1 /* 2 Routines to compute overlapping regions of a parallel MPI matrix 3 and to find submatrices that were shared across processors. 4 */ 5 #include <../src/mat/impls/aij/seq/aij.h> 6 #include <../src/mat/impls/aij/mpi/mpiaij.h> 7 #include <petscbt.h> 8 #include <petscsf.h> 9 10 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once(Mat,PetscInt,IS*); 11 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local(Mat,PetscInt,char**,PetscInt*,PetscInt**,PetscTable*); 12 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive(Mat,PetscInt,PetscInt**,PetscInt**,PetscInt*); 13 extern PetscErrorCode MatGetRow_MPIAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); 14 extern PetscErrorCode MatRestoreRow_MPIAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); 15 16 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once_Scalable(Mat,PetscInt,IS*); 17 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local_Scalable(Mat,PetscInt,IS*); 18 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Send_Scalable(Mat,PetscInt,PetscMPIInt,PetscMPIInt *,PetscInt *, PetscInt *,PetscInt **,PetscInt **); 19 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive_Scalable(Mat,PetscInt,IS*,PetscInt,PetscInt *); 20 21 22 PetscErrorCode MatIncreaseOverlap_MPIAIJ(Mat C,PetscInt imax,IS is[],PetscInt ov) 23 { 24 PetscErrorCode ierr; 25 PetscInt i; 26 27 PetscFunctionBegin; 28 if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified"); 29 for (i=0; i<ov; ++i) { 30 ierr = MatIncreaseOverlap_MPIAIJ_Once(C,imax,is);CHKERRQ(ierr); 31 } 32 PetscFunctionReturn(0); 33 } 34 35 PetscErrorCode MatIncreaseOverlap_MPIAIJ_Scalable(Mat C,PetscInt imax,IS is[],PetscInt ov) 36 { 37 PetscErrorCode ierr; 38 PetscInt i; 39 40 PetscFunctionBegin; 41 if (ov < 0) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified"); 42 for (i=0; i<ov; ++i) { 43 ierr = MatIncreaseOverlap_MPIAIJ_Once_Scalable(C,imax,is);CHKERRQ(ierr); 44 } 45 PetscFunctionReturn(0); 46 } 47 48 49 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once_Scalable(Mat mat,PetscInt nidx,IS is[]) 50 { 51 PetscErrorCode ierr; 52 MPI_Comm comm; 53 PetscInt *length,length_i,tlength,*remoterows,nrrows,reducednrrows,*rrow_ranks,*rrow_isids,i,j,owner; 54 PetscInt *tosizes,*tosizes_temp,*toffsets,*fromsizes,*todata,*fromdata; 55 PetscInt nrecvrows,*sbsizes = 0,*sbdata = 0; 56 const PetscInt *indices_i,**indices; 57 PetscLayout rmap; 58 PetscMPIInt rank,size,*toranks,*fromranks,nto,nfrom; 59 PetscSF sf; 60 PetscSFNode *remote; 61 62 PetscFunctionBegin; 63 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 64 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 65 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 66 /* get row map to determine where rows should be going */ 67 ierr = MatGetLayouts(mat,&rmap,NULL);CHKERRQ(ierr); 68 /* retrieve IS data and put all together so that we 69 * can optimize communication 70 * */ 71 ierr = PetscCalloc2(nidx,(PetscInt ***)&indices,nidx,&length);CHKERRQ(ierr); 72 for (i=0,tlength=0; i<nidx; i++){ 73 ierr = ISGetLocalSize(is[i],&length[i]);CHKERRQ(ierr); 74 tlength += length[i]; 75 ierr = ISGetIndices(is[i],&indices[i]);CHKERRQ(ierr); 76 } 77 /* find these rows on remote processors */ 78 ierr = PetscCalloc3(tlength,&remoterows,tlength,&rrow_ranks,tlength,&rrow_isids);CHKERRQ(ierr); 79 ierr = PetscCalloc3(size,&toranks,2*size,&tosizes,size,&tosizes_temp);CHKERRQ(ierr); 80 nrrows = 0; 81 for (i=0; i<nidx; i++){ 82 length_i = length[i]; 83 indices_i = indices[i]; 84 for (j=0; j<length_i; j++){ 85 owner = -1; 86 ierr = PetscLayoutFindOwner(rmap,indices_i[j],&owner);CHKERRQ(ierr); 87 /* remote processors */ 88 if (owner != rank){ 89 tosizes_temp[owner]++; /* number of rows to owner */ 90 rrow_ranks[nrrows] = owner; /* processor */ 91 rrow_isids[nrrows] = i; /* is id */ 92 remoterows[nrrows++] = indices_i[j]; /* row */ 93 } 94 } 95 ierr = ISRestoreIndices(is[i],&indices[i]);CHKERRQ(ierr); 96 } 97 ierr = PetscFree2(indices,length);CHKERRQ(ierr); 98 /* test if we need to exchange messages 99 * generally speaking, we do not need to exchange 100 * data when overlap is 1 101 * */ 102 ierr = MPIU_Allreduce(&nrrows,&reducednrrows,1,MPIU_INT,MPIU_MAX,comm);CHKERRQ(ierr); 103 /* we do not have any messages 104 * It usually corresponds to overlap 1 105 * */ 106 if (!reducednrrows){ 107 ierr = PetscFree3(toranks,tosizes,tosizes_temp);CHKERRQ(ierr); 108 ierr = PetscFree3(remoterows,rrow_ranks,rrow_isids);CHKERRQ(ierr); 109 ierr = MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);CHKERRQ(ierr); 110 PetscFunctionReturn(0); 111 } 112 nto = 0; 113 /* send sizes and ranks for building a two-sided communcation */ 114 for (i=0; i<size; i++){ 115 if (tosizes_temp[i]){ 116 tosizes[nto*2] = tosizes_temp[i]*2; /* size */ 117 tosizes_temp[i] = nto; /* a map from processor to index */ 118 toranks[nto++] = i; /* processor */ 119 } 120 } 121 ierr = PetscCalloc1(nto+1,&toffsets);CHKERRQ(ierr); 122 for (i=0; i<nto; i++){ 123 toffsets[i+1] = toffsets[i]+tosizes[2*i]; /* offsets */ 124 tosizes[2*i+1] = toffsets[i]; /* offsets to send */ 125 } 126 /* send information to other processors */ 127 ierr = PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);CHKERRQ(ierr); 128 nrecvrows = 0; 129 for (i=0; i<nfrom; i++) nrecvrows += fromsizes[2*i]; 130 ierr = PetscMalloc1(nrecvrows,&remote);CHKERRQ(ierr); 131 nrecvrows = 0; 132 for (i=0; i<nfrom; i++){ 133 for (j=0; j<fromsizes[2*i]; j++){ 134 remote[nrecvrows].rank = fromranks[i]; 135 remote[nrecvrows++].index = fromsizes[2*i+1]+j; 136 } 137 } 138 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 139 ierr = PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); 140 /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */ 141 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 142 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 143 /* message pair <no of is, row> */ 144 ierr = PetscCalloc2(2*nrrows,&todata,nrecvrows,&fromdata);CHKERRQ(ierr); 145 for (i=0; i<nrrows; i++){ 146 owner = rrow_ranks[i]; /* processor */ 147 j = tosizes_temp[owner]; /* index */ 148 todata[toffsets[j]++] = rrow_isids[i]; 149 todata[toffsets[j]++] = remoterows[i]; 150 } 151 ierr = PetscFree3(toranks,tosizes,tosizes_temp);CHKERRQ(ierr); 152 ierr = PetscFree3(remoterows,rrow_ranks,rrow_isids);CHKERRQ(ierr); 153 ierr = PetscFree(toffsets);CHKERRQ(ierr); 154 ierr = PetscSFBcastBegin(sf,MPIU_INT,todata,fromdata);CHKERRQ(ierr); 155 ierr = PetscSFBcastEnd(sf,MPIU_INT,todata,fromdata);CHKERRQ(ierr); 156 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 157 /* send rows belonging to the remote so that then we could get the overlapping data back */ 158 ierr = MatIncreaseOverlap_MPIAIJ_Send_Scalable(mat,nidx,nfrom,fromranks,fromsizes,fromdata,&sbsizes,&sbdata);CHKERRQ(ierr); 159 ierr = PetscFree2(todata,fromdata);CHKERRQ(ierr); 160 ierr = PetscFree(fromsizes);CHKERRQ(ierr); 161 ierr = PetscCommBuildTwoSided(comm,2,MPIU_INT,nfrom,fromranks,sbsizes,&nto,&toranks,&tosizes);CHKERRQ(ierr); 162 ierr = PetscFree(fromranks);CHKERRQ(ierr); 163 nrecvrows = 0; 164 for (i=0; i<nto; i++) nrecvrows += tosizes[2*i]; 165 ierr = PetscCalloc1(nrecvrows,&todata);CHKERRQ(ierr); 166 ierr = PetscMalloc1(nrecvrows,&remote);CHKERRQ(ierr); 167 nrecvrows = 0; 168 for (i=0; i<nto; i++){ 169 for (j=0; j<tosizes[2*i]; j++){ 170 remote[nrecvrows].rank = toranks[i]; 171 remote[nrecvrows++].index = tosizes[2*i+1]+j; 172 } 173 } 174 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 175 ierr = PetscSFSetGraph(sf,nrecvrows,nrecvrows,NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); 176 /* use two-sided communication by default since OPENMPI has some bugs for one-sided one */ 177 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 178 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 179 /* overlap communication and computation */ 180 ierr = PetscSFBcastBegin(sf,MPIU_INT,sbdata,todata);CHKERRQ(ierr); 181 ierr = MatIncreaseOverlap_MPIAIJ_Local_Scalable(mat,nidx,is);CHKERRQ(ierr); 182 ierr = PetscSFBcastEnd(sf,MPIU_INT,sbdata,todata);CHKERRQ(ierr); 183 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 184 ierr = PetscFree2(sbdata,sbsizes);CHKERRQ(ierr); 185 ierr = MatIncreaseOverlap_MPIAIJ_Receive_Scalable(mat,nidx,is,nrecvrows,todata);CHKERRQ(ierr); 186 ierr = PetscFree(toranks);CHKERRQ(ierr); 187 ierr = PetscFree(tosizes);CHKERRQ(ierr); 188 ierr = PetscFree(todata);CHKERRQ(ierr); 189 PetscFunctionReturn(0); 190 } 191 192 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive_Scalable(Mat mat,PetscInt nidx, IS is[], PetscInt nrecvs, PetscInt *recvdata) 193 { 194 PetscInt *isz,isz_i,i,j,is_id, data_size; 195 PetscInt col,lsize,max_lsize,*indices_temp, *indices_i; 196 const PetscInt *indices_i_temp; 197 PetscErrorCode ierr; 198 199 PetscFunctionBegin; 200 max_lsize = 0; 201 ierr = PetscMalloc1(nidx,&isz);CHKERRQ(ierr); 202 for (i=0; i<nidx; i++){ 203 ierr = ISGetLocalSize(is[i],&lsize);CHKERRQ(ierr); 204 max_lsize = lsize>max_lsize ? lsize:max_lsize; 205 isz[i] = lsize; 206 } 207 ierr = PetscMalloc1((max_lsize+nrecvs)*nidx,&indices_temp);CHKERRQ(ierr); 208 for (i=0; i<nidx; i++){ 209 ierr = ISGetIndices(is[i],&indices_i_temp);CHKERRQ(ierr); 210 ierr = PetscMemcpy(indices_temp+i*(max_lsize+nrecvs),indices_i_temp, sizeof(PetscInt)*isz[i]);CHKERRQ(ierr); 211 ierr = ISRestoreIndices(is[i],&indices_i_temp);CHKERRQ(ierr); 212 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 213 } 214 /* retrieve information to get row id and its overlap */ 215 for (i=0; i<nrecvs; ){ 216 is_id = recvdata[i++]; 217 data_size = recvdata[i++]; 218 indices_i = indices_temp+(max_lsize+nrecvs)*is_id; 219 isz_i = isz[is_id]; 220 for (j=0; j< data_size; j++){ 221 col = recvdata[i++]; 222 indices_i[isz_i++] = col; 223 } 224 isz[is_id] = isz_i; 225 } 226 /* remove duplicate entities */ 227 for (i=0; i<nidx; i++){ 228 indices_i = indices_temp+(max_lsize+nrecvs)*i; 229 isz_i = isz[i]; 230 ierr = PetscSortRemoveDupsInt(&isz_i,indices_i);CHKERRQ(ierr); 231 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz_i,indices_i,PETSC_COPY_VALUES,&is[i]);CHKERRQ(ierr); 232 } 233 ierr = PetscFree(isz);CHKERRQ(ierr); 234 ierr = PetscFree(indices_temp);CHKERRQ(ierr); 235 PetscFunctionReturn(0); 236 } 237 238 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Send_Scalable(Mat mat,PetscInt nidx, PetscMPIInt nfrom,PetscMPIInt *fromranks,PetscInt *fromsizes, PetscInt *fromrows, PetscInt **sbrowsizes, PetscInt **sbrows) 239 { 240 PetscLayout rmap,cmap; 241 PetscInt i,j,k,l,*rows_i,*rows_data_ptr,**rows_data,max_fszs,rows_pos,*rows_pos_i; 242 PetscInt is_id,tnz,an,bn,rstart,cstart,row,start,end,col,totalrows,*sbdata; 243 PetscInt *indv_counts,indvc_ij,*sbsizes,*indices_tmp,*offsets; 244 const PetscInt *gcols,*ai,*aj,*bi,*bj; 245 Mat amat,bmat; 246 PetscMPIInt rank; 247 PetscBool done; 248 MPI_Comm comm; 249 PetscErrorCode ierr; 250 251 PetscFunctionBegin; 252 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 253 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 254 ierr = MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);CHKERRQ(ierr); 255 /* Even if the mat is symmetric, we still assume it is not symmetric */ 256 ierr = MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);CHKERRQ(ierr); 257 if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n"); 258 ierr = MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);CHKERRQ(ierr); 259 if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n"); 260 /* total number of nonzero values is used to estimate the memory usage in the next step */ 261 tnz = ai[an]+bi[bn]; 262 ierr = MatGetLayouts(mat,&rmap,&cmap);CHKERRQ(ierr); 263 ierr = PetscLayoutGetRange(rmap,&rstart,NULL);CHKERRQ(ierr); 264 ierr = PetscLayoutGetRange(cmap,&cstart,NULL);CHKERRQ(ierr); 265 /* to find the longest message */ 266 max_fszs = 0; 267 for (i=0; i<nfrom; i++) max_fszs = fromsizes[2*i]>max_fszs ? fromsizes[2*i]:max_fszs; 268 /* better way to estimate number of nonzero in the mat??? */ 269 ierr = PetscCalloc5(max_fszs*nidx,&rows_data_ptr,nidx,&rows_data,nidx,&rows_pos_i,nfrom*nidx,&indv_counts,tnz,&indices_tmp);CHKERRQ(ierr); 270 for (i=0; i<nidx; i++) rows_data[i] = rows_data_ptr+max_fszs*i; 271 rows_pos = 0; 272 totalrows = 0; 273 for (i=0; i<nfrom; i++){ 274 ierr = PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);CHKERRQ(ierr); 275 /* group data together */ 276 for (j=0; j<fromsizes[2*i]; j+=2){ 277 is_id = fromrows[rows_pos++];/* no of is */ 278 rows_i = rows_data[is_id]; 279 rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++];/* row */ 280 } 281 /* estimate a space to avoid multiple allocations */ 282 for (j=0; j<nidx; j++){ 283 indvc_ij = 0; 284 rows_i = rows_data[j]; 285 for (l=0; l<rows_pos_i[j]; l++){ 286 row = rows_i[l]-rstart; 287 start = ai[row]; 288 end = ai[row+1]; 289 for (k=start; k<end; k++){ /* Amat */ 290 col = aj[k] + cstart; 291 indices_tmp[indvc_ij++] = col;/* do not count the rows from the original rank */ 292 } 293 start = bi[row]; 294 end = bi[row+1]; 295 for (k=start; k<end; k++) { /* Bmat */ 296 col = gcols[bj[k]]; 297 indices_tmp[indvc_ij++] = col; 298 } 299 } 300 ierr = PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);CHKERRQ(ierr); 301 indv_counts[i*nidx+j] = indvc_ij; 302 totalrows += indvc_ij; 303 } 304 } 305 /* message triple <no of is, number of rows, rows> */ 306 ierr = PetscCalloc2(totalrows+nidx*nfrom*2,&sbdata,2*nfrom,&sbsizes);CHKERRQ(ierr); 307 totalrows = 0; 308 rows_pos = 0; 309 /* use this code again */ 310 for (i=0;i<nfrom;i++){ 311 ierr = PetscMemzero(rows_pos_i,sizeof(PetscInt)*nidx);CHKERRQ(ierr); 312 for (j=0; j<fromsizes[2*i]; j+=2){ 313 is_id = fromrows[rows_pos++]; 314 rows_i = rows_data[is_id]; 315 rows_i[rows_pos_i[is_id]++] = fromrows[rows_pos++]; 316 } 317 /* add data */ 318 for (j=0; j<nidx; j++){ 319 if (!indv_counts[i*nidx+j]) continue; 320 indvc_ij = 0; 321 sbdata[totalrows++] = j; 322 sbdata[totalrows++] = indv_counts[i*nidx+j]; 323 sbsizes[2*i] += 2; 324 rows_i = rows_data[j]; 325 for (l=0; l<rows_pos_i[j]; l++){ 326 row = rows_i[l]-rstart; 327 start = ai[row]; 328 end = ai[row+1]; 329 for (k=start; k<end; k++){ /* Amat */ 330 col = aj[k] + cstart; 331 indices_tmp[indvc_ij++] = col; 332 } 333 start = bi[row]; 334 end = bi[row+1]; 335 for (k=start; k<end; k++) { /* Bmat */ 336 col = gcols[bj[k]]; 337 indices_tmp[indvc_ij++] = col; 338 } 339 } 340 ierr = PetscSortRemoveDupsInt(&indvc_ij,indices_tmp);CHKERRQ(ierr); 341 sbsizes[2*i] += indvc_ij; 342 ierr = PetscMemcpy(sbdata+totalrows,indices_tmp,sizeof(PetscInt)*indvc_ij);CHKERRQ(ierr); 343 totalrows += indvc_ij; 344 } 345 } 346 ierr = PetscCalloc1(nfrom+1,&offsets);CHKERRQ(ierr); 347 for (i=0; i<nfrom; i++){ 348 offsets[i+1] = offsets[i] + sbsizes[2*i]; 349 sbsizes[2*i+1] = offsets[i]; 350 } 351 ierr = PetscFree(offsets);CHKERRQ(ierr); 352 if (sbrowsizes) *sbrowsizes = sbsizes; 353 if (sbrows) *sbrows = sbdata; 354 ierr = PetscFree5(rows_data_ptr,rows_data,rows_pos_i,indv_counts,indices_tmp);CHKERRQ(ierr); 355 ierr = MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);CHKERRQ(ierr); 356 ierr = MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);CHKERRQ(ierr); 357 PetscFunctionReturn(0); 358 } 359 360 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local_Scalable(Mat mat,PetscInt nidx, IS is[]) 361 { 362 const PetscInt *gcols,*ai,*aj,*bi,*bj, *indices; 363 PetscInt tnz,an,bn,i,j,row,start,end,rstart,cstart,col,k,*indices_temp; 364 PetscInt lsize,lsize_tmp,owner; 365 PetscMPIInt rank; 366 Mat amat,bmat; 367 PetscBool done; 368 PetscLayout cmap,rmap; 369 MPI_Comm comm; 370 PetscErrorCode ierr; 371 372 PetscFunctionBegin; 373 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 374 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 375 ierr = MatMPIAIJGetSeqAIJ(mat,&amat,&bmat,&gcols);CHKERRQ(ierr); 376 ierr = MatGetRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);CHKERRQ(ierr); 377 if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n"); 378 ierr = MatGetRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);CHKERRQ(ierr); 379 if (!done) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"can not get row IJ \n"); 380 /* is it a safe way to compute number of nonzero values ? */ 381 tnz = ai[an]+bi[bn]; 382 ierr = MatGetLayouts(mat,&rmap,&cmap);CHKERRQ(ierr); 383 ierr = PetscLayoutGetRange(rmap,&rstart,NULL);CHKERRQ(ierr); 384 ierr = PetscLayoutGetRange(cmap,&cstart,NULL);CHKERRQ(ierr); 385 /* it is a better way to estimate memory than the old implementation 386 * where global size of matrix is used 387 * */ 388 ierr = PetscMalloc1(tnz,&indices_temp);CHKERRQ(ierr); 389 for (i=0; i<nidx; i++) { 390 ierr = ISGetLocalSize(is[i],&lsize);CHKERRQ(ierr); 391 ierr = ISGetIndices(is[i],&indices);CHKERRQ(ierr); 392 lsize_tmp = 0; 393 for (j=0; j<lsize; j++) { 394 owner = -1; 395 row = indices[j]; 396 ierr = PetscLayoutFindOwner(rmap,row,&owner);CHKERRQ(ierr); 397 if (owner != rank) continue; 398 /* local number */ 399 row -= rstart; 400 start = ai[row]; 401 end = ai[row+1]; 402 for (k=start; k<end; k++) { /* Amat */ 403 col = aj[k] + cstart; 404 indices_temp[lsize_tmp++] = col; 405 } 406 start = bi[row]; 407 end = bi[row+1]; 408 for (k=start; k<end; k++) { /* Bmat */ 409 col = gcols[bj[k]]; 410 indices_temp[lsize_tmp++] = col; 411 } 412 } 413 ierr = ISRestoreIndices(is[i],&indices);CHKERRQ(ierr); 414 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 415 ierr = PetscSortRemoveDupsInt(&lsize_tmp,indices_temp);CHKERRQ(ierr); 416 ierr = ISCreateGeneral(PETSC_COMM_SELF,lsize_tmp,indices_temp,PETSC_COPY_VALUES,&is[i]);CHKERRQ(ierr); 417 } 418 ierr = PetscFree(indices_temp);CHKERRQ(ierr); 419 ierr = MatRestoreRowIJ(amat,0,PETSC_FALSE,PETSC_FALSE,&an,&ai,&aj,&done);CHKERRQ(ierr); 420 ierr = MatRestoreRowIJ(bmat,0,PETSC_FALSE,PETSC_FALSE,&bn,&bi,&bj,&done);CHKERRQ(ierr); 421 PetscFunctionReturn(0); 422 } 423 424 425 /* 426 Sample message format: 427 If a processor A wants processor B to process some elements corresponding 428 to index sets is[1],is[5] 429 mesg [0] = 2 (no of index sets in the mesg) 430 ----------- 431 mesg [1] = 1 => is[1] 432 mesg [2] = sizeof(is[1]); 433 ----------- 434 mesg [3] = 5 => is[5] 435 mesg [4] = sizeof(is[5]); 436 ----------- 437 mesg [5] 438 mesg [n] datas[1] 439 ----------- 440 mesg[n+1] 441 mesg[m] data(is[5]) 442 ----------- 443 444 Notes: 445 nrqs - no of requests sent (or to be sent out) 446 nrqr - no of requests recieved (which have to be or which have been processed 447 */ 448 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Once(Mat C,PetscInt imax,IS is[]) 449 { 450 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 451 PetscMPIInt *w1,*w2,nrqr,*w3,*w4,*onodes1,*olengths1,*onodes2,*olengths2; 452 const PetscInt **idx,*idx_i; 453 PetscInt *n,**data,len; 454 #if defined(PETSC_USE_CTABLE) 455 PetscTable *table_data,table_data_i; 456 PetscInt *tdata,tcount,tcount_max; 457 #else 458 PetscInt *data_i,*d_p; 459 #endif 460 PetscErrorCode ierr; 461 PetscMPIInt size,rank,tag1,tag2; 462 PetscInt M,i,j,k,**rbuf,row,proc = 0,nrqs,msz,**outdat,**ptr; 463 PetscInt *ctr,*pa,*tmp,*isz,*isz1,**xdata,**rbuf2; 464 PetscBT *table; 465 MPI_Comm comm; 466 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2; 467 MPI_Status *s_status,*recv_status; 468 char *t_p; 469 470 PetscFunctionBegin; 471 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 472 size = c->size; 473 rank = c->rank; 474 M = C->rmap->N; 475 476 ierr = PetscObjectGetNewTag((PetscObject)C,&tag1);CHKERRQ(ierr); 477 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 478 479 ierr = PetscMalloc2(imax,&idx,imax,&n);CHKERRQ(ierr); 480 481 for (i=0; i<imax; i++) { 482 ierr = ISGetIndices(is[i],&idx[i]);CHKERRQ(ierr); 483 ierr = ISGetLocalSize(is[i],&n[i]);CHKERRQ(ierr); 484 } 485 486 /* evaluate communication - mesg to who,length of mesg, and buffer space 487 required. Based on this, buffers are allocated, and data copied into them */ 488 ierr = PetscMalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); 489 ierr = PetscMemzero(w1,size*sizeof(PetscMPIInt));CHKERRQ(ierr); /* initialise work vector*/ 490 ierr = PetscMemzero(w2,size*sizeof(PetscMPIInt));CHKERRQ(ierr); /* initialise work vector*/ 491 ierr = PetscMemzero(w3,size*sizeof(PetscMPIInt));CHKERRQ(ierr); /* initialise work vector*/ 492 for (i=0; i<imax; i++) { 493 ierr = PetscMemzero(w4,size*sizeof(PetscMPIInt));CHKERRQ(ierr); /* initialise work vector*/ 494 idx_i = idx[i]; 495 len = n[i]; 496 for (j=0; j<len; j++) { 497 row = idx_i[j]; 498 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries"); 499 ierr = PetscLayoutFindOwner(C->rmap,row,&proc);CHKERRQ(ierr); 500 w4[proc]++; 501 } 502 for (j=0; j<size; j++) { 503 if (w4[j]) { w1[j] += w4[j]; w3[j]++;} 504 } 505 } 506 507 nrqs = 0; /* no of outgoing messages */ 508 msz = 0; /* total mesg length (for all proc */ 509 w1[rank] = 0; /* no mesg sent to intself */ 510 w3[rank] = 0; 511 for (i=0; i<size; i++) { 512 if (w1[i]) {w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 513 } 514 /* pa - is list of processors to communicate with */ 515 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); 516 for (i=0,j=0; i<size; i++) { 517 if (w1[i]) {pa[j] = i; j++;} 518 } 519 520 /* Each message would have a header = 1 + 2*(no of IS) + data */ 521 for (i=0; i<nrqs; i++) { 522 j = pa[i]; 523 w1[j] += w2[j] + 2*w3[j]; 524 msz += w1[j]; 525 } 526 527 /* Determine the number of messages to expect, their lengths, from from-ids */ 528 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 529 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 530 531 /* Now post the Irecvs corresponding to these messages */ 532 ierr = PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf,&r_waits1);CHKERRQ(ierr); 533 534 /* Allocate Memory for outgoing messages */ 535 ierr = PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);CHKERRQ(ierr); 536 ierr = PetscMemzero(outdat,size*sizeof(PetscInt*));CHKERRQ(ierr); 537 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 538 539 { 540 PetscInt *iptr = tmp,ict = 0; 541 for (i=0; i<nrqs; i++) { 542 j = pa[i]; 543 iptr += ict; 544 outdat[j] = iptr; 545 ict = w1[j]; 546 } 547 } 548 549 /* Form the outgoing messages */ 550 /* plug in the headers */ 551 for (i=0; i<nrqs; i++) { 552 j = pa[i]; 553 outdat[j][0] = 0; 554 ierr = PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 555 ptr[j] = outdat[j] + 2*w3[j] + 1; 556 } 557 558 /* Memory for doing local proc's work */ 559 { 560 PetscInt M_BPB_imax = 0; 561 #if defined(PETSC_USE_CTABLE) 562 ierr = PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);CHKERRQ(ierr); 563 ierr = PetscMalloc1(imax,&table_data);CHKERRQ(ierr); 564 for (i=0; i<imax; i++) { 565 ierr = PetscTableCreate(n[i]+1,M+1,&table_data[i]);CHKERRQ(ierr); 566 } 567 ierr = PetscCalloc4(imax,&table, imax,&data, imax,&isz, M_BPB_imax,&t_p);CHKERRQ(ierr); 568 for (i=0; i<imax; i++) { 569 table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i; 570 } 571 #else 572 PetscInt Mimax = 0; 573 ierr = PetscIntMultError(M,imax, &Mimax);CHKERRQ(ierr); 574 ierr = PetscIntMultError((M/PETSC_BITS_PER_BYTE+1),imax, &M_BPB_imax);CHKERRQ(ierr); 575 ierr = PetscCalloc5(imax,&table, imax,&data, imax,&isz, Mimax,&d_p, M_BPB_imax,&t_p);CHKERRQ(ierr); 576 for (i=0; i<imax; i++) { 577 table[i] = t_p + (M/PETSC_BITS_PER_BYTE+1)*i; 578 data[i] = d_p + M*i; 579 } 580 #endif 581 } 582 583 /* Parse the IS and update local tables and the outgoing buf with the data */ 584 { 585 PetscInt n_i,isz_i,*outdat_j,ctr_j; 586 PetscBT table_i; 587 588 for (i=0; i<imax; i++) { 589 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 590 n_i = n[i]; 591 table_i = table[i]; 592 idx_i = idx[i]; 593 #if defined(PETSC_USE_CTABLE) 594 table_data_i = table_data[i]; 595 #else 596 data_i = data[i]; 597 #endif 598 isz_i = isz[i]; 599 for (j=0; j<n_i; j++) { /* parse the indices of each IS */ 600 row = idx_i[j]; 601 ierr = PetscLayoutFindOwner(C->rmap,row,&proc);CHKERRQ(ierr); 602 if (proc != rank) { /* copy to the outgoing buffer */ 603 ctr[proc]++; 604 *ptr[proc] = row; 605 ptr[proc]++; 606 } else if (!PetscBTLookupSet(table_i,row)) { 607 #if defined(PETSC_USE_CTABLE) 608 ierr = PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);CHKERRQ(ierr); 609 #else 610 data_i[isz_i] = row; /* Update the local table */ 611 #endif 612 isz_i++; 613 } 614 } 615 /* Update the headers for the current IS */ 616 for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */ 617 if ((ctr_j = ctr[j])) { 618 outdat_j = outdat[j]; 619 k = ++outdat_j[0]; 620 outdat_j[2*k] = ctr_j; 621 outdat_j[2*k-1] = i; 622 } 623 } 624 isz[i] = isz_i; 625 } 626 } 627 628 /* Now post the sends */ 629 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 630 for (i=0; i<nrqs; ++i) { 631 j = pa[i]; 632 ierr = MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);CHKERRQ(ierr); 633 } 634 635 /* No longer need the original indices */ 636 for (i=0; i<imax; ++i) { 637 ierr = ISRestoreIndices(is[i],idx+i);CHKERRQ(ierr); 638 } 639 ierr = PetscFree2(idx,n);CHKERRQ(ierr); 640 641 for (i=0; i<imax; ++i) { 642 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 643 } 644 645 /* Do Local work */ 646 #if defined(PETSC_USE_CTABLE) 647 ierr = MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,NULL,table_data);CHKERRQ(ierr); 648 #else 649 ierr = MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,data,NULL);CHKERRQ(ierr); 650 #endif 651 652 /* Receive messages */ 653 ierr = PetscMalloc1(nrqr+1,&recv_status);CHKERRQ(ierr); 654 if (nrqr) {ierr = MPI_Waitall(nrqr,r_waits1,recv_status);CHKERRQ(ierr);} 655 656 ierr = PetscMalloc1(nrqs+1,&s_status);CHKERRQ(ierr); 657 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status);CHKERRQ(ierr);} 658 659 /* Phase 1 sends are complete - deallocate buffers */ 660 ierr = PetscFree4(outdat,ptr,tmp,ctr);CHKERRQ(ierr); 661 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 662 663 ierr = PetscMalloc1(nrqr+1,&xdata);CHKERRQ(ierr); 664 ierr = PetscMalloc1(nrqr+1,&isz1);CHKERRQ(ierr); 665 ierr = MatIncreaseOverlap_MPIAIJ_Receive(C,nrqr,rbuf,xdata,isz1);CHKERRQ(ierr); 666 ierr = PetscFree(rbuf[0]);CHKERRQ(ierr); 667 ierr = PetscFree(rbuf);CHKERRQ(ierr); 668 669 670 /* Send the data back */ 671 /* Do a global reduction to know the buffer space req for incoming messages */ 672 { 673 PetscMPIInt *rw1; 674 675 ierr = PetscCalloc1(size,&rw1);CHKERRQ(ierr); 676 677 for (i=0; i<nrqr; ++i) { 678 proc = recv_status[i].MPI_SOURCE; 679 680 if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch"); 681 rw1[proc] = isz1[i]; 682 } 683 ierr = PetscFree(onodes1);CHKERRQ(ierr); 684 ierr = PetscFree(olengths1);CHKERRQ(ierr); 685 686 /* Determine the number of messages to expect, their lengths, from from-ids */ 687 ierr = PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);CHKERRQ(ierr); 688 ierr = PetscFree(rw1);CHKERRQ(ierr); 689 } 690 /* Now post the Irecvs corresponding to these messages */ 691 ierr = PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);CHKERRQ(ierr); 692 693 /* Now post the sends */ 694 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 695 for (i=0; i<nrqr; ++i) { 696 j = recv_status[i].MPI_SOURCE; 697 ierr = MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);CHKERRQ(ierr); 698 } 699 700 /* receive work done on other processors */ 701 { 702 PetscInt is_no,ct1,max,*rbuf2_i,isz_i,jmax; 703 PetscMPIInt idex; 704 PetscBT table_i; 705 MPI_Status *status2; 706 707 ierr = PetscMalloc1((PetscMax(nrqr,nrqs)+1),&status2);CHKERRQ(ierr); 708 for (i=0; i<nrqs; ++i) { 709 ierr = MPI_Waitany(nrqs,r_waits2,&idex,status2+i);CHKERRQ(ierr); 710 /* Process the message */ 711 rbuf2_i = rbuf2[idex]; 712 ct1 = 2*rbuf2_i[0]+1; 713 jmax = rbuf2[idex][0]; 714 for (j=1; j<=jmax; j++) { 715 max = rbuf2_i[2*j]; 716 is_no = rbuf2_i[2*j-1]; 717 isz_i = isz[is_no]; 718 table_i = table[is_no]; 719 #if defined(PETSC_USE_CTABLE) 720 table_data_i = table_data[is_no]; 721 #else 722 data_i = data[is_no]; 723 #endif 724 for (k=0; k<max; k++,ct1++) { 725 row = rbuf2_i[ct1]; 726 if (!PetscBTLookupSet(table_i,row)) { 727 #if defined(PETSC_USE_CTABLE) 728 ierr = PetscTableAdd(table_data_i,row+1,isz_i+1,INSERT_VALUES);CHKERRQ(ierr); 729 #else 730 data_i[isz_i] = row; 731 #endif 732 isz_i++; 733 } 734 } 735 isz[is_no] = isz_i; 736 } 737 } 738 739 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,status2);CHKERRQ(ierr);} 740 ierr = PetscFree(status2);CHKERRQ(ierr); 741 } 742 743 #if defined(PETSC_USE_CTABLE) 744 tcount_max = 0; 745 for (i=0; i<imax; ++i) { 746 table_data_i = table_data[i]; 747 ierr = PetscTableGetCount(table_data_i,&tcount);CHKERRQ(ierr); 748 if (tcount_max < tcount) tcount_max = tcount; 749 } 750 ierr = PetscMalloc1(tcount_max+1,&tdata);CHKERRQ(ierr); 751 #endif 752 753 for (i=0; i<imax; ++i) { 754 #if defined(PETSC_USE_CTABLE) 755 PetscTablePosition tpos; 756 table_data_i = table_data[i]; 757 758 ierr = PetscTableGetHeadPosition(table_data_i,&tpos);CHKERRQ(ierr); 759 while (tpos) { 760 ierr = PetscTableGetNext(table_data_i,&tpos,&k,&j);CHKERRQ(ierr); 761 tdata[--j] = --k; 762 } 763 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz[i],tdata,PETSC_COPY_VALUES,is+i);CHKERRQ(ierr); 764 #else 765 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz[i],data[i],PETSC_COPY_VALUES,is+i);CHKERRQ(ierr); 766 #endif 767 } 768 769 ierr = PetscFree(onodes2);CHKERRQ(ierr); 770 ierr = PetscFree(olengths2);CHKERRQ(ierr); 771 772 ierr = PetscFree(pa);CHKERRQ(ierr); 773 ierr = PetscFree(rbuf2[0]);CHKERRQ(ierr); 774 ierr = PetscFree(rbuf2);CHKERRQ(ierr); 775 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 776 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 777 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 778 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 779 ierr = PetscFree(s_status);CHKERRQ(ierr); 780 ierr = PetscFree(recv_status);CHKERRQ(ierr); 781 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 782 ierr = PetscFree(xdata);CHKERRQ(ierr); 783 ierr = PetscFree(isz1);CHKERRQ(ierr); 784 #if defined(PETSC_USE_CTABLE) 785 for (i=0; i<imax; i++) { 786 ierr = PetscTableDestroy((PetscTable*)&table_data[i]);CHKERRQ(ierr); 787 } 788 ierr = PetscFree(table_data);CHKERRQ(ierr); 789 ierr = PetscFree(tdata);CHKERRQ(ierr); 790 ierr = PetscFree4(table,data,isz,t_p);CHKERRQ(ierr); 791 #else 792 ierr = PetscFree5(table,data,isz,d_p,t_p);CHKERRQ(ierr); 793 #endif 794 PetscFunctionReturn(0); 795 } 796 797 /* 798 MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do 799 the work on the local processor. 800 801 Inputs: 802 C - MAT_MPIAIJ; 803 imax - total no of index sets processed at a time; 804 table - an array of char - size = m bits. 805 806 Output: 807 isz - array containing the count of the solution elements corresponding 808 to each index set; 809 data or table_data - pointer to the solutions 810 */ 811 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data,PetscTable *table_data) 812 { 813 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 814 Mat A = c->A,B = c->B; 815 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data; 816 PetscInt start,end,val,max,rstart,cstart,*ai,*aj; 817 PetscInt *bi,*bj,*garray,i,j,k,row,isz_i; 818 PetscBT table_i; 819 #if defined(PETSC_USE_CTABLE) 820 PetscTable table_data_i; 821 PetscErrorCode ierr; 822 PetscTablePosition tpos; 823 PetscInt tcount,*tdata; 824 #else 825 PetscInt *data_i; 826 #endif 827 828 PetscFunctionBegin; 829 rstart = C->rmap->rstart; 830 cstart = C->cmap->rstart; 831 ai = a->i; 832 aj = a->j; 833 bi = b->i; 834 bj = b->j; 835 garray = c->garray; 836 837 for (i=0; i<imax; i++) { 838 #if defined(PETSC_USE_CTABLE) 839 /* copy existing entries of table_data_i into tdata[] */ 840 table_data_i = table_data[i]; 841 ierr = PetscTableGetCount(table_data_i,&tcount);CHKERRQ(ierr); 842 if (tcount != isz[i]) SETERRQ3(PETSC_COMM_SELF,0," tcount %d != isz[%d] %d",tcount,i,isz[i]); 843 844 ierr = PetscMalloc1(tcount,&tdata);CHKERRQ(ierr); 845 ierr = PetscTableGetHeadPosition(table_data_i,&tpos);CHKERRQ(ierr); 846 while (tpos) { 847 ierr = PetscTableGetNext(table_data_i,&tpos,&row,&j);CHKERRQ(ierr); 848 tdata[--j] = --row; 849 if (j > tcount - 1) SETERRQ2(PETSC_COMM_SELF,0," j %d >= tcount %d",j,tcount); 850 } 851 #else 852 data_i = data[i]; 853 #endif 854 table_i = table[i]; 855 isz_i = isz[i]; 856 max = isz[i]; 857 858 for (j=0; j<max; j++) { 859 #if defined(PETSC_USE_CTABLE) 860 row = tdata[j] - rstart; 861 #else 862 row = data_i[j] - rstart; 863 #endif 864 start = ai[row]; 865 end = ai[row+1]; 866 for (k=start; k<end; k++) { /* Amat */ 867 val = aj[k] + cstart; 868 if (!PetscBTLookupSet(table_i,val)) { 869 #if defined(PETSC_USE_CTABLE) 870 ierr = PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);CHKERRQ(ierr); 871 #else 872 data_i[isz_i] = val; 873 #endif 874 isz_i++; 875 } 876 } 877 start = bi[row]; 878 end = bi[row+1]; 879 for (k=start; k<end; k++) { /* Bmat */ 880 val = garray[bj[k]]; 881 if (!PetscBTLookupSet(table_i,val)) { 882 #if defined(PETSC_USE_CTABLE) 883 ierr = PetscTableAdd(table_data_i,val+1,isz_i+1,INSERT_VALUES);CHKERRQ(ierr); 884 #else 885 data_i[isz_i] = val; 886 #endif 887 isz_i++; 888 } 889 } 890 } 891 isz[i] = isz_i; 892 893 #if defined(PETSC_USE_CTABLE) 894 ierr = PetscFree(tdata);CHKERRQ(ierr); 895 #endif 896 } 897 PetscFunctionReturn(0); 898 } 899 900 /* 901 MatIncreaseOverlap_MPIAIJ_Receive - Process the recieved messages, 902 and return the output 903 904 Input: 905 C - the matrix 906 nrqr - no of messages being processed. 907 rbuf - an array of pointers to the recieved requests 908 909 Output: 910 xdata - array of messages to be sent back 911 isz1 - size of each message 912 913 For better efficiency perhaps we should malloc separately each xdata[i], 914 then if a remalloc is required we need only copy the data for that one row 915 rather then all previous rows as it is now where a single large chunck of 916 memory is used. 917 918 */ 919 static PetscErrorCode MatIncreaseOverlap_MPIAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1) 920 { 921 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 922 Mat A = c->A,B = c->B; 923 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data; 924 PetscErrorCode ierr; 925 PetscInt rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k; 926 PetscInt row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end; 927 PetscInt val,max1,max2,m,no_malloc =0,*tmp,new_estimate,ctr; 928 PetscInt *rbuf_i,kmax,rbuf_0; 929 PetscBT xtable; 930 931 PetscFunctionBegin; 932 m = C->rmap->N; 933 rstart = C->rmap->rstart; 934 cstart = C->cmap->rstart; 935 ai = a->i; 936 aj = a->j; 937 bi = b->i; 938 bj = b->j; 939 garray = c->garray; 940 941 942 for (i=0,ct=0,total_sz=0; i<nrqr; ++i) { 943 rbuf_i = rbuf[i]; 944 rbuf_0 = rbuf_i[0]; 945 ct += rbuf_0; 946 for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j]; 947 } 948 949 if (C->rmap->n) max1 = ct*(a->nz + b->nz)/C->rmap->n; 950 else max1 = 1; 951 mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1); 952 ierr = PetscMalloc1(mem_estimate,&xdata[0]);CHKERRQ(ierr); 953 ++no_malloc; 954 ierr = PetscBTCreate(m,&xtable);CHKERRQ(ierr); 955 ierr = PetscMemzero(isz1,nrqr*sizeof(PetscInt));CHKERRQ(ierr); 956 957 ct3 = 0; 958 for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */ 959 rbuf_i = rbuf[i]; 960 rbuf_0 = rbuf_i[0]; 961 ct1 = 2*rbuf_0+1; 962 ct2 = ct1; 963 ct3 += ct1; 964 for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/ 965 ierr = PetscBTMemzero(m,xtable);CHKERRQ(ierr); 966 oct2 = ct2; 967 kmax = rbuf_i[2*j]; 968 for (k=0; k<kmax; k++,ct1++) { 969 row = rbuf_i[ct1]; 970 if (!PetscBTLookupSet(xtable,row)) { 971 if (!(ct3 < mem_estimate)) { 972 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 973 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 974 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 975 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 976 xdata[0] = tmp; 977 mem_estimate = new_estimate; ++no_malloc; 978 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 979 } 980 xdata[i][ct2++] = row; 981 ct3++; 982 } 983 } 984 for (k=oct2,max2=ct2; k<max2; k++) { 985 row = xdata[i][k] - rstart; 986 start = ai[row]; 987 end = ai[row+1]; 988 for (l=start; l<end; l++) { 989 val = aj[l] + cstart; 990 if (!PetscBTLookupSet(xtable,val)) { 991 if (!(ct3 < mem_estimate)) { 992 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 993 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 994 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 995 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 996 xdata[0] = tmp; 997 mem_estimate = new_estimate; ++no_malloc; 998 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 999 } 1000 xdata[i][ct2++] = val; 1001 ct3++; 1002 } 1003 } 1004 start = bi[row]; 1005 end = bi[row+1]; 1006 for (l=start; l<end; l++) { 1007 val = garray[bj[l]]; 1008 if (!PetscBTLookupSet(xtable,val)) { 1009 if (!(ct3 < mem_estimate)) { 1010 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 1011 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 1012 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 1013 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 1014 xdata[0] = tmp; 1015 mem_estimate = new_estimate; ++no_malloc; 1016 for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 1017 } 1018 xdata[i][ct2++] = val; 1019 ct3++; 1020 } 1021 } 1022 } 1023 /* Update the header*/ 1024 xdata[i][2*j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/ 1025 xdata[i][2*j-1] = rbuf_i[2*j-1]; 1026 } 1027 xdata[i][0] = rbuf_0; 1028 xdata[i+1] = xdata[i] + ct2; 1029 isz1[i] = ct2; /* size of each message */ 1030 } 1031 ierr = PetscBTDestroy(&xtable);CHKERRQ(ierr); 1032 ierr = PetscInfo3(C,"Allocated %D bytes, required %D bytes, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);CHKERRQ(ierr); 1033 PetscFunctionReturn(0); 1034 } 1035 /* -------------------------------------------------------------------------*/ 1036 extern PetscErrorCode MatGetSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*); 1037 extern PetscErrorCode MatAssemblyEnd_SeqAIJ(Mat,MatAssemblyType); 1038 /* 1039 Every processor gets the entire matrix 1040 */ 1041 PetscErrorCode MatGetSubMatrix_MPIAIJ_All(Mat A,MatGetSubMatrixOption flag,MatReuse scall,Mat *Bin[]) 1042 { 1043 Mat B; 1044 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1045 Mat_SeqAIJ *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data; 1046 PetscErrorCode ierr; 1047 PetscMPIInt size,rank,*recvcounts = 0,*displs = 0; 1048 PetscInt sendcount,i,*rstarts = A->rmap->range,n,cnt,j; 1049 PetscInt m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf; 1050 MatScalar *sendbuf,*recvbuf,*a_sendbuf,*b_sendbuf; 1051 1052 PetscFunctionBegin; 1053 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&size);CHKERRQ(ierr); 1054 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 1055 1056 if (scall == MAT_INITIAL_MATRIX) { 1057 /* ---------------------------------------------------------------- 1058 Tell every processor the number of nonzeros per row 1059 */ 1060 ierr = PetscMalloc1(A->rmap->N,&lens);CHKERRQ(ierr); 1061 for (i=A->rmap->rstart; i<A->rmap->rend; i++) { 1062 lens[i] = ad->i[i-A->rmap->rstart+1] - ad->i[i-A->rmap->rstart] + bd->i[i-A->rmap->rstart+1] - bd->i[i-A->rmap->rstart]; 1063 } 1064 ierr = PetscMalloc2(size,&recvcounts,size,&displs);CHKERRQ(ierr); 1065 for (i=0; i<size; i++) { 1066 recvcounts[i] = A->rmap->range[i+1] - A->rmap->range[i]; 1067 displs[i] = A->rmap->range[i]; 1068 } 1069 #if defined(PETSC_HAVE_MPI_IN_PLACE) 1070 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1071 #else 1072 sendcount = A->rmap->rend - A->rmap->rstart; 1073 ierr = MPI_Allgatherv(lens+A->rmap->rstart,sendcount,MPIU_INT,lens,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1074 #endif 1075 /* --------------------------------------------------------------- 1076 Create the sequential matrix of the same type as the local block diagonal 1077 */ 1078 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 1079 ierr = MatSetSizes(B,A->rmap->N,A->cmap->N,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1080 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 1081 ierr = MatSetType(B,((PetscObject)a->A)->type_name);CHKERRQ(ierr); 1082 ierr = MatSeqAIJSetPreallocation(B,0,lens);CHKERRQ(ierr); 1083 ierr = PetscMalloc1(1,Bin);CHKERRQ(ierr); 1084 **Bin = B; 1085 b = (Mat_SeqAIJ*)B->data; 1086 1087 /*-------------------------------------------------------------------- 1088 Copy my part of matrix column indices over 1089 */ 1090 sendcount = ad->nz + bd->nz; 1091 jsendbuf = b->j + b->i[rstarts[rank]]; 1092 a_jsendbuf = ad->j; 1093 b_jsendbuf = bd->j; 1094 n = A->rmap->rend - A->rmap->rstart; 1095 cnt = 0; 1096 for (i=0; i<n; i++) { 1097 1098 /* put in lower diagonal portion */ 1099 m = bd->i[i+1] - bd->i[i]; 1100 while (m > 0) { 1101 /* is it above diagonal (in bd (compressed) numbering) */ 1102 if (garray[*b_jsendbuf] > A->rmap->rstart + i) break; 1103 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 1104 m--; 1105 } 1106 1107 /* put in diagonal portion */ 1108 for (j=ad->i[i]; j<ad->i[i+1]; j++) { 1109 jsendbuf[cnt++] = A->rmap->rstart + *a_jsendbuf++; 1110 } 1111 1112 /* put in upper diagonal portion */ 1113 while (m-- > 0) { 1114 jsendbuf[cnt++] = garray[*b_jsendbuf++]; 1115 } 1116 } 1117 if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt); 1118 1119 /*-------------------------------------------------------------------- 1120 Gather all column indices to all processors 1121 */ 1122 for (i=0; i<size; i++) { 1123 recvcounts[i] = 0; 1124 for (j=A->rmap->range[i]; j<A->rmap->range[i+1]; j++) { 1125 recvcounts[i] += lens[j]; 1126 } 1127 } 1128 displs[0] = 0; 1129 for (i=1; i<size; i++) { 1130 displs[i] = displs[i-1] + recvcounts[i-1]; 1131 } 1132 #if defined(PETSC_HAVE_MPI_IN_PLACE) 1133 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1134 #else 1135 ierr = MPI_Allgatherv(jsendbuf,sendcount,MPIU_INT,b->j,recvcounts,displs,MPIU_INT,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1136 #endif 1137 /*-------------------------------------------------------------------- 1138 Assemble the matrix into useable form (note numerical values not yet set) 1139 */ 1140 /* set the b->ilen (length of each row) values */ 1141 ierr = PetscMemcpy(b->ilen,lens,A->rmap->N*sizeof(PetscInt));CHKERRQ(ierr); 1142 /* set the b->i indices */ 1143 b->i[0] = 0; 1144 for (i=1; i<=A->rmap->N; i++) { 1145 b->i[i] = b->i[i-1] + lens[i-1]; 1146 } 1147 ierr = PetscFree(lens);CHKERRQ(ierr); 1148 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1149 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1150 1151 } else { 1152 B = **Bin; 1153 b = (Mat_SeqAIJ*)B->data; 1154 } 1155 1156 /*-------------------------------------------------------------------- 1157 Copy my part of matrix numerical values into the values location 1158 */ 1159 if (flag == MAT_GET_VALUES) { 1160 sendcount = ad->nz + bd->nz; 1161 sendbuf = b->a + b->i[rstarts[rank]]; 1162 a_sendbuf = ad->a; 1163 b_sendbuf = bd->a; 1164 b_sendj = bd->j; 1165 n = A->rmap->rend - A->rmap->rstart; 1166 cnt = 0; 1167 for (i=0; i<n; i++) { 1168 1169 /* put in lower diagonal portion */ 1170 m = bd->i[i+1] - bd->i[i]; 1171 while (m > 0) { 1172 /* is it above diagonal (in bd (compressed) numbering) */ 1173 if (garray[*b_sendj] > A->rmap->rstart + i) break; 1174 sendbuf[cnt++] = *b_sendbuf++; 1175 m--; 1176 b_sendj++; 1177 } 1178 1179 /* put in diagonal portion */ 1180 for (j=ad->i[i]; j<ad->i[i+1]; j++) { 1181 sendbuf[cnt++] = *a_sendbuf++; 1182 } 1183 1184 /* put in upper diagonal portion */ 1185 while (m-- > 0) { 1186 sendbuf[cnt++] = *b_sendbuf++; 1187 b_sendj++; 1188 } 1189 } 1190 if (cnt != sendcount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupted PETSc matrix: nz given %D actual nz %D",sendcount,cnt); 1191 1192 /* ----------------------------------------------------------------- 1193 Gather all numerical values to all processors 1194 */ 1195 if (!recvcounts) { 1196 ierr = PetscMalloc2(size,&recvcounts,size,&displs);CHKERRQ(ierr); 1197 } 1198 for (i=0; i<size; i++) { 1199 recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]]; 1200 } 1201 displs[0] = 0; 1202 for (i=1; i<size; i++) { 1203 displs[i] = displs[i-1] + recvcounts[i-1]; 1204 } 1205 recvbuf = b->a; 1206 #if defined(PETSC_HAVE_MPI_IN_PLACE) 1207 ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1208 #else 1209 ierr = MPI_Allgatherv(sendbuf,sendcount,MPIU_SCALAR,recvbuf,recvcounts,displs,MPIU_SCALAR,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1210 #endif 1211 } /* endof (flag == MAT_GET_VALUES) */ 1212 ierr = PetscFree2(recvcounts,displs);CHKERRQ(ierr); 1213 1214 if (A->symmetric) { 1215 ierr = MatSetOption(B,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 1216 } else if (A->hermitian) { 1217 ierr = MatSetOption(B,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr); 1218 } else if (A->structurally_symmetric) { 1219 ierr = MatSetOption(B,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); 1220 } 1221 PetscFunctionReturn(0); 1222 } 1223 1224 PetscErrorCode MatDestroy_MPIAIJ_MatGetSubmatrices(Mat C) 1225 { 1226 PetscErrorCode ierr; 1227 Mat_SeqAIJ *c = (Mat_SeqAIJ*)C->data; 1228 Mat_SubMat *submatj = c->submatis1; 1229 PetscInt i; 1230 1231 PetscFunctionBegin; 1232 if (!submatj->id) { /* delete data that are linked only to submats[id=0] */ 1233 ierr = PetscFree4(submatj->sbuf1,submatj->ptr,submatj->tmp,submatj->ctr);CHKERRQ(ierr); 1234 1235 for (i=0; i<submatj->nrqr; ++i) { 1236 ierr = PetscFree(submatj->sbuf2[i]);CHKERRQ(ierr); 1237 } 1238 ierr = PetscFree3(submatj->sbuf2,submatj->req_size,submatj->req_source1);CHKERRQ(ierr); 1239 1240 if (submatj->rbuf1) { 1241 ierr = PetscFree(submatj->rbuf1[0]);CHKERRQ(ierr); 1242 ierr = PetscFree(submatj->rbuf1);CHKERRQ(ierr); 1243 } 1244 1245 for (i=0; i<submatj->nrqs; ++i) { 1246 ierr = PetscFree(submatj->rbuf3[i]);CHKERRQ(ierr); 1247 } 1248 ierr = PetscFree3(submatj->req_source2,submatj->rbuf2,submatj->rbuf3);CHKERRQ(ierr); 1249 ierr = PetscFree(submatj->pa);CHKERRQ(ierr); 1250 } 1251 1252 #if defined(PETSC_USE_CTABLE) 1253 ierr = PetscTableDestroy((PetscTable*)&submatj->rmap);CHKERRQ(ierr); 1254 if (submatj->cmap_loc) {ierr = PetscFree(submatj->cmap_loc);CHKERRQ(ierr);} 1255 ierr = PetscFree(submatj->rmap_loc);CHKERRQ(ierr); 1256 #else 1257 ierr = PetscFree(submatj->rmap);CHKERRQ(ierr); 1258 #endif 1259 1260 if (!submatj->allcolumns) { 1261 #if defined(PETSC_USE_CTABLE) 1262 ierr = PetscTableDestroy((PetscTable*)&submatj->cmap);CHKERRQ(ierr); 1263 #else 1264 ierr = PetscFree(submatj->cmap);CHKERRQ(ierr); 1265 #endif 1266 } 1267 ierr = submatj->destroy(C);CHKERRQ(ierr); 1268 ierr = PetscFree(submatj->row2proc);CHKERRQ(ierr); 1269 1270 ierr = PetscFree(submatj);CHKERRQ(ierr); 1271 PetscFunctionReturn(0); 1272 } 1273 1274 PetscErrorCode MatGetSubMatrices_MPIAIJ_SingleIS_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool allcolumns,Mat *submats) 1275 { 1276 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 1277 Mat submat,A = c->A,B = c->B; 1278 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data,*subc; 1279 PetscInt *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j,nzA,nzB; 1280 PetscInt cstart = C->cmap->rstart,cend = C->cmap->rend,rstart = C->rmap->rstart,*bmap = c->garray; 1281 const PetscInt *icol,*irow; 1282 PetscInt nrow,ncol,start; 1283 PetscErrorCode ierr; 1284 PetscMPIInt rank,size,tag1,tag2,tag3,tag4,*w1,*w2,nrqr; 1285 PetscInt **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,ct3,**rbuf1,row,proc; 1286 PetscInt nrqs=0,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol,*iptr; 1287 PetscInt **rbuf3,*req_source1,*req_source2,**sbuf_aj,**rbuf2,max1,nnz; 1288 PetscInt *lens,rmax,ncols,*cols,Crow; 1289 #if defined(PETSC_USE_CTABLE) 1290 PetscTable cmap,rmap; 1291 PetscInt *cmap_loc,*rmap_loc; 1292 #else 1293 PetscInt *cmap,*rmap; 1294 #endif 1295 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*sbuf1_i,*rbuf2_i,*rbuf3_i; 1296 PetscInt *cworkB,lwrite,*subcols,*row2proc; 1297 PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a,*subvals=NULL; 1298 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 1299 MPI_Request *r_waits4,*s_waits3 = NULL,*s_waits4; 1300 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3 = NULL,*s_status2; 1301 MPI_Status *r_status3 = NULL,*r_status4,*s_status4; 1302 MPI_Comm comm; 1303 PetscScalar **rbuf4,**sbuf_aa,*vals,*sbuf_aa_i,*rbuf4_i; 1304 PetscMPIInt *onodes1,*olengths1,idex,end; 1305 Mat_SubMat *smatis1; 1306 PetscBool isrowsorted; 1307 1308 PetscFunctionBegin; 1309 if (ismax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This routine only works when all processes have ismax=1"); 1310 1311 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1312 size = c->size; 1313 rank = c->rank; 1314 1315 ierr = ISSorted(isrow[0],&isrowsorted);CHKERRQ(ierr); 1316 if (!isrowsorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow[0] must be sorted"); 1317 1318 ierr = ISGetIndices(isrow[0],&irow);CHKERRQ(ierr); 1319 ierr = ISGetLocalSize(isrow[0],&nrow);CHKERRQ(ierr); 1320 if (allcolumns) { 1321 icol = NULL; 1322 ncol = C->cmap->N; 1323 } else { 1324 ierr = ISGetIndices(iscol[0],&icol);CHKERRQ(ierr); 1325 ierr = ISGetLocalSize(iscol[0],&ncol);CHKERRQ(ierr); 1326 } 1327 1328 if (scall == MAT_INITIAL_MATRIX) { 1329 PetscInt *sbuf2_i,*cworkA,lwrite,ctmp; 1330 1331 /* Get some new tags to keep the communication clean */ 1332 tag1 = ((PetscObject)C)->tag; 1333 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 1334 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 1335 1336 /* evaluate communication - mesg to who, length of mesg, and buffer space 1337 required. Based on this, buffers are allocated, and data copied into them */ 1338 ierr = PetscCalloc2(size,&w1,size,&w2);CHKERRQ(ierr); 1339 ierr = PetscMalloc1(nrow,&row2proc);CHKERRQ(ierr); 1340 1341 /* w1[proc] = num of rows owned by proc -- to be requested */ 1342 proc = 0; 1343 nrqs = 0; /* num of outgoing messages */ 1344 for (j=0; j<nrow; j++) { 1345 row = irow[j]; /* sorted! */ 1346 while (row >= C->rmap->range[proc+1]) proc++; 1347 w1[proc]++; 1348 row2proc[j] = proc; /* map row index to proc */ 1349 1350 if (proc != rank && !w2[proc]) { 1351 w2[proc] = 1; nrqs++; 1352 } 1353 } 1354 w1[rank] = 0; /* rows owned by self will not be requested */ 1355 1356 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 1357 for (proc=0,j=0; proc<size; proc++) { 1358 if (w1[proc]) { pa[j++] = proc;} 1359 } 1360 1361 /* Each message would have a header = 1 + 2*(num of IS) + data (here,num of IS = 1) */ 1362 msz = 0; /* total mesg length (for all procs) */ 1363 for (i=0; i<nrqs; i++) { 1364 proc = pa[i]; 1365 w1[proc] += 3; 1366 msz += w1[proc]; 1367 } 1368 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 1369 1370 /* Determine nrqr, the number of messages to expect, their lengths, from from-ids */ 1371 /* if w2[proc]=1, a message of length w1[proc] will be sent to proc; */ 1372 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 1373 1374 /* Input: nrqs: nsend; nrqr: nrecv; w1: msg length to be sent; 1375 Output: onodes1: recv node-ids; olengths1: corresponding recv message length */ 1376 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 1377 1378 /* Now post the Irecvs corresponding to these messages */ 1379 ierr = PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 1380 1381 ierr = PetscFree(onodes1);CHKERRQ(ierr); 1382 ierr = PetscFree(olengths1);CHKERRQ(ierr); 1383 1384 /* Allocate Memory for outgoing messages */ 1385 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 1386 ierr = PetscMemzero(sbuf1,size*sizeof(PetscInt*));CHKERRQ(ierr); 1387 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 1388 1389 /* subf1[pa[0]] = tmp, subf1[pa[i]] = subf1[pa[i-1]] + w1[pa[i-1]] */ 1390 iptr = tmp; 1391 for (i=0; i<nrqs; i++) { 1392 proc = pa[i]; 1393 sbuf1[proc] = iptr; 1394 iptr += w1[proc]; 1395 } 1396 1397 /* Form the outgoing messages */ 1398 /* Initialize the header space */ 1399 for (i=0; i<nrqs; i++) { 1400 proc = pa[i]; 1401 ierr = PetscMemzero(sbuf1[proc],3*sizeof(PetscInt));CHKERRQ(ierr); 1402 ptr[proc] = sbuf1[proc] + 3; 1403 } 1404 1405 /* Parse the isrow and copy data into outbuf */ 1406 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 1407 for (j=0; j<nrow; j++) { /* parse the indices of each IS */ 1408 proc = row2proc[j]; 1409 if (proc != rank) { /* copy to the outgoing buf*/ 1410 *ptr[proc] = irow[j]; 1411 ctr[proc]++; ptr[proc]++; 1412 } 1413 } 1414 1415 /* Update the headers for the current IS */ 1416 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 1417 if ((ctr_j = ctr[j])) { 1418 sbuf1_j = sbuf1[j]; 1419 k = ++sbuf1_j[0]; 1420 sbuf1_j[2*k] = ctr_j; 1421 sbuf1_j[2*k-1] = 0; 1422 } 1423 } 1424 1425 /* Now post the sends */ 1426 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 1427 for (i=0; i<nrqs; ++i) { 1428 proc = pa[i]; 1429 ierr = MPI_Isend(sbuf1[proc],w1[proc],MPIU_INT,proc,tag1,comm,s_waits1+i);CHKERRQ(ierr); 1430 } 1431 1432 /* Post Receives to capture the buffer size */ 1433 ierr = PetscMalloc4(nrqs+1,&r_status2,nrqr+1,&s_waits2,nrqs+1,&r_waits2,nrqr+1,&s_status2);CHKERRQ(ierr); 1434 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 1435 1436 rbuf2[0] = tmp + msz; 1437 for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + w1[pa[i-1]]; 1438 1439 for (i=0; i<nrqs; ++i) { 1440 proc = pa[i]; 1441 ierr = MPI_Irecv(rbuf2[i],w1[proc],MPIU_INT,proc,tag2,comm,r_waits2+i);CHKERRQ(ierr); 1442 } 1443 1444 ierr = PetscFree2(w1,w2);CHKERRQ(ierr); 1445 1446 /* Send to other procs the buf size they should allocate */ 1447 /* Receive messages*/ 1448 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 1449 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 1450 1451 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRQ(ierr); 1452 for (i=0; i<nrqr; ++i) { 1453 req_size[i] = 0; 1454 rbuf1_i = rbuf1[i]; 1455 start = 2*rbuf1_i[0] + 1; 1456 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRQ(ierr); 1457 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 1458 sbuf2_i = sbuf2[i]; 1459 for (j=start; j<end; j++) { 1460 k = rbuf1_i[j] - rstart; 1461 ncols = ai[k+1] - ai[k] + bi[k+1] - bi[k]; 1462 sbuf2_i[j] = ncols; 1463 req_size[i] += ncols; 1464 } 1465 req_source1[i] = r_status1[i].MPI_SOURCE; 1466 1467 /* form the header */ 1468 sbuf2_i[0] = req_size[i]; 1469 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 1470 1471 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 1472 } 1473 1474 ierr = PetscFree(r_status1);CHKERRQ(ierr); 1475 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 1476 1477 /* rbuf2 is received, Post recv column indices a->j */ 1478 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRQ(ierr); 1479 1480 ierr = PetscMalloc4(nrqs+1,&r_waits3,nrqr+1,&s_waits3,nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 1481 for (i=0; i<nrqs; ++i) { 1482 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 1483 req_source2[i] = r_status2[i].MPI_SOURCE; 1484 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRQ(ierr); 1485 } 1486 1487 /* Wait on sends1 and sends2 */ 1488 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 1489 ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr); 1490 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 1491 ierr = PetscFree(s_status1);CHKERRQ(ierr); 1492 1493 ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr); 1494 ierr = PetscFree4(r_status2,s_waits2,r_waits2,s_status2);CHKERRQ(ierr); 1495 1496 /* Now allocate sending buffers for a->j, and send them off */ 1497 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 1498 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 1499 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 1500 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 1501 1502 for (i=0; i<nrqr; i++) { /* for each requested message */ 1503 rbuf1_i = rbuf1[i]; 1504 sbuf_aj_i = sbuf_aj[i]; 1505 ct1 = 2*rbuf1_i[0] + 1; 1506 ct2 = 0; 1507 /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ1(PETSC_COMM_SELF,0,"max1 %d != 1",max1); */ 1508 1509 kmax = rbuf1[i][2]; 1510 for (k=0; k<kmax; k++,ct1++) { /* for each row */ 1511 row = rbuf1_i[ct1] - rstart; 1512 nzA = ai[row+1] - ai[row]; 1513 nzB = bi[row+1] - bi[row]; 1514 ncols = nzA + nzB; 1515 cworkA = aj + ai[row]; cworkB = bj + bi[row]; 1516 1517 /* load the column indices for this row into cols*/ 1518 cols = sbuf_aj_i + ct2; 1519 1520 lwrite = 0; 1521 for (l=0; l<nzB; l++) { 1522 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp; 1523 } 1524 for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l]; 1525 for (l=0; l<nzB; l++) { 1526 if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp; 1527 } 1528 1529 ct2 += ncols; 1530 } 1531 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 1532 } 1533 1534 /* create column map (cmap): global col of C -> local col of submat */ 1535 #if defined(PETSC_USE_CTABLE) 1536 if (!allcolumns) { 1537 ierr = PetscTableCreate(ncol+1,C->cmap->N+1,&cmap);CHKERRQ(ierr); 1538 ierr = PetscCalloc1(C->cmap->n,&cmap_loc);CHKERRQ(ierr); 1539 for (j=0; j<ncol; j++) { /* use array cmap_loc[] for local col indices */ 1540 if (icol[j] >= cstart && icol[j] <cend) { 1541 cmap_loc[icol[j] - cstart] = j+1; 1542 } else { /* use PetscTable for non-local col indices */ 1543 ierr = PetscTableAdd(cmap,icol[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1544 } 1545 } 1546 } else { 1547 cmap = NULL; 1548 cmap_loc = NULL; 1549 } 1550 ierr = PetscCalloc1(C->rmap->n,&rmap_loc);CHKERRQ(ierr); 1551 #else 1552 if (!allcolumns) { 1553 ierr = PetscCalloc1(C->cmap->N,&cmap);CHKERRQ(ierr); 1554 for (j=0; j<ncol; j++) cmap[icol[j]] = j+1; 1555 } else { 1556 cmap = NULL; 1557 } 1558 #endif 1559 1560 /* Create lens for MatSeqAIJSetPreallocation() */ 1561 ierr = PetscCalloc1(nrow,&lens);CHKERRQ(ierr); 1562 1563 /* Compute lens from local part of C */ 1564 for (j=0; j<nrow; j++) { 1565 row = irow[j]; 1566 proc = row2proc[j]; 1567 if (proc == rank) { 1568 /* diagonal part A = c->A */ 1569 ncols = ai[row-rstart+1] - ai[row-rstart]; 1570 cols = aj + ai[row-rstart]; 1571 if (!allcolumns) { 1572 for (k=0; k<ncols; k++) { 1573 #if defined(PETSC_USE_CTABLE) 1574 tcol = cmap_loc[cols[k]]; 1575 #else 1576 tcol = cmap[cols[k]+cstart]; 1577 #endif 1578 if (tcol) lens[j]++; 1579 } 1580 } else { /* allcolumns */ 1581 lens[j] = ncols; 1582 } 1583 1584 /* off-diagonal part B = c->B */ 1585 ncols = bi[row-rstart+1] - bi[row-rstart]; 1586 cols = bj + bi[row-rstart]; 1587 if (!allcolumns) { 1588 for (k=0; k<ncols; k++) { 1589 #if defined(PETSC_USE_CTABLE) 1590 ierr = PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);CHKERRQ(ierr); 1591 #else 1592 tcol = cmap[bmap[cols[k]]]; 1593 #endif 1594 if (tcol) lens[j]++; 1595 } 1596 } else { /* allcolumns */ 1597 lens[j] += ncols; 1598 } 1599 } 1600 } 1601 1602 /* Create row map (rmap): global row of C -> local row of submat */ 1603 #if defined(PETSC_USE_CTABLE) 1604 ierr = PetscTableCreate(nrow+1,C->rmap->N+1,&rmap);CHKERRQ(ierr); 1605 for (j=0; j<nrow; j++) { 1606 row = irow[j]; 1607 proc = row2proc[j]; 1608 if (proc == rank) { /* a local row */ 1609 rmap_loc[row - rstart] = j; 1610 } else { 1611 ierr = PetscTableAdd(rmap,irow[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1612 } 1613 } 1614 #else 1615 ierr = PetscCalloc1(C->rmap->N,&rmap);CHKERRQ(ierr); 1616 for (j=0; j<nrow; j++) { 1617 rmap[irow[j]] = j; 1618 } 1619 #endif 1620 1621 /* Update lens from offproc data */ 1622 /* recv a->j is done */ 1623 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRQ(ierr); 1624 for (i=0; i<nrqs; i++) { 1625 proc = pa[i]; 1626 sbuf1_i = sbuf1[proc]; 1627 /* jmax = sbuf1_i[0]; if (jmax != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"jmax !=1"); */ 1628 ct1 = 2 + 1; 1629 ct2 = 0; 1630 rbuf2_i = rbuf2[i]; /* received length of C->j */ 1631 rbuf3_i = rbuf3[i]; /* received C->j */ 1632 1633 /* is_no = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */ 1634 max1 = sbuf1_i[2]; 1635 for (k=0; k<max1; k++,ct1++) { 1636 #if defined(PETSC_USE_CTABLE) 1637 ierr = PetscTableFind(rmap,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 1638 row--; 1639 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1640 #else 1641 row = rmap[sbuf1_i[ct1]]; /* the row index in submat */ 1642 #endif 1643 /* Now, store row index of submat in sbuf1_i[ct1] */ 1644 sbuf1_i[ct1] = row; 1645 1646 nnz = rbuf2_i[ct1]; 1647 if (!allcolumns) { 1648 for (l=0; l<nnz; l++,ct2++) { 1649 #if defined(PETSC_USE_CTABLE) 1650 if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) { 1651 tcol = cmap_loc[rbuf3_i[ct2] - cstart]; 1652 } else { 1653 ierr = PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1654 } 1655 #else 1656 tcol = cmap[rbuf3_i[ct2]]; /* column index in submat */ 1657 #endif 1658 if (tcol) lens[row]++; 1659 } 1660 } else { /* allcolumns */ 1661 lens[row] += nnz; 1662 } 1663 } 1664 } 1665 ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr); 1666 ierr = PetscFree4(r_waits3,s_waits3,r_status3,s_status3);CHKERRQ(ierr); 1667 1668 /* Create the submatrices */ 1669 ierr = MatCreate(PETSC_COMM_SELF,&submat);CHKERRQ(ierr); 1670 ierr = MatSetSizes(submat,nrow,ncol,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1671 1672 ierr = ISGetBlockSize(isrow[0],&i);CHKERRQ(ierr); 1673 ierr = ISGetBlockSize(iscol[0],&j);CHKERRQ(ierr); 1674 ierr = MatSetBlockSizes(submat,i,j);CHKERRQ(ierr); 1675 ierr = MatSetType(submat,((PetscObject)A)->type_name);CHKERRQ(ierr); 1676 ierr = MatSeqAIJSetPreallocation(submat,0,lens);CHKERRQ(ierr); 1677 1678 /* create struct Mat_SubMat and attached it to submat */ 1679 ierr = PetscNew(&smatis1);CHKERRQ(ierr); 1680 subc = (Mat_SeqAIJ*)submat->data; 1681 subc->submatis1 = smatis1; 1682 1683 smatis1->id = 0; 1684 smatis1->nrqs = nrqs; 1685 smatis1->nrqr = nrqr; 1686 smatis1->rbuf1 = rbuf1; 1687 smatis1->rbuf2 = rbuf2; 1688 smatis1->rbuf3 = rbuf3; 1689 smatis1->sbuf2 = sbuf2; 1690 smatis1->req_source2 = req_source2; 1691 1692 smatis1->sbuf1 = sbuf1; 1693 smatis1->ptr = ptr; 1694 smatis1->tmp = tmp; 1695 smatis1->ctr = ctr; 1696 1697 smatis1->pa = pa; 1698 smatis1->req_size = req_size; 1699 smatis1->req_source1 = req_source1; 1700 1701 smatis1->allcolumns = allcolumns; 1702 smatis1->singleis = PETSC_TRUE; 1703 smatis1->row2proc = row2proc; 1704 smatis1->rmap = rmap; 1705 smatis1->cmap = cmap; 1706 #if defined(PETSC_USE_CTABLE) 1707 smatis1->rmap_loc = rmap_loc; 1708 smatis1->cmap_loc = cmap_loc; 1709 #endif 1710 1711 smatis1->destroy = submat->ops->destroy; 1712 submat->ops->destroy = MatDestroy_MPIAIJ_MatGetSubmatrices; 1713 submat->factortype = C->factortype; 1714 1715 /* compute rmax */ 1716 rmax = 0; 1717 for (i=0; i<nrow; i++) rmax = PetscMax(rmax,lens[i]); 1718 1719 } else { /* scall == MAT_REUSE_MATRIX */ 1720 submat = submats[0]; 1721 if (submat->rmap->n != nrow || submat->cmap->n != ncol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 1722 1723 subc = (Mat_SeqAIJ*)submat->data; 1724 rmax = subc->rmax; 1725 smatis1 = subc->submatis1; 1726 nrqs = smatis1->nrqs; 1727 nrqr = smatis1->nrqr; 1728 rbuf1 = smatis1->rbuf1; 1729 rbuf2 = smatis1->rbuf2; 1730 rbuf3 = smatis1->rbuf3; 1731 req_source2 = smatis1->req_source2; 1732 1733 sbuf1 = smatis1->sbuf1; 1734 sbuf2 = smatis1->sbuf2; 1735 ptr = smatis1->ptr; 1736 tmp = smatis1->tmp; 1737 ctr = smatis1->ctr; 1738 1739 pa = smatis1->pa; 1740 req_size = smatis1->req_size; 1741 req_source1 = smatis1->req_source1; 1742 1743 allcolumns = smatis1->allcolumns; 1744 row2proc = smatis1->row2proc; 1745 rmap = smatis1->rmap; 1746 cmap = smatis1->cmap; 1747 #if defined(PETSC_USE_CTABLE) 1748 rmap_loc = smatis1->rmap_loc; 1749 cmap_loc = smatis1->cmap_loc; 1750 #endif 1751 } 1752 1753 /* Post recv matrix values */ 1754 ierr = PetscMalloc3(nrqs+1,&rbuf4, rmax,&subcols, rmax,&subvals);CHKERRQ(ierr); 1755 ierr = PetscMalloc4(nrqs+1,&r_waits4,nrqr+1,&s_waits4,nrqs+1,&r_status4,nrqr+1,&s_status4);CHKERRQ(ierr); 1756 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 1757 for (i=0; i<nrqs; ++i) { 1758 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);CHKERRQ(ierr); 1759 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRQ(ierr); 1760 } 1761 1762 /* Allocate sending buffers for a->a, and send them off */ 1763 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 1764 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 1765 ierr = PetscMalloc1(j+1,&sbuf_aa[0]);CHKERRQ(ierr); 1766 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]; 1767 1768 for (i=0; i<nrqr; i++) { 1769 rbuf1_i = rbuf1[i]; 1770 sbuf_aa_i = sbuf_aa[i]; 1771 ct1 = 2*rbuf1_i[0]+1; 1772 ct2 = 0; 1773 /* max1=rbuf1_i[0]; if (max1 != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"max1 !=1"); */ 1774 1775 kmax = rbuf1_i[2]; 1776 for (k=0; k<kmax; k++,ct1++) { 1777 row = rbuf1_i[ct1] - rstart; 1778 nzA = ai[row+1] - ai[row]; 1779 nzB = bi[row+1] - bi[row]; 1780 ncols = nzA + nzB; 1781 cworkB = bj + bi[row]; 1782 vworkA = a_a + ai[row]; 1783 vworkB = b_a + bi[row]; 1784 1785 /* load the column values for this row into vals*/ 1786 vals = sbuf_aa_i + ct2; 1787 1788 lwrite = 0; 1789 for (l=0; l<nzB; l++) { 1790 if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l]; 1791 } 1792 for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l]; 1793 for (l=0; l<nzB; l++) { 1794 if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l]; 1795 } 1796 1797 ct2 += ncols; 1798 } 1799 ierr = MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRQ(ierr); 1800 } 1801 1802 /* Assemble submat */ 1803 /* First assemble the local rows */ 1804 for (j=0; j<nrow; j++) { 1805 row = irow[j]; 1806 proc = row2proc[j]; 1807 if (proc == rank) { 1808 Crow = row - rstart; /* local row index of C */ 1809 #if defined(PETSC_USE_CTABLE) 1810 row = rmap_loc[Crow]; /* row index of submat */ 1811 #else 1812 row = rmap[row]; 1813 #endif 1814 1815 if (allcolumns) { 1816 /* diagonal part A = c->A */ 1817 ncols = ai[Crow+1] - ai[Crow]; 1818 cols = aj + ai[Crow]; 1819 vals = a->a + ai[Crow]; 1820 i = 0; 1821 for (k=0; k<ncols; k++) { 1822 subcols[i] = cols[k] + cstart; 1823 subvals[i++] = vals[k]; 1824 } 1825 1826 /* off-diagonal part B = c->B */ 1827 ncols = bi[Crow+1] - bi[Crow]; 1828 cols = bj + bi[Crow]; 1829 vals = b->a + bi[Crow]; 1830 for (k=0; k<ncols; k++) { 1831 subcols[i] = bmap[cols[k]]; 1832 subvals[i++] = vals[k]; 1833 } 1834 1835 ierr = MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);CHKERRQ(ierr); 1836 1837 } else { /* !allcolumns */ 1838 #if defined(PETSC_USE_CTABLE) 1839 /* diagonal part A = c->A */ 1840 ncols = ai[Crow+1] - ai[Crow]; 1841 cols = aj + ai[Crow]; 1842 vals = a->a + ai[Crow]; 1843 i = 0; 1844 for (k=0; k<ncols; k++) { 1845 tcol = cmap_loc[cols[k]]; 1846 if (tcol) { 1847 subcols[i] = --tcol; 1848 subvals[i++] = vals[k]; 1849 } 1850 } 1851 1852 /* off-diagonal part B = c->B */ 1853 ncols = bi[Crow+1] - bi[Crow]; 1854 cols = bj + bi[Crow]; 1855 vals = b->a + bi[Crow]; 1856 for (k=0; k<ncols; k++) { 1857 ierr = PetscTableFind(cmap,bmap[cols[k]]+1,&tcol);CHKERRQ(ierr); 1858 if (tcol) { 1859 subcols[i] = --tcol; 1860 subvals[i++] = vals[k]; 1861 } 1862 } 1863 #else 1864 /* diagonal part A = c->A */ 1865 ncols = ai[Crow+1] - ai[Crow]; 1866 cols = aj + ai[Crow]; 1867 vals = a->a + ai[Crow]; 1868 i = 0; 1869 for (k=0; k<ncols; k++) { 1870 tcol = cmap[cols[k]+cstart]; 1871 if (tcol) { 1872 subcols[i] = --tcol; 1873 subvals[i++] = vals[k]; 1874 } 1875 } 1876 1877 /* off-diagonal part B = c->B */ 1878 ncols = bi[Crow+1] - bi[Crow]; 1879 cols = bj + bi[Crow]; 1880 vals = b->a + bi[Crow]; 1881 for (k=0; k<ncols; k++) { 1882 tcol = cmap[bmap[cols[k]]]; 1883 if (tcol) { 1884 subcols[i] = --tcol; 1885 subvals[i++] = vals[k]; 1886 } 1887 } 1888 #endif 1889 ierr = MatSetValues_SeqAIJ(submat,1,&row,i,subcols,subvals,INSERT_VALUES);CHKERRQ(ierr); 1890 } 1891 } 1892 } 1893 1894 /* Now assemble the off-proc rows */ 1895 for (i=0; i<nrqs; i++) { /* for each requested message */ 1896 /* recv values from other processes */ 1897 ierr = MPI_Waitany(nrqs,r_waits4,&idex,r_status4+i);CHKERRQ(ierr); 1898 proc = pa[idex]; 1899 sbuf1_i = sbuf1[proc]; 1900 /* jmax = sbuf1_i[0]; if (jmax != 1)SETERRQ1(PETSC_COMM_SELF,0,"jmax %d != 1",jmax); */ 1901 ct1 = 2 + 1; 1902 ct2 = 0; /* count of received C->j */ 1903 ct3 = 0; /* count of received C->j that will be inserted into submat */ 1904 rbuf2_i = rbuf2[idex]; /* int** received length of C->j from other processes */ 1905 rbuf3_i = rbuf3[idex]; /* int** received C->j from other processes */ 1906 rbuf4_i = rbuf4[idex]; /* scalar** received C->a from other processes */ 1907 1908 /* is_no = sbuf1_i[2*j-1]; if (is_no != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"is_no !=0"); */ 1909 max1 = sbuf1_i[2]; /* num of rows */ 1910 for (k=0; k<max1; k++,ct1++) { /* for each recved row */ 1911 row = sbuf1_i[ct1]; /* row index of submat */ 1912 if (!allcolumns) { 1913 idex = 0; 1914 if (scall == MAT_INITIAL_MATRIX) { 1915 nnz = rbuf2_i[ct1]; /* num of C entries in this row */ 1916 for (l=0; l<nnz; l++,ct2++) { /* for each recved column */ 1917 #if defined(PETSC_USE_CTABLE) 1918 if (rbuf3_i[ct2] >= cstart && rbuf3_i[ct2] <cend) { 1919 tcol = cmap_loc[rbuf3_i[ct2] - cstart]; 1920 } else { 1921 ierr = PetscTableFind(cmap,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1922 } 1923 #else 1924 tcol = cmap[rbuf3_i[ct2]]; 1925 #endif 1926 if (tcol) { 1927 subcols[idex] = --tcol; 1928 subvals[idex++] = rbuf4_i[ct2]; 1929 1930 /* We receive an entire column of C, but a subset of it needs to be inserted into submat. 1931 For reuse, we replace received C->j with index that should be inserted to submat */ 1932 rbuf3_i[ct3++] = ct2; 1933 } 1934 } 1935 ierr = MatSetValues_SeqAIJ(submat,1,&row,idex,subcols,subvals,INSERT_VALUES);CHKERRQ(ierr); 1936 1937 } else { /* scall == MAT_REUSE_MATRIX */ 1938 submat = submats[0]; 1939 subc = (Mat_SeqAIJ*)submat->data; 1940 1941 nnz = subc->i[row+1] - subc->i[row]; /* num of submat entries in this row */ 1942 for (l=0; l<nnz; l++) { 1943 ct2 = rbuf3_i[ct3++]; /* index of rbuf4_i[] which needs to be inserted into submat */ 1944 subvals[idex++] = rbuf4_i[ct2]; 1945 } 1946 1947 bj = subc->j + subc->i[row]; 1948 ierr = MatSetValues_SeqAIJ(submat,1,&row,nnz,bj,subvals,INSERT_VALUES);CHKERRQ(ierr); 1949 } 1950 } else { /* allcolumns */ 1951 nnz = rbuf2_i[ct1]; /* num of C entries in this row */ 1952 ierr = MatSetValues_SeqAIJ(submat,1,&row,nnz,rbuf3_i+ct2,rbuf4_i+ct2,INSERT_VALUES);CHKERRQ(ierr); 1953 ct2 += nnz; 1954 } 1955 } 1956 } 1957 1958 /* sending a->a are done */ 1959 ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr); 1960 ierr = PetscFree4(r_waits4,s_waits4,r_status4,s_status4);CHKERRQ(ierr); 1961 1962 ierr = MatAssemblyBegin(submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1963 ierr = MatAssemblyEnd(submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1964 submats[0] = submat; 1965 1966 /* Restore the indices */ 1967 ierr = ISRestoreIndices(isrow[0],&irow);CHKERRQ(ierr); 1968 if (!allcolumns) { 1969 ierr = ISRestoreIndices(iscol[0],&icol);CHKERRQ(ierr); 1970 } 1971 1972 /* Destroy allocated memory */ 1973 for (i=0; i<nrqs; ++i) { 1974 ierr = PetscFree3(rbuf4[i],subcols,subvals);CHKERRQ(ierr); 1975 } 1976 ierr = PetscFree3(rbuf4,subcols,subvals);CHKERRQ(ierr); 1977 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 1978 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 1979 1980 if (scall == MAT_INITIAL_MATRIX) { 1981 ierr = PetscFree(lens);CHKERRQ(ierr); 1982 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 1983 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 1984 } 1985 PetscFunctionReturn(0); 1986 } 1987 1988 PetscErrorCode MatGetSubMatrices_MPIAIJ_SingleIS(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 1989 { 1990 PetscErrorCode ierr; 1991 PetscInt ncol; 1992 PetscBool colflag,allcolumns=PETSC_FALSE; 1993 1994 PetscFunctionBegin; 1995 /* Allocate memory to hold all the submatrices */ 1996 if (scall == MAT_INITIAL_MATRIX) { 1997 ierr = PetscMalloc1(1,submat);CHKERRQ(ierr); 1998 } 1999 2000 /* Check for special case: each processor gets entire matrix columns */ 2001 ierr = ISIdentity(iscol[0],&colflag);CHKERRQ(ierr); 2002 ierr = ISGetLocalSize(iscol[0],&ncol);CHKERRQ(ierr); 2003 if (colflag && ncol == C->cmap->N) allcolumns = PETSC_TRUE; 2004 2005 ierr = MatGetSubMatrices_MPIAIJ_SingleIS_Local(C,ismax,isrow,iscol,scall,allcolumns,*submat);CHKERRQ(ierr); 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatGetSubMatrices_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 2010 { 2011 PetscErrorCode ierr; 2012 PetscInt nmax,nstages,i,pos,max_no,nrow,ncol,in[2],out[2]; 2013 PetscBool rowflag,colflag,wantallmatrix=PETSC_FALSE; 2014 Mat_SeqAIJ *subc; 2015 Mat_SubMat *smat; 2016 2017 PetscFunctionBegin; 2018 /* Check for special case: each processor has a single IS */ 2019 if (C->submat_singleis) { /* flag is set in PCSetUp_ASM() to skip MPIU_Allreduce() */ 2020 ierr = MatGetSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 2021 C->submat_singleis = PETSC_FALSE; /* resume its default value in case C will be used for non-singlis */ 2022 PetscFunctionReturn(0); 2023 } 2024 2025 if (scall == MAT_REUSE_MATRIX && !ismax) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"n=0 is not supported for MatGetSubMatrices(mat,n,isrow,iscol,MAT_REUSE_MATRIX,...). Set n=1 with zero-length isrow and iscolumn instead"); 2026 2027 /* Collect global wantallmatrix and nstages */ 2028 nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt)); 2029 if (!nmax) nmax = 1; 2030 2031 if (scall == MAT_INITIAL_MATRIX) { 2032 /* Collect global wantallmatrix and nstages */ 2033 if (ismax == 1 && C->rmap->N == C->cmap->N) { 2034 ierr = ISIdentity(*isrow,&rowflag);CHKERRQ(ierr); 2035 ierr = ISIdentity(*iscol,&colflag);CHKERRQ(ierr); 2036 ierr = ISGetLocalSize(*isrow,&nrow);CHKERRQ(ierr); 2037 ierr = ISGetLocalSize(*iscol,&ncol);CHKERRQ(ierr); 2038 if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) { 2039 wantallmatrix = PETSC_TRUE; 2040 2041 ierr = PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);CHKERRQ(ierr); 2042 } 2043 } 2044 2045 /* Determine the number of stages through which submatrices are done 2046 Each stage will extract nmax submatrices. 2047 nmax is determined by the matrix column dimension. 2048 If the original matrix has 20M columns, only one submatrix per stage is allowed, etc. 2049 */ 2050 nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */ 2051 2052 in[0] = -1*(PetscInt)wantallmatrix; 2053 in[1] = nstages; 2054 ierr = MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 2055 wantallmatrix = (PetscBool)(-out[0]); 2056 nstages = out[1]; /* Make sure every processor loops through the global nstages */ 2057 2058 } else { /* MAT_REUSE_MATRIX */ 2059 subc = (Mat_SeqAIJ*)((*submat)[0]->data); 2060 smat = subc->submatis1; 2061 if (!smat) { 2062 /* smat is not generated by MatGetSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */ 2063 wantallmatrix = PETSC_TRUE; 2064 } else if (smat->singleis) { 2065 ierr = MatGetSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } else { 2068 nstages = smat->nstages; 2069 } 2070 } 2071 2072 if (wantallmatrix) { 2073 ierr = MatGetSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);CHKERRQ(ierr); 2074 PetscFunctionReturn(0); 2075 } 2076 2077 /* Allocate memory to hold all the submatrices */ 2078 if (scall == MAT_INITIAL_MATRIX) { 2079 ierr = PetscMalloc1(ismax+1,submat);CHKERRQ(ierr); 2080 } 2081 2082 for (i=0,pos=0; i<nstages; i++) { 2083 if (pos+nmax <= ismax) max_no = nmax; 2084 else if (pos == ismax) max_no = 0; 2085 else max_no = ismax-pos; 2086 ierr = MatGetSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);CHKERRQ(ierr); 2087 pos += max_no; 2088 } 2089 2090 if (scall == MAT_INITIAL_MATRIX && ismax) { 2091 /* save nstages for reuse */ 2092 subc = (Mat_SeqAIJ*)((*submat)[0]->data); 2093 smat = subc->submatis1; 2094 if (!smat) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"smat does not exit"); 2095 smat->nstages = nstages; 2096 } 2097 PetscFunctionReturn(0); 2098 } 2099 2100 /* -------------------------------------------------------------------------*/ 2101 PetscErrorCode MatGetSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats) 2102 { 2103 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 2104 Mat A = c->A; 2105 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc; 2106 const PetscInt **icol,**irow; 2107 PetscInt *nrow,*ncol,start; 2108 PetscErrorCode ierr; 2109 PetscMPIInt rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr; 2110 PetscInt **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1; 2111 PetscInt nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol; 2112 PetscInt **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2; 2113 PetscInt **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax; 2114 #if defined(PETSC_USE_CTABLE) 2115 PetscTable *cmap,cmap_i=NULL,*rmap,rmap_i; 2116 #else 2117 PetscInt **cmap,*cmap_i=NULL,**rmap,*rmap_i; 2118 #endif 2119 const PetscInt *irow_i; 2120 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i; 2121 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 2122 MPI_Request *r_waits4,*s_waits3,*s_waits4; 2123 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 2124 MPI_Status *r_status3,*r_status4,*s_status4; 2125 MPI_Comm comm; 2126 PetscScalar **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i; 2127 PetscMPIInt *onodes1,*olengths1,end; 2128 PetscInt **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row; 2129 Mat_SubMat **smats,*smat_i; 2130 PetscBool *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE; 2131 PetscInt *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen; 2132 2133 PetscFunctionBegin; 2134 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2135 size = c->size; 2136 rank = c->rank; 2137 2138 ierr = PetscMalloc5(ismax,&smats,ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax,&allcolumns);CHKERRQ(ierr); 2139 ierr = PetscMalloc5(ismax,&irow,ismax,&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);CHKERRQ(ierr); 2140 2141 for (i=0; i<ismax; i++) { 2142 ierr = ISSorted(iscol[i],&issorted[i]);CHKERRQ(ierr); 2143 if (!issorted[i]) iscsorted = issorted[i]; 2144 2145 ierr = ISSorted(isrow[i],&issorted[i]);CHKERRQ(ierr); 2146 2147 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 2148 ierr = ISGetLocalSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 2149 2150 /* Check for special case: allcolumn */ 2151 ierr = ISIdentity(iscol[i],&colflag);CHKERRQ(ierr); 2152 ierr = ISGetLocalSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 2153 if (colflag && ncol[i] == C->cmap->N) { 2154 allcolumns[i] = PETSC_TRUE; 2155 icol[i] = NULL; 2156 } else { 2157 allcolumns[i] = PETSC_FALSE; 2158 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 2159 } 2160 } 2161 2162 if (scall == MAT_REUSE_MATRIX) { 2163 /* Assumes new rows are same length as the old rows */ 2164 for (i=0; i<ismax; i++) { 2165 subc = (Mat_SeqAIJ*)(submats[i]->data); 2166 if ((submats[i]->rmap->n != nrow[i]) || (submats[i]->cmap->n != ncol[i])) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 2167 2168 /* Initial matrix as if empty */ 2169 ierr = PetscMemzero(subc->ilen,submats[i]->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2170 2171 /* Initial matrix as if empty */ 2172 submats[i]->factortype = C->factortype; 2173 2174 smat_i = subc->submatis1; 2175 smats[i] = smat_i; 2176 2177 nrqs = smat_i->nrqs; 2178 nrqr = smat_i->nrqr; 2179 rbuf1 = smat_i->rbuf1; 2180 rbuf2 = smat_i->rbuf2; 2181 rbuf3 = smat_i->rbuf3; 2182 req_source2 = smat_i->req_source2; 2183 2184 sbuf1 = smat_i->sbuf1; 2185 sbuf2 = smat_i->sbuf2; 2186 ptr = smat_i->ptr; 2187 tmp = smat_i->tmp; 2188 ctr = smat_i->ctr; 2189 2190 pa = smat_i->pa; 2191 req_size = smat_i->req_size; 2192 req_source1 = smat_i->req_source1; 2193 2194 allcolumns[i] = smat_i->allcolumns; 2195 row2proc[i] = smat_i->row2proc; 2196 rmap[i] = smat_i->rmap; 2197 cmap[i] = smat_i->cmap; 2198 } 2199 } else { /* scall == MAT_INITIAL_MATRIX */ 2200 /* Get some new tags to keep the communication clean */ 2201 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 2202 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 2203 2204 /* evaluate communication - mesg to who, length of mesg, and buffer space 2205 required. Based on this, buffers are allocated, and data copied into them*/ 2206 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); /* mesg size, initialize work vectors */ 2207 2208 for (i=0; i<ismax; i++) { 2209 jmax = nrow[i]; 2210 irow_i = irow[i]; 2211 2212 ierr = PetscMalloc1(jmax,&row2proc_i);CHKERRQ(ierr); 2213 row2proc[i] = row2proc_i; 2214 2215 if (issorted[i]) proc = 0; 2216 for (j=0; j<jmax; j++) { 2217 if (!issorted[i]) proc = 0; 2218 row = irow_i[j]; 2219 while (row >= C->rmap->range[proc+1]) proc++; 2220 w4[proc]++; 2221 row2proc_i[j] = proc; /* map row index to proc */ 2222 } 2223 for (j=0; j<size; j++) { 2224 if (w4[j]) { w1[j] += w4[j]; w3[j]++; w4[j] = 0;} 2225 } 2226 } 2227 2228 nrqs = 0; /* no of outgoing messages */ 2229 msz = 0; /* total mesg length (for all procs) */ 2230 w1[rank] = 0; /* no mesg sent to self */ 2231 w3[rank] = 0; 2232 for (i=0; i<size; i++) { 2233 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 2234 } 2235 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 2236 for (i=0,j=0; i<size; i++) { 2237 if (w1[i]) { pa[j] = i; j++; } 2238 } 2239 2240 /* Each message would have a header = 1 + 2*(no of IS) + data */ 2241 for (i=0; i<nrqs; i++) { 2242 j = pa[i]; 2243 w1[j] += w2[j] + 2* w3[j]; 2244 msz += w1[j]; 2245 } 2246 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 2247 2248 /* Determine the number of messages to expect, their lengths, from from-ids */ 2249 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 2250 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 2251 2252 /* Now post the Irecvs corresponding to these messages */ 2253 tag0 = ((PetscObject)C)->tag; 2254 ierr = PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 2255 2256 ierr = PetscFree(onodes1);CHKERRQ(ierr); 2257 ierr = PetscFree(olengths1);CHKERRQ(ierr); 2258 2259 /* Allocate Memory for outgoing messages */ 2260 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 2261 ierr = PetscMemzero(sbuf1,size*sizeof(PetscInt*));CHKERRQ(ierr); 2262 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 2263 2264 { 2265 PetscInt *iptr = tmp; 2266 k = 0; 2267 for (i=0; i<nrqs; i++) { 2268 j = pa[i]; 2269 iptr += k; 2270 sbuf1[j] = iptr; 2271 k = w1[j]; 2272 } 2273 } 2274 2275 /* Form the outgoing messages. Initialize the header space */ 2276 for (i=0; i<nrqs; i++) { 2277 j = pa[i]; 2278 sbuf1[j][0] = 0; 2279 ierr = PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 2280 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 2281 } 2282 2283 /* Parse the isrow and copy data into outbuf */ 2284 for (i=0; i<ismax; i++) { 2285 row2proc_i = row2proc[i]; 2286 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 2287 irow_i = irow[i]; 2288 jmax = nrow[i]; 2289 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 2290 proc = row2proc_i[j]; 2291 if (proc != rank) { /* copy to the outgoing buf*/ 2292 ctr[proc]++; 2293 *ptr[proc] = irow_i[j]; 2294 ptr[proc]++; 2295 } 2296 } 2297 /* Update the headers for the current IS */ 2298 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 2299 if ((ctr_j = ctr[j])) { 2300 sbuf1_j = sbuf1[j]; 2301 k = ++sbuf1_j[0]; 2302 sbuf1_j[2*k] = ctr_j; 2303 sbuf1_j[2*k-1] = i; 2304 } 2305 } 2306 } 2307 2308 /* Now post the sends */ 2309 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 2310 for (i=0; i<nrqs; ++i) { 2311 j = pa[i]; 2312 ierr = MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);CHKERRQ(ierr); 2313 } 2314 2315 /* Post Receives to capture the buffer size */ 2316 ierr = PetscMalloc1(nrqs+1,&r_waits2);CHKERRQ(ierr); 2317 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 2318 rbuf2[0] = tmp + msz; 2319 for (i=1; i<nrqs; ++i) { 2320 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 2321 } 2322 for (i=0; i<nrqs; ++i) { 2323 j = pa[i]; 2324 ierr = MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);CHKERRQ(ierr); 2325 } 2326 2327 /* Send to other procs the buf size they should allocate */ 2328 /* Receive messages*/ 2329 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 2330 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 2331 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 2332 { 2333 PetscInt *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart; 2334 PetscInt *sbuf2_i; 2335 2336 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRQ(ierr); 2337 for (i=0; i<nrqr; ++i) { 2338 req_size[i] = 0; 2339 rbuf1_i = rbuf1[i]; 2340 start = 2*rbuf1_i[0] + 1; 2341 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRQ(ierr); 2342 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 2343 sbuf2_i = sbuf2[i]; 2344 for (j=start; j<end; j++) { 2345 id = rbuf1_i[j] - rstart; 2346 ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id]; 2347 sbuf2_i[j] = ncols; 2348 req_size[i] += ncols; 2349 } 2350 req_source1[i] = r_status1[i].MPI_SOURCE; 2351 /* form the header */ 2352 sbuf2_i[0] = req_size[i]; 2353 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 2354 2355 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 2356 } 2357 } 2358 ierr = PetscFree(r_status1);CHKERRQ(ierr); 2359 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 2360 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 2361 2362 /* Receive messages*/ 2363 ierr = PetscMalloc1(nrqs+1,&r_waits3);CHKERRQ(ierr); 2364 ierr = PetscMalloc1(nrqs+1,&r_status2);CHKERRQ(ierr); 2365 2366 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRQ(ierr); 2367 for (i=0; i<nrqs; ++i) { 2368 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 2369 req_source2[i] = r_status2[i].MPI_SOURCE; 2370 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRQ(ierr); 2371 } 2372 ierr = PetscFree(r_status2);CHKERRQ(ierr); 2373 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 2374 2375 /* Wait on sends1 and sends2 */ 2376 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 2377 ierr = PetscMalloc1(nrqr+1,&s_status2);CHKERRQ(ierr); 2378 2379 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr);} 2380 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr);} 2381 ierr = PetscFree(s_status1);CHKERRQ(ierr); 2382 ierr = PetscFree(s_status2);CHKERRQ(ierr); 2383 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 2384 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 2385 2386 /* Now allocate sending buffers for a->j, and send them off */ 2387 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 2388 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2389 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 2390 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 2391 2392 ierr = PetscMalloc1(nrqr+1,&s_waits3);CHKERRQ(ierr); 2393 { 2394 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite; 2395 PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2396 PetscInt cend = C->cmap->rend; 2397 PetscInt *a_j = a->j,*b_j = b->j,ctmp; 2398 2399 for (i=0; i<nrqr; i++) { 2400 rbuf1_i = rbuf1[i]; 2401 sbuf_aj_i = sbuf_aj[i]; 2402 ct1 = 2*rbuf1_i[0] + 1; 2403 ct2 = 0; 2404 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2405 kmax = rbuf1[i][2*j]; 2406 for (k=0; k<kmax; k++,ct1++) { 2407 row = rbuf1_i[ct1] - rstart; 2408 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2409 ncols = nzA + nzB; 2410 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 2411 2412 /* load the column indices for this row into cols */ 2413 cols = sbuf_aj_i + ct2; 2414 2415 lwrite = 0; 2416 for (l=0; l<nzB; l++) { 2417 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp; 2418 } 2419 for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l]; 2420 for (l=0; l<nzB; l++) { 2421 if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp; 2422 } 2423 2424 ct2 += ncols; 2425 } 2426 } 2427 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 2428 } 2429 } 2430 ierr = PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 2431 2432 /* create col map: global col of C -> local col of submatrices */ 2433 { 2434 const PetscInt *icol_i; 2435 #if defined(PETSC_USE_CTABLE) 2436 for (i=0; i<ismax; i++) { 2437 if (!allcolumns[i]) { 2438 ierr = PetscTableCreate(ncol[i]+1,C->cmap->N+1,&cmap[i]);CHKERRQ(ierr); 2439 2440 jmax = ncol[i]; 2441 icol_i = icol[i]; 2442 cmap_i = cmap[i]; 2443 for (j=0; j<jmax; j++) { 2444 ierr = PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2445 } 2446 } else cmap[i] = NULL; 2447 } 2448 #else 2449 for (i=0; i<ismax; i++) { 2450 if (!allcolumns[i]) { 2451 ierr = PetscCalloc1(C->cmap->N,&cmap[i]);CHKERRQ(ierr); 2452 jmax = ncol[i]; 2453 icol_i = icol[i]; 2454 cmap_i = cmap[i]; 2455 for (j=0; j<jmax; j++) { 2456 cmap_i[icol_i[j]] = j+1; 2457 } 2458 } else cmap[i] = NULL; 2459 } 2460 #endif 2461 } 2462 2463 /* Create lens which is required for MatCreate... */ 2464 for (i=0,j=0; i<ismax; i++) j += nrow[i]; 2465 ierr = PetscMalloc1(ismax,&lens);CHKERRQ(ierr); 2466 2467 if (ismax) { 2468 ierr = PetscCalloc1(j,&lens[0]);CHKERRQ(ierr); 2469 } 2470 for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1]; 2471 2472 /* Update lens from local data */ 2473 for (i=0; i<ismax; i++) { 2474 row2proc_i = row2proc[i]; 2475 jmax = nrow[i]; 2476 if (!allcolumns[i]) cmap_i = cmap[i]; 2477 irow_i = irow[i]; 2478 lens_i = lens[i]; 2479 for (j=0; j<jmax; j++) { 2480 row = irow_i[j]; 2481 proc = row2proc_i[j]; 2482 if (proc == rank) { 2483 ierr = MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2484 if (!allcolumns[i]) { 2485 for (k=0; k<ncols; k++) { 2486 #if defined(PETSC_USE_CTABLE) 2487 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2488 #else 2489 tcol = cmap_i[cols[k]]; 2490 #endif 2491 if (tcol) lens_i[j]++; 2492 } 2493 } else { /* allcolumns */ 2494 lens_i[j] = ncols; 2495 } 2496 ierr = MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2497 } 2498 } 2499 } 2500 2501 /* Create row map: global row of C -> local row of submatrices */ 2502 #if defined(PETSC_USE_CTABLE) 2503 for (i=0; i<ismax; i++) { 2504 ierr = PetscTableCreate(nrow[i]+1,C->rmap->N+1,&rmap[i]);CHKERRQ(ierr); 2505 irow_i = irow[i]; 2506 jmax = nrow[i]; 2507 for (j=0; j<jmax; j++) { 2508 ierr = PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2509 } 2510 } 2511 #else 2512 for (i=0; i<ismax; i++) { 2513 ierr = PetscCalloc1(C->rmap->N,&rmap[i]);CHKERRQ(ierr); 2514 rmap_i = rmap[i]; 2515 irow_i = irow[i]; 2516 jmax = nrow[i]; 2517 for (j=0; j<jmax; j++) { 2518 rmap_i[irow_i[j]] = j; 2519 } 2520 } 2521 #endif 2522 2523 /* Update lens from offproc data */ 2524 { 2525 PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i; 2526 2527 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRQ(ierr); 2528 for (tmp2=0; tmp2<nrqs; tmp2++) { 2529 sbuf1_i = sbuf1[pa[tmp2]]; 2530 jmax = sbuf1_i[0]; 2531 ct1 = 2*jmax+1; 2532 ct2 = 0; 2533 rbuf2_i = rbuf2[tmp2]; 2534 rbuf3_i = rbuf3[tmp2]; 2535 for (j=1; j<=jmax; j++) { 2536 is_no = sbuf1_i[2*j-1]; 2537 max1 = sbuf1_i[2*j]; 2538 lens_i = lens[is_no]; 2539 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2540 rmap_i = rmap[is_no]; 2541 for (k=0; k<max1; k++,ct1++) { 2542 #if defined(PETSC_USE_CTABLE) 2543 ierr = PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 2544 row--; 2545 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 2546 #else 2547 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 2548 #endif 2549 max2 = rbuf2_i[ct1]; 2550 for (l=0; l<max2; l++,ct2++) { 2551 if (!allcolumns[is_no]) { 2552 #if defined(PETSC_USE_CTABLE) 2553 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2554 #else 2555 tcol = cmap_i[rbuf3_i[ct2]]; 2556 #endif 2557 if (tcol) lens_i[row]++; 2558 } else { /* allcolumns */ 2559 lens_i[row]++; /* lens_i[row] += max2 ? */ 2560 } 2561 } 2562 } 2563 } 2564 } 2565 } 2566 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 2567 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr);} 2568 ierr = PetscFree2(r_status3,s_status3);CHKERRQ(ierr); 2569 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 2570 2571 /* Create the submatrices */ 2572 for (i=0; i<ismax; i++) { 2573 PetscInt rbs,cbs; 2574 2575 ierr = ISGetBlockSize(isrow[i],&rbs);CHKERRQ(ierr); 2576 ierr = ISGetBlockSize(iscol[i],&cbs);CHKERRQ(ierr); 2577 2578 ierr = MatCreate(PETSC_COMM_SELF,submats+i);CHKERRQ(ierr); 2579 ierr = MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2580 2581 ierr = MatSetBlockSizes(submats[i],rbs,cbs);CHKERRQ(ierr); 2582 ierr = MatSetType(submats[i],((PetscObject)A)->type_name);CHKERRQ(ierr); 2583 ierr = MatSeqAIJSetPreallocation(submats[i],0,lens[i]);CHKERRQ(ierr); 2584 2585 /* create struct Mat_SubMat and attached it to submat */ 2586 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 2587 subc = (Mat_SeqAIJ*)submats[i]->data; 2588 subc->submatis1 = smat_i; 2589 smats[i] = smat_i; 2590 2591 smat_i->destroy = submats[i]->ops->destroy; 2592 submats[i]->ops->destroy = MatDestroy_MPIAIJ_MatGetSubmatrices; 2593 submats[i]->factortype = C->factortype; 2594 2595 smat_i->id = i; 2596 smat_i->nrqs = nrqs; 2597 smat_i->nrqr = nrqr; 2598 smat_i->rbuf1 = rbuf1; 2599 smat_i->rbuf2 = rbuf2; 2600 smat_i->rbuf3 = rbuf3; 2601 smat_i->sbuf2 = sbuf2; 2602 smat_i->req_source2 = req_source2; 2603 2604 smat_i->sbuf1 = sbuf1; 2605 smat_i->ptr = ptr; 2606 smat_i->tmp = tmp; 2607 smat_i->ctr = ctr; 2608 2609 smat_i->pa = pa; 2610 smat_i->req_size = req_size; 2611 smat_i->req_source1 = req_source1; 2612 2613 smat_i->allcolumns = allcolumns[i]; 2614 smat_i->singleis = PETSC_FALSE; 2615 smat_i->row2proc = row2proc[i]; 2616 smat_i->rmap = rmap[i]; 2617 smat_i->cmap = cmap[i]; 2618 } 2619 2620 if (ismax) {ierr = PetscFree(lens[0]);CHKERRQ(ierr);} 2621 ierr = PetscFree(lens);CHKERRQ(ierr); 2622 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 2623 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 2624 2625 } /* endof scall == MAT_INITIAL_MATRIX */ 2626 2627 /* Post recv matrix values */ 2628 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 2629 ierr = PetscMalloc1(nrqs+1,&rbuf4);CHKERRQ(ierr); 2630 ierr = PetscMalloc1(nrqs+1,&r_waits4);CHKERRQ(ierr); 2631 ierr = PetscMalloc1(nrqs+1,&r_status4);CHKERRQ(ierr); 2632 ierr = PetscMalloc1(nrqr+1,&s_status4);CHKERRQ(ierr); 2633 for (i=0; i<nrqs; ++i) { 2634 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);CHKERRQ(ierr); 2635 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRQ(ierr); 2636 } 2637 2638 /* Allocate sending buffers for a->a, and send them off */ 2639 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 2640 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2641 ierr = PetscMalloc1(j+1,&sbuf_aa[0]);CHKERRQ(ierr); 2642 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]; 2643 2644 ierr = PetscMalloc1(nrqr+1,&s_waits4);CHKERRQ(ierr); 2645 { 2646 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite; 2647 PetscInt cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2648 PetscInt cend = C->cmap->rend; 2649 PetscInt *b_j = b->j; 2650 PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a; 2651 2652 for (i=0; i<nrqr; i++) { 2653 rbuf1_i = rbuf1[i]; 2654 sbuf_aa_i = sbuf_aa[i]; 2655 ct1 = 2*rbuf1_i[0]+1; 2656 ct2 = 0; 2657 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2658 kmax = rbuf1_i[2*j]; 2659 for (k=0; k<kmax; k++,ct1++) { 2660 row = rbuf1_i[ct1] - rstart; 2661 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2662 ncols = nzA + nzB; 2663 cworkB = b_j + b_i[row]; 2664 vworkA = a_a + a_i[row]; 2665 vworkB = b_a + b_i[row]; 2666 2667 /* load the column values for this row into vals*/ 2668 vals = sbuf_aa_i+ct2; 2669 2670 lwrite = 0; 2671 for (l=0; l<nzB; l++) { 2672 if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l]; 2673 } 2674 for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l]; 2675 for (l=0; l<nzB; l++) { 2676 if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l]; 2677 } 2678 2679 ct2 += ncols; 2680 } 2681 } 2682 ierr = MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRQ(ierr); 2683 } 2684 } 2685 2686 if (!ismax) { 2687 ierr = PetscFree(rbuf1[0]);CHKERRQ(ierr); 2688 ierr = PetscFree(rbuf1);CHKERRQ(ierr); 2689 } 2690 2691 /* Assemble the matrices */ 2692 /* First assemble the local rows */ 2693 for (i=0; i<ismax; i++) { 2694 row2proc_i = row2proc[i]; 2695 subc = (Mat_SeqAIJ*)submats[i]->data; 2696 imat_ilen = subc->ilen; 2697 imat_j = subc->j; 2698 imat_i = subc->i; 2699 imat_a = subc->a; 2700 2701 if (!allcolumns[i]) cmap_i = cmap[i]; 2702 rmap_i = rmap[i]; 2703 irow_i = irow[i]; 2704 jmax = nrow[i]; 2705 for (j=0; j<jmax; j++) { 2706 row = irow_i[j]; 2707 proc = row2proc_i[j]; 2708 if (proc == rank) { 2709 old_row = row; 2710 #if defined(PETSC_USE_CTABLE) 2711 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2712 row--; 2713 #else 2714 row = rmap_i[row]; 2715 #endif 2716 ilen_row = imat_ilen[row]; 2717 ierr = MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2718 mat_i = imat_i[row]; 2719 mat_a = imat_a + mat_i; 2720 mat_j = imat_j + mat_i; 2721 if (!allcolumns[i]) { 2722 for (k=0; k<ncols; k++) { 2723 #if defined(PETSC_USE_CTABLE) 2724 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2725 #else 2726 tcol = cmap_i[cols[k]]; 2727 #endif 2728 if (tcol) { 2729 *mat_j++ = tcol - 1; 2730 *mat_a++ = vals[k]; 2731 ilen_row++; 2732 } 2733 } 2734 } else { /* allcolumns */ 2735 for (k=0; k<ncols; k++) { 2736 *mat_j++ = cols[k]; /* global col index! */ 2737 *mat_a++ = vals[k]; 2738 ilen_row++; 2739 } 2740 } 2741 ierr = MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2742 2743 imat_ilen[row] = ilen_row; 2744 } 2745 } 2746 } 2747 2748 /* Now assemble the off proc rows */ 2749 ierr = MPI_Waitall(nrqs,r_waits4,r_status4);CHKERRQ(ierr); 2750 for (tmp2=0; tmp2<nrqs; tmp2++) { 2751 sbuf1_i = sbuf1[pa[tmp2]]; 2752 jmax = sbuf1_i[0]; 2753 ct1 = 2*jmax + 1; 2754 ct2 = 0; 2755 rbuf2_i = rbuf2[tmp2]; 2756 rbuf3_i = rbuf3[tmp2]; 2757 rbuf4_i = rbuf4[tmp2]; 2758 for (j=1; j<=jmax; j++) { 2759 is_no = sbuf1_i[2*j-1]; 2760 rmap_i = rmap[is_no]; 2761 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2762 subc = (Mat_SeqAIJ*)submats[is_no]->data; 2763 imat_ilen = subc->ilen; 2764 imat_j = subc->j; 2765 imat_i = subc->i; 2766 imat_a = subc->a; 2767 max1 = sbuf1_i[2*j]; 2768 for (k=0; k<max1; k++,ct1++) { 2769 row = sbuf1_i[ct1]; 2770 #if defined(PETSC_USE_CTABLE) 2771 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2772 row--; 2773 #else 2774 row = rmap_i[row]; 2775 #endif 2776 ilen = imat_ilen[row]; 2777 mat_i = imat_i[row]; 2778 mat_a = imat_a + mat_i; 2779 mat_j = imat_j + mat_i; 2780 max2 = rbuf2_i[ct1]; 2781 if (!allcolumns[is_no]) { 2782 for (l=0; l<max2; l++,ct2++) { 2783 #if defined(PETSC_USE_CTABLE) 2784 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2785 #else 2786 tcol = cmap_i[rbuf3_i[ct2]]; 2787 #endif 2788 if (tcol) { 2789 *mat_j++ = tcol - 1; 2790 *mat_a++ = rbuf4_i[ct2]; 2791 ilen++; 2792 } 2793 } 2794 } else { /* allcolumns */ 2795 for (l=0; l<max2; l++,ct2++) { 2796 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 2797 *mat_a++ = rbuf4_i[ct2]; 2798 ilen++; 2799 } 2800 } 2801 imat_ilen[row] = ilen; 2802 } 2803 } 2804 } 2805 2806 if (!iscsorted) { /* sort column indices of the rows */ 2807 for (i=0; i<ismax; i++) { 2808 subc = (Mat_SeqAIJ*)submats[i]->data; 2809 imat_j = subc->j; 2810 imat_i = subc->i; 2811 imat_a = subc->a; 2812 imat_ilen = subc->ilen; 2813 2814 if (allcolumns[i]) continue; 2815 jmax = nrow[i]; 2816 for (j=0; j<jmax; j++) { 2817 PetscInt ilen; 2818 2819 mat_i = imat_i[j]; 2820 mat_a = imat_a + mat_i; 2821 mat_j = imat_j + mat_i; 2822 ilen = imat_ilen[j]; 2823 ierr = PetscSortIntWithScalarArray(ilen,mat_j,mat_a);CHKERRQ(ierr); 2824 } 2825 } 2826 } 2827 2828 ierr = PetscFree(r_status4);CHKERRQ(ierr); 2829 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 2830 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr);} 2831 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 2832 ierr = PetscFree(s_status4);CHKERRQ(ierr); 2833 2834 /* Restore the indices */ 2835 for (i=0; i<ismax; i++) { 2836 ierr = ISRestoreIndices(isrow[i],irow+i);CHKERRQ(ierr); 2837 if (!allcolumns[i]) { 2838 ierr = ISRestoreIndices(iscol[i],icol+i);CHKERRQ(ierr); 2839 } 2840 } 2841 2842 for (i=0; i<ismax; i++) { 2843 ierr = MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2844 ierr = MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2845 } 2846 2847 /* Destroy allocated memory */ 2848 if (!ismax) { 2849 ierr = PetscFree(pa);CHKERRQ(ierr); 2850 2851 ierr = PetscFree4(sbuf1,ptr,tmp,ctr);CHKERRQ(ierr); 2852 for (i=0; i<nrqr; ++i) { 2853 ierr = PetscFree(sbuf2[i]);CHKERRQ(ierr); 2854 } 2855 for (i=0; i<nrqs; ++i) { 2856 ierr = PetscFree(rbuf3[i]);CHKERRQ(ierr); 2857 } 2858 2859 ierr = PetscFree3(sbuf2,req_size,req_source1);CHKERRQ(ierr); 2860 ierr = PetscFree3(req_source2,rbuf2,rbuf3);CHKERRQ(ierr); 2861 } 2862 2863 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 2864 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 2865 ierr = PetscFree5(irow,icol,nrow,ncol,issorted);CHKERRQ(ierr); 2866 2867 for (i=0; i<nrqs; ++i) { 2868 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 2869 } 2870 ierr = PetscFree(rbuf4);CHKERRQ(ierr); 2871 2872 ierr = PetscFree5(smats,row2proc,cmap,rmap,allcolumns);CHKERRQ(ierr); 2873 PetscFunctionReturn(0); 2874 } 2875 2876 /* 2877 Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B. 2878 Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset 2879 of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n). 2880 If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B. 2881 After that B's columns are mapped into C's global column space, so that C is in the "disassembled" 2882 state, and needs to be "assembled" later by compressing B's column space. 2883 2884 This function may be called in lieu of preallocation, so C should not be expected to be preallocated. 2885 Following this call, C->A & C->B have been created, even if empty. 2886 */ 2887 PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B) 2888 { 2889 /* If making this function public, change the error returned in this function away from _PLIB. */ 2890 PetscErrorCode ierr; 2891 Mat_MPIAIJ *aij; 2892 Mat_SeqAIJ *Baij; 2893 PetscBool seqaij,Bdisassembled; 2894 PetscInt m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count; 2895 PetscScalar v; 2896 const PetscInt *rowindices,*colindices; 2897 2898 PetscFunctionBegin; 2899 /* Check to make sure the component matrices (and embeddings) are compatible with C. */ 2900 if (A) { 2901 ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2902 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type"); 2903 if (rowemb) { 2904 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2905 if (m != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with diag matrix row size %D",m,A->rmap->n); 2906 } else { 2907 if (C->rmap->n != A->rmap->n) { 2908 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2909 } 2910 } 2911 if (dcolemb) { 2912 ierr = ISGetLocalSize(dcolemb,&n);CHKERRQ(ierr); 2913 if (n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag col IS of size %D is incompatible with diag matrix col size %D",n,A->cmap->n); 2914 } else { 2915 if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix"); 2916 } 2917 } 2918 if (B) { 2919 ierr = PetscObjectTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2920 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type"); 2921 if (rowemb) { 2922 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2923 if (m != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Row IS of size %D is incompatible with off-diag matrix row size %D",m,A->rmap->n); 2924 } else { 2925 if (C->rmap->n != B->rmap->n) { 2926 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2927 } 2928 } 2929 if (ocolemb) { 2930 ierr = ISGetLocalSize(ocolemb,&n);CHKERRQ(ierr); 2931 if (n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag col IS of size %D is incompatible with off-diag matrix col size %D",n,B->cmap->n); 2932 } else { 2933 if (C->cmap->N - C->cmap->n != B->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is col-incompatible with the MPIAIJ matrix"); 2934 } 2935 } 2936 2937 aij = (Mat_MPIAIJ*)(C->data); 2938 if (!aij->A) { 2939 /* Mimic parts of MatMPIAIJSetPreallocation() */ 2940 ierr = MatCreate(PETSC_COMM_SELF,&aij->A);CHKERRQ(ierr); 2941 ierr = MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);CHKERRQ(ierr); 2942 ierr = MatSetBlockSizesFromMats(aij->A,C,C);CHKERRQ(ierr); 2943 ierr = MatSetType(aij->A,MATSEQAIJ);CHKERRQ(ierr); 2944 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);CHKERRQ(ierr); 2945 } 2946 if (A) { 2947 ierr = MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);CHKERRQ(ierr); 2948 } else { 2949 ierr = MatSetUp(aij->A);CHKERRQ(ierr); 2950 } 2951 if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */ 2952 /* 2953 If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and 2954 need to "disassemble" B -- convert it to using C's global indices. 2955 To insert the values we take the safer, albeit more expensive, route of MatSetValues(). 2956 2957 If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate; 2958 we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out. 2959 2960 TODO: Put B's values into aij->B's aij structure in place using the embedding ISs? 2961 At least avoid calling MatSetValues() and the implied searches? 2962 */ 2963 2964 if (B && pattern == DIFFERENT_NONZERO_PATTERN) { 2965 #if defined(PETSC_USE_CTABLE) 2966 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 2967 #else 2968 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 2969 /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */ 2970 if (aij->B) { 2971 ierr = PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2972 } 2973 #endif 2974 ngcol = 0; 2975 if (aij->lvec) { 2976 ierr = VecGetSize(aij->lvec,&ngcol);CHKERRQ(ierr); 2977 } 2978 if (aij->garray) { 2979 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 2980 ierr = PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));CHKERRQ(ierr); 2981 } 2982 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 2983 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 2984 } 2985 if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) { 2986 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 2987 } 2988 if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) { 2989 ierr = MatZeroEntries(aij->B);CHKERRQ(ierr); 2990 } 2991 } 2992 Bdisassembled = PETSC_FALSE; 2993 if (!aij->B) { 2994 ierr = MatCreate(PETSC_COMM_SELF,&aij->B);CHKERRQ(ierr); 2995 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);CHKERRQ(ierr); 2996 ierr = MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);CHKERRQ(ierr); 2997 ierr = MatSetBlockSizesFromMats(aij->B,B,B);CHKERRQ(ierr); 2998 ierr = MatSetType(aij->B,MATSEQAIJ);CHKERRQ(ierr); 2999 Bdisassembled = PETSC_TRUE; 3000 } 3001 if (B) { 3002 Baij = (Mat_SeqAIJ*)(B->data); 3003 if (pattern == DIFFERENT_NONZERO_PATTERN) { 3004 ierr = PetscMalloc1(B->rmap->n,&nz);CHKERRQ(ierr); 3005 for (i=0; i<B->rmap->n; i++) { 3006 nz[i] = Baij->i[i+1] - Baij->i[i]; 3007 } 3008 ierr = MatSeqAIJSetPreallocation(aij->B,0,nz);CHKERRQ(ierr); 3009 ierr = PetscFree(nz);CHKERRQ(ierr); 3010 } 3011 3012 ierr = PetscLayoutGetRange(C->rmap,&rstart,&rend);CHKERRQ(ierr); 3013 shift = rend-rstart; 3014 count = 0; 3015 rowindices = NULL; 3016 colindices = NULL; 3017 if (rowemb) { 3018 ierr = ISGetIndices(rowemb,&rowindices);CHKERRQ(ierr); 3019 } 3020 if (ocolemb) { 3021 ierr = ISGetIndices(ocolemb,&colindices);CHKERRQ(ierr); 3022 } 3023 for (i=0; i<B->rmap->n; i++) { 3024 PetscInt row; 3025 row = i; 3026 if (rowindices) row = rowindices[i]; 3027 for (j=Baij->i[i]; j<Baij->i[i+1]; j++) { 3028 col = Baij->j[count]; 3029 if (colindices) col = colindices[col]; 3030 if (Bdisassembled && col>=rstart) col += shift; 3031 v = Baij->a[count]; 3032 ierr = MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);CHKERRQ(ierr); 3033 ++count; 3034 } 3035 } 3036 /* No assembly for aij->B is necessary. */ 3037 /* FIXME: set aij->B's nonzerostate correctly. */ 3038 } else { 3039 ierr = MatSetUp(aij->B);CHKERRQ(ierr); 3040 } 3041 C->preallocated = PETSC_TRUE; 3042 C->was_assembled = PETSC_FALSE; 3043 C->assembled = PETSC_FALSE; 3044 /* 3045 C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ(). 3046 Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's. 3047 */ 3048 PetscFunctionReturn(0); 3049 } 3050 3051 /* 3052 B uses local indices with column indices ranging between 0 and N-n; they must be interpreted using garray. 3053 */ 3054 PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B) 3055 { 3056 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) (C->data); 3057 3058 PetscFunctionBegin; 3059 PetscValidPointer(A,2); 3060 PetscValidPointer(B,3); 3061 /* FIXME: make sure C is assembled */ 3062 *A = aij->A; 3063 *B = aij->B; 3064 /* Note that we don't incref *A and *B, so be careful! */ 3065 PetscFunctionReturn(0); 3066 } 3067 3068 /* 3069 Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C. 3070 NOT SCALABLE due to the use of ISGetNonlocalIS() (see below). 3071 */ 3072 PetscErrorCode MatGetSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[], 3073 PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**), 3074 PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*), 3075 PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat), 3076 PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat)) 3077 { 3078 PetscErrorCode ierr; 3079 PetscMPIInt isize,flag; 3080 PetscInt i,ii,cismax,ispar; 3081 Mat *A,*B; 3082 IS *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p; 3083 3084 PetscFunctionBegin; 3085 if (!ismax) PetscFunctionReturn(0); 3086 3087 for (i = 0, cismax = 0; i < ismax; ++i) { 3088 PetscMPIInt isize; 3089 ierr = MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);CHKERRQ(ierr); 3090 if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator"); 3091 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm, &isize);CHKERRQ(ierr); 3092 if (isize > 1) ++cismax; 3093 } 3094 3095 /* 3096 If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction. 3097 ispar counts the number of parallel ISs across C's comm. 3098 */ 3099 ierr = MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 3100 if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */ 3101 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104 3105 /* if (ispar) */ 3106 /* 3107 Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only. 3108 These are used to extract the off-diag portion of the resulting parallel matrix. 3109 The row IS for the off-diag portion is the same as for the diag portion, 3110 so we merely alias (without increfing) the row IS, while skipping those that are sequential. 3111 */ 3112 ierr = PetscMalloc2(cismax,&cisrow,cismax,&ciscol);CHKERRQ(ierr); 3113 ierr = PetscMalloc1(cismax,&ciscol_p);CHKERRQ(ierr); 3114 for (i = 0, ii = 0; i < ismax; ++i) { 3115 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3116 if (isize > 1) { 3117 /* 3118 TODO: This is the part that's ***NOT SCALABLE***. 3119 To fix this we need to extract just the indices of C's nonzero columns 3120 that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal 3121 part of iscol[i] -- without actually computing ciscol[ii]. This also has 3122 to be done without serializing on the IS list, so, most likely, it is best 3123 done by rewriting MatGetSubMatrices_MPIAIJ() directly. 3124 */ 3125 ierr = ISGetNonlocalIS(iscol[i],&(ciscol[ii]));CHKERRQ(ierr); 3126 /* Now we have to 3127 (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices 3128 were sorted on each rank, concatenated they might no longer be sorted; 3129 (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the 3130 indices in the nondecreasing order to the original index positions. 3131 If ciscol[ii] is strictly increasing, the permutation IS is NULL. 3132 */ 3133 ierr = ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);CHKERRQ(ierr); 3134 ierr = ISSort(ciscol[ii]);CHKERRQ(ierr); 3135 ++ii; 3136 } 3137 } 3138 ierr = PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);CHKERRQ(ierr); 3139 for (i = 0, ii = 0; i < ismax; ++i) { 3140 PetscInt j,issize; 3141 const PetscInt *indices; 3142 3143 /* 3144 Permute the indices into a nondecreasing order. Reject row and col indices with duplicates. 3145 */ 3146 ierr = ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);CHKERRQ(ierr); 3147 ierr = ISSort(isrow[i]);CHKERRQ(ierr); 3148 ierr = ISGetLocalSize(isrow[i],&issize);CHKERRQ(ierr); 3149 ierr = ISGetIndices(isrow[i],&indices);CHKERRQ(ierr); 3150 for (j = 1; j < issize; ++j) { 3151 if (indices[j] == indices[j-1]) { 3152 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in row IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]); 3153 } 3154 } 3155 ierr = ISRestoreIndices(isrow[i],&indices);CHKERRQ(ierr); 3156 3157 3158 ierr = ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);CHKERRQ(ierr); 3159 ierr = ISSort(iscol[i]);CHKERRQ(ierr); 3160 ierr = ISGetLocalSize(iscol[i],&issize);CHKERRQ(ierr); 3161 ierr = ISGetIndices(iscol[i],&indices);CHKERRQ(ierr); 3162 for (j = 1; j < issize; ++j) { 3163 if (indices[j-1] == indices[j]) { 3164 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Repeated indices in col IS %D: indices at %D and %D are both %D",i,j-1,j,indices[j]); 3165 } 3166 } 3167 ierr = ISRestoreIndices(iscol[i],&indices);CHKERRQ(ierr); 3168 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3169 if (isize > 1) { 3170 cisrow[ii] = isrow[i]; 3171 ++ii; 3172 } 3173 } 3174 /* 3175 Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate 3176 array of sequential matrices underlying the resulting parallel matrices. 3177 Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or 3178 contain duplicates. 3179 3180 There are as many diag matrices as there are original index sets. There are only as many parallel 3181 and off-diag matrices, as there are parallel (comm size > 1) index sets. 3182 3183 ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq(): 3184 - If the array of MPI matrices already exists and is being reused, we need to allocate the array 3185 and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq 3186 will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them 3187 with A[i] and B[ii] extracted from the corresponding MPI submat. 3188 - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii] 3189 will have a different order from what getsubmats_seq expects. To handle this case -- indicated 3190 by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii] 3191 (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its 3192 values into A[i] and B[ii] sitting inside the corresponding submat. 3193 - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding 3194 A[i], B[ii], AA[i] or BB[ii] matrices. 3195 */ 3196 /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */ 3197 if (scall == MAT_INITIAL_MATRIX) { 3198 ierr = PetscMalloc1(ismax,submat);CHKERRQ(ierr); 3199 } 3200 3201 /* Now obtain the sequential A and B submatrices separately. */ 3202 /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */ 3203 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr); 3204 ierr = (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 3205 3206 /* 3207 If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential 3208 matrices A & B have been extracted directly into the parallel matrices containing them, or 3209 simply into the sequential matrix identical with the corresponding A (if isize == 1). 3210 Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected 3211 to have the same sparsity pattern. 3212 Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap 3213 must be constructed for C. This is done by setseqmat(s). 3214 */ 3215 for (i = 0, ii = 0; i < ismax; ++i) { 3216 /* 3217 TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol? 3218 That way we can avoid sorting and computing permutations when reusing. 3219 To this end: 3220 - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX 3221 - if caching arrays to hold the ISs, make and compose a container for them so that it can 3222 be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents). 3223 */ 3224 MatStructure pattern; 3225 pattern = DIFFERENT_NONZERO_PATTERN; 3226 3227 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3228 /* Construct submat[i] from the Seq pieces A (and B, if necessary). */ 3229 if (isize > 1) { 3230 if (scall == MAT_INITIAL_MATRIX) { 3231 ierr = MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);CHKERRQ(ierr); 3232 ierr = MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3233 ierr = MatSetType((*submat)[i],MATMPIAIJ);CHKERRQ(ierr); 3234 ierr = PetscLayoutSetUp((*submat)[i]->rmap);CHKERRQ(ierr); 3235 ierr = PetscLayoutSetUp((*submat)[i]->cmap);CHKERRQ(ierr); 3236 } 3237 /* 3238 For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix. 3239 */ 3240 { 3241 Mat AA,BB; 3242 AA = A[i]; 3243 BB = B[ii]; 3244 if (AA || BB) { 3245 ierr = setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);CHKERRQ(ierr); 3246 ierr = MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3247 ierr = MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3248 } 3249 3250 ierr = MatDestroy(&AA);CHKERRQ(ierr); 3251 ierr = MatDestroy(&BB);CHKERRQ(ierr); 3252 } 3253 ierr = ISDestroy(ciscol+ii);CHKERRQ(ierr); 3254 ierr = ISDestroy(ciscol_p+ii);CHKERRQ(ierr); 3255 ++ii; 3256 } else { /* if (isize == 1) */ 3257 if (scall == MAT_REUSE_MATRIX) { 3258 ierr = MatDestroy(&(*submat)[i]);CHKERRQ(ierr); 3259 } 3260 if (isrow_p[i] || iscol_p[i]) { 3261 ierr = MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);CHKERRQ(ierr); 3262 ierr = setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);CHKERRQ(ierr); 3263 /* Otherwise A is extracted straight into (*submats)[i]. */ 3264 /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */ 3265 ierr = MatDestroy(A+i);CHKERRQ(ierr); 3266 } else (*submat)[i] = A[i]; 3267 } 3268 ierr = ISDestroy(&isrow_p[i]);CHKERRQ(ierr); 3269 ierr = ISDestroy(&iscol_p[i]);CHKERRQ(ierr); 3270 } 3271 ierr = PetscFree2(cisrow,ciscol);CHKERRQ(ierr); 3272 ierr = PetscFree2(isrow_p,iscol_p);CHKERRQ(ierr); 3273 ierr = PetscFree(ciscol_p);CHKERRQ(ierr); 3274 ierr = PetscFree(A);CHKERRQ(ierr); 3275 ierr = PetscFree(B);CHKERRQ(ierr); 3276 PetscFunctionReturn(0); 3277 } 3278 3279 PetscErrorCode MatGetSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 3280 { 3281 PetscErrorCode ierr; 3282 3283 PetscFunctionBegin; 3284 ierr = MatGetSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatGetSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);CHKERRQ(ierr); 3285 PetscFunctionReturn(0); 3286 } 3287