3430 ierr = PetscMalloc2(rend-rstart,PetscInt,&dlens,rend-rstart,PetscInt,&odlens);CHKERRQ(ierr); 3431 ierr = PetscMalloc3(Mbs,PetscInt,&mask,Mbs,PetscInt,&masked1,Mbs,PetscInt,&masked2);CHKERRQ(ierr); 3432 ierr = PetscMemzero(mask,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3433 ierr = PetscMemzero(masked1,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3434 ierr = PetscMemzero(masked2,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3435 rowcount = 0; nzcount = 0; 3436 for (i=0; i<mbs; i++) { 3437 dcount = 0; 3438 odcount = 0; 3439 for (j=0; j<bs; j++) { 3440 kmax = locrowlens[rowcount]; 3441 for (k=0; k<kmax; k++) { 3442 tmp = mycols[nzcount++]/bs; 3443 if (!mask[tmp]) { 3444 mask[tmp] = 1; 3445 if (tmp < rstart || tmp >= rend) masked2[odcount++] = tmp; 3446 else masked1[dcount++] = tmp; 3447 } 3448 } 3449 rowcount++; 3450 } 3451 3452 dlens[i] = dcount; 3453 odlens[i] = odcount; 3454 3455 /* zero out the mask elements we set */ 3456 for (j=0; j<dcount; j++) mask[masked1[j]] = 0; 3457 for (j=0; j<odcount; j++) mask[masked2[j]] = 0; 3458 } 3459 3460 3461 if (!sizesset) { 3462 ierr = MatSetSizes(newmat,m,m,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 3463 } 3464 ierr = MatMPIBAIJSetPreallocation(newmat,bs,0,dlens,0,odlens);CHKERRQ(ierr); 3465 3466 if (!rank) { 3467 ierr = PetscMalloc((maxnz+1)*sizeof(PetscScalar),&buf);CHKERRQ(ierr); 3468 /* read in my part of the matrix numerical values */ 3469 nz = procsnz[0]; 3470 vals = buf; 3471 mycols = ibuf; 3472 if (size == 1) nz -= extra_rows; 3473 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3474 if (size == 1) { 3475 for (i=0; i< extra_rows; i++) vals[nz+i] = 1.0; 3476 } 3477 3478 /* insert into matrix */ 3479 jj = rstart*bs; 3480 for (i=0; i<m; i++) { 3481 ierr = MatSetValues_MPIBAIJ(newmat,1,&jj,locrowlens[i],mycols,vals,INSERT_VALUES);CHKERRQ(ierr); 3482 mycols += locrowlens[i]; 3483 vals += locrowlens[i]; 3484 jj++; 3485 } 3486 /* read in other processors (except the last one) and ship out */ 3487 for (i=1; i<size-1; i++) { 3488 nz = procsnz[i]; 3489 vals = buf; 3490 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3491 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newmat)->tag,comm);CHKERRQ(ierr); 3492 } 3493 /* the last proc */ 3494 if (size != 1) { 3495 nz = procsnz[i] - extra_rows; 3496 vals = buf; 3497 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3498 for (i=0; i<extra_rows; i++) vals[nz+i] = 1.0; 3499 ierr = MPIULong_Send(vals,nz+extra_rows,MPIU_SCALAR,size-1,((PetscObject)newmat)->tag,comm);CHKERRQ(ierr); 3500 } 3501 ierr = PetscFree(procsnz);CHKERRQ(ierr); 3502 } else { 3503 /* receive numeric values */ 3504 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&buf);CHKERRQ(ierr); 3505 3506 /* receive message of values*/ 3507 vals = buf; 3508 mycols = ibuf; 3509 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newmat)->tag,comm);CHKERRQ(ierr); 3510 3511 /* insert into matrix */ 3512 jj = rstart*bs; 3513 for (i=0; i<m; i++) { 3514 ierr = MatSetValues_MPIBAIJ(newmat,1,&jj,locrowlens[i],mycols,vals,INSERT_VALUES);CHKERRQ(ierr); 3515 mycols += locrowlens[i]; 3516 vals += locrowlens[i]; 3517 jj++; 3518 } 3519 } 3520 ierr = PetscFree(locrowlens);CHKERRQ(ierr); 3521 ierr = PetscFree(buf);CHKERRQ(ierr); 3522 ierr = PetscFree(ibuf);CHKERRQ(ierr); 3523 ierr = PetscFree2(rowners,browners);CHKERRQ(ierr); 3524 ierr = PetscFree2(dlens,odlens);CHKERRQ(ierr); 3525 ierr = PetscFree3(mask,masked1,masked2);CHKERRQ(ierr); 3526 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3527 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3528 PetscFunctionReturn(0); 3529 } 3530 3531 #undef __FUNCT__ 3532 #define __FUNCT__ "MatMPIBAIJSetHashTableFactor" 3533 /*@ 3534 MatMPIBAIJSetHashTableFactor - Sets the factor required to compute the size of the HashTable. 3535 3536 Input Parameters: 3537 . mat - the matrix 3538 . fact - factor 3539 3540 Not Collective, each process can use a different factor 3541 3542 Level: advanced 3543 3544 Notes: 3545 This can also be set by the command line option: -mat_use_hash_table <fact> 3546 3547 .keywords: matrix, hashtable, factor, HT 3548 3549 .seealso: MatSetOption() 3550 @*/ 3551 PetscErrorCode MatMPIBAIJSetHashTableFactor(Mat mat,PetscReal fact) 3552 { 3553 PetscErrorCode ierr; 3554 3555 PetscFunctionBegin; 3556 ierr = PetscTryMethod(mat,"MatSetHashTableFactor_C",(Mat,PetscReal),(mat,fact));CHKERRQ(ierr); 3557 PetscFunctionReturn(0); 3558 } 3559 3560 #undef __FUNCT__ 3561 #define __FUNCT__ "MatSetHashTableFactor_MPIBAIJ" 3562 PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat mat,PetscReal fact) 3563 { 3564 Mat_MPIBAIJ *baij; 3565 3566 PetscFunctionBegin; 3567 baij = (Mat_MPIBAIJ*)mat->data; 3568 baij->ht_fact = fact; 3569 PetscFunctionReturn(0); 3570 } 3571 3572 #undef __FUNCT__ 3573 #define __FUNCT__ "MatMPIBAIJGetSeqBAIJ" 3574 PetscErrorCode MatMPIBAIJGetSeqBAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 3575 { 3576 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 3577 3578 PetscFunctionBegin; 3579 *Ad = a->A; 3580 *Ao = a->B; 3581 *colmap = a->garray; 3582 PetscFunctionReturn(0); 3583 } 3584 3585 /* 3586 Special version for direct calls from Fortran (to eliminate two function call overheads 3587 */ 3588 #if defined(PETSC_HAVE_FORTRAN_CAPS) 3589 #define matmpibaijsetvaluesblocked_ MATMPIBAIJSETVALUESBLOCKED 3590 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 3591 #define matmpibaijsetvaluesblocked_ matmpibaijsetvaluesblocked 3592 #endif 3593 3594 #undef __FUNCT__ 3595 #define __FUNCT__ "matmpibiajsetvaluesblocked" 3596 /*@C 3597 MatMPIBAIJSetValuesBlocked - Direct Fortran call to replace call to MatSetValuesBlocked() 3598 3599 Collective on Mat 3600 3601 Input Parameters: 3602 + mat - the matrix 3603 . min - number of input rows 3604 . im - input rows 3605 . nin - number of input columns 3606 . in - input columns 3607 . v - numerical values input 3608 - addvin - INSERT_VALUES or ADD_VALUES 3609 3610 Notes: This has a complete copy of MatSetValuesBlocked_MPIBAIJ() which is terrible code un-reuse. 3611 3612 Level: advanced 3613 3614 .seealso: MatSetValuesBlocked() 3615 @*/ 3616 PetscErrorCode matmpibaijsetvaluesblocked_(Mat *matin,PetscInt *min,const PetscInt im[],PetscInt *nin,const PetscInt in[],const MatScalar v[],InsertMode *addvin) 3617 { 3618 /* convert input arguments to C version */ 3619 Mat mat = *matin; 3620 PetscInt m = *min, n = *nin; 3621 InsertMode addv = *addvin; 3622 3623 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 3624 const MatScalar *value; 3625 MatScalar *barray = baij->barray; 3626 PetscBool roworiented = baij->roworiented; 3627 PetscErrorCode ierr; 3628 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 3629 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 3630 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 3631 3632 PetscFunctionBegin; 3633 /* tasks normally handled by MatSetValuesBlocked() */ 3634 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 3635 #if defined(PETSC_USE_DEBUG) 3636 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 3637 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 3638 #endif 3639 if (mat->assembled) { 3640 mat->was_assembled = PETSC_TRUE; 3641 mat->assembled = PETSC_FALSE; 3642 } 3643 ierr = PetscLogEventBegin(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3644 3645 3646 if (!barray) { 3647 ierr = PetscMalloc(bs2*sizeof(MatScalar),&barray);CHKERRQ(ierr); 3648 baij->barray = barray; 3649 } 3650 3651 if (roworiented) stepval = (n-1)*bs; 3652 else stepval = (m-1)*bs; 3653 3654 for (i=0; i<m; i++) { 3655 if (im[i] < 0) continue; 3656 #if defined(PETSC_USE_DEBUG) 3657 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); 3658 #endif 3659 if (im[i] >= rstart && im[i] < rend) { 3660 row = im[i] - rstart; 3661 for (j=0; j<n; j++) { 3662 /* If NumCol = 1 then a copy is not required */ 3663 if ((roworiented) && (n == 1)) { 3664 barray = (MatScalar*)v + i*bs2; 3665 } else if ((!roworiented) && (m == 1)) { 3666 barray = (MatScalar*)v + j*bs2; 3667 } else { /* Here a copy is required */ 3668 if (roworiented) { 3669 value = v + i*(stepval+bs)*bs + j*bs; 3670 } else { 3671 value = v + j*(stepval+bs)*bs + i*bs; 3672 } 3673 for (ii=0; ii<bs; ii++,value+=stepval) { 3674 for (jj=0; jj<bs; jj++) { 3675 *barray++ = *value++; 3676 } 3677 } 3678 barray -=bs2; 3679 } 3680 3681 if (in[j] >= cstart && in[j] < cend) { 3682 col = in[j] - cstart; 3683 ierr = MatSetValuesBlocked_SeqBAIJ(baij->A,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 3684 } else if (in[j] < 0) continue; 3685 #if defined(PETSC_USE_DEBUG) 3686 else if (in[j] >= baij->Nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large, col %D max %D",in[j],baij->Nbs-1); 3687 #endif 3688 else { 3689 if (mat->was_assembled) { 3690 if (!baij->colmap) { 3691 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 3692 } 3693 3694 #if defined(PETSC_USE_DEBUG) 3695 #if defined(PETSC_USE_CTABLE) 3696 { PetscInt data; 3697 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 3698 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3699 } 3700 #else 3701 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 3702 #endif 3703 #endif 3704 #if defined(PETSC_USE_CTABLE) 3705 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 3706 col = (col - 1)/bs; 3707 #else 3708 col = (baij->colmap[in[j]] - 1)/bs; 3709 #endif 3710 if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 3711 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 3712 col = in[j]; 3713 } 3714 } else col = in[j]; 3715 ierr = MatSetValuesBlocked_SeqBAIJ(baij->B,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 3716 } 3717 } 3718 } else { 3719 if (!baij->donotstash) { 3720 if (roworiented) { 3721 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3722 } else { 3723 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 3724 } 3725 } 3726 } 3727 } 3728 3729 /* task normally handled by MatSetValuesBlocked() */ 3730 ierr = PetscLogEventEnd(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 3731 PetscFunctionReturn(0); 3732 } 3733 3734 #undef __FUNCT__ 3735 #define __FUNCT__ "MatCreateMPIBAIJWithArrays" 3736 /*@ 3737 MatCreateMPIBAIJWithArrays - creates a MPI BAIJ matrix using arrays that contain in standard 3738 CSR format the local rows. 3739 3740 Collective on MPI_Comm 3741 3742 Input Parameters: 3743 + comm - MPI communicator 3744 . bs - the block size, only a block size of 1 is supported 3745 . m - number of local rows (Cannot be PETSC_DECIDE) 3746 . n - This value should be the same as the local size used in creating the 3747 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3748 calculated if N is given) For square matrices n is almost always m. 3749 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3750 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3751 . i - row indices 3752 . j - column indices 3753 - a - matrix values 3754 3755 Output Parameter: 3756 . mat - the matrix 3757 3758 Level: intermediate 3759 3760 Notes: 3761 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3762 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3763 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3764 3765 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3766 3767 .keywords: matrix, aij, compressed row, sparse, parallel 3768 3769 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3770 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3771 @*/ 3772 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) 3773 { 3774 PetscErrorCode ierr; 3775 3776 PetscFunctionBegin; 3777 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3778 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3779 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3780 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3781 ierr = MatSetType(*mat,MATMPISBAIJ);CHKERRQ(ierr); 3782 ierr = MatMPIBAIJSetPreallocationCSR(*mat,bs,i,j,a);CHKERRQ(ierr); 3783 PetscFunctionReturn(0); 3784 } 3785