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++) {if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart;} 29 } 30 31 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 32 if (idx) {ierr = PetscMalloc(A->rmap->n*sizeof(PetscInt),&idxb);CHKERRQ(ierr);} 33 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 34 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 35 36 for (i=0; i<A->rmap->n; i++){ 37 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) {va[i] = vb[i]; if (idx) idx[i] = A->cmap->bs*a->garray[idxb[i]/A->cmap->bs] + (idxb[i] % A->cmap->bs);} 38 } 39 40 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 41 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 42 ierr = PetscFree(idxb);CHKERRQ(ierr); 43 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 44 PetscFunctionReturn(0); 45 } 46 47 EXTERN_C_BEGIN 48 #undef __FUNCT__ 49 #define __FUNCT__ "MatStoreValues_MPIBAIJ" 50 PetscErrorCode MatStoreValues_MPIBAIJ(Mat mat) 51 { 52 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ *)mat->data; 53 PetscErrorCode ierr; 54 55 PetscFunctionBegin; 56 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 57 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 58 PetscFunctionReturn(0); 59 } 60 EXTERN_C_END 61 62 EXTERN_C_BEGIN 63 #undef __FUNCT__ 64 #define __FUNCT__ "MatRetrieveValues_MPIBAIJ" 65 PetscErrorCode MatRetrieveValues_MPIBAIJ(Mat mat) 66 { 67 Mat_MPIBAIJ *aij = (Mat_MPIBAIJ *)mat->data; 68 PetscErrorCode ierr; 69 70 PetscFunctionBegin; 71 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 72 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 73 PetscFunctionReturn(0); 74 } 75 EXTERN_C_END 76 77 /* 78 Local utility routine that creates a mapping from the global column 79 number to the local number in the off-diagonal part of the local 80 storage of the matrix. This is done in a non scalable way since the 81 length of colmap equals the global matrix length. 82 */ 83 #undef __FUNCT__ 84 #define __FUNCT__ "MatCreateColmap_MPIBAIJ_Private" 85 PetscErrorCode MatCreateColmap_MPIBAIJ_Private(Mat mat) 86 { 87 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 88 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 89 PetscErrorCode ierr; 90 PetscInt nbs = B->nbs,i,bs=mat->rmap->bs; 91 92 PetscFunctionBegin; 93 #if defined (PETSC_USE_CTABLE) 94 ierr = PetscTableCreate(baij->nbs,baij->Nbs+1,&baij->colmap);CHKERRQ(ierr); 95 for (i=0; i<nbs; i++){ 96 ierr = PetscTableAdd(baij->colmap,baij->garray[i]+1,i*bs+1,INSERT_VALUES);CHKERRQ(ierr); 97 } 98 #else 99 ierr = PetscMalloc((baij->Nbs+1)*sizeof(PetscInt),&baij->colmap);CHKERRQ(ierr); 100 ierr = PetscLogObjectMemory(mat,baij->Nbs*sizeof(PetscInt));CHKERRQ(ierr); 101 ierr = PetscMemzero(baij->colmap,baij->Nbs*sizeof(PetscInt));CHKERRQ(ierr); 102 for (i=0; i<nbs; i++) baij->colmap[baij->garray[i]] = i*bs+1; 103 #endif 104 PetscFunctionReturn(0); 105 } 106 107 #define MatSetValues_SeqBAIJ_A_Private(row,col,value,addv) \ 108 { \ 109 \ 110 brow = row/bs; \ 111 rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; \ 112 rmax = aimax[brow]; nrow = ailen[brow]; \ 113 bcol = col/bs; \ 114 ridx = row % bs; cidx = col % bs; \ 115 low = 0; high = nrow; \ 116 while (high-low > 3) { \ 117 t = (low+high)/2; \ 118 if (rp[t] > bcol) high = t; \ 119 else low = t; \ 120 } \ 121 for (_i=low; _i<high; _i++) { \ 122 if (rp[_i] > bcol) break; \ 123 if (rp[_i] == bcol) { \ 124 bap = ap + bs2*_i + bs*cidx + ridx; \ 125 if (addv == ADD_VALUES) *bap += value; \ 126 else *bap = value; \ 127 goto a_noinsert; \ 128 } \ 129 } \ 130 if (a->nonew == 1) goto a_noinsert; \ 131 if (a->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 132 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,aimax,a->nonew,MatScalar); \ 133 N = nrow++ - 1; \ 134 /* shift up all the later entries in this row */ \ 135 for (ii=N; ii>=_i; ii--) { \ 136 rp[ii+1] = rp[ii]; \ 137 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); \ 138 } \ 139 if (N>=_i) { ierr = PetscMemzero(ap+bs2*_i,bs2*sizeof(MatScalar));CHKERRQ(ierr); } \ 140 rp[_i] = bcol; \ 141 ap[bs2*_i + bs*cidx + ridx] = value; \ 142 a_noinsert:; \ 143 ailen[brow] = nrow; \ 144 } 145 146 #define MatSetValues_SeqBAIJ_B_Private(row,col,value,addv) \ 147 { \ 148 brow = row/bs; \ 149 rp = bj + bi[brow]; ap = ba + bs2*bi[brow]; \ 150 rmax = bimax[brow]; nrow = bilen[brow]; \ 151 bcol = col/bs; \ 152 ridx = row % bs; cidx = col % bs; \ 153 low = 0; high = nrow; \ 154 while (high-low > 3) { \ 155 t = (low+high)/2; \ 156 if (rp[t] > bcol) high = t; \ 157 else low = t; \ 158 } \ 159 for (_i=low; _i<high; _i++) { \ 160 if (rp[_i] > bcol) break; \ 161 if (rp[_i] == bcol) { \ 162 bap = ap + bs2*_i + bs*cidx + ridx; \ 163 if (addv == ADD_VALUES) *bap += value; \ 164 else *bap = value; \ 165 goto b_noinsert; \ 166 } \ 167 } \ 168 if (b->nonew == 1) goto b_noinsert; \ 169 if (b->nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) into matrix", row, col); \ 170 MatSeqXAIJReallocateAIJ(B,b->mbs,bs2,nrow,brow,bcol,rmax,ba,bi,bj,rp,ap,bimax,b->nonew,MatScalar); \ 171 CHKMEMQ;\ 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]; else value = v[i+j*m]; 226 MatSetValues_SeqBAIJ_A_Private(row,col,value,addv); 227 /* ierr = MatSetValues_SeqBAIJ(baij->A,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ 228 } else if (in[j] < 0) continue; 229 #if defined(PETSC_USE_DEBUG) 230 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); 231 #endif 232 else { 233 if (mat->was_assembled) { 234 if (!baij->colmap) { 235 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 236 } 237 #if defined (PETSC_USE_CTABLE) 238 ierr = PetscTableFind(baij->colmap,in[j]/bs + 1,&col);CHKERRQ(ierr); 239 col = col - 1; 240 #else 241 col = baij->colmap[in[j]/bs] - 1; 242 #endif 243 if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 244 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 245 col = in[j]; 246 /* Reinitialize the variables required by MatSetValues_SeqBAIJ_B_Private() */ 247 B = baij->B; 248 b = (Mat_SeqBAIJ*)(B)->data; 249 bimax=b->imax;bi=b->i;bilen=b->ilen;bj=b->j; 250 ba=b->a; 251 } else col += in[j]%bs; 252 } else col = in[j]; 253 if (roworiented) value = v[i*n+j]; else value = v[i+j*m]; 254 MatSetValues_SeqBAIJ_B_Private(row,col,value,addv); 255 /* ierr = MatSetValues_SeqBAIJ(baij->B,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ 256 } 257 } 258 } else { 259 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]); 260 if (!baij->donotstash) { 261 mat->assembled = PETSC_FALSE; 262 if (roworiented) { 263 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 264 } else { 265 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 266 } 267 } 268 } 269 } 270 PetscFunctionReturn(0); 271 } 272 273 #undef __FUNCT__ 274 #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ" 275 PetscErrorCode MatSetValuesBlocked_MPIBAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 276 { 277 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 278 const PetscScalar *value; 279 MatScalar *barray=baij->barray; 280 PetscBool roworiented = baij->roworiented; 281 PetscErrorCode ierr; 282 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 283 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 284 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 285 286 PetscFunctionBegin; 287 if(!barray) { 288 ierr = PetscMalloc(bs2*sizeof(MatScalar),&barray);CHKERRQ(ierr); 289 baij->barray = barray; 290 } 291 292 if (roworiented) { 293 stepval = (n-1)*bs; 294 } else { 295 stepval = (m-1)*bs; 296 } 297 for (i=0; i<m; i++) { 298 if (im[i] < 0) continue; 299 #if defined(PETSC_USE_DEBUG) 300 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); 301 #endif 302 if (im[i] >= rstart && im[i] < rend) { 303 row = im[i] - rstart; 304 for (j=0; j<n; j++) { 305 /* If NumCol = 1 then a copy is not required */ 306 if ((roworiented) && (n == 1)) { 307 barray = (MatScalar*)v + i*bs2; 308 } else if((!roworiented) && (m == 1)) { 309 barray = (MatScalar*)v + j*bs2; 310 } else { /* Here a copy is required */ 311 if (roworiented) { 312 value = v + (i*(stepval+bs) + j)*bs; 313 } else { 314 value = v + (j*(stepval+bs) + i)*bs; 315 } 316 for (ii=0; ii<bs; ii++,value+=bs+stepval) { 317 for (jj=0; jj<bs; jj++) { 318 barray[jj] = value[jj]; 319 } 320 barray += bs; 321 } 322 barray -= bs2; 323 } 324 325 if (in[j] >= cstart && in[j] < cend){ 326 col = in[j] - cstart; 327 ierr = MatSetValuesBlocked_SeqBAIJ(baij->A,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 328 } 329 else if (in[j] < 0) continue; 330 #if defined(PETSC_USE_DEBUG) 331 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); 332 #endif 333 else { 334 if (mat->was_assembled) { 335 if (!baij->colmap) { 336 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 337 } 338 339 #if defined(PETSC_USE_DEBUG) 340 #if defined (PETSC_USE_CTABLE) 341 { PetscInt data; 342 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 343 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 344 } 345 #else 346 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 347 #endif 348 #endif 349 #if defined (PETSC_USE_CTABLE) 350 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 351 col = (col - 1)/bs; 352 #else 353 col = (baij->colmap[in[j]] - 1)/bs; 354 #endif 355 if (col < 0 && !((Mat_SeqBAIJ*)(baij->B->data))->nonew) { 356 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 357 col = in[j]; 358 } 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]); 359 } 360 else col = in[j]; 361 ierr = MatSetValuesBlocked_SeqBAIJ(baij->B,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 362 } 363 } 364 } else { 365 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]); 366 if (!baij->donotstash) { 367 if (roworiented) { 368 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 369 } else { 370 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 371 } 372 } 373 } 374 } 375 PetscFunctionReturn(0); 376 } 377 378 #define HASH_KEY 0.6180339887 379 #define HASH(size,key,tmp) (tmp = (key)*HASH_KEY,(PetscInt)((size)*(tmp-(PetscInt)tmp))) 380 /* #define HASH(size,key) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 381 /* #define HASH(size,key,tmp) ((PetscInt)((size)*fmod(((key)*HASH_KEY),1))) */ 382 #undef __FUNCT__ 383 #define __FUNCT__ "MatSetValues_MPIBAIJ_HT" 384 PetscErrorCode MatSetValues_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 385 { 386 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 387 PetscBool roworiented = baij->roworiented; 388 PetscErrorCode ierr; 389 PetscInt i,j,row,col; 390 PetscInt rstart_orig=mat->rmap->rstart; 391 PetscInt rend_orig=mat->rmap->rend,Nbs=baij->Nbs; 392 PetscInt h1,key,size=baij->ht_size,bs=mat->rmap->bs,*HT=baij->ht,idx; 393 PetscReal tmp; 394 MatScalar **HD = baij->hd,value; 395 #if defined(PETSC_USE_DEBUG) 396 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 397 #endif 398 399 PetscFunctionBegin; 400 if (v) PetscValidScalarPointer(v,6); 401 for (i=0; i<m; i++) { 402 #if defined(PETSC_USE_DEBUG) 403 if (im[i] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row"); 404 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); 405 #endif 406 row = im[i]; 407 if (row >= rstart_orig && row < rend_orig) { 408 for (j=0; j<n; j++) { 409 col = in[j]; 410 if (roworiented) value = v[i*n+j]; else value = v[i+j*m]; 411 /* Look up PetscInto the Hash Table */ 412 key = (row/bs)*Nbs+(col/bs)+1; 413 h1 = HASH(size,key,tmp); 414 415 416 idx = h1; 417 #if defined(PETSC_USE_DEBUG) 418 insert_ct++; 419 total_ct++; 420 if (HT[idx] != key) { 421 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++); 422 if (idx == size) { 423 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++); 424 if (idx == h1) { 425 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 426 } 427 } 428 } 429 #else 430 if (HT[idx] != key) { 431 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++); 432 if (idx == size) { 433 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++); 434 if (idx == h1) { 435 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 436 } 437 } 438 } 439 #endif 440 /* A HASH table entry is found, so insert the values at the correct address */ 441 if (addv == ADD_VALUES) *(HD[idx]+ (col % bs)*bs + (row % bs)) += value; 442 else *(HD[idx]+ (col % bs)*bs + (row % bs)) = value; 443 } 444 } else { 445 if (!baij->donotstash) { 446 if (roworiented) { 447 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,PETSC_FALSE);CHKERRQ(ierr); 448 } else { 449 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,PETSC_FALSE);CHKERRQ(ierr); 450 } 451 } 452 } 453 } 454 #if defined(PETSC_USE_DEBUG) 455 baij->ht_total_ct = total_ct; 456 baij->ht_insert_ct = insert_ct; 457 #endif 458 PetscFunctionReturn(0); 459 } 460 461 #undef __FUNCT__ 462 #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ_HT" 463 PetscErrorCode MatSetValuesBlocked_MPIBAIJ_HT(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 464 { 465 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 466 PetscBool roworiented = baij->roworiented; 467 PetscErrorCode ierr; 468 PetscInt i,j,ii,jj,row,col; 469 PetscInt rstart=baij->rstartbs; 470 PetscInt rend=mat->rmap->rend,stepval,bs=mat->rmap->bs,bs2=baij->bs2,nbs2=n*bs2; 471 PetscInt h1,key,size=baij->ht_size,idx,*HT=baij->ht,Nbs=baij->Nbs; 472 PetscReal tmp; 473 MatScalar **HD = baij->hd,*baij_a; 474 const PetscScalar *v_t,*value; 475 #if defined(PETSC_USE_DEBUG) 476 PetscInt total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; 477 #endif 478 479 PetscFunctionBegin; 480 481 if (roworiented) { 482 stepval = (n-1)*bs; 483 } else { 484 stepval = (m-1)*bs; 485 } 486 for (i=0; i<m; i++) { 487 #if defined(PETSC_USE_DEBUG) 488 if (im[i] < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",im[i]); 489 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); 490 #endif 491 row = im[i]; 492 v_t = v + i*nbs2; 493 if (row >= rstart && row < rend) { 494 for (j=0; j<n; j++) { 495 col = in[j]; 496 497 /* Look up into the Hash Table */ 498 key = row*Nbs+col+1; 499 h1 = HASH(size,key,tmp); 500 501 idx = h1; 502 #if defined(PETSC_USE_DEBUG) 503 total_ct++; 504 insert_ct++; 505 if (HT[idx] != key) { 506 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++,total_ct++); 507 if (idx == size) { 508 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++,total_ct++); 509 if (idx == h1) { 510 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 511 } 512 } 513 } 514 #else 515 if (HT[idx] != key) { 516 for (idx=h1; (idx<size) && (HT[idx]!=key); idx++); 517 if (idx == size) { 518 for (idx=0; (idx<h1) && (HT[idx]!=key); idx++); 519 if (idx == h1) { 520 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"(%D,%D) has no entry in the hash table", row, col); 521 } 522 } 523 } 524 #endif 525 baij_a = HD[idx]; 526 if (roworiented) { 527 /*value = v + i*(stepval+bs)*bs + j*bs;*/ 528 /* value = v + (i*(stepval+bs)+j)*bs; */ 529 value = v_t; 530 v_t += bs; 531 if (addv == ADD_VALUES) { 532 for (ii=0; ii<bs; ii++,value+=stepval) { 533 for (jj=ii; jj<bs2; jj+=bs) { 534 baij_a[jj] += *value++; 535 } 536 } 537 } else { 538 for (ii=0; ii<bs; ii++,value+=stepval) { 539 for (jj=ii; jj<bs2; jj+=bs) { 540 baij_a[jj] = *value++; 541 } 542 } 543 } 544 } else { 545 value = v + j*(stepval+bs)*bs + i*bs; 546 if (addv == ADD_VALUES) { 547 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 548 for (jj=0; jj<bs; jj++) { 549 baij_a[jj] += *value++; 550 } 551 } 552 } else { 553 for (ii=0; ii<bs; ii++,value+=stepval,baij_a+=bs) { 554 for (jj=0; jj<bs; jj++) { 555 baij_a[jj] = *value++; 556 } 557 } 558 } 559 } 560 } 561 } else { 562 if (!baij->donotstash) { 563 if (roworiented) { 564 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 565 } else { 566 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 567 } 568 } 569 } 570 } 571 #if defined(PETSC_USE_DEBUG) 572 baij->ht_total_ct = total_ct; 573 baij->ht_insert_ct = insert_ct; 574 #endif 575 PetscFunctionReturn(0); 576 } 577 578 #undef __FUNCT__ 579 #define __FUNCT__ "MatGetValues_MPIBAIJ" 580 PetscErrorCode MatGetValues_MPIBAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 581 { 582 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 583 PetscErrorCode ierr; 584 PetscInt bs=mat->rmap->bs,i,j,bsrstart = mat->rmap->rstart,bsrend = mat->rmap->rend; 585 PetscInt bscstart = mat->cmap->rstart,bscend = mat->cmap->rend,row,col,data; 586 587 PetscFunctionBegin; 588 for (i=0; i<m; i++) { 589 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 590 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); 591 if (idxm[i] >= bsrstart && idxm[i] < bsrend) { 592 row = idxm[i] - bsrstart; 593 for (j=0; j<n; j++) { 594 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 595 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); 596 if (idxn[j] >= bscstart && idxn[j] < bscend){ 597 col = idxn[j] - bscstart; 598 ierr = MatGetValues_SeqBAIJ(baij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 599 } else { 600 if (!baij->colmap) { 601 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 602 } 603 #if defined (PETSC_USE_CTABLE) 604 ierr = PetscTableFind(baij->colmap,idxn[j]/bs+1,&data);CHKERRQ(ierr); 605 data --; 606 #else 607 data = baij->colmap[idxn[j]/bs]-1; 608 #endif 609 if((data < 0) || (baij->garray[data/bs] != idxn[j]/bs)) *(v+i*n+j) = 0.0; 610 else { 611 col = data + idxn[j]%bs; 612 ierr = MatGetValues_SeqBAIJ(baij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 613 } 614 } 615 } 616 } else { 617 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 618 } 619 } 620 PetscFunctionReturn(0); 621 } 622 623 #undef __FUNCT__ 624 #define __FUNCT__ "MatNorm_MPIBAIJ" 625 PetscErrorCode MatNorm_MPIBAIJ(Mat mat,NormType type,PetscReal *nrm) 626 { 627 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 628 Mat_SeqBAIJ *amat = (Mat_SeqBAIJ*)baij->A->data,*bmat = (Mat_SeqBAIJ*)baij->B->data; 629 PetscErrorCode ierr; 630 PetscInt i,j,bs2=baij->bs2,bs=baij->A->rmap->bs,nz,row,col; 631 PetscReal sum = 0.0; 632 MatScalar *v; 633 634 PetscFunctionBegin; 635 if (baij->size == 1) { 636 ierr = MatNorm(baij->A,type,nrm);CHKERRQ(ierr); 637 } else { 638 if (type == NORM_FROBENIUS) { 639 v = amat->a; 640 nz = amat->nz*bs2; 641 for (i=0; i<nz; i++) { 642 #if defined(PETSC_USE_COMPLEX) 643 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 644 #else 645 sum += (*v)*(*v); v++; 646 #endif 647 } 648 v = bmat->a; 649 nz = bmat->nz*bs2; 650 for (i=0; i<nz; i++) { 651 #if defined(PETSC_USE_COMPLEX) 652 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 653 #else 654 sum += (*v)*(*v); v++; 655 #endif 656 } 657 ierr = MPI_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_SUM,((PetscObject)mat)->comm);CHKERRQ(ierr); 658 *nrm = PetscSqrtReal(*nrm); 659 } else if (type == NORM_1) { /* max column sum */ 660 PetscReal *tmp,*tmp2; 661 PetscInt *jj,*garray=baij->garray,cstart=baij->rstartbs; 662 ierr = PetscMalloc2(mat->cmap->N,PetscReal,&tmp,mat->cmap->N,PetscReal,&tmp2);CHKERRQ(ierr); 663 ierr = PetscMemzero(tmp,mat->cmap->N*sizeof(PetscReal));CHKERRQ(ierr); 664 v = amat->a; jj = amat->j; 665 for (i=0; i<amat->nz; i++) { 666 for (j=0; j<bs; j++){ 667 col = bs*(cstart + *jj) + j; /* column index */ 668 for (row=0; row<bs; row++){ 669 tmp[col] += PetscAbsScalar(*v); v++; 670 } 671 } 672 jj++; 673 } 674 v = bmat->a; jj = bmat->j; 675 for (i=0; i<bmat->nz; i++) { 676 for (j=0; j<bs; j++){ 677 col = bs*garray[*jj] + j; 678 for (row=0; row<bs; row++){ 679 tmp[col] += PetscAbsScalar(*v); v++; 680 } 681 } 682 jj++; 683 } 684 ierr = MPI_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,((PetscObject)mat)->comm);CHKERRQ(ierr); 685 *nrm = 0.0; 686 for (j=0; j<mat->cmap->N; j++) { 687 if (tmp2[j] > *nrm) *nrm = tmp2[j]; 688 } 689 ierr = PetscFree2(tmp,tmp2);CHKERRQ(ierr); 690 } else if (type == NORM_INFINITY) { /* max row sum */ 691 PetscReal *sums; 692 ierr = PetscMalloc(bs*sizeof(PetscReal),&sums);CHKERRQ(ierr); 693 sum = 0.0; 694 for (j=0; j<amat->mbs; j++) { 695 for (row=0; row<bs; row++) sums[row] = 0.0; 696 v = amat->a + bs2*amat->i[j]; 697 nz = amat->i[j+1]-amat->i[j]; 698 for (i=0; i<nz; i++) { 699 for (col=0; col<bs; col++){ 700 for (row=0; row<bs; row++){ 701 sums[row] += PetscAbsScalar(*v); v++; 702 } 703 } 704 } 705 v = bmat->a + bs2*bmat->i[j]; 706 nz = bmat->i[j+1]-bmat->i[j]; 707 for (i=0; i<nz; i++) { 708 for (col=0; col<bs; col++){ 709 for (row=0; row<bs; row++){ 710 sums[row] += PetscAbsScalar(*v); v++; 711 } 712 } 713 } 714 for (row=0; row<bs; row++){ 715 if (sums[row] > sum) sum = sums[row]; 716 } 717 } 718 ierr = MPI_Allreduce(&sum,nrm,1,MPIU_REAL,MPIU_MAX,((PetscObject)mat)->comm);CHKERRQ(ierr); 719 ierr = PetscFree(sums);CHKERRQ(ierr); 720 } else SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_SUP,"No support for this norm yet"); 721 } 722 PetscFunctionReturn(0); 723 } 724 725 /* 726 Creates the hash table, and sets the table 727 This table is created only once. 728 If new entried need to be added to the matrix 729 then the hash table has to be destroyed and 730 recreated. 731 */ 732 #undef __FUNCT__ 733 #define __FUNCT__ "MatCreateHashTable_MPIBAIJ_Private" 734 PetscErrorCode MatCreateHashTable_MPIBAIJ_Private(Mat mat,PetscReal factor) 735 { 736 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 737 Mat A = baij->A,B=baij->B; 738 Mat_SeqBAIJ *a=(Mat_SeqBAIJ *)A->data,*b=(Mat_SeqBAIJ *)B->data; 739 PetscInt i,j,k,nz=a->nz+b->nz,h1,*ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j; 740 PetscErrorCode ierr; 741 PetscInt ht_size,bs2=baij->bs2,rstart=baij->rstartbs; 742 PetscInt cstart=baij->cstartbs,*garray=baij->garray,row,col,Nbs=baij->Nbs; 743 PetscInt *HT,key; 744 MatScalar **HD; 745 PetscReal tmp; 746 #if defined(PETSC_USE_INFO) 747 PetscInt ct=0,max=0; 748 #endif 749 750 PetscFunctionBegin; 751 if (baij->ht) PetscFunctionReturn(0); 752 753 baij->ht_size = (PetscInt)(factor*nz); 754 ht_size = baij->ht_size; 755 756 /* Allocate Memory for Hash Table */ 757 ierr = PetscMalloc2(ht_size,MatScalar*,&baij->hd,ht_size,PetscInt,&baij->ht);CHKERRQ(ierr); 758 ierr = PetscMemzero(baij->hd,ht_size*sizeof(MatScalar*));CHKERRQ(ierr); 759 ierr = PetscMemzero(baij->ht,ht_size*sizeof(PetscInt));CHKERRQ(ierr); 760 HD = baij->hd; 761 HT = baij->ht; 762 763 /* Loop Over A */ 764 for (i=0; i<a->mbs; i++) { 765 for (j=ai[i]; j<ai[i+1]; j++) { 766 row = i+rstart; 767 col = aj[j]+cstart; 768 769 key = row*Nbs + col + 1; 770 h1 = HASH(ht_size,key,tmp); 771 for (k=0; k<ht_size; k++){ 772 if (!HT[(h1+k)%ht_size]) { 773 HT[(h1+k)%ht_size] = key; 774 HD[(h1+k)%ht_size] = a->a + j*bs2; 775 break; 776 #if defined(PETSC_USE_INFO) 777 } else { 778 ct++; 779 #endif 780 } 781 } 782 #if defined(PETSC_USE_INFO) 783 if (k> max) max = k; 784 #endif 785 } 786 } 787 /* Loop Over B */ 788 for (i=0; i<b->mbs; i++) { 789 for (j=bi[i]; j<bi[i+1]; j++) { 790 row = i+rstart; 791 col = garray[bj[j]]; 792 key = row*Nbs + col + 1; 793 h1 = HASH(ht_size,key,tmp); 794 for (k=0; k<ht_size; k++){ 795 if (!HT[(h1+k)%ht_size]) { 796 HT[(h1+k)%ht_size] = key; 797 HD[(h1+k)%ht_size] = b->a + j*bs2; 798 break; 799 #if defined(PETSC_USE_INFO) 800 } else { 801 ct++; 802 #endif 803 } 804 } 805 #if defined(PETSC_USE_INFO) 806 if (k> max) max = k; 807 #endif 808 } 809 } 810 811 /* Print Summary */ 812 #if defined(PETSC_USE_INFO) 813 for (i=0,j=0; i<ht_size; i++) { 814 if (HT[i]) {j++;} 815 } 816 ierr = PetscInfo2(mat,"Average Search = %5.2f,max search = %D\n",(!j)? 0.0:((PetscReal)(ct+j))/j,max);CHKERRQ(ierr); 817 #endif 818 PetscFunctionReturn(0); 819 } 820 821 #undef __FUNCT__ 822 #define __FUNCT__ "MatAssemblyBegin_MPIBAIJ" 823 PetscErrorCode MatAssemblyBegin_MPIBAIJ(Mat mat,MatAssemblyType mode) 824 { 825 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 826 PetscErrorCode ierr; 827 PetscInt nstash,reallocs; 828 InsertMode addv; 829 830 PetscFunctionBegin; 831 if (baij->donotstash || mat->nooffprocentries) { 832 PetscFunctionReturn(0); 833 } 834 835 /* make sure all processors are either in INSERTMODE or ADDMODE */ 836 ierr = MPI_Allreduce(&mat->insertmode,&addv,1,MPI_INT,MPI_BOR,((PetscObject)mat)->comm);CHKERRQ(ierr); 837 if (addv == (ADD_VALUES|INSERT_VALUES)) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Some processors inserted others added"); 838 mat->insertmode = addv; /* in case this processor had no cache */ 839 840 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 841 ierr = MatStashScatterBegin_Private(mat,&mat->bstash,baij->rangebs);CHKERRQ(ierr); 842 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 843 ierr = PetscInfo2(mat,"Stash has %D entries,uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 844 ierr = MatStashGetInfo_Private(&mat->bstash,&nstash,&reallocs);CHKERRQ(ierr); 845 ierr = PetscInfo2(mat,"Block-Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 846 PetscFunctionReturn(0); 847 } 848 849 #undef __FUNCT__ 850 #define __FUNCT__ "MatAssemblyEnd_MPIBAIJ" 851 PetscErrorCode MatAssemblyEnd_MPIBAIJ(Mat mat,MatAssemblyType mode) 852 { 853 Mat_MPIBAIJ *baij=(Mat_MPIBAIJ*)mat->data; 854 Mat_SeqBAIJ *a=(Mat_SeqBAIJ*)baij->A->data; 855 PetscErrorCode ierr; 856 PetscInt i,j,rstart,ncols,flg,bs2=baij->bs2; 857 PetscInt *row,*col; 858 PetscBool r1,r2,r3,other_disassembled; 859 MatScalar *val; 860 InsertMode addv = mat->insertmode; 861 PetscMPIInt n; 862 863 /* do not use 'b=(Mat_SeqBAIJ*)baij->B->data' as B can be reset in disassembly */ 864 PetscFunctionBegin; 865 if (!baij->donotstash && !mat->nooffprocentries) { 866 while (1) { 867 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 868 if (!flg) break; 869 870 for (i=0; i<n;) { 871 /* Now identify the consecutive vals belonging to the same row */ 872 for (j=i,rstart=row[j]; j<n; j++) { if (row[j] != rstart) break; } 873 if (j < n) ncols = j-i; 874 else ncols = n-i; 875 /* Now assemble all these values with a single function call */ 876 ierr = MatSetValues_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i,addv);CHKERRQ(ierr); 877 i = j; 878 } 879 } 880 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 881 /* Now process the block-stash. Since the values are stashed column-oriented, 882 set the roworiented flag to column oriented, and after MatSetValues() 883 restore the original flags */ 884 r1 = baij->roworiented; 885 r2 = a->roworiented; 886 r3 = ((Mat_SeqBAIJ*)baij->B->data)->roworiented; 887 baij->roworiented = PETSC_FALSE; 888 a->roworiented = PETSC_FALSE; 889 (((Mat_SeqBAIJ*)baij->B->data))->roworiented = PETSC_FALSE; /* b->roworiented */ 890 while (1) { 891 ierr = MatStashScatterGetMesg_Private(&mat->bstash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 892 if (!flg) break; 893 894 for (i=0; i<n;) { 895 /* Now identify the consecutive vals belonging to the same row */ 896 for (j=i,rstart=row[j]; j<n; j++) { if (row[j] != rstart) break; } 897 if (j < n) ncols = j-i; 898 else ncols = n-i; 899 ierr = MatSetValuesBlocked_MPIBAIJ(mat,1,row+i,ncols,col+i,val+i*bs2,addv);CHKERRQ(ierr); 900 i = j; 901 } 902 } 903 ierr = MatStashScatterEnd_Private(&mat->bstash);CHKERRQ(ierr); 904 baij->roworiented = r1; 905 a->roworiented = r2; 906 ((Mat_SeqBAIJ*)baij->B->data)->roworiented = r3; /* b->roworiented */ 907 } 908 909 ierr = MatAssemblyBegin(baij->A,mode);CHKERRQ(ierr); 910 ierr = MatAssemblyEnd(baij->A,mode);CHKERRQ(ierr); 911 912 /* determine if any processor has disassembled, if so we must 913 also disassemble ourselfs, in order that we may reassemble. */ 914 /* 915 if nonzero structure of submatrix B cannot change then we know that 916 no processor disassembled thus we can skip this stuff 917 */ 918 if (!((Mat_SeqBAIJ*)baij->B->data)->nonew) { 919 ierr = MPI_Allreduce(&mat->was_assembled,&other_disassembled,1,MPI_INT,MPI_PROD,((PetscObject)mat)->comm);CHKERRQ(ierr); 920 if (mat->was_assembled && !other_disassembled) { 921 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 922 } 923 } 924 925 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 926 ierr = MatSetUpMultiply_MPIBAIJ(mat);CHKERRQ(ierr); 927 } 928 ierr = MatSetOption(baij->B,MAT_CHECK_COMPRESSED_ROW,PETSC_FALSE);CHKERRQ(ierr); 929 ierr = MatAssemblyBegin(baij->B,mode);CHKERRQ(ierr); 930 ierr = MatAssemblyEnd(baij->B,mode);CHKERRQ(ierr); 931 932 #if defined(PETSC_USE_INFO) 933 if (baij->ht && mode== MAT_FINAL_ASSEMBLY) { 934 ierr = PetscInfo1(mat,"Average Hash Table Search in MatSetValues = %5.2f\n",((PetscReal)baij->ht_total_ct)/baij->ht_insert_ct);CHKERRQ(ierr); 935 baij->ht_total_ct = 0; 936 baij->ht_insert_ct = 0; 937 } 938 #endif 939 if (baij->ht_flag && !baij->ht && mode == MAT_FINAL_ASSEMBLY) { 940 ierr = MatCreateHashTable_MPIBAIJ_Private(mat,baij->ht_fact);CHKERRQ(ierr); 941 mat->ops->setvalues = MatSetValues_MPIBAIJ_HT; 942 mat->ops->setvaluesblocked = MatSetValuesBlocked_MPIBAIJ_HT; 943 } 944 945 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 946 baij->rowvalues = 0; 947 PetscFunctionReturn(0); 948 } 949 950 #undef __FUNCT__ 951 #define __FUNCT__ "MatView_MPIBAIJ_ASCIIorDraworSocket" 952 static PetscErrorCode MatView_MPIBAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 953 { 954 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 955 PetscErrorCode ierr; 956 PetscMPIInt size = baij->size,rank = baij->rank; 957 PetscInt bs = mat->rmap->bs; 958 PetscBool iascii,isdraw; 959 PetscViewer sviewer; 960 PetscViewerFormat format; 961 962 PetscFunctionBegin; 963 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 964 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 965 if (iascii) { 966 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 967 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 968 MatInfo info; 969 ierr = MPI_Comm_rank(((PetscObject)mat)->comm,&rank);CHKERRQ(ierr); 970 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 971 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 972 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D bs %D mem %D\n", 973 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,mat->rmap->bs,(PetscInt)info.memory);CHKERRQ(ierr); 974 ierr = MatGetInfo(baij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 975 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 976 ierr = MatGetInfo(baij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 977 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 978 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 979 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr); 980 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 981 ierr = VecScatterView(baij->Mvctx,viewer);CHKERRQ(ierr); 982 PetscFunctionReturn(0); 983 } else if (format == PETSC_VIEWER_ASCII_INFO) { 984 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 985 PetscFunctionReturn(0); 986 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 987 PetscFunctionReturn(0); 988 } 989 } 990 991 if (isdraw) { 992 PetscDraw draw; 993 PetscBool isnull; 994 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 995 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 996 } 997 998 if (size == 1) { 999 ierr = PetscObjectSetName((PetscObject)baij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1000 ierr = MatView(baij->A,viewer);CHKERRQ(ierr); 1001 } else { 1002 /* assemble the entire matrix onto first processor. */ 1003 Mat A; 1004 Mat_SeqBAIJ *Aloc; 1005 PetscInt M = mat->rmap->N,N = mat->cmap->N,*ai,*aj,col,i,j,k,*rvals,mbs = baij->mbs; 1006 MatScalar *a; 1007 1008 /* Here we are creating a temporary matrix, so will assume MPIBAIJ is acceptable */ 1009 /* Perhaps this should be the type of mat? */ 1010 ierr = MatCreate(((PetscObject)mat)->comm,&A);CHKERRQ(ierr); 1011 if (!rank) { 1012 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1013 } else { 1014 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1015 } 1016 ierr = MatSetType(A,MATMPIBAIJ);CHKERRQ(ierr); 1017 ierr = MatMPIBAIJSetPreallocation(A,mat->rmap->bs,0,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr); 1018 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1019 ierr = PetscLogObjectParent(mat,A);CHKERRQ(ierr); 1020 1021 /* copy over the A part */ 1022 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1023 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1024 ierr = PetscMalloc(bs*sizeof(PetscInt),&rvals);CHKERRQ(ierr); 1025 1026 for (i=0; i<mbs; i++) { 1027 rvals[0] = bs*(baij->rstartbs + i); 1028 for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; } 1029 for (j=ai[i]; j<ai[i+1]; j++) { 1030 col = (baij->cstartbs+aj[j])*bs; 1031 for (k=0; k<bs; k++) { 1032 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1033 col++; a += bs; 1034 } 1035 } 1036 } 1037 /* copy over the B part */ 1038 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1039 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1040 for (i=0; i<mbs; i++) { 1041 rvals[0] = bs*(baij->rstartbs + i); 1042 for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; } 1043 for (j=ai[i]; j<ai[i+1]; j++) { 1044 col = baij->garray[aj[j]]*bs; 1045 for (k=0; k<bs; k++) { 1046 ierr = MatSetValues_MPIBAIJ(A,bs,rvals,1,&col,a,INSERT_VALUES);CHKERRQ(ierr); 1047 col++; a += bs; 1048 } 1049 } 1050 } 1051 ierr = PetscFree(rvals);CHKERRQ(ierr); 1052 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1053 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1054 /* 1055 Everyone has to call to draw the matrix since the graphics waits are 1056 synchronized across all processors that share the PetscDraw object 1057 */ 1058 ierr = PetscViewerGetSingleton(viewer,&sviewer);CHKERRQ(ierr); 1059 if (!rank) { 1060 ierr = PetscObjectSetName((PetscObject)((Mat_MPIBAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1061 /* Set the type name to MATMPIBAIJ so that the correct type can be printed out by PetscObjectPrintClassNamePrefixType() in MatView_SeqBAIJ_ASCII()*/ 1062 PetscStrcpy(((PetscObject)((Mat_MPIBAIJ*)(A->data))->A)->type_name,MATMPIBAIJ); 1063 ierr = MatView(((Mat_MPIBAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1064 } 1065 ierr = PetscViewerRestoreSingleton(viewer,&sviewer);CHKERRQ(ierr); 1066 ierr = MatDestroy(&A);CHKERRQ(ierr); 1067 } 1068 PetscFunctionReturn(0); 1069 } 1070 1071 #undef __FUNCT__ 1072 #define __FUNCT__ "MatView_MPIBAIJ_Binary" 1073 static PetscErrorCode MatView_MPIBAIJ_Binary(Mat mat,PetscViewer viewer) 1074 { 1075 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)mat->data; 1076 Mat_SeqBAIJ* A = (Mat_SeqBAIJ*)a->A->data; 1077 Mat_SeqBAIJ* B = (Mat_SeqBAIJ*)a->B->data; 1078 PetscErrorCode ierr; 1079 PetscInt i,*row_lens,*crow_lens,bs = mat->rmap->bs,j,k,bs2=a->bs2,header[4],nz,rlen; 1080 PetscInt *range=0,nzmax,*column_indices,cnt,col,*garray = a->garray,cstart = mat->cmap->rstart/bs,len,pcnt,l,ll; 1081 int fd; 1082 PetscScalar *column_values; 1083 FILE *file; 1084 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1085 PetscInt message_count,flowcontrolcount; 1086 1087 PetscFunctionBegin; 1088 ierr = MPI_Comm_rank(((PetscObject)mat)->comm,&rank);CHKERRQ(ierr); 1089 ierr = MPI_Comm_size(((PetscObject)mat)->comm,&size);CHKERRQ(ierr); 1090 nz = bs2*(A->nz + B->nz); 1091 rlen = mat->rmap->n; 1092 if (!rank) { 1093 header[0] = MAT_FILE_CLASSID; 1094 header[1] = mat->rmap->N; 1095 header[2] = mat->cmap->N; 1096 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,((PetscObject)mat)->comm);CHKERRQ(ierr); 1097 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1098 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1099 /* get largest number of rows any processor has */ 1100 range = mat->rmap->range; 1101 for (i=1; i<size; i++) { 1102 rlen = PetscMax(rlen,range[i+1] - range[i]); 1103 } 1104 } else { 1105 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,((PetscObject)mat)->comm);CHKERRQ(ierr); 1106 } 1107 1108 ierr = PetscMalloc((rlen/bs)*sizeof(PetscInt),&crow_lens);CHKERRQ(ierr); 1109 /* compute lengths of each row */ 1110 for (i=0; i<a->mbs; i++) { 1111 crow_lens[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1112 } 1113 /* store the row lengths to the file */ 1114 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1115 if (!rank) { 1116 MPI_Status status; 1117 ierr = PetscMalloc(rlen*sizeof(PetscInt),&row_lens);CHKERRQ(ierr); 1118 rlen = (range[1] - range[0])/bs; 1119 for (i=0; i<rlen; i++) { 1120 for (j=0; j<bs; j++) { 1121 row_lens[i*bs+j] = bs*crow_lens[i]; 1122 } 1123 } 1124 ierr = PetscBinaryWrite(fd,row_lens,bs*rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1125 for (i=1; i<size; i++) { 1126 rlen = (range[i+1] - range[i])/bs; 1127 ierr = PetscViewerFlowControlStepMaster(viewer,i,message_count,flowcontrolcount);CHKERRQ(ierr); 1128 ierr = MPI_Recv(crow_lens,rlen,MPIU_INT,i,tag,((PetscObject)mat)->comm,&status);CHKERRQ(ierr); 1129 for (k=0; k<rlen; k++) { 1130 for (j=0; j<bs; j++) { 1131 row_lens[k*bs+j] = bs*crow_lens[k]; 1132 } 1133 } 1134 ierr = PetscBinaryWrite(fd,row_lens,bs*rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1135 } 1136 ierr = PetscViewerFlowControlEndMaster(viewer,message_count);CHKERRQ(ierr); 1137 ierr = PetscFree(row_lens);CHKERRQ(ierr); 1138 } else { 1139 ierr = PetscViewerFlowControlStepWorker(viewer,rank,message_count);CHKERRQ(ierr); 1140 ierr = MPI_Send(crow_lens,mat->rmap->n/bs,MPIU_INT,0,tag,((PetscObject)mat)->comm);CHKERRQ(ierr); 1141 ierr = PetscViewerFlowControlEndWorker(viewer,message_count);CHKERRQ(ierr); 1142 } 1143 ierr = PetscFree(crow_lens);CHKERRQ(ierr); 1144 1145 /* load up the local column indices. Include for all rows not just one for each block row since process 0 does not have the 1146 information needed to make it for each row from a block row. This does require more communication but still not more than 1147 the communication needed for the nonzero values */ 1148 nzmax = nz; /* space a largest processor needs */ 1149 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,((PetscObject)mat)->comm);CHKERRQ(ierr); 1150 ierr = PetscMalloc(nzmax*sizeof(PetscInt),&column_indices);CHKERRQ(ierr); 1151 cnt = 0; 1152 for (i=0; i<a->mbs; i++) { 1153 pcnt = cnt; 1154 for (j=B->i[i]; j<B->i[i+1]; j++) { 1155 if ( (col = garray[B->j[j]]) > cstart) break; 1156 for (l=0; l<bs; l++) { 1157 column_indices[cnt++] = bs*col+l; 1158 } 1159 } 1160 for (k=A->i[i]; k<A->i[i+1]; k++) { 1161 for (l=0; l<bs; l++) { 1162 column_indices[cnt++] = bs*(A->j[k] + cstart)+l; 1163 } 1164 } 1165 for (; j<B->i[i+1]; j++) { 1166 for (l=0; l<bs; l++) { 1167 column_indices[cnt++] = bs*garray[B->j[j]]+l; 1168 } 1169 } 1170 len = cnt - pcnt; 1171 for (k=1; k<bs; k++) { 1172 ierr = PetscMemcpy(&column_indices[cnt],&column_indices[pcnt],len*sizeof(PetscInt));CHKERRQ(ierr); 1173 cnt += len; 1174 } 1175 } 1176 if (cnt != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,nz); 1177 1178 /* store the columns to the file */ 1179 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1180 if (!rank) { 1181 MPI_Status status; 1182 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1183 for (i=1; i<size; i++) { 1184 ierr = PetscViewerFlowControlStepMaster(viewer,i,message_count,flowcontrolcount);CHKERRQ(ierr); 1185 ierr = MPI_Recv(&cnt,1,MPIU_INT,i,tag,((PetscObject)mat)->comm,&status);CHKERRQ(ierr); 1186 ierr = MPI_Recv(column_indices,cnt,MPIU_INT,i,tag,((PetscObject)mat)->comm,&status);CHKERRQ(ierr); 1187 ierr = PetscBinaryWrite(fd,column_indices,cnt,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1188 } 1189 ierr = PetscViewerFlowControlEndMaster(viewer,message_count);CHKERRQ(ierr); 1190 } else { 1191 ierr = PetscViewerFlowControlStepWorker(viewer,rank,message_count);CHKERRQ(ierr); 1192 ierr = MPI_Send(&cnt,1,MPIU_INT,0,tag,((PetscObject)mat)->comm);CHKERRQ(ierr); 1193 ierr = MPI_Send(column_indices,cnt,MPIU_INT,0,tag,((PetscObject)mat)->comm);CHKERRQ(ierr); 1194 ierr = PetscViewerFlowControlEndWorker(viewer,message_count);CHKERRQ(ierr); 1195 } 1196 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1197 1198 /* load up the numerical values */ 1199 ierr = PetscMalloc(nzmax*sizeof(PetscScalar),&column_values);CHKERRQ(ierr); 1200 cnt = 0; 1201 for (i=0; i<a->mbs; i++) { 1202 rlen = bs*(B->i[i+1] - B->i[i] + A->i[i+1] - A->i[i]); 1203 for (j=B->i[i]; j<B->i[i+1]; j++) { 1204 if ( garray[B->j[j]] > cstart) break; 1205 for (l=0; l<bs; l++) { 1206 for (ll=0; ll<bs; ll++) { 1207 column_values[cnt + l*rlen + ll] = B->a[bs2*j+l+bs*ll]; 1208 } 1209 } 1210 cnt += bs; 1211 } 1212 for (k=A->i[i]; k<A->i[i+1]; k++) { 1213 for (l=0; l<bs; l++) { 1214 for (ll=0; ll<bs; ll++) { 1215 column_values[cnt + l*rlen + ll] = A->a[bs2*k+l+bs*ll]; 1216 } 1217 } 1218 cnt += bs; 1219 } 1220 for (; j<B->i[i+1]; j++) { 1221 for (l=0; l<bs; l++) { 1222 for (ll=0; ll<bs; ll++) { 1223 column_values[cnt + l*rlen + ll] = B->a[bs2*j+l+bs*ll]; 1224 } 1225 } 1226 cnt += bs; 1227 } 1228 cnt += (bs-1)*rlen; 1229 } 1230 if (cnt != nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,nz); 1231 1232 /* store the column values to the file */ 1233 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1234 if (!rank) { 1235 MPI_Status status; 1236 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1237 for (i=1; i<size; i++) { 1238 ierr = PetscViewerFlowControlStepMaster(viewer,i,message_count,flowcontrolcount);CHKERRQ(ierr); 1239 ierr = MPI_Recv(&cnt,1,MPIU_INT,i,tag,((PetscObject)mat)->comm,&status);CHKERRQ(ierr); 1240 ierr = MPI_Recv(column_values,cnt,MPIU_SCALAR,i,tag,((PetscObject)mat)->comm,&status);CHKERRQ(ierr); 1241 ierr = PetscBinaryWrite(fd,column_values,cnt,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1242 } 1243 ierr = PetscViewerFlowControlEndMaster(viewer,message_count);CHKERRQ(ierr); 1244 } else { 1245 ierr = PetscViewerFlowControlStepWorker(viewer,rank,message_count);CHKERRQ(ierr); 1246 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,((PetscObject)mat)->comm);CHKERRQ(ierr); 1247 ierr = MPI_Send(column_values,nz,MPIU_SCALAR,0,tag,((PetscObject)mat)->comm);CHKERRQ(ierr); 1248 ierr = PetscViewerFlowControlEndWorker(viewer,message_count);CHKERRQ(ierr); 1249 } 1250 ierr = PetscFree(column_values);CHKERRQ(ierr); 1251 1252 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1253 if (file) { 1254 fprintf(file,"-matload_block_size %d\n",(int)mat->rmap->bs); 1255 } 1256 PetscFunctionReturn(0); 1257 } 1258 1259 #undef __FUNCT__ 1260 #define __FUNCT__ "MatView_MPIBAIJ" 1261 PetscErrorCode MatView_MPIBAIJ(Mat mat,PetscViewer viewer) 1262 { 1263 PetscErrorCode ierr; 1264 PetscBool iascii,isdraw,issocket,isbinary; 1265 1266 PetscFunctionBegin; 1267 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1268 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1269 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1270 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1271 if (iascii || isdraw || issocket) { 1272 ierr = MatView_MPIBAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1273 } else if (isbinary) { 1274 ierr = MatView_MPIBAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1275 } else { 1276 SETERRQ1(((PetscObject)mat)->comm,PETSC_ERR_SUP,"Viewer type %s not supported by MPIBAIJ matrices",((PetscObject)viewer)->type_name); 1277 } 1278 PetscFunctionReturn(0); 1279 } 1280 1281 #undef __FUNCT__ 1282 #define __FUNCT__ "MatDestroy_MPIBAIJ" 1283 PetscErrorCode MatDestroy_MPIBAIJ(Mat mat) 1284 { 1285 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1286 PetscErrorCode ierr; 1287 1288 PetscFunctionBegin; 1289 #if defined(PETSC_USE_LOG) 1290 PetscLogObjectState((PetscObject)mat,"Rows=%D,Cols=%D",mat->rmap->N,mat->cmap->N); 1291 #endif 1292 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1293 ierr = MatStashDestroy_Private(&mat->bstash);CHKERRQ(ierr); 1294 ierr = MatDestroy(&baij->A);CHKERRQ(ierr); 1295 ierr = MatDestroy(&baij->B);CHKERRQ(ierr); 1296 #if defined (PETSC_USE_CTABLE) 1297 ierr = PetscTableDestroy(&baij->colmap);CHKERRQ(ierr); 1298 #else 1299 ierr = PetscFree(baij->colmap);CHKERRQ(ierr); 1300 #endif 1301 ierr = PetscFree(baij->garray);CHKERRQ(ierr); 1302 ierr = VecDestroy(&baij->lvec);CHKERRQ(ierr); 1303 ierr = VecScatterDestroy(&baij->Mvctx);CHKERRQ(ierr); 1304 ierr = PetscFree2(baij->rowvalues,baij->rowindices);CHKERRQ(ierr); 1305 ierr = PetscFree(baij->barray);CHKERRQ(ierr); 1306 ierr = PetscFree2(baij->hd,baij->ht);CHKERRQ(ierr); 1307 ierr = PetscFree(baij->rangebs);CHKERRQ(ierr); 1308 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1309 1310 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1311 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 1312 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 1313 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatGetDiagonalBlock_C","",PETSC_NULL);CHKERRQ(ierr); 1314 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 1315 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIBAIJSetPreallocationCSR_C","",PETSC_NULL);CHKERRQ(ierr); 1316 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C","",PETSC_NULL);CHKERRQ(ierr); 1317 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatSetHashTableFactor_C","",PETSC_NULL);CHKERRQ(ierr); 1318 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpisbaij_C","",PETSC_NULL);CHKERRQ(ierr); 1319 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpibaij_mpibstrm_C","",PETSC_NULL);CHKERRQ(ierr); 1320 PetscFunctionReturn(0); 1321 } 1322 1323 #undef __FUNCT__ 1324 #define __FUNCT__ "MatMult_MPIBAIJ" 1325 PetscErrorCode MatMult_MPIBAIJ(Mat A,Vec xx,Vec yy) 1326 { 1327 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1328 PetscErrorCode ierr; 1329 PetscInt nt; 1330 1331 PetscFunctionBegin; 1332 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 1333 if (nt != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A and xx"); 1334 ierr = VecGetLocalSize(yy,&nt);CHKERRQ(ierr); 1335 if (nt != A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible parition of A and yy"); 1336 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1337 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 1338 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1339 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 1340 PetscFunctionReturn(0); 1341 } 1342 1343 #undef __FUNCT__ 1344 #define __FUNCT__ "MatMultAdd_MPIBAIJ" 1345 PetscErrorCode MatMultAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1346 { 1347 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1348 PetscErrorCode ierr; 1349 1350 PetscFunctionBegin; 1351 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1352 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1353 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1354 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 1355 PetscFunctionReturn(0); 1356 } 1357 1358 #undef __FUNCT__ 1359 #define __FUNCT__ "MatMultTranspose_MPIBAIJ" 1360 PetscErrorCode MatMultTranspose_MPIBAIJ(Mat A,Vec xx,Vec yy) 1361 { 1362 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1363 PetscErrorCode ierr; 1364 PetscBool merged; 1365 1366 PetscFunctionBegin; 1367 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 1368 /* do nondiagonal part */ 1369 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1370 if (!merged) { 1371 /* send it on its way */ 1372 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1373 /* do local part */ 1374 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1375 /* receive remote parts: note this assumes the values are not actually */ 1376 /* inserted in yy until the next line */ 1377 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1378 } else { 1379 /* do local part */ 1380 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 1381 /* send it on its way */ 1382 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1383 /* values actually were received in the Begin() but we need to call this nop */ 1384 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1385 } 1386 PetscFunctionReturn(0); 1387 } 1388 1389 #undef __FUNCT__ 1390 #define __FUNCT__ "MatMultTransposeAdd_MPIBAIJ" 1391 PetscErrorCode MatMultTransposeAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1392 { 1393 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1394 PetscErrorCode ierr; 1395 1396 PetscFunctionBegin; 1397 /* do nondiagonal part */ 1398 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1399 /* send it on its way */ 1400 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1401 /* do local part */ 1402 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1403 /* receive remote parts: note this assumes the values are not actually */ 1404 /* inserted in yy until the next line, which is true for my implementation*/ 1405 /* but is not perhaps always true. */ 1406 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1407 PetscFunctionReturn(0); 1408 } 1409 1410 /* 1411 This only works correctly for square matrices where the subblock A->A is the 1412 diagonal block 1413 */ 1414 #undef __FUNCT__ 1415 #define __FUNCT__ "MatGetDiagonal_MPIBAIJ" 1416 PetscErrorCode MatGetDiagonal_MPIBAIJ(Mat A,Vec v) 1417 { 1418 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1419 PetscErrorCode ierr; 1420 1421 PetscFunctionBegin; 1422 if (A->rmap->N != A->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1423 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1424 PetscFunctionReturn(0); 1425 } 1426 1427 #undef __FUNCT__ 1428 #define __FUNCT__ "MatScale_MPIBAIJ" 1429 PetscErrorCode MatScale_MPIBAIJ(Mat A,PetscScalar aa) 1430 { 1431 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1432 PetscErrorCode ierr; 1433 1434 PetscFunctionBegin; 1435 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1436 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1437 PetscFunctionReturn(0); 1438 } 1439 1440 #undef __FUNCT__ 1441 #define __FUNCT__ "MatGetRow_MPIBAIJ" 1442 PetscErrorCode MatGetRow_MPIBAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1443 { 1444 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 1445 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1446 PetscErrorCode ierr; 1447 PetscInt bs = matin->rmap->bs,bs2 = mat->bs2,i,*cworkA,*cworkB,**pcA,**pcB; 1448 PetscInt nztot,nzA,nzB,lrow,brstart = matin->rmap->rstart,brend = matin->rmap->rend; 1449 PetscInt *cmap,*idx_p,cstart = mat->cstartbs; 1450 1451 PetscFunctionBegin; 1452 if (row < brstart || row >= brend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local rows"); 1453 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1454 mat->getrowactive = PETSC_TRUE; 1455 1456 if (!mat->rowvalues && (idx || v)) { 1457 /* 1458 allocate enough space to hold information from the longest row. 1459 */ 1460 Mat_SeqBAIJ *Aa = (Mat_SeqBAIJ*)mat->A->data,*Ba = (Mat_SeqBAIJ*)mat->B->data; 1461 PetscInt max = 1,mbs = mat->mbs,tmp; 1462 for (i=0; i<mbs; i++) { 1463 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1464 if (max < tmp) { max = tmp; } 1465 } 1466 ierr = PetscMalloc2(max*bs2,PetscScalar,&mat->rowvalues,max*bs2,PetscInt,&mat->rowindices);CHKERRQ(ierr); 1467 } 1468 lrow = row - brstart; 1469 1470 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1471 if (!v) {pvA = 0; pvB = 0;} 1472 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1473 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1474 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1475 nztot = nzA + nzB; 1476 1477 cmap = mat->garray; 1478 if (v || idx) { 1479 if (nztot) { 1480 /* Sort by increasing column numbers, assuming A and B already sorted */ 1481 PetscInt imark = -1; 1482 if (v) { 1483 *v = v_p = mat->rowvalues; 1484 for (i=0; i<nzB; i++) { 1485 if (cmap[cworkB[i]/bs] < cstart) v_p[i] = vworkB[i]; 1486 else break; 1487 } 1488 imark = i; 1489 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1490 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1491 } 1492 if (idx) { 1493 *idx = idx_p = mat->rowindices; 1494 if (imark > -1) { 1495 for (i=0; i<imark; i++) { 1496 idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs; 1497 } 1498 } else { 1499 for (i=0; i<nzB; i++) { 1500 if (cmap[cworkB[i]/bs] < cstart) 1501 idx_p[i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs ; 1502 else break; 1503 } 1504 imark = i; 1505 } 1506 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart*bs + cworkA[i]; 1507 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]/bs]*bs + cworkB[i]%bs ; 1508 } 1509 } else { 1510 if (idx) *idx = 0; 1511 if (v) *v = 0; 1512 } 1513 } 1514 *nz = nztot; 1515 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1516 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1517 PetscFunctionReturn(0); 1518 } 1519 1520 #undef __FUNCT__ 1521 #define __FUNCT__ "MatRestoreRow_MPIBAIJ" 1522 PetscErrorCode MatRestoreRow_MPIBAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1523 { 1524 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1525 1526 PetscFunctionBegin; 1527 if (!baij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow not called"); 1528 baij->getrowactive = PETSC_FALSE; 1529 PetscFunctionReturn(0); 1530 } 1531 1532 #undef __FUNCT__ 1533 #define __FUNCT__ "MatZeroEntries_MPIBAIJ" 1534 PetscErrorCode MatZeroEntries_MPIBAIJ(Mat A) 1535 { 1536 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1537 PetscErrorCode ierr; 1538 1539 PetscFunctionBegin; 1540 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 1541 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 1542 PetscFunctionReturn(0); 1543 } 1544 1545 #undef __FUNCT__ 1546 #define __FUNCT__ "MatGetInfo_MPIBAIJ" 1547 PetscErrorCode MatGetInfo_MPIBAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1548 { 1549 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)matin->data; 1550 Mat A = a->A,B = a->B; 1551 PetscErrorCode ierr; 1552 PetscReal isend[5],irecv[5]; 1553 1554 PetscFunctionBegin; 1555 info->block_size = (PetscReal)matin->rmap->bs; 1556 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1557 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1558 isend[3] = info->memory; isend[4] = info->mallocs; 1559 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1560 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1561 isend[3] += info->memory; isend[4] += info->mallocs; 1562 if (flag == MAT_LOCAL) { 1563 info->nz_used = isend[0]; 1564 info->nz_allocated = isend[1]; 1565 info->nz_unneeded = isend[2]; 1566 info->memory = isend[3]; 1567 info->mallocs = isend[4]; 1568 } else if (flag == MAT_GLOBAL_MAX) { 1569 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,((PetscObject)matin)->comm);CHKERRQ(ierr); 1570 info->nz_used = irecv[0]; 1571 info->nz_allocated = irecv[1]; 1572 info->nz_unneeded = irecv[2]; 1573 info->memory = irecv[3]; 1574 info->mallocs = irecv[4]; 1575 } else if (flag == MAT_GLOBAL_SUM) { 1576 ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,((PetscObject)matin)->comm);CHKERRQ(ierr); 1577 info->nz_used = irecv[0]; 1578 info->nz_allocated = irecv[1]; 1579 info->nz_unneeded = irecv[2]; 1580 info->memory = irecv[3]; 1581 info->mallocs = irecv[4]; 1582 } else { 1583 SETERRQ1(((PetscObject)matin)->comm,PETSC_ERR_ARG_WRONG,"Unknown MatInfoType argument %d",(int)flag); 1584 } 1585 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1586 info->fill_ratio_needed = 0; 1587 info->factor_mallocs = 0; 1588 PetscFunctionReturn(0); 1589 } 1590 1591 #undef __FUNCT__ 1592 #define __FUNCT__ "MatSetOption_MPIBAIJ" 1593 PetscErrorCode MatSetOption_MPIBAIJ(Mat A,MatOption op,PetscBool flg) 1594 { 1595 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1596 PetscErrorCode ierr; 1597 1598 PetscFunctionBegin; 1599 switch (op) { 1600 case MAT_NEW_NONZERO_LOCATIONS: 1601 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1602 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1603 case MAT_KEEP_NONZERO_PATTERN: 1604 case MAT_NEW_NONZERO_LOCATION_ERR: 1605 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1606 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1607 break; 1608 case MAT_ROW_ORIENTED: 1609 a->roworiented = flg; 1610 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1611 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1612 break; 1613 case MAT_NEW_DIAGONALS: 1614 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1615 break; 1616 case MAT_IGNORE_OFF_PROC_ENTRIES: 1617 a->donotstash = flg; 1618 break; 1619 case MAT_USE_HASH_TABLE: 1620 a->ht_flag = flg; 1621 break; 1622 case MAT_SYMMETRIC: 1623 case MAT_STRUCTURALLY_SYMMETRIC: 1624 case MAT_HERMITIAN: 1625 case MAT_SYMMETRY_ETERNAL: 1626 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1627 break; 1628 default: 1629 SETERRQ1(((PetscObject)A)->comm,PETSC_ERR_SUP,"unknown option %d",op); 1630 } 1631 PetscFunctionReturn(0); 1632 } 1633 1634 #undef __FUNCT__ 1635 #define __FUNCT__ "MatTranspose_MPIBAIJ" 1636 PetscErrorCode MatTranspose_MPIBAIJ(Mat A,MatReuse reuse,Mat *matout) 1637 { 1638 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data; 1639 Mat_SeqBAIJ *Aloc; 1640 Mat B; 1641 PetscErrorCode ierr; 1642 PetscInt M=A->rmap->N,N=A->cmap->N,*ai,*aj,i,*rvals,j,k,col; 1643 PetscInt bs=A->rmap->bs,mbs=baij->mbs; 1644 MatScalar *a; 1645 1646 PetscFunctionBegin; 1647 if (reuse == MAT_REUSE_MATRIX && A == *matout && M != N) SETERRQ(((PetscObject)A)->comm,PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1648 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1649 ierr = MatCreate(((PetscObject)A)->comm,&B);CHKERRQ(ierr); 1650 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1651 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1652 /* Do not know preallocation information, but must set block size */ 1653 ierr = MatMPIBAIJSetPreallocation(B,A->rmap->bs,PETSC_DECIDE,PETSC_NULL,PETSC_DECIDE,PETSC_NULL);CHKERRQ(ierr); 1654 } else { 1655 B = *matout; 1656 } 1657 1658 /* copy over the A part */ 1659 Aloc = (Mat_SeqBAIJ*)baij->A->data; 1660 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1661 ierr = PetscMalloc(bs*sizeof(PetscInt),&rvals);CHKERRQ(ierr); 1662 1663 for (i=0; i<mbs; i++) { 1664 rvals[0] = bs*(baij->rstartbs + i); 1665 for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; } 1666 for (j=ai[i]; j<ai[i+1]; j++) { 1667 col = (baij->cstartbs+aj[j])*bs; 1668 for (k=0; k<bs; k++) { 1669 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1670 col++; a += bs; 1671 } 1672 } 1673 } 1674 /* copy over the B part */ 1675 Aloc = (Mat_SeqBAIJ*)baij->B->data; 1676 ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1677 for (i=0; i<mbs; i++) { 1678 rvals[0] = bs*(baij->rstartbs + i); 1679 for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; } 1680 for (j=ai[i]; j<ai[i+1]; j++) { 1681 col = baij->garray[aj[j]]*bs; 1682 for (k=0; k<bs; k++) { 1683 ierr = MatSetValues_MPIBAIJ(B,1,&col,bs,rvals,a,INSERT_VALUES);CHKERRQ(ierr); 1684 col++; a += bs; 1685 } 1686 } 1687 } 1688 ierr = PetscFree(rvals);CHKERRQ(ierr); 1689 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1690 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1691 1692 if (reuse == MAT_INITIAL_MATRIX || *matout != A) { 1693 *matout = B; 1694 } else { 1695 ierr = MatHeaderMerge(A,B);CHKERRQ(ierr); 1696 } 1697 PetscFunctionReturn(0); 1698 } 1699 1700 #undef __FUNCT__ 1701 #define __FUNCT__ "MatDiagonalScale_MPIBAIJ" 1702 PetscErrorCode MatDiagonalScale_MPIBAIJ(Mat mat,Vec ll,Vec rr) 1703 { 1704 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 1705 Mat a = baij->A,b = baij->B; 1706 PetscErrorCode ierr; 1707 PetscInt s1,s2,s3; 1708 1709 PetscFunctionBegin; 1710 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1711 if (rr) { 1712 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1713 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1714 /* Overlap communication with computation. */ 1715 ierr = VecScatterBegin(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1716 } 1717 if (ll) { 1718 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1719 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1720 ierr = (*b->ops->diagonalscale)(b,ll,PETSC_NULL);CHKERRQ(ierr); 1721 } 1722 /* scale the diagonal block */ 1723 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 1724 1725 if (rr) { 1726 /* Do a scatter end and then right scale the off-diagonal block */ 1727 ierr = VecScatterEnd(baij->Mvctx,rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1728 ierr = (*b->ops->diagonalscale)(b,PETSC_NULL,baij->lvec);CHKERRQ(ierr); 1729 } 1730 1731 PetscFunctionReturn(0); 1732 } 1733 1734 #undef __FUNCT__ 1735 #define __FUNCT__ "MatZeroRows_MPIBAIJ" 1736 PetscErrorCode MatZeroRows_MPIBAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1737 { 1738 Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; 1739 PetscErrorCode ierr; 1740 PetscMPIInt imdex,size = l->size,n,rank = l->rank; 1741 PetscInt i,*owners = A->rmap->range; 1742 PetscInt *nprocs,j,idx,nsends,row; 1743 PetscInt nmax,*svalues,*starts,*owner,nrecvs; 1744 PetscInt *rvalues,tag = ((PetscObject)A)->tag,count,base,slen,*source,lastidx = -1; 1745 PetscInt *lens,*lrows,*values,rstart_bs=A->rmap->rstart; 1746 MPI_Comm comm = ((PetscObject)A)->comm; 1747 MPI_Request *send_waits,*recv_waits; 1748 MPI_Status recv_status,*send_status; 1749 const PetscScalar *xx; 1750 PetscScalar *bb; 1751 #if defined(PETSC_DEBUG) 1752 PetscBool found = PETSC_FALSE; 1753 #endif 1754 1755 PetscFunctionBegin; 1756 /* first count number of contributors to each processor */ 1757 ierr = PetscMalloc(2*size*sizeof(PetscInt),&nprocs);CHKERRQ(ierr); 1758 ierr = PetscMemzero(nprocs,2*size*sizeof(PetscInt));CHKERRQ(ierr); 1759 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&owner);CHKERRQ(ierr); /* see note*/ 1760 j = 0; 1761 for (i=0; i<N; i++) { 1762 if (lastidx > (idx = rows[i])) j = 0; 1763 lastidx = idx; 1764 for (; j<size; j++) { 1765 if (idx >= owners[j] && idx < owners[j+1]) { 1766 nprocs[2*j]++; 1767 nprocs[2*j+1] = 1; 1768 owner[i] = j; 1769 #if defined(PETSC_DEBUG) 1770 found = PETSC_TRUE; 1771 #endif 1772 break; 1773 } 1774 } 1775 #if defined(PETSC_DEBUG) 1776 if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index out of range"); 1777 found = PETSC_FALSE; 1778 #endif 1779 } 1780 nsends = 0; for (i=0; i<size; i++) { nsends += nprocs[2*i+1];} 1781 1782 if (A->nooffproczerorows) { 1783 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"); 1784 nrecvs = nsends; 1785 nmax = N; 1786 } else { 1787 /* inform other processors of number of messages and max length*/ 1788 ierr = PetscMaxSum(comm,nprocs,&nmax,&nrecvs);CHKERRQ(ierr); 1789 } 1790 1791 /* post receives: */ 1792 ierr = PetscMalloc((nrecvs+1)*(nmax+1)*sizeof(PetscInt),&rvalues);CHKERRQ(ierr); 1793 ierr = PetscMalloc((nrecvs+1)*sizeof(MPI_Request),&recv_waits);CHKERRQ(ierr); 1794 for (i=0; i<nrecvs; i++) { 1795 ierr = MPI_Irecv(rvalues+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag,comm,recv_waits+i);CHKERRQ(ierr); 1796 } 1797 1798 /* do sends: 1799 1) starts[i] gives the starting index in svalues for stuff going to 1800 the ith processor 1801 */ 1802 ierr = PetscMalloc((N+1)*sizeof(PetscInt),&svalues);CHKERRQ(ierr); 1803 ierr = PetscMalloc((nsends+1)*sizeof(MPI_Request),&send_waits);CHKERRQ(ierr); 1804 ierr = PetscMalloc((size+1)*sizeof(PetscInt),&starts);CHKERRQ(ierr); 1805 starts[0] = 0; 1806 for (i=1; i<size; i++) { starts[i] = starts[i-1] + nprocs[2*i-2];} 1807 for (i=0; i<N; i++) { 1808 svalues[starts[owner[i]]++] = rows[i]; 1809 } 1810 1811 starts[0] = 0; 1812 for (i=1; i<size+1; i++) { starts[i] = starts[i-1] + nprocs[2*i-2];} 1813 count = 0; 1814 for (i=0; i<size; i++) { 1815 if (nprocs[2*i+1]) { 1816 ierr = MPI_Isend(svalues+starts[i],nprocs[2*i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr); 1817 } 1818 } 1819 ierr = PetscFree(starts);CHKERRQ(ierr); 1820 1821 base = owners[rank]; 1822 1823 /* wait on receives */ 1824 ierr = PetscMalloc2(nrecvs+1,PetscInt,&lens,nrecvs+1,PetscInt,&source);CHKERRQ(ierr); 1825 count = nrecvs; 1826 slen = 0; 1827 while (count) { 1828 ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr); 1829 /* unpack receives into our local space */ 1830 ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr); 1831 source[imdex] = recv_status.MPI_SOURCE; 1832 lens[imdex] = n; 1833 slen += n; 1834 count--; 1835 } 1836 ierr = PetscFree(recv_waits);CHKERRQ(ierr); 1837 1838 /* move the data into the send scatter */ 1839 ierr = PetscMalloc((slen+1)*sizeof(PetscInt),&lrows);CHKERRQ(ierr); 1840 count = 0; 1841 for (i=0; i<nrecvs; i++) { 1842 values = rvalues + i*nmax; 1843 for (j=0; j<lens[i]; j++) { 1844 lrows[count++] = values[j] - base; 1845 } 1846 } 1847 ierr = PetscFree(rvalues);CHKERRQ(ierr); 1848 ierr = PetscFree2(lens,source);CHKERRQ(ierr); 1849 ierr = PetscFree(owner);CHKERRQ(ierr); 1850 ierr = PetscFree(nprocs);CHKERRQ(ierr); 1851 1852 /* fix right hand side if needed */ 1853 if (x && b) { 1854 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1855 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1856 for (i=0; i<slen; i++) { 1857 bb[lrows[i]] = diag*xx[lrows[i]]; 1858 } 1859 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1860 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1861 } 1862 1863 /* actually zap the local rows */ 1864 /* 1865 Zero the required rows. If the "diagonal block" of the matrix 1866 is square and the user wishes to set the diagonal we use separate 1867 code so that MatSetValues() is not called for each diagonal allocating 1868 new memory, thus calling lots of mallocs and slowing things down. 1869 1870 */ 1871 /* must zero l->B before l->A because the (diag) case below may put values into l->B*/ 1872 ierr = MatZeroRows_SeqBAIJ(l->B,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1873 if ((diag != 0.0) && (l->A->rmap->N == l->A->cmap->N)) { 1874 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,diag,0,0);CHKERRQ(ierr); 1875 } else if (diag != 0.0) { 1876 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1877 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\ 1878 MAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 1879 for (i=0; i<slen; i++) { 1880 row = lrows[i] + rstart_bs; 1881 ierr = MatSetValues(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1882 } 1883 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1884 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1885 } else { 1886 ierr = MatZeroRows_SeqBAIJ(l->A,slen,lrows,0.0,0,0);CHKERRQ(ierr); 1887 } 1888 1889 ierr = PetscFree(lrows);CHKERRQ(ierr); 1890 1891 /* wait on sends */ 1892 if (nsends) { 1893 ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr); 1894 ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr); 1895 ierr = PetscFree(send_status);CHKERRQ(ierr); 1896 } 1897 ierr = PetscFree(send_waits);CHKERRQ(ierr); 1898 ierr = PetscFree(svalues);CHKERRQ(ierr); 1899 1900 PetscFunctionReturn(0); 1901 } 1902 1903 #undef __FUNCT__ 1904 #define __FUNCT__ "MatSetUnfactored_MPIBAIJ" 1905 PetscErrorCode MatSetUnfactored_MPIBAIJ(Mat A) 1906 { 1907 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1908 PetscErrorCode ierr; 1909 1910 PetscFunctionBegin; 1911 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 1912 PetscFunctionReturn(0); 1913 } 1914 1915 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat,MatDuplicateOption,Mat *); 1916 1917 #undef __FUNCT__ 1918 #define __FUNCT__ "MatEqual_MPIBAIJ" 1919 PetscErrorCode MatEqual_MPIBAIJ(Mat A,Mat B,PetscBool *flag) 1920 { 1921 Mat_MPIBAIJ *matB = (Mat_MPIBAIJ*)B->data,*matA = (Mat_MPIBAIJ*)A->data; 1922 Mat a,b,c,d; 1923 PetscBool flg; 1924 PetscErrorCode ierr; 1925 1926 PetscFunctionBegin; 1927 a = matA->A; b = matA->B; 1928 c = matB->A; d = matB->B; 1929 1930 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 1931 if (flg) { 1932 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 1933 } 1934 ierr = MPI_Allreduce(&flg,flag,1,MPI_INT,MPI_LAND,((PetscObject)A)->comm);CHKERRQ(ierr); 1935 PetscFunctionReturn(0); 1936 } 1937 1938 #undef __FUNCT__ 1939 #define __FUNCT__ "MatCopy_MPIBAIJ" 1940 PetscErrorCode MatCopy_MPIBAIJ(Mat A,Mat B,MatStructure str) 1941 { 1942 PetscErrorCode ierr; 1943 Mat_MPIBAIJ *a = (Mat_MPIBAIJ *)A->data; 1944 Mat_MPIBAIJ *b = (Mat_MPIBAIJ *)B->data; 1945 1946 PetscFunctionBegin; 1947 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 1948 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 1949 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1950 } else { 1951 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 1952 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 1953 } 1954 PetscFunctionReturn(0); 1955 } 1956 1957 #undef __FUNCT__ 1958 #define __FUNCT__ "MatSetUp_MPIBAIJ" 1959 PetscErrorCode MatSetUp_MPIBAIJ(Mat A) 1960 { 1961 PetscErrorCode ierr; 1962 1963 PetscFunctionBegin; 1964 ierr = MatMPIBAIJSetPreallocation(A,A->rmap->bs,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 1965 PetscFunctionReturn(0); 1966 } 1967 1968 #undef __FUNCT__ 1969 #define __FUNCT__ "MatAXPY_MPIBAIJ" 1970 PetscErrorCode MatAXPY_MPIBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1971 { 1972 PetscErrorCode ierr; 1973 Mat_MPIBAIJ *xx=(Mat_MPIBAIJ *)X->data,*yy=(Mat_MPIBAIJ *)Y->data; 1974 PetscBLASInt bnz,one=1; 1975 Mat_SeqBAIJ *x,*y; 1976 1977 PetscFunctionBegin; 1978 if (str == SAME_NONZERO_PATTERN) { 1979 PetscScalar alpha = a; 1980 x = (Mat_SeqBAIJ *)xx->A->data; 1981 y = (Mat_SeqBAIJ *)yy->A->data; 1982 bnz = PetscBLASIntCast(x->nz); 1983 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 1984 x = (Mat_SeqBAIJ *)xx->B->data; 1985 y = (Mat_SeqBAIJ *)yy->B->data; 1986 bnz = PetscBLASIntCast(x->nz); 1987 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 1988 } else { 1989 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1990 } 1991 PetscFunctionReturn(0); 1992 } 1993 1994 #undef __FUNCT__ 1995 #define __FUNCT__ "MatRealPart_MPIBAIJ" 1996 PetscErrorCode MatRealPart_MPIBAIJ(Mat A) 1997 { 1998 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 1999 PetscErrorCode ierr; 2000 2001 PetscFunctionBegin; 2002 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2003 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2004 PetscFunctionReturn(0); 2005 } 2006 2007 #undef __FUNCT__ 2008 #define __FUNCT__ "MatImaginaryPart_MPIBAIJ" 2009 PetscErrorCode MatImaginaryPart_MPIBAIJ(Mat A) 2010 { 2011 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2016 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2017 PetscFunctionReturn(0); 2018 } 2019 2020 #undef __FUNCT__ 2021 #define __FUNCT__ "MatGetSubMatrix_MPIBAIJ" 2022 PetscErrorCode MatGetSubMatrix_MPIBAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 2023 { 2024 PetscErrorCode ierr; 2025 IS iscol_local; 2026 PetscInt csize; 2027 2028 PetscFunctionBegin; 2029 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 2030 if (call == MAT_REUSE_MATRIX) { 2031 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 2032 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 2033 } else { 2034 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2035 } 2036 ierr = MatGetSubMatrix_MPIBAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 2037 if (call == MAT_INITIAL_MATRIX) { 2038 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 2039 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 2040 } 2041 PetscFunctionReturn(0); 2042 } 2043 extern PetscErrorCode MatGetSubMatrices_MPIBAIJ_local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool*,PetscBool*,Mat*); 2044 #undef __FUNCT__ 2045 #define __FUNCT__ "MatGetSubMatrix_MPIBAIJ_Private" 2046 /* 2047 Not great since it makes two copies of the submatrix, first an SeqBAIJ 2048 in local and then by concatenating the local matrices the end result. 2049 Writing it directly would be much like MatGetSubMatrices_MPIBAIJ() 2050 */ 2051 PetscErrorCode MatGetSubMatrix_MPIBAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 2052 { 2053 PetscErrorCode ierr; 2054 PetscMPIInt rank,size; 2055 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs; 2056 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal,ncol,nrow; 2057 Mat M,Mreuse; 2058 MatScalar *vwork,*aa; 2059 MPI_Comm comm = ((PetscObject)mat)->comm; 2060 IS isrow_new, iscol_new; 2061 PetscBool idflag,allrows, allcols; 2062 Mat_SeqBAIJ *aij; 2063 2064 2065 PetscFunctionBegin; 2066 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2067 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2068 /* The compression and expansion should be avoided. Doesn't point 2069 out errors, might change the indices, hence buggey */ 2070 ierr = ISCompressIndicesGeneral(mat->rmap->N,mat->rmap->n,mat->rmap->bs,1,&isrow,&isrow_new);CHKERRQ(ierr); 2071 ierr = ISCompressIndicesGeneral(mat->cmap->N,mat->cmap->n,mat->cmap->bs,1,&iscol,&iscol_new);CHKERRQ(ierr); 2072 2073 /* Check for special case: each processor gets entire matrix columns */ 2074 ierr = ISIdentity(iscol,&idflag);CHKERRQ(ierr); 2075 ierr = ISGetLocalSize(iscol,&ncol);CHKERRQ(ierr); 2076 if (idflag && ncol == mat->cmap->N){ 2077 allcols = PETSC_TRUE; 2078 } else { 2079 allcols = PETSC_FALSE; 2080 } 2081 2082 ierr = ISIdentity(isrow,&idflag);CHKERRQ(ierr); 2083 ierr = ISGetLocalSize(isrow,&nrow);CHKERRQ(ierr); 2084 if (idflag && nrow == mat->rmap->N){ 2085 allrows = PETSC_TRUE; 2086 } else { 2087 allrows = PETSC_FALSE; 2088 } 2089 if (call == MAT_REUSE_MATRIX) { 2090 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject *)&Mreuse);CHKERRQ(ierr); 2091 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 2092 ierr = MatGetSubMatrices_MPIBAIJ_local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,&allrows,&allcols,&Mreuse);CHKERRQ(ierr); 2093 } else { 2094 ierr = MatGetSubMatrices_MPIBAIJ_local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&allrows,&allcols,&Mreuse);CHKERRQ(ierr); 2095 } 2096 ierr = ISDestroy(&isrow_new); CHKERRQ(ierr); 2097 ierr = ISDestroy(&iscol_new); CHKERRQ(ierr); 2098 /* 2099 m - number of local rows 2100 n - number of columns (same on all processors) 2101 rstart - first row in new global matrix generated 2102 */ 2103 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 2104 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 2105 m = m/bs; 2106 n = n/bs; 2107 2108 if (call == MAT_INITIAL_MATRIX) { 2109 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 2110 ii = aij->i; 2111 jj = aij->j; 2112 2113 /* 2114 Determine the number of non-zeros in the diagonal and off-diagonal 2115 portions of the matrix in order to do correct preallocation 2116 */ 2117 2118 /* first get start and end of "diagonal" columns */ 2119 if (csize == PETSC_DECIDE) { 2120 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 2121 if (mglobal == n*bs) { /* square matrix */ 2122 nlocal = m; 2123 } else { 2124 nlocal = n/size + ((n % size) > rank); 2125 } 2126 } else { 2127 nlocal = csize/bs; 2128 } 2129 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2130 rstart = rend - nlocal; 2131 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); 2132 2133 /* next, compute all the lengths */ 2134 ierr = PetscMalloc((2*m+1)*sizeof(PetscInt),&dlens);CHKERRQ(ierr); 2135 olens = dlens + m; 2136 for (i=0; i<m; i++) { 2137 jend = ii[i+1] - ii[i]; 2138 olen = 0; 2139 dlen = 0; 2140 for (j=0; j<jend; j++) { 2141 if (*jj < rstart || *jj >= rend) olen++; 2142 else dlen++; 2143 jj++; 2144 } 2145 olens[i] = olen; 2146 dlens[i] = dlen; 2147 } 2148 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 2149 ierr = MatSetSizes(M,bs*m,bs*nlocal,PETSC_DECIDE,bs*n);CHKERRQ(ierr); 2150 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 2151 ierr = MatMPIBAIJSetPreallocation(M,bs,0,dlens,0,olens);CHKERRQ(ierr); 2152 ierr = PetscFree(dlens);CHKERRQ(ierr); 2153 } else { 2154 PetscInt ml,nl; 2155 2156 M = *newmat; 2157 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 2158 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 2159 ierr = MatZeroEntries(M);CHKERRQ(ierr); 2160 /* 2161 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 2162 rather than the slower MatSetValues(). 2163 */ 2164 M->was_assembled = PETSC_TRUE; 2165 M->assembled = PETSC_FALSE; 2166 } 2167 ierr = MatSetOption(M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 2168 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 2169 aij = (Mat_SeqBAIJ*)(Mreuse)->data; 2170 ii = aij->i; 2171 jj = aij->j; 2172 aa = aij->a; 2173 for (i=0; i<m; i++) { 2174 row = rstart/bs + i; 2175 nz = ii[i+1] - ii[i]; 2176 cwork = jj; jj += nz; 2177 vwork = aa; aa += nz; 2178 ierr = MatSetValuesBlocked_MPIBAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 2179 } 2180 2181 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2182 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2183 *newmat = M; 2184 2185 /* save submatrix used in processor for next request */ 2186 if (call == MAT_INITIAL_MATRIX) { 2187 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 2188 ierr = PetscObjectDereference((PetscObject)Mreuse);CHKERRQ(ierr); 2189 } 2190 2191 PetscFunctionReturn(0); 2192 } 2193 2194 #undef __FUNCT__ 2195 #define __FUNCT__ "MatPermute_MPIBAIJ" 2196 PetscErrorCode MatPermute_MPIBAIJ(Mat A,IS rowp,IS colp,Mat *B) 2197 { 2198 MPI_Comm comm,pcomm; 2199 PetscInt first,local_size,nrows; 2200 const PetscInt *rows; 2201 PetscMPIInt size; 2202 IS crowp,growp,irowp,lrowp,lcolp,icolp; 2203 PetscErrorCode ierr; 2204 2205 PetscFunctionBegin; 2206 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 2207 /* make a collective version of 'rowp' */ 2208 ierr = PetscObjectGetComm((PetscObject)rowp,&pcomm);CHKERRQ(ierr); 2209 if (pcomm==comm) { 2210 crowp = rowp; 2211 } else { 2212 ierr = ISGetSize(rowp,&nrows);CHKERRQ(ierr); 2213 ierr = ISGetIndices(rowp,&rows);CHKERRQ(ierr); 2214 ierr = ISCreateGeneral(comm,nrows,rows,PETSC_COPY_VALUES,&crowp);CHKERRQ(ierr); 2215 ierr = ISRestoreIndices(rowp,&rows);CHKERRQ(ierr); 2216 } 2217 /* collect the global row permutation and invert it */ 2218 ierr = ISAllGather(crowp,&growp);CHKERRQ(ierr); 2219 ierr = ISSetPermutation(growp);CHKERRQ(ierr); 2220 if (pcomm!=comm) { 2221 ierr = ISDestroy(&crowp);CHKERRQ(ierr); 2222 } 2223 ierr = ISInvertPermutation(growp,PETSC_DECIDE,&irowp);CHKERRQ(ierr); 2224 /* get the local target indices */ 2225 ierr = MatGetOwnershipRange(A,&first,PETSC_NULL);CHKERRQ(ierr); 2226 ierr = MatGetLocalSize(A,&local_size,PETSC_NULL);CHKERRQ(ierr); 2227 ierr = ISGetIndices(irowp,&rows);CHKERRQ(ierr); 2228 ierr = ISCreateGeneral(MPI_COMM_SELF,local_size,rows+first,PETSC_COPY_VALUES,&lrowp);CHKERRQ(ierr); 2229 ierr = ISRestoreIndices(irowp,&rows);CHKERRQ(ierr); 2230 ierr = ISDestroy(&irowp);CHKERRQ(ierr); 2231 /* the column permutation is so much easier; 2232 make a local version of 'colp' and invert it */ 2233 ierr = PetscObjectGetComm((PetscObject)colp,&pcomm);CHKERRQ(ierr); 2234 ierr = MPI_Comm_size(pcomm,&size);CHKERRQ(ierr); 2235 if (size==1) { 2236 lcolp = colp; 2237 } else { 2238 ierr = ISGetSize(colp,&nrows);CHKERRQ(ierr); 2239 ierr = ISGetIndices(colp,&rows);CHKERRQ(ierr); 2240 ierr = ISCreateGeneral(MPI_COMM_SELF,nrows,rows,PETSC_COPY_VALUES,&lcolp);CHKERRQ(ierr); 2241 } 2242 ierr = ISSetPermutation(lcolp);CHKERRQ(ierr); 2243 ierr = ISInvertPermutation(lcolp,PETSC_DECIDE,&icolp);CHKERRQ(ierr); 2244 ierr = ISSetPermutation(icolp);CHKERRQ(ierr); 2245 if (size>1) { 2246 ierr = ISRestoreIndices(colp,&rows);CHKERRQ(ierr); 2247 ierr = ISDestroy(&lcolp);CHKERRQ(ierr); 2248 } 2249 /* now we just get the submatrix */ 2250 ierr = MatGetSubMatrix_MPIBAIJ_Private(A,lrowp,icolp,local_size,MAT_INITIAL_MATRIX,B);CHKERRQ(ierr); 2251 /* clean up */ 2252 ierr = ISDestroy(&lrowp);CHKERRQ(ierr); 2253 ierr = ISDestroy(&icolp);CHKERRQ(ierr); 2254 PetscFunctionReturn(0); 2255 } 2256 2257 #undef __FUNCT__ 2258 #define __FUNCT__ "MatGetGhosts_MPIBAIJ" 2259 PetscErrorCode MatGetGhosts_MPIBAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 2260 { 2261 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*) mat->data; 2262 Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; 2263 2264 PetscFunctionBegin; 2265 if (nghosts) { *nghosts = B->nbs;} 2266 if (ghosts) {*ghosts = baij->garray;} 2267 PetscFunctionReturn(0); 2268 } 2269 2270 extern PetscErrorCode MatCreateColmap_MPIBAIJ_Private(Mat); 2271 2272 #undef __FUNCT__ 2273 #define __FUNCT__ "MatFDColoringCreate_MPIBAIJ" 2274 /* 2275 This routine is almost identical to MatFDColoringCreate_MPIBAIJ()! 2276 */ 2277 PetscErrorCode MatFDColoringCreate_MPIBAIJ(Mat mat,ISColoring iscoloring,MatFDColoring c) 2278 { 2279 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 2280 PetscErrorCode ierr; 2281 PetscMPIInt size,*ncolsonproc,*disp,nn; 2282 PetscInt bs,i,n,nrows,j,k,m,*rows = 0,*A_ci,*A_cj,ncols,col; 2283 const PetscInt *is; 2284 PetscInt nis = iscoloring->n,nctot,*cols,*B_ci,*B_cj; 2285 PetscInt *rowhit,M,cstart,cend,colb; 2286 PetscInt *columnsforrow,l; 2287 IS *isa; 2288 PetscBool done,flg; 2289 ISLocalToGlobalMapping map = mat->cmap->bmapping; 2290 PetscInt *ltog = (map ? map->indices : (PetscInt*) PETSC_NULL) ,ctype=c->ctype; 2291 2292 PetscFunctionBegin; 2293 if (!mat->assembled) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Matrix must be assembled first; MatAssemblyBegin/End();"); 2294 if (ctype == IS_COLORING_GHOSTED && !map) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_INCOMP,"When using ghosted differencing matrix must have local to global mapping provided with MatSetLocalToGlobalMappingBlock"); 2295 2296 ierr = ISColoringGetIS(iscoloring,PETSC_IGNORE,&isa);CHKERRQ(ierr); 2297 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 2298 M = mat->rmap->n/bs; 2299 cstart = mat->cmap->rstart/bs; 2300 cend = mat->cmap->rend/bs; 2301 c->M = mat->rmap->N/bs; /* set the global rows and columns and local rows */ 2302 c->N = mat->cmap->N/bs; 2303 c->m = mat->rmap->n/bs; 2304 c->rstart = mat->rmap->rstart/bs; 2305 2306 c->ncolors = nis; 2307 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->ncolumns);CHKERRQ(ierr); 2308 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columns);CHKERRQ(ierr); 2309 ierr = PetscMalloc(nis*sizeof(PetscInt),&c->nrows);CHKERRQ(ierr); 2310 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->rows);CHKERRQ(ierr); 2311 ierr = PetscMalloc(nis*sizeof(PetscInt*),&c->columnsforrow);CHKERRQ(ierr); 2312 ierr = PetscLogObjectMemory(c,5*nis*sizeof(PetscInt));CHKERRQ(ierr); 2313 2314 /* Allow access to data structures of local part of matrix */ 2315 if (!baij->colmap) { 2316 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 2317 } 2318 ierr = MatGetColumnIJ(baij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 2319 ierr = MatGetColumnIJ(baij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 2320 2321 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&rowhit);CHKERRQ(ierr); 2322 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&columnsforrow);CHKERRQ(ierr); 2323 2324 for (i=0; i<nis; i++) { 2325 ierr = ISGetLocalSize(isa[i],&n);CHKERRQ(ierr); 2326 ierr = ISGetIndices(isa[i],&is);CHKERRQ(ierr); 2327 c->ncolumns[i] = n; 2328 if (n) { 2329 ierr = PetscMalloc(n*sizeof(PetscInt),&c->columns[i]);CHKERRQ(ierr); 2330 ierr = PetscLogObjectMemory(c,n*sizeof(PetscInt));CHKERRQ(ierr); 2331 ierr = PetscMemcpy(c->columns[i],is,n*sizeof(PetscInt));CHKERRQ(ierr); 2332 } else { 2333 c->columns[i] = 0; 2334 } 2335 2336 if (ctype == IS_COLORING_GLOBAL){ 2337 /* Determine the total (parallel) number of columns of this color */ 2338 ierr = MPI_Comm_size(((PetscObject)mat)->comm,&size);CHKERRQ(ierr); 2339 ierr = PetscMalloc2(size,PetscMPIInt,&ncolsonproc,size,PetscMPIInt,&disp);CHKERRQ(ierr); 2340 2341 nn = PetscMPIIntCast(n); 2342 ierr = MPI_Allgather(&nn,1,MPI_INT,ncolsonproc,1,MPI_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 2343 nctot = 0; for (j=0; j<size; j++) {nctot += ncolsonproc[j];} 2344 if (!nctot) { 2345 ierr = PetscInfo(mat,"Coloring of matrix has some unneeded colors with no corresponding rows\n");CHKERRQ(ierr); 2346 } 2347 2348 disp[0] = 0; 2349 for (j=1; j<size; j++) { 2350 disp[j] = disp[j-1] + ncolsonproc[j-1]; 2351 } 2352 2353 /* Get complete list of columns for color on each processor */ 2354 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 2355 ierr = MPI_Allgatherv((void*)is,n,MPIU_INT,cols,ncolsonproc,disp,MPIU_INT,((PetscObject)mat)->comm);CHKERRQ(ierr); 2356 ierr = PetscFree2(ncolsonproc,disp);CHKERRQ(ierr); 2357 } else if (ctype == IS_COLORING_GHOSTED){ 2358 /* Determine local number of columns of this color on this process, including ghost points */ 2359 nctot = n; 2360 ierr = PetscMalloc((nctot+1)*sizeof(PetscInt),&cols);CHKERRQ(ierr); 2361 ierr = PetscMemcpy(cols,is,n*sizeof(PetscInt));CHKERRQ(ierr); 2362 } else { 2363 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not provided for this MatFDColoring type"); 2364 } 2365 2366 /* 2367 Mark all rows affect by these columns 2368 */ 2369 /* Temporary option to allow for debugging/testing */ 2370 flg = PETSC_FALSE; 2371 ierr = PetscOptionsGetBool(PETSC_NULL,"-matfdcoloring_slow",&flg,PETSC_NULL);CHKERRQ(ierr); 2372 if (!flg) {/*-----------------------------------------------------------------------------*/ 2373 /* crude, fast version */ 2374 ierr = PetscMemzero(rowhit,M*sizeof(PetscInt));CHKERRQ(ierr); 2375 /* loop over columns*/ 2376 for (j=0; j<nctot; j++) { 2377 if (ctype == IS_COLORING_GHOSTED) { 2378 col = ltog[cols[j]]; 2379 } else { 2380 col = cols[j]; 2381 } 2382 if (col >= cstart && col < cend) { 2383 /* column is in diagonal block of matrix */ 2384 rows = A_cj + A_ci[col-cstart]; 2385 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 2386 } else { 2387 #if defined (PETSC_USE_CTABLE) 2388 ierr = PetscTableFind(baij->colmap,col+1,&colb);CHKERRQ(ierr); 2389 colb --; 2390 #else 2391 colb = baij->colmap[col] - 1; 2392 #endif 2393 if (colb == -1) { 2394 m = 0; 2395 } else { 2396 colb = colb/bs; 2397 rows = B_cj + B_ci[colb]; 2398 m = B_ci[colb+1] - B_ci[colb]; 2399 } 2400 } 2401 /* loop over columns marking them in rowhit */ 2402 for (k=0; k<m; k++) { 2403 rowhit[*rows++] = col + 1; 2404 } 2405 } 2406 2407 /* count the number of hits */ 2408 nrows = 0; 2409 for (j=0; j<M; j++) { 2410 if (rowhit[j]) nrows++; 2411 } 2412 c->nrows[i] = nrows; 2413 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 2414 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 2415 ierr = PetscLogObjectMemory(c,2*(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 2416 nrows = 0; 2417 for (j=0; j<M; j++) { 2418 if (rowhit[j]) { 2419 c->rows[i][nrows] = j; 2420 c->columnsforrow[i][nrows] = rowhit[j] - 1; 2421 nrows++; 2422 } 2423 } 2424 } else {/*-------------------------------------------------------------------------------*/ 2425 /* slow version, using rowhit as a linked list */ 2426 PetscInt currentcol,fm,mfm; 2427 rowhit[M] = M; 2428 nrows = 0; 2429 /* loop over columns*/ 2430 for (j=0; j<nctot; j++) { 2431 if (ctype == IS_COLORING_GHOSTED) { 2432 col = ltog[cols[j]]; 2433 } else { 2434 col = cols[j]; 2435 } 2436 if (col >= cstart && col < cend) { 2437 /* column is in diagonal block of matrix */ 2438 rows = A_cj + A_ci[col-cstart]; 2439 m = A_ci[col-cstart+1] - A_ci[col-cstart]; 2440 } else { 2441 #if defined (PETSC_USE_CTABLE) 2442 ierr = PetscTableFind(baij->colmap,col+1,&colb);CHKERRQ(ierr); 2443 colb --; 2444 #else 2445 colb = baij->colmap[col] - 1; 2446 #endif 2447 if (colb == -1) { 2448 m = 0; 2449 } else { 2450 colb = colb/bs; 2451 rows = B_cj + B_ci[colb]; 2452 m = B_ci[colb+1] - B_ci[colb]; 2453 } 2454 } 2455 2456 /* loop over columns marking them in rowhit */ 2457 fm = M; /* fm points to first entry in linked list */ 2458 for (k=0; k<m; k++) { 2459 currentcol = *rows++; 2460 /* is it already in the list? */ 2461 do { 2462 mfm = fm; 2463 fm = rowhit[fm]; 2464 } while (fm < currentcol); 2465 /* not in list so add it */ 2466 if (fm != currentcol) { 2467 nrows++; 2468 columnsforrow[currentcol] = col; 2469 /* next three lines insert new entry into linked list */ 2470 rowhit[mfm] = currentcol; 2471 rowhit[currentcol] = fm; 2472 fm = currentcol; 2473 /* fm points to present position in list since we know the columns are sorted */ 2474 } else { 2475 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid coloring of matrix detected"); 2476 } 2477 } 2478 } 2479 c->nrows[i] = nrows; 2480 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->rows[i]);CHKERRQ(ierr); 2481 ierr = PetscMalloc((nrows+1)*sizeof(PetscInt),&c->columnsforrow[i]);CHKERRQ(ierr); 2482 ierr = PetscLogObjectMemory(c,(nrows+1)*sizeof(PetscInt));CHKERRQ(ierr); 2483 /* now store the linked list of rows into c->rows[i] */ 2484 nrows = 0; 2485 fm = rowhit[M]; 2486 do { 2487 c->rows[i][nrows] = fm; 2488 c->columnsforrow[i][nrows++] = columnsforrow[fm]; 2489 fm = rowhit[fm]; 2490 } while (fm < M); 2491 } /* ---------------------------------------------------------------------------------------*/ 2492 ierr = PetscFree(cols);CHKERRQ(ierr); 2493 } 2494 2495 /* Optimize by adding the vscale, and scaleforrow[][] fields */ 2496 /* 2497 vscale will contain the "diagonal" on processor scalings followed by the off processor 2498 */ 2499 if (ctype == IS_COLORING_GLOBAL) { 2500 PetscInt *garray; 2501 ierr = PetscMalloc(baij->B->cmap->n*sizeof(PetscInt),&garray);CHKERRQ(ierr); 2502 for (i=0; i<baij->B->cmap->n/bs; i++) { 2503 for (j=0; j<bs; j++) { 2504 garray[i*bs+j] = bs*baij->garray[i]+j; 2505 } 2506 } 2507 ierr = VecCreateGhost(((PetscObject)mat)->comm,baij->A->rmap->n,PETSC_DETERMINE,baij->B->cmap->n,garray,&c->vscale);CHKERRQ(ierr); 2508 ierr = PetscFree(garray);CHKERRQ(ierr); 2509 CHKMEMQ; 2510 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 2511 for (k=0; k<c->ncolors; k++) { 2512 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 2513 for (l=0; l<c->nrows[k]; l++) { 2514 col = c->columnsforrow[k][l]; 2515 if (col >= cstart && col < cend) { 2516 /* column is in diagonal block of matrix */ 2517 colb = col - cstart; 2518 } else { 2519 /* column is in "off-processor" part */ 2520 #if defined (PETSC_USE_CTABLE) 2521 ierr = PetscTableFind(baij->colmap,col+1,&colb);CHKERRQ(ierr); 2522 colb --; 2523 #else 2524 colb = baij->colmap[col] - 1; 2525 #endif 2526 colb = colb/bs; 2527 colb += cend - cstart; 2528 } 2529 c->vscaleforrow[k][l] = colb; 2530 } 2531 } 2532 } else if (ctype == IS_COLORING_GHOSTED) { 2533 /* Get gtol mapping */ 2534 PetscInt N = mat->cmap->N, *gtol; 2535 ierr = PetscMalloc((N+1)*sizeof(PetscInt),>ol);CHKERRQ(ierr); 2536 for (i=0; i<N; i++) gtol[i] = -1; 2537 for (i=0; i<map->n; i++) gtol[ltog[i]] = i; 2538 2539 c->vscale = 0; /* will be created in MatFDColoringApply() */ 2540 ierr = PetscMalloc(c->ncolors*sizeof(PetscInt*),&c->vscaleforrow);CHKERRQ(ierr); 2541 for (k=0; k<c->ncolors; k++) { 2542 ierr = PetscMalloc((c->nrows[k]+1)*sizeof(PetscInt),&c->vscaleforrow[k]);CHKERRQ(ierr); 2543 for (l=0; l<c->nrows[k]; l++) { 2544 col = c->columnsforrow[k][l]; /* global column index */ 2545 c->vscaleforrow[k][l] = gtol[col]; /* local column index */ 2546 } 2547 } 2548 ierr = PetscFree(gtol);CHKERRQ(ierr); 2549 } 2550 ierr = ISColoringRestoreIS(iscoloring,&isa);CHKERRQ(ierr); 2551 2552 ierr = PetscFree(rowhit);CHKERRQ(ierr); 2553 ierr = PetscFree(columnsforrow);CHKERRQ(ierr); 2554 ierr = MatRestoreColumnIJ(baij->A,0,PETSC_FALSE,PETSC_FALSE,&ncols,&A_ci,&A_cj,&done);CHKERRQ(ierr); 2555 ierr = MatRestoreColumnIJ(baij->B,0,PETSC_FALSE,PETSC_FALSE,&ncols,&B_ci,&B_cj,&done);CHKERRQ(ierr); 2556 CHKMEMQ; 2557 PetscFunctionReturn(0); 2558 } 2559 2560 #undef __FUNCT__ 2561 #define __FUNCT__ "MatGetSeqNonzeroStructure_MPIBAIJ" 2562 PetscErrorCode MatGetSeqNonzeroStructure_MPIBAIJ(Mat A,Mat *newmat) 2563 { 2564 Mat B; 2565 Mat_MPIBAIJ *a = (Mat_MPIBAIJ *)A->data; 2566 Mat_SeqBAIJ *ad = (Mat_SeqBAIJ*)a->A->data,*bd = (Mat_SeqBAIJ*)a->B->data; 2567 Mat_SeqAIJ *b; 2568 PetscErrorCode ierr; 2569 PetscMPIInt size,rank,*recvcounts = 0,*displs = 0; 2570 PetscInt sendcount,i,*rstarts = A->rmap->range,n,cnt,j,bs = A->rmap->bs; 2571 PetscInt m,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf; 2572 2573 PetscFunctionBegin; 2574 ierr = MPI_Comm_size(((PetscObject)A)->comm,&size);CHKERRQ(ierr); 2575 ierr = MPI_Comm_rank(((PetscObject)A)->comm,&rank);CHKERRQ(ierr); 2576 2577 /* ---------------------------------------------------------------- 2578 Tell every processor the number of nonzeros per row 2579 */ 2580 ierr = PetscMalloc((A->rmap->N/bs)*sizeof(PetscInt),&lens);CHKERRQ(ierr); 2581 for (i=A->rmap->rstart/bs; i<A->rmap->rend/bs; i++) { 2582 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]; 2583 } 2584 sendcount = A->rmap->rend/bs - A->rmap->rstart/bs; 2585 ierr = PetscMalloc(2*size*sizeof(PetscMPIInt),&recvcounts);CHKERRQ(ierr); 2586 displs = recvcounts + size; 2587 for (i=0; i<size; i++) { 2588 recvcounts[i] = A->rmap->range[i+1]/bs - A->rmap->range[i]/bs; 2589 displs[i] = A->rmap->range[i]/bs; 2590 } 2591 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2592 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,((PetscObject)A)->comm);CHKERRQ(ierr); 2593 #else 2594 ierr = MPI_Allgatherv(lens+A->rmap->rstart/bs,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,((PetscObject)A)->comm);CHKERRQ(ierr); 2595 #endif 2596 /* --------------------------------------------------------------- 2597 Create the sequential matrix of the same type as the local block diagonal 2598 */ 2599 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 2600 ierr = MatSetSizes(B,A->rmap->N/bs,A->cmap->N/bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2601 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 2602 ierr = MatSeqAIJSetPreallocation(B,0,lens);CHKERRQ(ierr); 2603 b = (Mat_SeqAIJ *)B->data; 2604 2605 /*-------------------------------------------------------------------- 2606 Copy my part of matrix column indices over 2607 */ 2608 sendcount = ad->nz + bd->nz; 2609 jsendbuf = b->j + b->i[rstarts[rank]/bs]; 2610 a_jsendbuf = ad->j; 2611 b_jsendbuf = bd->j; 2612 n = A->rmap->rend/bs - A->rmap->rstart/bs; 2613 cnt = 0; 2614 for (i=0; i<n; i++) { 2615 2616 /* put in lower diagonal portion */ 2617 m = bd->i[i+1] - bd->i[i]; 2618 while (m > 0) { 2619 /* is it above diagonal (in bd (compressed) numbering) */ 2620 if (garray[*b_jsendbuf] > A->rmap->rstart/bs + i) break; 2621 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2622 m--; 2623 } 2624 2625 /* put in diagonal portion */ 2626 for (j=ad->i[i]; j<ad->i[i+1]; j++) { 2627 jsendbuf[cnt++] = A->rmap->rstart/bs + *a_jsendbuf++; 2628 } 2629 2630 /* put in upper diagonal portion */ 2631 while (m-- > 0) { 2632 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 2633 } 2634 } 2635 if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt); 2636 2637 /*-------------------------------------------------------------------- 2638 Gather all column indices to all processors 2639 */ 2640 for (i=0; i<size; i++) { 2641 recvcounts[i] = 0; 2642 for (j=A->rmap->range[i]/bs; j<A->rmap->range[i+1]/bs; j++) { 2643 recvcounts[i] += lens[j]; 2644 } 2645 } 2646 displs[0] = 0; 2647 for (i=1; i<size; i++) { 2648 displs[i] = displs[i-1] + recvcounts[i-1]; 2649 } 2650 #if defined(PETSC_HAVE_MPI_IN_PLACE) 2651 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,((PetscObject)A)->comm);CHKERRQ(ierr); 2652 #else 2653 ierr = MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,((PetscObject)A)->comm);CHKERRQ(ierr); 2654 #endif 2655 /*-------------------------------------------------------------------- 2656 Assemble the matrix into useable form (note numerical values not yet set) 2657 */ 2658 /* set the b->ilen (length of each row) values */ 2659 ierr = PetscMemcpy(b->ilen,lens,(A->rmap->N/bs)*sizeof(PetscInt));CHKERRQ(ierr); 2660 /* set the b->i indices */ 2661 b->i[0] = 0; 2662 for (i=1; i<=A->rmap->N/bs; i++) { 2663 b->i[i] = b->i[i-1] + lens[i-1]; 2664 } 2665 ierr = PetscFree(lens);CHKERRQ(ierr); 2666 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2667 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2668 ierr = PetscFree(recvcounts);CHKERRQ(ierr); 2669 2670 if (A->symmetric){ 2671 ierr = MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2672 } else if (A->hermitian) { 2673 ierr = MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr); 2674 } else if (A->structurally_symmetric) { 2675 ierr = MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 2676 } 2677 *newmat = B; 2678 PetscFunctionReturn(0); 2679 } 2680 2681 #undef __FUNCT__ 2682 #define __FUNCT__ "MatSOR_MPIBAIJ" 2683 PetscErrorCode MatSOR_MPIBAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 2684 { 2685 Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; 2686 PetscErrorCode ierr; 2687 Vec bb1 = 0; 2688 2689 PetscFunctionBegin; 2690 if (flag == SOR_APPLY_UPPER) { 2691 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2692 PetscFunctionReturn(0); 2693 } 2694 2695 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS) { 2696 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 2697 } 2698 2699 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP){ 2700 if (flag & SOR_ZERO_INITIAL_GUESS) { 2701 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2702 its--; 2703 } 2704 2705 while (its--) { 2706 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2707 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2708 2709 /* update rhs: bb1 = bb - B*x */ 2710 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2711 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2712 2713 /* local sweep */ 2714 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2715 } 2716 } else if (flag & SOR_LOCAL_FORWARD_SWEEP){ 2717 if (flag & SOR_ZERO_INITIAL_GUESS) { 2718 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2719 its--; 2720 } 2721 while (its--) { 2722 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2723 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2724 2725 /* update rhs: bb1 = bb - B*x */ 2726 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2727 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2728 2729 /* local sweep */ 2730 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2731 } 2732 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP){ 2733 if (flag & SOR_ZERO_INITIAL_GUESS) { 2734 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 2735 its--; 2736 } 2737 while (its--) { 2738 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2739 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2740 2741 /* update rhs: bb1 = bb - B*x */ 2742 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 2743 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 2744 2745 /* local sweep */ 2746 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 2747 } 2748 } else SETERRQ(((PetscObject)matin)->comm,PETSC_ERR_SUP,"Parallel version of SOR requested not supported"); 2749 2750 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 2751 PetscFunctionReturn(0); 2752 } 2753 2754 extern PetscErrorCode MatFDColoringApply_BAIJ(Mat,MatFDColoring,Vec,MatStructure*,void*); 2755 2756 #undef __FUNCT__ 2757 #define __FUNCT__ "MatInvertBlockDiagonal_MPIBAIJ" 2758 PetscErrorCode MatInvertBlockDiagonal_MPIBAIJ(Mat A,const PetscScalar **values) 2759 { 2760 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; 2761 PetscErrorCode ierr; 2762 2763 PetscFunctionBegin; 2764 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2765 PetscFunctionReturn(0); 2766 } 2767 2768 2769 /* -------------------------------------------------------------------*/ 2770 static struct _MatOps MatOps_Values = { 2771 MatSetValues_MPIBAIJ, 2772 MatGetRow_MPIBAIJ, 2773 MatRestoreRow_MPIBAIJ, 2774 MatMult_MPIBAIJ, 2775 /* 4*/ MatMultAdd_MPIBAIJ, 2776 MatMultTranspose_MPIBAIJ, 2777 MatMultTransposeAdd_MPIBAIJ, 2778 0, 2779 0, 2780 0, 2781 /*10*/ 0, 2782 0, 2783 0, 2784 MatSOR_MPIBAIJ, 2785 MatTranspose_MPIBAIJ, 2786 /*15*/ MatGetInfo_MPIBAIJ, 2787 MatEqual_MPIBAIJ, 2788 MatGetDiagonal_MPIBAIJ, 2789 MatDiagonalScale_MPIBAIJ, 2790 MatNorm_MPIBAIJ, 2791 /*20*/ MatAssemblyBegin_MPIBAIJ, 2792 MatAssemblyEnd_MPIBAIJ, 2793 MatSetOption_MPIBAIJ, 2794 MatZeroEntries_MPIBAIJ, 2795 /*24*/ MatZeroRows_MPIBAIJ, 2796 0, 2797 0, 2798 0, 2799 0, 2800 /*29*/ MatSetUp_MPIBAIJ, 2801 0, 2802 0, 2803 0, 2804 0, 2805 /*34*/ MatDuplicate_MPIBAIJ, 2806 0, 2807 0, 2808 0, 2809 0, 2810 /*39*/ MatAXPY_MPIBAIJ, 2811 MatGetSubMatrices_MPIBAIJ, 2812 MatIncreaseOverlap_MPIBAIJ, 2813 MatGetValues_MPIBAIJ, 2814 MatCopy_MPIBAIJ, 2815 /*44*/ 0, 2816 MatScale_MPIBAIJ, 2817 0, 2818 0, 2819 0, 2820 /*49*/ 0, 2821 0, 2822 0, 2823 0, 2824 0, 2825 /*54*/ MatFDColoringCreate_MPIBAIJ, 2826 0, 2827 MatSetUnfactored_MPIBAIJ, 2828 MatPermute_MPIBAIJ, 2829 MatSetValuesBlocked_MPIBAIJ, 2830 /*59*/ MatGetSubMatrix_MPIBAIJ, 2831 MatDestroy_MPIBAIJ, 2832 MatView_MPIBAIJ, 2833 0, 2834 0, 2835 /*64*/ 0, 2836 0, 2837 0, 2838 0, 2839 0, 2840 /*69*/ MatGetRowMaxAbs_MPIBAIJ, 2841 0, 2842 0, 2843 0, 2844 0, 2845 /*74*/ 0, 2846 MatFDColoringApply_BAIJ, 2847 0, 2848 0, 2849 0, 2850 /*79*/ 0, 2851 0, 2852 0, 2853 0, 2854 MatLoad_MPIBAIJ, 2855 /*84*/ 0, 2856 0, 2857 0, 2858 0, 2859 0, 2860 /*89*/ 0, 2861 0, 2862 0, 2863 0, 2864 0, 2865 /*94*/ 0, 2866 0, 2867 0, 2868 0, 2869 0, 2870 /*99*/ 0, 2871 0, 2872 0, 2873 0, 2874 0, 2875 /*104*/0, 2876 MatRealPart_MPIBAIJ, 2877 MatImaginaryPart_MPIBAIJ, 2878 0, 2879 0, 2880 /*109*/0, 2881 0, 2882 0, 2883 0, 2884 0, 2885 /*114*/MatGetSeqNonzeroStructure_MPIBAIJ, 2886 0, 2887 MatGetGhosts_MPIBAIJ, 2888 0, 2889 0, 2890 /*119*/0, 2891 0, 2892 0, 2893 0, 2894 0, 2895 /*124*/0, 2896 0, 2897 MatInvertBlockDiagonal_MPIBAIJ 2898 }; 2899 2900 EXTERN_C_BEGIN 2901 #undef __FUNCT__ 2902 #define __FUNCT__ "MatGetDiagonalBlock_MPIBAIJ" 2903 PetscErrorCode MatGetDiagonalBlock_MPIBAIJ(Mat A,Mat *a) 2904 { 2905 PetscFunctionBegin; 2906 *a = ((Mat_MPIBAIJ *)A->data)->A; 2907 PetscFunctionReturn(0); 2908 } 2909 EXTERN_C_END 2910 2911 EXTERN_C_BEGIN 2912 extern PetscErrorCode MatConvert_MPIBAIJ_MPISBAIJ(Mat, MatType,MatReuse,Mat*); 2913 EXTERN_C_END 2914 2915 EXTERN_C_BEGIN 2916 #undef __FUNCT__ 2917 #define __FUNCT__ "MatMPIBAIJSetPreallocationCSR_MPIBAIJ" 2918 PetscErrorCode MatMPIBAIJSetPreallocationCSR_MPIBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[],const PetscScalar V[]) 2919 { 2920 PetscInt m,rstart,cstart,cend; 2921 PetscInt i,j,d,nz,nz_max=0,*d_nnz=0,*o_nnz=0; 2922 const PetscInt *JJ=0; 2923 PetscScalar *values=0; 2924 PetscErrorCode ierr; 2925 2926 PetscFunctionBegin; 2927 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 2928 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 2929 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2930 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2931 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 2932 m = B->rmap->n/bs; 2933 rstart = B->rmap->rstart/bs; 2934 cstart = B->cmap->rstart/bs; 2935 cend = B->cmap->rend/bs; 2936 2937 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 2938 ierr = PetscMalloc2(m,PetscInt,&d_nnz,m,PetscInt,&o_nnz);CHKERRQ(ierr); 2939 for (i=0; i<m; i++) { 2940 nz = ii[i+1] - ii[i]; 2941 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative number of columns %D",i,nz); 2942 nz_max = PetscMax(nz_max,nz); 2943 JJ = jj + ii[i]; 2944 for (j=0; j<nz; j++) { 2945 if (*JJ >= cstart) break; 2946 JJ++; 2947 } 2948 d = 0; 2949 for (; j<nz; j++) { 2950 if (*JJ++ >= cend) break; 2951 d++; 2952 } 2953 d_nnz[i] = d; 2954 o_nnz[i] = nz - d; 2955 } 2956 ierr = MatMPIBAIJSetPreallocation(B,bs,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 2957 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 2958 2959 values = (PetscScalar*)V; 2960 if (!values) { 2961 ierr = PetscMalloc(bs*bs*nz_max*sizeof(PetscScalar),&values);CHKERRQ(ierr); 2962 ierr = PetscMemzero(values,bs*bs*nz_max*sizeof(PetscScalar));CHKERRQ(ierr); 2963 } 2964 for (i=0; i<m; i++) { 2965 PetscInt row = i + rstart; 2966 PetscInt ncols = ii[i+1] - ii[i]; 2967 const PetscInt *icols = jj + ii[i]; 2968 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 2969 ierr = MatSetValuesBlocked_MPIBAIJ(B,1,&row,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 2970 } 2971 2972 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 2973 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2974 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2975 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2976 PetscFunctionReturn(0); 2977 } 2978 EXTERN_C_END 2979 2980 #undef __FUNCT__ 2981 #define __FUNCT__ "MatMPIBAIJSetPreallocationCSR" 2982 /*@C 2983 MatMPIBAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in BAIJ format 2984 (the default parallel PETSc format). 2985 2986 Collective on MPI_Comm 2987 2988 Input Parameters: 2989 + A - the matrix 2990 . bs - the block size 2991 . i - the indices into j for the start of each local row (starts with zero) 2992 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2993 - v - optional values in the matrix 2994 2995 Level: developer 2996 2997 .keywords: matrix, aij, compressed row, sparse, parallel 2998 2999 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIBAIJSetPreallocation(), MatCreateAIJ(), MPIAIJ 3000 @*/ 3001 PetscErrorCode MatMPIBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3002 { 3003 PetscErrorCode ierr; 3004 3005 PetscFunctionBegin; 3006 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3007 PetscValidType(B,1); 3008 PetscValidLogicalCollectiveInt(B,bs,2); 3009 ierr = PetscTryMethod(B,"MatMPIBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 3010 PetscFunctionReturn(0); 3011 } 3012 3013 EXTERN_C_BEGIN 3014 #undef __FUNCT__ 3015 #define __FUNCT__ "MatMPIBAIJSetPreallocation_MPIBAIJ" 3016 PetscErrorCode MatMPIBAIJSetPreallocation_MPIBAIJ(Mat B,PetscInt bs,PetscInt d_nz,PetscInt *d_nnz,PetscInt o_nz,PetscInt *o_nnz) 3017 { 3018 Mat_MPIBAIJ *b; 3019 PetscErrorCode ierr; 3020 PetscInt i; 3021 PetscBool d_realalloc = PETSC_FALSE,o_realalloc = PETSC_FALSE; 3022 3023 PetscFunctionBegin; 3024 if (d_nz >= 0 || d_nnz) d_realalloc = PETSC_TRUE; 3025 if (o_nz >= 0 || o_nnz) o_realalloc = PETSC_TRUE; 3026 3027 if (d_nz == PETSC_DEFAULT || d_nz == PETSC_DECIDE) d_nz = 5; 3028 if (o_nz == PETSC_DEFAULT || o_nz == PETSC_DECIDE) o_nz = 2; 3029 if (d_nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"d_nz cannot be less than 0: value %D",d_nz); 3030 if (o_nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"o_nz cannot be less than 0: value %D",o_nz); 3031 3032 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 3033 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 3034 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3035 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3036 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 3037 3038 if (d_nnz) { 3039 for (i=0; i<B->rmap->n/bs; i++) { 3040 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]); 3041 } 3042 } 3043 if (o_nnz) { 3044 for (i=0; i<B->rmap->n/bs; i++) { 3045 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]); 3046 } 3047 } 3048 3049 b = (Mat_MPIBAIJ*)B->data; 3050 b->bs2 = bs*bs; 3051 b->mbs = B->rmap->n/bs; 3052 b->nbs = B->cmap->n/bs; 3053 b->Mbs = B->rmap->N/bs; 3054 b->Nbs = B->cmap->N/bs; 3055 3056 for (i=0; i<=b->size; i++) { 3057 b->rangebs[i] = B->rmap->range[i]/bs; 3058 } 3059 b->rstartbs = B->rmap->rstart/bs; 3060 b->rendbs = B->rmap->rend/bs; 3061 b->cstartbs = B->cmap->rstart/bs; 3062 b->cendbs = B->cmap->rend/bs; 3063 3064 if (!B->preallocated) { 3065 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 3066 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 3067 ierr = MatSetType(b->A,MATSEQBAIJ);CHKERRQ(ierr); 3068 ierr = PetscLogObjectParent(B,b->A);CHKERRQ(ierr); 3069 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 3070 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 3071 ierr = MatSetType(b->B,MATSEQBAIJ);CHKERRQ(ierr); 3072 ierr = PetscLogObjectParent(B,b->B);CHKERRQ(ierr); 3073 ierr = MatStashCreate_Private(((PetscObject)B)->comm,bs,&B->bstash);CHKERRQ(ierr); 3074 } 3075 3076 ierr = MatSeqBAIJSetPreallocation(b->A,bs,d_nz,d_nnz);CHKERRQ(ierr); 3077 ierr = MatSeqBAIJSetPreallocation(b->B,bs,o_nz,o_nnz);CHKERRQ(ierr); 3078 /* Do not error if the user did not give real preallocation information. Ugly because this would overwrite a previous user call to MatSetOption(). */ 3079 if (!d_realalloc) {ierr = MatSetOption(b->A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);} 3080 if (!o_realalloc) {ierr = MatSetOption(b->B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);} 3081 B->preallocated = PETSC_TRUE; 3082 PetscFunctionReturn(0); 3083 } 3084 EXTERN_C_END 3085 3086 EXTERN_C_BEGIN 3087 extern PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat,Vec); 3088 extern PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat,PetscReal); 3089 EXTERN_C_END 3090 3091 3092 EXTERN_C_BEGIN 3093 #undef __FUNCT__ 3094 #define __FUNCT__ "MatConvert_MPIBAIJ_MPIAdj" 3095 PetscErrorCode MatConvert_MPIBAIJ_MPIAdj(Mat B, const MatType newtype,MatReuse reuse,Mat *adj) 3096 { 3097 Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)B->data; 3098 PetscErrorCode ierr; 3099 Mat_SeqBAIJ *d = (Mat_SeqBAIJ*) b->A->data,*o = (Mat_SeqBAIJ*) b->B->data; 3100 PetscInt M = B->rmap->n/B->rmap->bs,i,*ii,*jj,cnt,j,k,rstart = B->rmap->rstart/B->rmap->bs; 3101 const PetscInt *id = d->i, *jd = d->j, *io = o->i, *jo = o->j, *garray = b->garray; 3102 3103 PetscFunctionBegin; 3104 ierr = PetscMalloc((M+1)*sizeof(PetscInt),&ii);CHKERRQ(ierr); 3105 ii[0] = 0; 3106 CHKMEMQ; 3107 for (i=0; i<M; i++) { 3108 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]); 3109 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]); 3110 ii[i+1] = ii[i] + id[i+1] - id[i] + io[i+1] - io[i]; 3111 /* remove one from count of matrix has diagonal */ 3112 for (j=id[i]; j<id[i+1]; j++) { 3113 if (jd[j] == i) {ii[i+1]--;break;} 3114 } 3115 CHKMEMQ; 3116 } 3117 ierr = PetscMalloc(ii[M]*sizeof(PetscInt),&jj);CHKERRQ(ierr); 3118 cnt = 0; 3119 for (i=0; i<M; i++) { 3120 for (j=io[i]; j<io[i+1]; j++) { 3121 if (garray[jo[j]] > rstart) break; 3122 jj[cnt++] = garray[jo[j]]; 3123 CHKMEMQ; 3124 } 3125 for (k=id[i]; k<id[i+1]; k++) { 3126 if (jd[k] != i) { 3127 jj[cnt++] = rstart + jd[k]; 3128 CHKMEMQ; 3129 } 3130 } 3131 for (;j<io[i+1]; j++) { 3132 jj[cnt++] = garray[jo[j]]; 3133 CHKMEMQ; 3134 } 3135 } 3136 ierr = MatCreateMPIAdj(((PetscObject)B)->comm,M,B->cmap->N/B->rmap->bs,ii,jj,PETSC_NULL,adj);CHKERRQ(ierr); 3137 PetscFunctionReturn(0); 3138 } 3139 EXTERN_C_END 3140 3141 #include <../src/mat/impls/aij/mpi/mpiaij.h> 3142 EXTERN_C_BEGIN 3143 PetscErrorCode MatConvert_SeqBAIJ_SeqAIJ(Mat,const MatType,MatReuse,Mat*); 3144 EXTERN_C_END 3145 3146 EXTERN_C_BEGIN 3147 #undef __FUNCT__ 3148 #define __FUNCT__ "MatConvert_MPIBAIJ_MPIAIJ" 3149 PetscErrorCode MatConvert_MPIBAIJ_MPIAIJ(Mat A,const MatType newtype,MatReuse reuse,Mat *newmat) 3150 { 3151 PetscErrorCode ierr; 3152 Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; 3153 Mat B; 3154 Mat_MPIAIJ *b; 3155 3156 PetscFunctionBegin; 3157 if (!A->assembled) SETERRQ(((PetscObject)A)->comm,PETSC_ERR_SUP,"Matrix must be assembled"); 3158 3159 ierr = MatCreate(((PetscObject)A)->comm,&B);CHKERRQ(ierr); 3160 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 3161 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 3162 ierr = MatSeqAIJSetPreallocation(B,0,PETSC_NULL);CHKERRQ(ierr); 3163 ierr = MatMPIAIJSetPreallocation(B,0,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr); 3164 b = (Mat_MPIAIJ*) B->data; 3165 3166 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 3167 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 3168 ierr = MatDisAssemble_MPIBAIJ(A);CHKERRQ(ierr); 3169 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->A, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->A);CHKERRQ(ierr); 3170 ierr = MatConvert_SeqBAIJ_SeqAIJ(a->B, MATSEQAIJ, MAT_INITIAL_MATRIX, &b->B);CHKERRQ(ierr); 3171 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3172 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3173 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3174 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3175 if (reuse == MAT_REUSE_MATRIX) { 3176 ierr = MatHeaderReplace(A,B);CHKERRQ(ierr); 3177 } else { 3178 *newmat = B; 3179 } 3180 PetscFunctionReturn(0); 3181 } 3182 EXTERN_C_END 3183 3184 EXTERN_C_BEGIN 3185 #if defined(PETSC_HAVE_MUMPS) 3186 extern PetscErrorCode MatGetFactor_baij_mumps(Mat,MatFactorType,Mat*); 3187 #endif 3188 EXTERN_C_END 3189 3190 /*MC 3191 MATMPIBAIJ - MATMPIBAIJ = "mpibaij" - A matrix type to be used for distributed block sparse matrices. 3192 3193 Options Database Keys: 3194 + -mat_type mpibaij - sets the matrix type to "mpibaij" during a call to MatSetFromOptions() 3195 . -mat_block_size <bs> - set the blocksize used to store the matrix 3196 - -mat_use_hash_table <fact> 3197 3198 Level: beginner 3199 3200 .seealso: MatCreateMPIBAIJ 3201 M*/ 3202 3203 EXTERN_C_BEGIN 3204 extern PetscErrorCode MatConvert_MPIBAIJ_MPIBSTRM(Mat,const MatType,MatReuse,Mat*); 3205 EXTERN_C_END 3206 3207 EXTERN_C_BEGIN 3208 #undef __FUNCT__ 3209 #define __FUNCT__ "MatCreate_MPIBAIJ" 3210 PetscErrorCode MatCreate_MPIBAIJ(Mat B) 3211 { 3212 Mat_MPIBAIJ *b; 3213 PetscErrorCode ierr; 3214 PetscBool flg; 3215 3216 PetscFunctionBegin; 3217 ierr = PetscNewLog(B,Mat_MPIBAIJ,&b);CHKERRQ(ierr); 3218 B->data = (void*)b; 3219 3220 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 3221 B->assembled = PETSC_FALSE; 3222 3223 B->insertmode = NOT_SET_VALUES; 3224 ierr = MPI_Comm_rank(((PetscObject)B)->comm,&b->rank);CHKERRQ(ierr); 3225 ierr = MPI_Comm_size(((PetscObject)B)->comm,&b->size);CHKERRQ(ierr); 3226 3227 /* build local table of row and column ownerships */ 3228 ierr = PetscMalloc((b->size+1)*sizeof(PetscInt),&b->rangebs);CHKERRQ(ierr); 3229 3230 /* build cache for off array entries formed */ 3231 ierr = MatStashCreate_Private(((PetscObject)B)->comm,1,&B->stash);CHKERRQ(ierr); 3232 b->donotstash = PETSC_FALSE; 3233 b->colmap = PETSC_NULL; 3234 b->garray = PETSC_NULL; 3235 b->roworiented = PETSC_TRUE; 3236 3237 /* stuff used in block assembly */ 3238 b->barray = 0; 3239 3240 /* stuff used for matrix vector multiply */ 3241 b->lvec = 0; 3242 b->Mvctx = 0; 3243 3244 /* stuff for MatGetRow() */ 3245 b->rowindices = 0; 3246 b->rowvalues = 0; 3247 b->getrowactive = PETSC_FALSE; 3248 3249 /* hash table stuff */ 3250 b->ht = 0; 3251 b->hd = 0; 3252 b->ht_size = 0; 3253 b->ht_flag = PETSC_FALSE; 3254 b->ht_fact = 0; 3255 b->ht_total_ct = 0; 3256 b->ht_insert_ct = 0; 3257 3258 /* stuff for MatGetSubMatrices_MPIBAIJ_local() */ 3259 b->ijonly = PETSC_FALSE; 3260 3261 ierr = PetscOptionsBegin(((PetscObject)B)->comm,PETSC_NULL,"Options for loading MPIBAIJ matrix 1","Mat");CHKERRQ(ierr); 3262 ierr = PetscOptionsBool("-mat_use_hash_table","Use hash table to save memory in constructing matrix","MatSetOption",PETSC_FALSE,&flg,PETSC_NULL);CHKERRQ(ierr); 3263 if (flg) { 3264 PetscReal fact = 1.39; 3265 ierr = MatSetOption(B,MAT_USE_HASH_TABLE,PETSC_TRUE);CHKERRQ(ierr); 3266 ierr = PetscOptionsReal("-mat_use_hash_table","Use hash table factor","MatMPIBAIJSetHashTableFactor",fact,&fact,PETSC_NULL);CHKERRQ(ierr); 3267 if (fact <= 1.0) fact = 1.39; 3268 ierr = MatMPIBAIJSetHashTableFactor(B,fact);CHKERRQ(ierr); 3269 ierr = PetscInfo1(B,"Hash table Factor used %5.2f\n",fact);CHKERRQ(ierr); 3270 } 3271 ierr = PetscOptionsEnd();CHKERRQ(ierr); 3272 3273 #if defined(PETSC_HAVE_MUMPS) 3274 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", "MatGetFactor_baij_mumps",MatGetFactor_baij_mumps);CHKERRQ(ierr); 3275 #endif 3276 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_mpibaij_mpiadj_C", 3277 "MatConvert_MPIBAIJ_MPIAdj", 3278 MatConvert_MPIBAIJ_MPIAdj);CHKERRQ(ierr); 3279 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_mpibaij_mpiaij_C", 3280 "MatConvert_MPIBAIJ_MPIAIJ", 3281 MatConvert_MPIBAIJ_MPIAIJ);CHKERRQ(ierr); 3282 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_mpibaij_mpisbaij_C", 3283 "MatConvert_MPIBAIJ_MPISBAIJ", 3284 MatConvert_MPIBAIJ_MPISBAIJ);CHKERRQ(ierr); 3285 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 3286 "MatStoreValues_MPIBAIJ", 3287 MatStoreValues_MPIBAIJ);CHKERRQ(ierr); 3288 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 3289 "MatRetrieveValues_MPIBAIJ", 3290 MatRetrieveValues_MPIBAIJ);CHKERRQ(ierr); 3291 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetDiagonalBlock_C", 3292 "MatGetDiagonalBlock_MPIBAIJ", 3293 MatGetDiagonalBlock_MPIBAIJ);CHKERRQ(ierr); 3294 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMPIBAIJSetPreallocation_C", 3295 "MatMPIBAIJSetPreallocation_MPIBAIJ", 3296 MatMPIBAIJSetPreallocation_MPIBAIJ);CHKERRQ(ierr); 3297 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMPIBAIJSetPreallocationCSR_C", 3298 "MatMPIBAIJSetPreallocationCSR_MPIBAIJ", 3299 MatMPIBAIJSetPreallocationCSR_MPIBAIJ);CHKERRQ(ierr); 3300 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatDiagonalScaleLocal_C", 3301 "MatDiagonalScaleLocal_MPIBAIJ", 3302 MatDiagonalScaleLocal_MPIBAIJ);CHKERRQ(ierr); 3303 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSetHashTableFactor_C", 3304 "MatSetHashTableFactor_MPIBAIJ", 3305 MatSetHashTableFactor_MPIBAIJ);CHKERRQ(ierr); 3306 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_mpibaij_mpibstrm_C", 3307 "MatConvert_MPIBAIJ_MPIBSTRM", 3308 MatConvert_MPIBAIJ_MPIBSTRM);CHKERRQ(ierr); 3309 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIBAIJ);CHKERRQ(ierr); 3310 PetscFunctionReturn(0); 3311 } 3312 EXTERN_C_END 3313 3314 /*MC 3315 MATBAIJ - MATBAIJ = "baij" - A matrix type to be used for block sparse matrices. 3316 3317 This matrix type is identical to MATSEQBAIJ when constructed with a single process communicator, 3318 and MATMPIBAIJ otherwise. 3319 3320 Options Database Keys: 3321 . -mat_type baij - sets the matrix type to "baij" during a call to MatSetFromOptions() 3322 3323 Level: beginner 3324 3325 .seealso: MatCreateBAIJ(),MATSEQBAIJ,MATMPIBAIJ, MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3326 M*/ 3327 3328 #undef __FUNCT__ 3329 #define __FUNCT__ "MatMPIBAIJSetPreallocation" 3330 /*@C 3331 MatMPIBAIJSetPreallocation - Allocates memory for a sparse parallel matrix in block AIJ format 3332 (block compressed row). For good matrix assembly performance 3333 the user should preallocate the matrix storage by setting the parameters 3334 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3335 performance can be increased by more than a factor of 50. 3336 3337 Collective on Mat 3338 3339 Input Parameters: 3340 + A - the matrix 3341 . bs - size of blockk 3342 . d_nz - number of block nonzeros per block row in diagonal portion of local 3343 submatrix (same for all local rows) 3344 . d_nnz - array containing the number of block nonzeros in the various block rows 3345 of the in diagonal portion of the local (possibly different for each block 3346 row) or PETSC_NULL. If you plan to factor the matrix you must leave room for the diagonal entry and 3347 set it even if it is zero. 3348 . o_nz - number of block nonzeros per block row in the off-diagonal portion of local 3349 submatrix (same for all local rows). 3350 - o_nnz - array containing the number of nonzeros in the various block rows of the 3351 off-diagonal portion of the local submatrix (possibly different for 3352 each block row) or PETSC_NULL. 3353 3354 If the *_nnz parameter is given then the *_nz parameter is ignored 3355 3356 Options Database Keys: 3357 + -mat_block_size - size of the blocks to use 3358 - -mat_use_hash_table <fact> 3359 3360 Notes: 3361 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3362 than it must be used on all processors that share the object for that argument. 3363 3364 Storage Information: 3365 For a square global matrix we define each processor's diagonal portion 3366 to be its local rows and the corresponding columns (a square submatrix); 3367 each processor's off-diagonal portion encompasses the remainder of the 3368 local matrix (a rectangular submatrix). 3369 3370 The user can specify preallocated storage for the diagonal part of 3371 the local submatrix with either d_nz or d_nnz (not both). Set 3372 d_nz=PETSC_DEFAULT and d_nnz=PETSC_NULL for PETSc to control dynamic 3373 memory allocation. Likewise, specify preallocated storage for the 3374 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3375 3376 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3377 the figure below we depict these three local rows and all columns (0-11). 3378 3379 .vb 3380 0 1 2 3 4 5 6 7 8 9 10 11 3381 ------------------- 3382 row 3 | o o o d d d o o o o o o 3383 row 4 | o o o d d d o o o o o o 3384 row 5 | o o o d d d o o o o o o 3385 ------------------- 3386 .ve 3387 3388 Thus, any entries in the d locations are stored in the d (diagonal) 3389 submatrix, and any entries in the o locations are stored in the 3390 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3391 stored simply in the MATSEQBAIJ format for compressed row storage. 3392 3393 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3394 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3395 In general, for PDE problems in which most nonzeros are near the diagonal, 3396 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3397 or you will get TERRIBLE performance; see the users' manual chapter on 3398 matrices. 3399 3400 You can call MatGetInfo() to get information on how effective the preallocation was; 3401 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3402 You can also run with the option -info and look for messages with the string 3403 malloc in them to see if additional memory allocation was needed. 3404 3405 Level: intermediate 3406 3407 .keywords: matrix, block, aij, compressed row, sparse, parallel 3408 3409 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocationCSR() 3410 @*/ 3411 PetscErrorCode MatMPIBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3412 { 3413 PetscErrorCode ierr; 3414 3415 PetscFunctionBegin; 3416 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3417 PetscValidType(B,1); 3418 PetscValidLogicalCollectiveInt(B,bs,2); 3419 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); 3420 PetscFunctionReturn(0); 3421 } 3422 3423 #undef __FUNCT__ 3424 #define __FUNCT__ "MatCreateBAIJ" 3425 /*@C 3426 MatCreateBAIJ - Creates a sparse parallel matrix in block AIJ format 3427 (block compressed row). For good matrix assembly performance 3428 the user should preallocate the matrix storage by setting the parameters 3429 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3430 performance can be increased by more than a factor of 50. 3431 3432 Collective on MPI_Comm 3433 3434 Input Parameters: 3435 + comm - MPI communicator 3436 . bs - size of blockk 3437 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3438 This value should be the same as the local size used in creating the 3439 y vector for the matrix-vector product y = Ax. 3440 . n - number of local columns (or PETSC_DECIDE to have calculated if N is given) 3441 This value should be the same as the local size used in creating the 3442 x vector for the matrix-vector product y = Ax. 3443 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3444 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3445 . d_nz - number of nonzero blocks per block row in diagonal portion of local 3446 submatrix (same for all local rows) 3447 . d_nnz - array containing the number of nonzero blocks in the various block rows 3448 of the in diagonal portion of the local (possibly different for each block 3449 row) or PETSC_NULL. If you plan to factor the matrix you must leave room for the diagonal entry 3450 and set it even if it is zero. 3451 . o_nz - number of nonzero blocks per block row in the off-diagonal portion of local 3452 submatrix (same for all local rows). 3453 - o_nnz - array containing the number of nonzero blocks in the various block rows of the 3454 off-diagonal portion of the local submatrix (possibly different for 3455 each block row) or PETSC_NULL. 3456 3457 Output Parameter: 3458 . A - the matrix 3459 3460 Options Database Keys: 3461 + -mat_block_size - size of the blocks to use 3462 - -mat_use_hash_table <fact> 3463 3464 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3465 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3466 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3467 3468 Notes: 3469 If the *_nnz parameter is given then the *_nz parameter is ignored 3470 3471 A nonzero block is any block that as 1 or more nonzeros in it 3472 3473 The user MUST specify either the local or global matrix dimensions 3474 (possibly both). 3475 3476 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor 3477 than it must be used on all processors that share the object for that argument. 3478 3479 Storage Information: 3480 For a square global matrix we define each processor's diagonal portion 3481 to be its local rows and the corresponding columns (a square submatrix); 3482 each processor's off-diagonal portion encompasses the remainder of the 3483 local matrix (a rectangular submatrix). 3484 3485 The user can specify preallocated storage for the diagonal part of 3486 the local submatrix with either d_nz or d_nnz (not both). Set 3487 d_nz=PETSC_DEFAULT and d_nnz=PETSC_NULL for PETSc to control dynamic 3488 memory allocation. Likewise, specify preallocated storage for the 3489 off-diagonal part of the local submatrix with o_nz or o_nnz (not both). 3490 3491 Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In 3492 the figure below we depict these three local rows and all columns (0-11). 3493 3494 .vb 3495 0 1 2 3 4 5 6 7 8 9 10 11 3496 ------------------- 3497 row 3 | o o o d d d o o o o o o 3498 row 4 | o o o d d d o o o o o o 3499 row 5 | o o o d d d o o o o o o 3500 ------------------- 3501 .ve 3502 3503 Thus, any entries in the d locations are stored in the d (diagonal) 3504 submatrix, and any entries in the o locations are stored in the 3505 o (off-diagonal) submatrix. Note that the d and the o submatrices are 3506 stored simply in the MATSEQBAIJ format for compressed row storage. 3507 3508 Now d_nz should indicate the number of block nonzeros per row in the d matrix, 3509 and o_nz should indicate the number of block nonzeros per row in the o matrix. 3510 In general, for PDE problems in which most nonzeros are near the diagonal, 3511 one expects d_nz >> o_nz. For large problems you MUST preallocate memory 3512 or you will get TERRIBLE performance; see the users' manual chapter on 3513 matrices. 3514 3515 Level: intermediate 3516 3517 .keywords: matrix, block, aij, compressed row, sparse, parallel 3518 3519 .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateBAIJ(), MatMPIBAIJSetPreallocation(), MatMPIBAIJSetPreallocationCSR() 3520 @*/ 3521 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) 3522 { 3523 PetscErrorCode ierr; 3524 PetscMPIInt size; 3525 3526 PetscFunctionBegin; 3527 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3528 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 3529 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3530 if (size > 1) { 3531 ierr = MatSetType(*A,MATMPIBAIJ);CHKERRQ(ierr); 3532 ierr = MatMPIBAIJSetPreallocation(*A,bs,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 3533 } else { 3534 ierr = MatSetType(*A,MATSEQBAIJ);CHKERRQ(ierr); 3535 ierr = MatSeqBAIJSetPreallocation(*A,bs,d_nz,d_nnz);CHKERRQ(ierr); 3536 } 3537 PetscFunctionReturn(0); 3538 } 3539 3540 #undef __FUNCT__ 3541 #define __FUNCT__ "MatDuplicate_MPIBAIJ" 3542 static PetscErrorCode MatDuplicate_MPIBAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 3543 { 3544 Mat mat; 3545 Mat_MPIBAIJ *a,*oldmat = (Mat_MPIBAIJ*)matin->data; 3546 PetscErrorCode ierr; 3547 PetscInt len=0; 3548 3549 PetscFunctionBegin; 3550 *newmat = 0; 3551 ierr = MatCreate(((PetscObject)matin)->comm,&mat);CHKERRQ(ierr); 3552 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 3553 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 3554 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 3555 3556 mat->factortype = matin->factortype; 3557 mat->preallocated = PETSC_TRUE; 3558 mat->assembled = PETSC_TRUE; 3559 mat->insertmode = NOT_SET_VALUES; 3560 3561 a = (Mat_MPIBAIJ*)mat->data; 3562 mat->rmap->bs = matin->rmap->bs; 3563 a->bs2 = oldmat->bs2; 3564 a->mbs = oldmat->mbs; 3565 a->nbs = oldmat->nbs; 3566 a->Mbs = oldmat->Mbs; 3567 a->Nbs = oldmat->Nbs; 3568 3569 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 3570 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 3571 3572 a->size = oldmat->size; 3573 a->rank = oldmat->rank; 3574 a->donotstash = oldmat->donotstash; 3575 a->roworiented = oldmat->roworiented; 3576 a->rowindices = 0; 3577 a->rowvalues = 0; 3578 a->getrowactive = PETSC_FALSE; 3579 a->barray = 0; 3580 a->rstartbs = oldmat->rstartbs; 3581 a->rendbs = oldmat->rendbs; 3582 a->cstartbs = oldmat->cstartbs; 3583 a->cendbs = oldmat->cendbs; 3584 3585 /* hash table stuff */ 3586 a->ht = 0; 3587 a->hd = 0; 3588 a->ht_size = 0; 3589 a->ht_flag = oldmat->ht_flag; 3590 a->ht_fact = oldmat->ht_fact; 3591 a->ht_total_ct = 0; 3592 a->ht_insert_ct = 0; 3593 3594 ierr = PetscMemcpy(a->rangebs,oldmat->rangebs,(a->size+1)*sizeof(PetscInt));CHKERRQ(ierr); 3595 if (oldmat->colmap) { 3596 #if defined (PETSC_USE_CTABLE) 3597 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 3598 #else 3599 ierr = PetscMalloc((a->Nbs)*sizeof(PetscInt),&a->colmap);CHKERRQ(ierr); 3600 ierr = PetscLogObjectMemory(mat,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3601 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(a->Nbs)*sizeof(PetscInt));CHKERRQ(ierr); 3602 #endif 3603 } else a->colmap = 0; 3604 3605 if (oldmat->garray && (len = ((Mat_SeqBAIJ*)(oldmat->B->data))->nbs)) { 3606 ierr = PetscMalloc(len*sizeof(PetscInt),&a->garray);CHKERRQ(ierr); 3607 ierr = PetscLogObjectMemory(mat,len*sizeof(PetscInt));CHKERRQ(ierr); 3608 ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); 3609 } else a->garray = 0; 3610 3611 ierr = MatStashCreate_Private(((PetscObject)matin)->comm,matin->rmap->bs,&mat->bstash);CHKERRQ(ierr); 3612 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 3613 ierr = PetscLogObjectParent(mat,a->lvec);CHKERRQ(ierr); 3614 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 3615 ierr = PetscLogObjectParent(mat,a->Mvctx);CHKERRQ(ierr); 3616 3617 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 3618 ierr = PetscLogObjectParent(mat,a->A);CHKERRQ(ierr); 3619 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 3620 ierr = PetscLogObjectParent(mat,a->B);CHKERRQ(ierr); 3621 ierr = PetscFListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 3622 *newmat = mat; 3623 3624 PetscFunctionReturn(0); 3625 } 3626 3627 #undef __FUNCT__ 3628 #define __FUNCT__ "MatLoad_MPIBAIJ" 3629 PetscErrorCode MatLoad_MPIBAIJ(Mat newmat,PetscViewer viewer) 3630 { 3631 PetscErrorCode ierr; 3632 int fd; 3633 PetscInt i,nz,j,rstart,rend; 3634 PetscScalar *vals,*buf; 3635 MPI_Comm comm = ((PetscObject)viewer)->comm; 3636 MPI_Status status; 3637 PetscMPIInt rank,size,maxnz; 3638 PetscInt header[4],*rowlengths = 0,M,N,m,*rowners,*cols; 3639 PetscInt *locrowlens = PETSC_NULL,*procsnz = PETSC_NULL,*browners = PETSC_NULL; 3640 PetscInt jj,*mycols,*ibuf,bs=1,Mbs,mbs,extra_rows,mmax; 3641 PetscMPIInt tag = ((PetscObject)viewer)->tag; 3642 PetscInt *dlens = PETSC_NULL,*odlens = PETSC_NULL,*mask = PETSC_NULL,*masked1 = PETSC_NULL,*masked2 = PETSC_NULL,rowcount,odcount; 3643 PetscInt dcount,kmax,k,nzcount,tmp,mend,sizesset=1,grows,gcols; 3644 3645 PetscFunctionBegin; 3646 ierr = PetscOptionsBegin(comm,PETSC_NULL,"Options for loading MPIBAIJ matrix 2","Mat");CHKERRQ(ierr); 3647 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,PETSC_NULL);CHKERRQ(ierr); 3648 ierr = PetscOptionsEnd();CHKERRQ(ierr); 3649 3650 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3651 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3652 if (!rank) { 3653 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 3654 ierr = PetscBinaryRead(fd,(char *)header,4,PETSC_INT);CHKERRQ(ierr); 3655 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 3656 } 3657 3658 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) sizesset = 0; 3659 3660 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 3661 M = header[1]; N = header[2]; 3662 3663 /* If global rows/cols are set to PETSC_DECIDE, set it to the sizes given in the file */ 3664 if (sizesset && newmat->rmap->N < 0) newmat->rmap->N = M; 3665 if (sizesset && newmat->cmap->N < 0) newmat->cmap->N = N; 3666 3667 /* If global sizes are set, check if they are consistent with that given in the file */ 3668 if (sizesset) { 3669 ierr = MatGetSize(newmat,&grows,&gcols);CHKERRQ(ierr); 3670 } 3671 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); 3672 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); 3673 3674 if (M != N) SETERRQ(((PetscObject)viewer)->comm,PETSC_ERR_SUP,"Can only do square matrices"); 3675 3676 /* 3677 This code adds extra rows to make sure the number of rows is 3678 divisible by the blocksize 3679 */ 3680 Mbs = M/bs; 3681 extra_rows = bs - M + bs*Mbs; 3682 if (extra_rows == bs) extra_rows = 0; 3683 else Mbs++; 3684 if (extra_rows && !rank) { 3685 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 3686 } 3687 3688 /* determine ownership of all rows */ 3689 if (newmat->rmap->n < 0) { /* PETSC_DECIDE */ 3690 mbs = Mbs/size + ((Mbs % size) > rank); 3691 m = mbs*bs; 3692 } else { /* User set */ 3693 m = newmat->rmap->n; 3694 mbs = m/bs; 3695 } 3696 ierr = PetscMalloc2(size+1,PetscInt,&rowners,size+1,PetscInt,&browners);CHKERRQ(ierr); 3697 ierr = MPI_Allgather(&mbs,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 3698 3699 /* process 0 needs enough room for process with most rows */ 3700 if (!rank) { 3701 mmax = rowners[1]; 3702 for (i=2; i<=size; i++) { 3703 mmax = PetscMax(mmax,rowners[i]); 3704 } 3705 mmax*=bs; 3706 } else mmax = m; 3707 3708 rowners[0] = 0; 3709 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 3710 for (i=0; i<=size; i++) browners[i] = rowners[i]*bs; 3711 rstart = rowners[rank]; 3712 rend = rowners[rank+1]; 3713 3714 /* distribute row lengths to all processors */ 3715 ierr = PetscMalloc((mmax+1)*sizeof(PetscInt),&locrowlens);CHKERRQ(ierr); 3716 if (!rank) { 3717 mend = m; 3718 if (size == 1) mend = mend - extra_rows; 3719 ierr = PetscBinaryRead(fd,locrowlens,mend,PETSC_INT);CHKERRQ(ierr); 3720 for (j=mend; j<m; j++) locrowlens[j] = 1; 3721 ierr = PetscMalloc(m*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 3722 ierr = PetscMalloc(size*sizeof(PetscInt),&procsnz);CHKERRQ(ierr); 3723 ierr = PetscMemzero(procsnz,size*sizeof(PetscInt));CHKERRQ(ierr); 3724 for (j=0; j<m; j++) { 3725 procsnz[0] += locrowlens[j]; 3726 } 3727 for (i=1; i<size; i++) { 3728 mend = browners[i+1] - browners[i]; 3729 if (i == size-1) mend = mend - extra_rows; 3730 ierr = PetscBinaryRead(fd,rowlengths,mend,PETSC_INT);CHKERRQ(ierr); 3731 for (j=mend; j<browners[i+1] - browners[i]; j++) rowlengths[j] = 1; 3732 /* calculate the number of nonzeros on each processor */ 3733 for (j=0; j<browners[i+1]-browners[i]; j++) { 3734 procsnz[i] += rowlengths[j]; 3735 } 3736 ierr = MPI_Send(rowlengths,browners[i+1]-browners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3737 } 3738 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 3739 } else { 3740 ierr = MPI_Recv(locrowlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 3741 } 3742 3743 if (!rank) { 3744 /* determine max buffer needed and allocate it */ 3745 maxnz = procsnz[0]; 3746 for (i=1; i<size; i++) { 3747 maxnz = PetscMax(maxnz,procsnz[i]); 3748 } 3749 ierr = PetscMalloc(maxnz*sizeof(PetscInt),&cols);CHKERRQ(ierr); 3750 3751 /* read in my part of the matrix column indices */ 3752 nz = procsnz[0]; 3753 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&ibuf);CHKERRQ(ierr); 3754 mycols = ibuf; 3755 if (size == 1) nz -= extra_rows; 3756 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 3757 if (size == 1) for (i=0; i< extra_rows; i++) { mycols[nz+i] = M+i; } 3758 3759 /* read in every ones (except the last) and ship off */ 3760 for (i=1; i<size-1; i++) { 3761 nz = procsnz[i]; 3762 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 3763 ierr = MPI_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 3764 } 3765 /* read in the stuff for the last proc */ 3766 if (size != 1) { 3767 nz = procsnz[size-1] - extra_rows; /* the extra rows are not on the disk */ 3768 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 3769 for (i=0; i<extra_rows; i++) cols[nz+i] = M+i; 3770 ierr = MPI_Send(cols,nz+extra_rows,MPIU_INT,size-1,tag,comm);CHKERRQ(ierr); 3771 } 3772 ierr = PetscFree(cols);CHKERRQ(ierr); 3773 } else { 3774 /* determine buffer space needed for message */ 3775 nz = 0; 3776 for (i=0; i<m; i++) { 3777 nz += locrowlens[i]; 3778 } 3779 ierr = PetscMalloc((nz+1)*sizeof(PetscInt),&ibuf);CHKERRQ(ierr); 3780 mycols = ibuf; 3781 /* receive message of column indices*/ 3782 ierr = MPI_Recv(mycols,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 3783 ierr = MPI_Get_count(&status,MPIU_INT,&maxnz);CHKERRQ(ierr); 3784 if (maxnz != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"something is wrong with file"); 3785 } 3786 3787 /* loop over local rows, determining number of off diagonal entries */ 3788 ierr = PetscMalloc2(rend-rstart,PetscInt,&dlens,rend-rstart,PetscInt,&odlens);CHKERRQ(ierr); 3789 ierr = PetscMalloc3(Mbs,PetscInt,&mask,Mbs,PetscInt,&masked1,Mbs,PetscInt,&masked2);CHKERRQ(ierr); 3790 ierr = PetscMemzero(mask,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3791 ierr = PetscMemzero(masked1,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3792 ierr = PetscMemzero(masked2,Mbs*sizeof(PetscInt));CHKERRQ(ierr); 3793 rowcount = 0; nzcount = 0; 3794 for (i=0; i<mbs; i++) { 3795 dcount = 0; 3796 odcount = 0; 3797 for (j=0; j<bs; j++) { 3798 kmax = locrowlens[rowcount]; 3799 for (k=0; k<kmax; k++) { 3800 tmp = mycols[nzcount++]/bs; 3801 if (!mask[tmp]) { 3802 mask[tmp] = 1; 3803 if (tmp < rstart || tmp >= rend) masked2[odcount++] = tmp; 3804 else masked1[dcount++] = tmp; 3805 } 3806 } 3807 rowcount++; 3808 } 3809 3810 dlens[i] = dcount; 3811 odlens[i] = odcount; 3812 3813 /* zero out the mask elements we set */ 3814 for (j=0; j<dcount; j++) mask[masked1[j]] = 0; 3815 for (j=0; j<odcount; j++) mask[masked2[j]] = 0; 3816 } 3817 3818 3819 if (!sizesset) { 3820 ierr = MatSetSizes(newmat,m,m,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 3821 } 3822 ierr = MatMPIBAIJSetPreallocation(newmat,bs,0,dlens,0,odlens);CHKERRQ(ierr); 3823 3824 if (!rank) { 3825 ierr = PetscMalloc((maxnz+1)*sizeof(PetscScalar),&buf);CHKERRQ(ierr); 3826 /* read in my part of the matrix numerical values */ 3827 nz = procsnz[0]; 3828 vals = buf; 3829 mycols = ibuf; 3830 if (size == 1) nz -= extra_rows; 3831 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3832 if (size == 1) for (i=0; i< extra_rows; i++) { vals[nz+i] = 1.0; } 3833 3834 /* insert into matrix */ 3835 jj = rstart*bs; 3836 for (i=0; i<m; i++) { 3837 ierr = MatSetValues_MPIBAIJ(newmat,1,&jj,locrowlens[i],mycols,vals,INSERT_VALUES);CHKERRQ(ierr); 3838 mycols += locrowlens[i]; 3839 vals += locrowlens[i]; 3840 jj++; 3841 } 3842 /* read in other processors (except the last one) and ship out */ 3843 for (i=1; i<size-1; i++) { 3844 nz = procsnz[i]; 3845 vals = buf; 3846 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3847 ierr = MPI_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newmat)->tag,comm);CHKERRQ(ierr); 3848 } 3849 /* the last proc */ 3850 if (size != 1){ 3851 nz = procsnz[i] - extra_rows; 3852 vals = buf; 3853 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 3854 for (i=0; i<extra_rows; i++) vals[nz+i] = 1.0; 3855 ierr = MPI_Send(vals,nz+extra_rows,MPIU_SCALAR,size-1,((PetscObject)newmat)->tag,comm);CHKERRQ(ierr); 3856 } 3857 ierr = PetscFree(procsnz);CHKERRQ(ierr); 3858 } else { 3859 /* receive numeric values */ 3860 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&buf);CHKERRQ(ierr); 3861 3862 /* receive message of values*/ 3863 vals = buf; 3864 mycols = ibuf; 3865 ierr = MPI_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newmat)->tag,comm,&status);CHKERRQ(ierr); 3866 ierr = MPI_Get_count(&status,MPIU_SCALAR,&maxnz);CHKERRQ(ierr); 3867 if (maxnz != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"something is wrong with file"); 3868 3869 /* insert into matrix */ 3870 jj = rstart*bs; 3871 for (i=0; i<m; i++) { 3872 ierr = MatSetValues_MPIBAIJ(newmat,1,&jj,locrowlens[i],mycols,vals,INSERT_VALUES);CHKERRQ(ierr); 3873 mycols += locrowlens[i]; 3874 vals += locrowlens[i]; 3875 jj++; 3876 } 3877 } 3878 ierr = PetscFree(locrowlens);CHKERRQ(ierr); 3879 ierr = PetscFree(buf);CHKERRQ(ierr); 3880 ierr = PetscFree(ibuf);CHKERRQ(ierr); 3881 ierr = PetscFree2(rowners,browners);CHKERRQ(ierr); 3882 ierr = PetscFree2(dlens,odlens);CHKERRQ(ierr); 3883 ierr = PetscFree3(mask,masked1,masked2);CHKERRQ(ierr); 3884 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3885 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3886 3887 PetscFunctionReturn(0); 3888 } 3889 3890 #undef __FUNCT__ 3891 #define __FUNCT__ "MatMPIBAIJSetHashTableFactor" 3892 /*@ 3893 MatMPIBAIJSetHashTableFactor - Sets the factor required to compute the size of the HashTable. 3894 3895 Input Parameters: 3896 . mat - the matrix 3897 . fact - factor 3898 3899 Not Collective, each process can use a different factor 3900 3901 Level: advanced 3902 3903 Notes: 3904 This can also be set by the command line option: -mat_use_hash_table <fact> 3905 3906 .keywords: matrix, hashtable, factor, HT 3907 3908 .seealso: MatSetOption() 3909 @*/ 3910 PetscErrorCode MatMPIBAIJSetHashTableFactor(Mat mat,PetscReal fact) 3911 { 3912 PetscErrorCode ierr; 3913 3914 PetscFunctionBegin; 3915 ierr = PetscTryMethod(mat,"MatSetHashTableFactor_C",(Mat,PetscReal),(mat,fact));CHKERRQ(ierr); 3916 PetscFunctionReturn(0); 3917 } 3918 3919 EXTERN_C_BEGIN 3920 #undef __FUNCT__ 3921 #define __FUNCT__ "MatSetHashTableFactor_MPIBAIJ" 3922 PetscErrorCode MatSetHashTableFactor_MPIBAIJ(Mat mat,PetscReal fact) 3923 { 3924 Mat_MPIBAIJ *baij; 3925 3926 PetscFunctionBegin; 3927 baij = (Mat_MPIBAIJ*)mat->data; 3928 baij->ht_fact = fact; 3929 PetscFunctionReturn(0); 3930 } 3931 EXTERN_C_END 3932 3933 #undef __FUNCT__ 3934 #define __FUNCT__ "MatMPIBAIJGetSeqBAIJ" 3935 PetscErrorCode MatMPIBAIJGetSeqBAIJ(Mat A,Mat *Ad,Mat *Ao,PetscInt *colmap[]) 3936 { 3937 Mat_MPIBAIJ *a = (Mat_MPIBAIJ *)A->data; 3938 PetscFunctionBegin; 3939 *Ad = a->A; 3940 *Ao = a->B; 3941 *colmap = a->garray; 3942 PetscFunctionReturn(0); 3943 } 3944 3945 /* 3946 Special version for direct calls from Fortran (to eliminate two function call overheads 3947 */ 3948 #if defined(PETSC_HAVE_FORTRAN_CAPS) 3949 #define matmpibaijsetvaluesblocked_ MATMPIBAIJSETVALUESBLOCKED 3950 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 3951 #define matmpibaijsetvaluesblocked_ matmpibaijsetvaluesblocked 3952 #endif 3953 3954 #undef __FUNCT__ 3955 #define __FUNCT__ "matmpibiajsetvaluesblocked" 3956 /*@C 3957 MatMPIBAIJSetValuesBlocked - Direct Fortran call to replace call to MatSetValuesBlocked() 3958 3959 Collective on Mat 3960 3961 Input Parameters: 3962 + mat - the matrix 3963 . min - number of input rows 3964 . im - input rows 3965 . nin - number of input columns 3966 . in - input columns 3967 . v - numerical values input 3968 - addvin - INSERT_VALUES or ADD_VALUES 3969 3970 Notes: This has a complete copy of MatSetValuesBlocked_MPIBAIJ() which is terrible code un-reuse. 3971 3972 Level: advanced 3973 3974 .seealso: MatSetValuesBlocked() 3975 @*/ 3976 PetscErrorCode matmpibaijsetvaluesblocked_(Mat *matin,PetscInt *min,const PetscInt im[],PetscInt *nin,const PetscInt in[],const MatScalar v[],InsertMode *addvin) 3977 { 3978 /* convert input arguments to C version */ 3979 Mat mat = *matin; 3980 PetscInt m = *min, n = *nin; 3981 InsertMode addv = *addvin; 3982 3983 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; 3984 const MatScalar *value; 3985 MatScalar *barray=baij->barray; 3986 PetscBool roworiented = baij->roworiented; 3987 PetscErrorCode ierr; 3988 PetscInt i,j,ii,jj,row,col,rstart=baij->rstartbs; 3989 PetscInt rend=baij->rendbs,cstart=baij->cstartbs,stepval; 3990 PetscInt cend=baij->cendbs,bs=mat->rmap->bs,bs2=baij->bs2; 3991 3992 PetscFunctionBegin; 3993 /* tasks normally handled by MatSetValuesBlocked() */ 3994 if (mat->insertmode == NOT_SET_VALUES) { 3995 mat->insertmode = addv; 3996 } 3997 #if defined(PETSC_USE_DEBUG) 3998 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 3999 if (mat->factortype) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix"); 4000 #endif 4001 if (mat->assembled) { 4002 mat->was_assembled = PETSC_TRUE; 4003 mat->assembled = PETSC_FALSE; 4004 } 4005 ierr = PetscLogEventBegin(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 4006 4007 4008 if(!barray) { 4009 ierr = PetscMalloc(bs2*sizeof(MatScalar),&barray);CHKERRQ(ierr); 4010 baij->barray = barray; 4011 } 4012 4013 if (roworiented) { 4014 stepval = (n-1)*bs; 4015 } else { 4016 stepval = (m-1)*bs; 4017 } 4018 for (i=0; i<m; i++) { 4019 if (im[i] < 0) continue; 4020 #if defined(PETSC_USE_DEBUG) 4021 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); 4022 #endif 4023 if (im[i] >= rstart && im[i] < rend) { 4024 row = im[i] - rstart; 4025 for (j=0; j<n; j++) { 4026 /* If NumCol = 1 then a copy is not required */ 4027 if ((roworiented) && (n == 1)) { 4028 barray = (MatScalar*)v + i*bs2; 4029 } else if((!roworiented) && (m == 1)) { 4030 barray = (MatScalar*)v + j*bs2; 4031 } else { /* Here a copy is required */ 4032 if (roworiented) { 4033 value = v + i*(stepval+bs)*bs + j*bs; 4034 } else { 4035 value = v + j*(stepval+bs)*bs + i*bs; 4036 } 4037 for (ii=0; ii<bs; ii++,value+=stepval) { 4038 for (jj=0; jj<bs; jj++) { 4039 *barray++ = *value++; 4040 } 4041 } 4042 barray -=bs2; 4043 } 4044 4045 if (in[j] >= cstart && in[j] < cend){ 4046 col = in[j] - cstart; 4047 ierr = MatSetValuesBlocked_SeqBAIJ(baij->A,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 4048 } 4049 else if (in[j] < 0) continue; 4050 #if defined(PETSC_USE_DEBUG) 4051 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); 4052 #endif 4053 else { 4054 if (mat->was_assembled) { 4055 if (!baij->colmap) { 4056 ierr = MatCreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); 4057 } 4058 4059 #if defined(PETSC_USE_DEBUG) 4060 #if defined (PETSC_USE_CTABLE) 4061 { PetscInt data; 4062 ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); 4063 if ((data - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 4064 } 4065 #else 4066 if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Incorrect colmap"); 4067 #endif 4068 #endif 4069 #if defined (PETSC_USE_CTABLE) 4070 ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); 4071 col = (col - 1)/bs; 4072 #else 4073 col = (baij->colmap[in[j]] - 1)/bs; 4074 #endif 4075 if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { 4076 ierr = MatDisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); 4077 col = in[j]; 4078 } 4079 } 4080 else col = in[j]; 4081 ierr = MatSetValuesBlocked_SeqBAIJ(baij->B,1,&row,1,&col,barray,addv);CHKERRQ(ierr); 4082 } 4083 } 4084 } else { 4085 if (!baij->donotstash) { 4086 if (roworiented) { 4087 ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 4088 } else { 4089 ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); 4090 } 4091 } 4092 } 4093 } 4094 4095 /* task normally handled by MatSetValuesBlocked() */ 4096 ierr = PetscLogEventEnd(MAT_SetValues,mat,0,0,0);CHKERRQ(ierr); 4097 PetscFunctionReturn(0); 4098 } 4099 4100 #undef __FUNCT__ 4101 #define __FUNCT__ "MatCreateMPIBAIJWithArrays" 4102 /*@ 4103 MatCreateMPIBAIJWithArrays - creates a MPI BAIJ matrix using arrays that contain in standard 4104 CSR format the local rows. 4105 4106 Collective on MPI_Comm 4107 4108 Input Parameters: 4109 + comm - MPI communicator 4110 . bs - the block size, only a block size of 1 is supported 4111 . m - number of local rows (Cannot be PETSC_DECIDE) 4112 . n - This value should be the same as the local size used in creating the 4113 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4114 calculated if N is given) For square matrices n is almost always m. 4115 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4116 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4117 . i - row indices 4118 . j - column indices 4119 - a - matrix values 4120 4121 Output Parameter: 4122 . mat - the matrix 4123 4124 Level: intermediate 4125 4126 Notes: 4127 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4128 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4129 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4130 4131 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4132 4133 .keywords: matrix, aij, compressed row, sparse, parallel 4134 4135 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4136 MPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4137 @*/ 4138 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) 4139 { 4140 PetscErrorCode ierr; 4141 4142 4143 PetscFunctionBegin; 4144 if (i[0]) { 4145 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4146 } 4147 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4148 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4149 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4150 ierr = MatSetType(*mat,MATMPISBAIJ);CHKERRQ(ierr); 4151 ierr = MatMPIBAIJSetPreallocationCSR(*mat,bs,i,j,a);CHKERRQ(ierr); 4152 PetscFunctionReturn(0); 4153 } 4154