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 if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt); 2029 else nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt)); 2030 if (!nmax) nmax = 1; 2031 2032 if (scall == MAT_INITIAL_MATRIX) { 2033 /* Collect global wantallmatrix and nstages */ 2034 if (ismax == 1 && C->rmap->N == C->cmap->N) { 2035 ierr = ISIdentity(*isrow,&rowflag);CHKERRQ(ierr); 2036 ierr = ISIdentity(*iscol,&colflag);CHKERRQ(ierr); 2037 ierr = ISGetLocalSize(*isrow,&nrow);CHKERRQ(ierr); 2038 ierr = ISGetLocalSize(*iscol,&ncol);CHKERRQ(ierr); 2039 if (rowflag && colflag && nrow == C->rmap->N && ncol == C->cmap->N) { 2040 wantallmatrix = PETSC_TRUE; 2041 2042 ierr = PetscOptionsGetBool(((PetscObject)C)->options,((PetscObject)C)->prefix,"-use_fast_submatrix",&wantallmatrix,NULL);CHKERRQ(ierr); 2043 } 2044 } 2045 2046 /* Determine the number of stages through which submatrices are done 2047 Each stage will extract nmax submatrices. 2048 nmax is determined by the matrix column dimension. 2049 If the original matrix has 20M columns, only one submatrix per stage is allowed, etc. 2050 */ 2051 nstages = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */ 2052 2053 in[0] = -1*(PetscInt)wantallmatrix; 2054 in[1] = nstages; 2055 ierr = MPIU_Allreduce(in,out,2,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 2056 wantallmatrix = (PetscBool)(-out[0]); 2057 nstages = out[1]; /* Make sure every processor loops through the global nstages */ 2058 2059 } else { /* MAT_REUSE_MATRIX */ 2060 subc = (Mat_SeqAIJ*)((*submat)[0]->data); 2061 smat = subc->submatis1; 2062 if (!smat) { 2063 /* smat is not generated by MatGetSubMatrix_MPIAIJ_All(...,MAT_INITIAL_MATRIX,...) */ 2064 wantallmatrix = PETSC_TRUE; 2065 } else if (smat->singleis) { 2066 ierr = MatGetSubMatrices_MPIAIJ_SingleIS(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 2067 PetscFunctionReturn(0); 2068 } else { 2069 nstages = smat->nstages; 2070 } 2071 } 2072 2073 if (wantallmatrix) { 2074 ierr = MatGetSubMatrix_MPIAIJ_All(C,MAT_GET_VALUES,scall,submat);CHKERRQ(ierr); 2075 PetscFunctionReturn(0); 2076 } 2077 2078 /* Allocate memory to hold all the submatrices */ 2079 if (scall == MAT_INITIAL_MATRIX) { 2080 ierr = PetscMalloc1(ismax+1,submat);CHKERRQ(ierr); 2081 } 2082 2083 for (i=0,pos=0; i<nstages; i++) { 2084 if (pos+nmax <= ismax) max_no = nmax; 2085 else if (pos == ismax) max_no = 0; 2086 else max_no = ismax-pos; 2087 ierr = MatGetSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);CHKERRQ(ierr); 2088 pos += max_no; 2089 } 2090 2091 if (scall == MAT_INITIAL_MATRIX && ismax) { 2092 /* save nstages for reuse */ 2093 subc = (Mat_SeqAIJ*)((*submat)[0]->data); 2094 smat = subc->submatis1; 2095 if (!smat) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"smat does not exit"); 2096 smat->nstages = nstages; 2097 } 2098 PetscFunctionReturn(0); 2099 } 2100 2101 /* -------------------------------------------------------------------------*/ 2102 PetscErrorCode MatGetSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats) 2103 { 2104 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 2105 Mat A = c->A; 2106 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc; 2107 const PetscInt **icol,**irow; 2108 PetscInt *nrow,*ncol,start; 2109 PetscErrorCode ierr; 2110 PetscMPIInt rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr; 2111 PetscInt **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1; 2112 PetscInt nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol; 2113 PetscInt **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2; 2114 PetscInt **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax; 2115 #if defined(PETSC_USE_CTABLE) 2116 PetscTable *cmap,cmap_i=NULL,*rmap,rmap_i; 2117 #else 2118 PetscInt **cmap,*cmap_i=NULL,**rmap,*rmap_i; 2119 #endif 2120 const PetscInt *irow_i; 2121 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i; 2122 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 2123 MPI_Request *r_waits4,*s_waits3,*s_waits4; 2124 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 2125 MPI_Status *r_status3,*r_status4,*s_status4; 2126 MPI_Comm comm; 2127 PetscScalar **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i; 2128 PetscMPIInt *onodes1,*olengths1,end; 2129 PetscInt **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row; 2130 Mat_SubMat **smats,*smat_i; 2131 PetscBool *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE; 2132 PetscInt *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen; 2133 2134 PetscFunctionBegin; 2135 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2136 size = c->size; 2137 rank = c->rank; 2138 2139 ierr = PetscMalloc5(ismax,&smats,ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax,&allcolumns);CHKERRQ(ierr); 2140 ierr = PetscMalloc5(ismax,&irow,ismax,&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);CHKERRQ(ierr); 2141 2142 for (i=0; i<ismax; i++) { 2143 ierr = ISSorted(iscol[i],&issorted[i]);CHKERRQ(ierr); 2144 if (!issorted[i]) iscsorted = issorted[i]; 2145 2146 ierr = ISSorted(isrow[i],&issorted[i]);CHKERRQ(ierr); 2147 2148 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 2149 ierr = ISGetLocalSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 2150 2151 /* Check for special case: allcolumn */ 2152 ierr = ISIdentity(iscol[i],&colflag);CHKERRQ(ierr); 2153 ierr = ISGetLocalSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 2154 if (colflag && ncol[i] == C->cmap->N) { 2155 allcolumns[i] = PETSC_TRUE; 2156 icol[i] = NULL; 2157 } else { 2158 allcolumns[i] = PETSC_FALSE; 2159 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 2160 } 2161 } 2162 2163 if (scall == MAT_REUSE_MATRIX) { 2164 /* Assumes new rows are same length as the old rows */ 2165 for (i=0; i<ismax; i++) { 2166 subc = (Mat_SeqAIJ*)(submats[i]->data); 2167 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"); 2168 2169 /* Initial matrix as if empty */ 2170 ierr = PetscMemzero(subc->ilen,submats[i]->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2171 2172 /* Initial matrix as if empty */ 2173 submats[i]->factortype = C->factortype; 2174 2175 smat_i = subc->submatis1; 2176 smats[i] = smat_i; 2177 2178 nrqs = smat_i->nrqs; 2179 nrqr = smat_i->nrqr; 2180 rbuf1 = smat_i->rbuf1; 2181 rbuf2 = smat_i->rbuf2; 2182 rbuf3 = smat_i->rbuf3; 2183 req_source2 = smat_i->req_source2; 2184 2185 sbuf1 = smat_i->sbuf1; 2186 sbuf2 = smat_i->sbuf2; 2187 ptr = smat_i->ptr; 2188 tmp = smat_i->tmp; 2189 ctr = smat_i->ctr; 2190 2191 pa = smat_i->pa; 2192 req_size = smat_i->req_size; 2193 req_source1 = smat_i->req_source1; 2194 2195 allcolumns[i] = smat_i->allcolumns; 2196 row2proc[i] = smat_i->row2proc; 2197 rmap[i] = smat_i->rmap; 2198 cmap[i] = smat_i->cmap; 2199 } 2200 } else { /* scall == MAT_INITIAL_MATRIX */ 2201 /* Get some new tags to keep the communication clean */ 2202 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 2203 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 2204 2205 /* evaluate communication - mesg to who, length of mesg, and buffer space 2206 required. Based on this, buffers are allocated, and data copied into them*/ 2207 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); /* mesg size, initialize work vectors */ 2208 2209 for (i=0; i<ismax; i++) { 2210 jmax = nrow[i]; 2211 irow_i = irow[i]; 2212 2213 ierr = PetscMalloc1(jmax,&row2proc_i);CHKERRQ(ierr); 2214 row2proc[i] = row2proc_i; 2215 2216 if (issorted[i]) proc = 0; 2217 for (j=0; j<jmax; j++) { 2218 if (!issorted[i]) proc = 0; 2219 row = irow_i[j]; 2220 while (row >= C->rmap->range[proc+1]) proc++; 2221 w4[proc]++; 2222 row2proc_i[j] = proc; /* map row index to proc */ 2223 } 2224 for (j=0; j<size; j++) { 2225 if (w4[j]) { w1[j] += w4[j]; w3[j]++; w4[j] = 0;} 2226 } 2227 } 2228 2229 nrqs = 0; /* no of outgoing messages */ 2230 msz = 0; /* total mesg length (for all procs) */ 2231 w1[rank] = 0; /* no mesg sent to self */ 2232 w3[rank] = 0; 2233 for (i=0; i<size; i++) { 2234 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 2235 } 2236 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 2237 for (i=0,j=0; i<size; i++) { 2238 if (w1[i]) { pa[j] = i; j++; } 2239 } 2240 2241 /* Each message would have a header = 1 + 2*(no of IS) + data */ 2242 for (i=0; i<nrqs; i++) { 2243 j = pa[i]; 2244 w1[j] += w2[j] + 2* w3[j]; 2245 msz += w1[j]; 2246 } 2247 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 2248 2249 /* Determine the number of messages to expect, their lengths, from from-ids */ 2250 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 2251 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 2252 2253 /* Now post the Irecvs corresponding to these messages */ 2254 tag0 = ((PetscObject)C)->tag; 2255 ierr = PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 2256 2257 ierr = PetscFree(onodes1);CHKERRQ(ierr); 2258 ierr = PetscFree(olengths1);CHKERRQ(ierr); 2259 2260 /* Allocate Memory for outgoing messages */ 2261 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 2262 ierr = PetscMemzero(sbuf1,size*sizeof(PetscInt*));CHKERRQ(ierr); 2263 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 2264 2265 { 2266 PetscInt *iptr = tmp; 2267 k = 0; 2268 for (i=0; i<nrqs; i++) { 2269 j = pa[i]; 2270 iptr += k; 2271 sbuf1[j] = iptr; 2272 k = w1[j]; 2273 } 2274 } 2275 2276 /* Form the outgoing messages. Initialize the header space */ 2277 for (i=0; i<nrqs; i++) { 2278 j = pa[i]; 2279 sbuf1[j][0] = 0; 2280 ierr = PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 2281 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 2282 } 2283 2284 /* Parse the isrow and copy data into outbuf */ 2285 for (i=0; i<ismax; i++) { 2286 row2proc_i = row2proc[i]; 2287 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 2288 irow_i = irow[i]; 2289 jmax = nrow[i]; 2290 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 2291 proc = row2proc_i[j]; 2292 if (proc != rank) { /* copy to the outgoing buf*/ 2293 ctr[proc]++; 2294 *ptr[proc] = irow_i[j]; 2295 ptr[proc]++; 2296 } 2297 } 2298 /* Update the headers for the current IS */ 2299 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 2300 if ((ctr_j = ctr[j])) { 2301 sbuf1_j = sbuf1[j]; 2302 k = ++sbuf1_j[0]; 2303 sbuf1_j[2*k] = ctr_j; 2304 sbuf1_j[2*k-1] = i; 2305 } 2306 } 2307 } 2308 2309 /* Now post the sends */ 2310 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 2311 for (i=0; i<nrqs; ++i) { 2312 j = pa[i]; 2313 ierr = MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);CHKERRQ(ierr); 2314 } 2315 2316 /* Post Receives to capture the buffer size */ 2317 ierr = PetscMalloc1(nrqs+1,&r_waits2);CHKERRQ(ierr); 2318 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 2319 rbuf2[0] = tmp + msz; 2320 for (i=1; i<nrqs; ++i) { 2321 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 2322 } 2323 for (i=0; i<nrqs; ++i) { 2324 j = pa[i]; 2325 ierr = MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);CHKERRQ(ierr); 2326 } 2327 2328 /* Send to other procs the buf size they should allocate */ 2329 /* Receive messages*/ 2330 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 2331 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 2332 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 2333 { 2334 PetscInt *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart; 2335 PetscInt *sbuf2_i; 2336 2337 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRQ(ierr); 2338 for (i=0; i<nrqr; ++i) { 2339 req_size[i] = 0; 2340 rbuf1_i = rbuf1[i]; 2341 start = 2*rbuf1_i[0] + 1; 2342 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRQ(ierr); 2343 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 2344 sbuf2_i = sbuf2[i]; 2345 for (j=start; j<end; j++) { 2346 id = rbuf1_i[j] - rstart; 2347 ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id]; 2348 sbuf2_i[j] = ncols; 2349 req_size[i] += ncols; 2350 } 2351 req_source1[i] = r_status1[i].MPI_SOURCE; 2352 /* form the header */ 2353 sbuf2_i[0] = req_size[i]; 2354 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 2355 2356 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 2357 } 2358 } 2359 ierr = PetscFree(r_status1);CHKERRQ(ierr); 2360 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 2361 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 2362 2363 /* Receive messages*/ 2364 ierr = PetscMalloc1(nrqs+1,&r_waits3);CHKERRQ(ierr); 2365 ierr = PetscMalloc1(nrqs+1,&r_status2);CHKERRQ(ierr); 2366 2367 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRQ(ierr); 2368 for (i=0; i<nrqs; ++i) { 2369 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 2370 req_source2[i] = r_status2[i].MPI_SOURCE; 2371 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRQ(ierr); 2372 } 2373 ierr = PetscFree(r_status2);CHKERRQ(ierr); 2374 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 2375 2376 /* Wait on sends1 and sends2 */ 2377 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 2378 ierr = PetscMalloc1(nrqr+1,&s_status2);CHKERRQ(ierr); 2379 2380 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr);} 2381 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr);} 2382 ierr = PetscFree(s_status1);CHKERRQ(ierr); 2383 ierr = PetscFree(s_status2);CHKERRQ(ierr); 2384 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 2385 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 2386 2387 /* Now allocate sending buffers for a->j, and send them off */ 2388 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 2389 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2390 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 2391 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 2392 2393 ierr = PetscMalloc1(nrqr+1,&s_waits3);CHKERRQ(ierr); 2394 { 2395 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite; 2396 PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2397 PetscInt cend = C->cmap->rend; 2398 PetscInt *a_j = a->j,*b_j = b->j,ctmp; 2399 2400 for (i=0; i<nrqr; i++) { 2401 rbuf1_i = rbuf1[i]; 2402 sbuf_aj_i = sbuf_aj[i]; 2403 ct1 = 2*rbuf1_i[0] + 1; 2404 ct2 = 0; 2405 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2406 kmax = rbuf1[i][2*j]; 2407 for (k=0; k<kmax; k++,ct1++) { 2408 row = rbuf1_i[ct1] - rstart; 2409 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2410 ncols = nzA + nzB; 2411 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 2412 2413 /* load the column indices for this row into cols */ 2414 cols = sbuf_aj_i + ct2; 2415 2416 lwrite = 0; 2417 for (l=0; l<nzB; l++) { 2418 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp; 2419 } 2420 for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l]; 2421 for (l=0; l<nzB; l++) { 2422 if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp; 2423 } 2424 2425 ct2 += ncols; 2426 } 2427 } 2428 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 2429 } 2430 } 2431 ierr = PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 2432 2433 /* create col map: global col of C -> local col of submatrices */ 2434 { 2435 const PetscInt *icol_i; 2436 #if defined(PETSC_USE_CTABLE) 2437 for (i=0; i<ismax; i++) { 2438 if (!allcolumns[i]) { 2439 ierr = PetscTableCreate(ncol[i]+1,C->cmap->N+1,&cmap[i]);CHKERRQ(ierr); 2440 2441 jmax = ncol[i]; 2442 icol_i = icol[i]; 2443 cmap_i = cmap[i]; 2444 for (j=0; j<jmax; j++) { 2445 ierr = PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2446 } 2447 } else cmap[i] = NULL; 2448 } 2449 #else 2450 for (i=0; i<ismax; i++) { 2451 if (!allcolumns[i]) { 2452 ierr = PetscCalloc1(C->cmap->N,&cmap[i]);CHKERRQ(ierr); 2453 jmax = ncol[i]; 2454 icol_i = icol[i]; 2455 cmap_i = cmap[i]; 2456 for (j=0; j<jmax; j++) { 2457 cmap_i[icol_i[j]] = j+1; 2458 } 2459 } else cmap[i] = NULL; 2460 } 2461 #endif 2462 } 2463 2464 /* Create lens which is required for MatCreate... */ 2465 for (i=0,j=0; i<ismax; i++) j += nrow[i]; 2466 ierr = PetscMalloc1(ismax,&lens);CHKERRQ(ierr); 2467 2468 if (ismax) { 2469 ierr = PetscCalloc1(j,&lens[0]);CHKERRQ(ierr); 2470 } 2471 for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1]; 2472 2473 /* Update lens from local data */ 2474 for (i=0; i<ismax; i++) { 2475 row2proc_i = row2proc[i]; 2476 jmax = nrow[i]; 2477 if (!allcolumns[i]) cmap_i = cmap[i]; 2478 irow_i = irow[i]; 2479 lens_i = lens[i]; 2480 for (j=0; j<jmax; j++) { 2481 row = irow_i[j]; 2482 proc = row2proc_i[j]; 2483 if (proc == rank) { 2484 ierr = MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2485 if (!allcolumns[i]) { 2486 for (k=0; k<ncols; k++) { 2487 #if defined(PETSC_USE_CTABLE) 2488 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2489 #else 2490 tcol = cmap_i[cols[k]]; 2491 #endif 2492 if (tcol) lens_i[j]++; 2493 } 2494 } else { /* allcolumns */ 2495 lens_i[j] = ncols; 2496 } 2497 ierr = MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2498 } 2499 } 2500 } 2501 2502 /* Create row map: global row of C -> local row of submatrices */ 2503 #if defined(PETSC_USE_CTABLE) 2504 for (i=0; i<ismax; i++) { 2505 ierr = PetscTableCreate(nrow[i]+1,C->rmap->N+1,&rmap[i]);CHKERRQ(ierr); 2506 irow_i = irow[i]; 2507 jmax = nrow[i]; 2508 for (j=0; j<jmax; j++) { 2509 ierr = PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2510 } 2511 } 2512 #else 2513 for (i=0; i<ismax; i++) { 2514 ierr = PetscCalloc1(C->rmap->N,&rmap[i]);CHKERRQ(ierr); 2515 rmap_i = rmap[i]; 2516 irow_i = irow[i]; 2517 jmax = nrow[i]; 2518 for (j=0; j<jmax; j++) { 2519 rmap_i[irow_i[j]] = j; 2520 } 2521 } 2522 #endif 2523 2524 /* Update lens from offproc data */ 2525 { 2526 PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i; 2527 2528 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRQ(ierr); 2529 for (tmp2=0; tmp2<nrqs; tmp2++) { 2530 sbuf1_i = sbuf1[pa[tmp2]]; 2531 jmax = sbuf1_i[0]; 2532 ct1 = 2*jmax+1; 2533 ct2 = 0; 2534 rbuf2_i = rbuf2[tmp2]; 2535 rbuf3_i = rbuf3[tmp2]; 2536 for (j=1; j<=jmax; j++) { 2537 is_no = sbuf1_i[2*j-1]; 2538 max1 = sbuf1_i[2*j]; 2539 lens_i = lens[is_no]; 2540 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2541 rmap_i = rmap[is_no]; 2542 for (k=0; k<max1; k++,ct1++) { 2543 #if defined(PETSC_USE_CTABLE) 2544 ierr = PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 2545 row--; 2546 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 2547 #else 2548 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 2549 #endif 2550 max2 = rbuf2_i[ct1]; 2551 for (l=0; l<max2; l++,ct2++) { 2552 if (!allcolumns[is_no]) { 2553 #if defined(PETSC_USE_CTABLE) 2554 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2555 #else 2556 tcol = cmap_i[rbuf3_i[ct2]]; 2557 #endif 2558 if (tcol) lens_i[row]++; 2559 } else { /* allcolumns */ 2560 lens_i[row]++; /* lens_i[row] += max2 ? */ 2561 } 2562 } 2563 } 2564 } 2565 } 2566 } 2567 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 2568 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr);} 2569 ierr = PetscFree2(r_status3,s_status3);CHKERRQ(ierr); 2570 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 2571 2572 /* Create the submatrices */ 2573 for (i=0; i<ismax; i++) { 2574 PetscInt rbs,cbs; 2575 2576 ierr = ISGetBlockSize(isrow[i],&rbs);CHKERRQ(ierr); 2577 ierr = ISGetBlockSize(iscol[i],&cbs);CHKERRQ(ierr); 2578 2579 ierr = MatCreate(PETSC_COMM_SELF,submats+i);CHKERRQ(ierr); 2580 ierr = MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2581 2582 ierr = MatSetBlockSizes(submats[i],rbs,cbs);CHKERRQ(ierr); 2583 ierr = MatSetType(submats[i],((PetscObject)A)->type_name);CHKERRQ(ierr); 2584 ierr = MatSeqAIJSetPreallocation(submats[i],0,lens[i]);CHKERRQ(ierr); 2585 2586 /* create struct Mat_SubMat and attached it to submat */ 2587 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 2588 subc = (Mat_SeqAIJ*)submats[i]->data; 2589 subc->submatis1 = smat_i; 2590 smats[i] = smat_i; 2591 2592 smat_i->destroy = submats[i]->ops->destroy; 2593 submats[i]->ops->destroy = MatDestroy_MPIAIJ_MatGetSubmatrices; 2594 submats[i]->factortype = C->factortype; 2595 2596 smat_i->id = i; 2597 smat_i->nrqs = nrqs; 2598 smat_i->nrqr = nrqr; 2599 smat_i->rbuf1 = rbuf1; 2600 smat_i->rbuf2 = rbuf2; 2601 smat_i->rbuf3 = rbuf3; 2602 smat_i->sbuf2 = sbuf2; 2603 smat_i->req_source2 = req_source2; 2604 2605 smat_i->sbuf1 = sbuf1; 2606 smat_i->ptr = ptr; 2607 smat_i->tmp = tmp; 2608 smat_i->ctr = ctr; 2609 2610 smat_i->pa = pa; 2611 smat_i->req_size = req_size; 2612 smat_i->req_source1 = req_source1; 2613 2614 smat_i->allcolumns = allcolumns[i]; 2615 smat_i->singleis = PETSC_FALSE; 2616 smat_i->row2proc = row2proc[i]; 2617 smat_i->rmap = rmap[i]; 2618 smat_i->cmap = cmap[i]; 2619 } 2620 2621 if (ismax) {ierr = PetscFree(lens[0]);CHKERRQ(ierr);} 2622 ierr = PetscFree(lens);CHKERRQ(ierr); 2623 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 2624 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 2625 2626 } /* endof scall == MAT_INITIAL_MATRIX */ 2627 2628 /* Post recv matrix values */ 2629 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 2630 ierr = PetscMalloc1(nrqs+1,&rbuf4);CHKERRQ(ierr); 2631 ierr = PetscMalloc1(nrqs+1,&r_waits4);CHKERRQ(ierr); 2632 ierr = PetscMalloc1(nrqs+1,&r_status4);CHKERRQ(ierr); 2633 ierr = PetscMalloc1(nrqr+1,&s_status4);CHKERRQ(ierr); 2634 for (i=0; i<nrqs; ++i) { 2635 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);CHKERRQ(ierr); 2636 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRQ(ierr); 2637 } 2638 2639 /* Allocate sending buffers for a->a, and send them off */ 2640 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 2641 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2642 ierr = PetscMalloc1(j+1,&sbuf_aa[0]);CHKERRQ(ierr); 2643 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]; 2644 2645 ierr = PetscMalloc1(nrqr+1,&s_waits4);CHKERRQ(ierr); 2646 { 2647 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite; 2648 PetscInt cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2649 PetscInt cend = C->cmap->rend; 2650 PetscInt *b_j = b->j; 2651 PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a; 2652 2653 for (i=0; i<nrqr; i++) { 2654 rbuf1_i = rbuf1[i]; 2655 sbuf_aa_i = sbuf_aa[i]; 2656 ct1 = 2*rbuf1_i[0]+1; 2657 ct2 = 0; 2658 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2659 kmax = rbuf1_i[2*j]; 2660 for (k=0; k<kmax; k++,ct1++) { 2661 row = rbuf1_i[ct1] - rstart; 2662 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2663 ncols = nzA + nzB; 2664 cworkB = b_j + b_i[row]; 2665 vworkA = a_a + a_i[row]; 2666 vworkB = b_a + b_i[row]; 2667 2668 /* load the column values for this row into vals*/ 2669 vals = sbuf_aa_i+ct2; 2670 2671 lwrite = 0; 2672 for (l=0; l<nzB; l++) { 2673 if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l]; 2674 } 2675 for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l]; 2676 for (l=0; l<nzB; l++) { 2677 if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l]; 2678 } 2679 2680 ct2 += ncols; 2681 } 2682 } 2683 ierr = MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRQ(ierr); 2684 } 2685 } 2686 2687 if (!ismax) { 2688 ierr = PetscFree(rbuf1[0]);CHKERRQ(ierr); 2689 ierr = PetscFree(rbuf1);CHKERRQ(ierr); 2690 } 2691 2692 /* Assemble the matrices */ 2693 /* First assemble the local rows */ 2694 for (i=0; i<ismax; i++) { 2695 row2proc_i = row2proc[i]; 2696 subc = (Mat_SeqAIJ*)submats[i]->data; 2697 imat_ilen = subc->ilen; 2698 imat_j = subc->j; 2699 imat_i = subc->i; 2700 imat_a = subc->a; 2701 2702 if (!allcolumns[i]) cmap_i = cmap[i]; 2703 rmap_i = rmap[i]; 2704 irow_i = irow[i]; 2705 jmax = nrow[i]; 2706 for (j=0; j<jmax; j++) { 2707 row = irow_i[j]; 2708 proc = row2proc_i[j]; 2709 if (proc == rank) { 2710 old_row = row; 2711 #if defined(PETSC_USE_CTABLE) 2712 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2713 row--; 2714 #else 2715 row = rmap_i[row]; 2716 #endif 2717 ilen_row = imat_ilen[row]; 2718 ierr = MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2719 mat_i = imat_i[row]; 2720 mat_a = imat_a + mat_i; 2721 mat_j = imat_j + mat_i; 2722 if (!allcolumns[i]) { 2723 for (k=0; k<ncols; k++) { 2724 #if defined(PETSC_USE_CTABLE) 2725 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2726 #else 2727 tcol = cmap_i[cols[k]]; 2728 #endif 2729 if (tcol) { 2730 *mat_j++ = tcol - 1; 2731 *mat_a++ = vals[k]; 2732 ilen_row++; 2733 } 2734 } 2735 } else { /* allcolumns */ 2736 for (k=0; k<ncols; k++) { 2737 *mat_j++ = cols[k]; /* global col index! */ 2738 *mat_a++ = vals[k]; 2739 ilen_row++; 2740 } 2741 } 2742 ierr = MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2743 2744 imat_ilen[row] = ilen_row; 2745 } 2746 } 2747 } 2748 2749 /* Now assemble the off proc rows */ 2750 ierr = MPI_Waitall(nrqs,r_waits4,r_status4);CHKERRQ(ierr); 2751 for (tmp2=0; tmp2<nrqs; tmp2++) { 2752 sbuf1_i = sbuf1[pa[tmp2]]; 2753 jmax = sbuf1_i[0]; 2754 ct1 = 2*jmax + 1; 2755 ct2 = 0; 2756 rbuf2_i = rbuf2[tmp2]; 2757 rbuf3_i = rbuf3[tmp2]; 2758 rbuf4_i = rbuf4[tmp2]; 2759 for (j=1; j<=jmax; j++) { 2760 is_no = sbuf1_i[2*j-1]; 2761 rmap_i = rmap[is_no]; 2762 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2763 subc = (Mat_SeqAIJ*)submats[is_no]->data; 2764 imat_ilen = subc->ilen; 2765 imat_j = subc->j; 2766 imat_i = subc->i; 2767 imat_a = subc->a; 2768 max1 = sbuf1_i[2*j]; 2769 for (k=0; k<max1; k++,ct1++) { 2770 row = sbuf1_i[ct1]; 2771 #if defined(PETSC_USE_CTABLE) 2772 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2773 row--; 2774 #else 2775 row = rmap_i[row]; 2776 #endif 2777 ilen = imat_ilen[row]; 2778 mat_i = imat_i[row]; 2779 mat_a = imat_a + mat_i; 2780 mat_j = imat_j + mat_i; 2781 max2 = rbuf2_i[ct1]; 2782 if (!allcolumns[is_no]) { 2783 for (l=0; l<max2; l++,ct2++) { 2784 #if defined(PETSC_USE_CTABLE) 2785 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2786 #else 2787 tcol = cmap_i[rbuf3_i[ct2]]; 2788 #endif 2789 if (tcol) { 2790 *mat_j++ = tcol - 1; 2791 *mat_a++ = rbuf4_i[ct2]; 2792 ilen++; 2793 } 2794 } 2795 } else { /* allcolumns */ 2796 for (l=0; l<max2; l++,ct2++) { 2797 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 2798 *mat_a++ = rbuf4_i[ct2]; 2799 ilen++; 2800 } 2801 } 2802 imat_ilen[row] = ilen; 2803 } 2804 } 2805 } 2806 2807 if (!iscsorted) { /* sort column indices of the rows */ 2808 for (i=0; i<ismax; i++) { 2809 subc = (Mat_SeqAIJ*)submats[i]->data; 2810 imat_j = subc->j; 2811 imat_i = subc->i; 2812 imat_a = subc->a; 2813 imat_ilen = subc->ilen; 2814 2815 if (allcolumns[i]) continue; 2816 jmax = nrow[i]; 2817 for (j=0; j<jmax; j++) { 2818 PetscInt ilen; 2819 2820 mat_i = imat_i[j]; 2821 mat_a = imat_a + mat_i; 2822 mat_j = imat_j + mat_i; 2823 ilen = imat_ilen[j]; 2824 ierr = PetscSortIntWithScalarArray(ilen,mat_j,mat_a);CHKERRQ(ierr); 2825 } 2826 } 2827 } 2828 2829 ierr = PetscFree(r_status4);CHKERRQ(ierr); 2830 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 2831 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr);} 2832 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 2833 ierr = PetscFree(s_status4);CHKERRQ(ierr); 2834 2835 /* Restore the indices */ 2836 for (i=0; i<ismax; i++) { 2837 ierr = ISRestoreIndices(isrow[i],irow+i);CHKERRQ(ierr); 2838 if (!allcolumns[i]) { 2839 ierr = ISRestoreIndices(iscol[i],icol+i);CHKERRQ(ierr); 2840 } 2841 } 2842 2843 for (i=0; i<ismax; i++) { 2844 ierr = MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2845 ierr = MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2846 } 2847 2848 /* Destroy allocated memory */ 2849 if (!ismax) { 2850 ierr = PetscFree(pa);CHKERRQ(ierr); 2851 2852 ierr = PetscFree4(sbuf1,ptr,tmp,ctr);CHKERRQ(ierr); 2853 for (i=0; i<nrqr; ++i) { 2854 ierr = PetscFree(sbuf2[i]);CHKERRQ(ierr); 2855 } 2856 for (i=0; i<nrqs; ++i) { 2857 ierr = PetscFree(rbuf3[i]);CHKERRQ(ierr); 2858 } 2859 2860 ierr = PetscFree3(sbuf2,req_size,req_source1);CHKERRQ(ierr); 2861 ierr = PetscFree3(req_source2,rbuf2,rbuf3);CHKERRQ(ierr); 2862 } 2863 2864 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 2865 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 2866 ierr = PetscFree5(irow,icol,nrow,ncol,issorted);CHKERRQ(ierr); 2867 2868 for (i=0; i<nrqs; ++i) { 2869 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 2870 } 2871 ierr = PetscFree(rbuf4);CHKERRQ(ierr); 2872 2873 ierr = PetscFree5(smats,row2proc,cmap,rmap,allcolumns);CHKERRQ(ierr); 2874 PetscFunctionReturn(0); 2875 } 2876 2877 /* 2878 Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B. 2879 Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset 2880 of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n). 2881 If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B. 2882 After that B's columns are mapped into C's global column space, so that C is in the "disassembled" 2883 state, and needs to be "assembled" later by compressing B's column space. 2884 2885 This function may be called in lieu of preallocation, so C should not be expected to be preallocated. 2886 Following this call, C->A & C->B have been created, even if empty. 2887 */ 2888 PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B) 2889 { 2890 /* If making this function public, change the error returned in this function away from _PLIB. */ 2891 PetscErrorCode ierr; 2892 Mat_MPIAIJ *aij; 2893 Mat_SeqAIJ *Baij; 2894 PetscBool seqaij,Bdisassembled; 2895 PetscInt m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count; 2896 PetscScalar v; 2897 const PetscInt *rowindices,*colindices; 2898 2899 PetscFunctionBegin; 2900 /* Check to make sure the component matrices (and embeddings) are compatible with C. */ 2901 if (A) { 2902 ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2903 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type"); 2904 if (rowemb) { 2905 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2906 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); 2907 } else { 2908 if (C->rmap->n != A->rmap->n) { 2909 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2910 } 2911 } 2912 if (dcolemb) { 2913 ierr = ISGetLocalSize(dcolemb,&n);CHKERRQ(ierr); 2914 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); 2915 } else { 2916 if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix"); 2917 } 2918 } 2919 if (B) { 2920 ierr = PetscObjectTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2921 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type"); 2922 if (rowemb) { 2923 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2924 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); 2925 } else { 2926 if (C->rmap->n != B->rmap->n) { 2927 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2928 } 2929 } 2930 if (ocolemb) { 2931 ierr = ISGetLocalSize(ocolemb,&n);CHKERRQ(ierr); 2932 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); 2933 } else { 2934 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"); 2935 } 2936 } 2937 2938 aij = (Mat_MPIAIJ*)(C->data); 2939 if (!aij->A) { 2940 /* Mimic parts of MatMPIAIJSetPreallocation() */ 2941 ierr = MatCreate(PETSC_COMM_SELF,&aij->A);CHKERRQ(ierr); 2942 ierr = MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);CHKERRQ(ierr); 2943 ierr = MatSetBlockSizesFromMats(aij->A,C,C);CHKERRQ(ierr); 2944 ierr = MatSetType(aij->A,MATSEQAIJ);CHKERRQ(ierr); 2945 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);CHKERRQ(ierr); 2946 } 2947 if (A) { 2948 ierr = MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);CHKERRQ(ierr); 2949 } else { 2950 ierr = MatSetUp(aij->A);CHKERRQ(ierr); 2951 } 2952 if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */ 2953 /* 2954 If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and 2955 need to "disassemble" B -- convert it to using C's global indices. 2956 To insert the values we take the safer, albeit more expensive, route of MatSetValues(). 2957 2958 If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate; 2959 we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out. 2960 2961 TODO: Put B's values into aij->B's aij structure in place using the embedding ISs? 2962 At least avoid calling MatSetValues() and the implied searches? 2963 */ 2964 2965 if (B && pattern == DIFFERENT_NONZERO_PATTERN) { 2966 #if defined(PETSC_USE_CTABLE) 2967 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 2968 #else 2969 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 2970 /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */ 2971 if (aij->B) { 2972 ierr = PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2973 } 2974 #endif 2975 ngcol = 0; 2976 if (aij->lvec) { 2977 ierr = VecGetSize(aij->lvec,&ngcol);CHKERRQ(ierr); 2978 } 2979 if (aij->garray) { 2980 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 2981 ierr = PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));CHKERRQ(ierr); 2982 } 2983 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 2984 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 2985 } 2986 if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) { 2987 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 2988 } 2989 if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) { 2990 ierr = MatZeroEntries(aij->B);CHKERRQ(ierr); 2991 } 2992 } 2993 Bdisassembled = PETSC_FALSE; 2994 if (!aij->B) { 2995 ierr = MatCreate(PETSC_COMM_SELF,&aij->B);CHKERRQ(ierr); 2996 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);CHKERRQ(ierr); 2997 ierr = MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);CHKERRQ(ierr); 2998 ierr = MatSetBlockSizesFromMats(aij->B,B,B);CHKERRQ(ierr); 2999 ierr = MatSetType(aij->B,MATSEQAIJ);CHKERRQ(ierr); 3000 Bdisassembled = PETSC_TRUE; 3001 } 3002 if (B) { 3003 Baij = (Mat_SeqAIJ*)(B->data); 3004 if (pattern == DIFFERENT_NONZERO_PATTERN) { 3005 ierr = PetscMalloc1(B->rmap->n,&nz);CHKERRQ(ierr); 3006 for (i=0; i<B->rmap->n; i++) { 3007 nz[i] = Baij->i[i+1] - Baij->i[i]; 3008 } 3009 ierr = MatSeqAIJSetPreallocation(aij->B,0,nz);CHKERRQ(ierr); 3010 ierr = PetscFree(nz);CHKERRQ(ierr); 3011 } 3012 3013 ierr = PetscLayoutGetRange(C->rmap,&rstart,&rend);CHKERRQ(ierr); 3014 shift = rend-rstart; 3015 count = 0; 3016 rowindices = NULL; 3017 colindices = NULL; 3018 if (rowemb) { 3019 ierr = ISGetIndices(rowemb,&rowindices);CHKERRQ(ierr); 3020 } 3021 if (ocolemb) { 3022 ierr = ISGetIndices(ocolemb,&colindices);CHKERRQ(ierr); 3023 } 3024 for (i=0; i<B->rmap->n; i++) { 3025 PetscInt row; 3026 row = i; 3027 if (rowindices) row = rowindices[i]; 3028 for (j=Baij->i[i]; j<Baij->i[i+1]; j++) { 3029 col = Baij->j[count]; 3030 if (colindices) col = colindices[col]; 3031 if (Bdisassembled && col>=rstart) col += shift; 3032 v = Baij->a[count]; 3033 ierr = MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);CHKERRQ(ierr); 3034 ++count; 3035 } 3036 } 3037 /* No assembly for aij->B is necessary. */ 3038 /* FIXME: set aij->B's nonzerostate correctly. */ 3039 } else { 3040 ierr = MatSetUp(aij->B);CHKERRQ(ierr); 3041 } 3042 C->preallocated = PETSC_TRUE; 3043 C->was_assembled = PETSC_FALSE; 3044 C->assembled = PETSC_FALSE; 3045 /* 3046 C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ(). 3047 Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's. 3048 */ 3049 PetscFunctionReturn(0); 3050 } 3051 3052 /* 3053 B uses local indices with column indices ranging between 0 and N-n; they must be interpreted using garray. 3054 */ 3055 PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B) 3056 { 3057 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) (C->data); 3058 3059 PetscFunctionBegin; 3060 PetscValidPointer(A,2); 3061 PetscValidPointer(B,3); 3062 /* FIXME: make sure C is assembled */ 3063 *A = aij->A; 3064 *B = aij->B; 3065 /* Note that we don't incref *A and *B, so be careful! */ 3066 PetscFunctionReturn(0); 3067 } 3068 3069 /* 3070 Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C. 3071 NOT SCALABLE due to the use of ISGetNonlocalIS() (see below). 3072 */ 3073 PetscErrorCode MatGetSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[], 3074 PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**), 3075 PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*), 3076 PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat), 3077 PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat)) 3078 { 3079 PetscErrorCode ierr; 3080 PetscMPIInt isize,flag; 3081 PetscInt i,ii,cismax,ispar; 3082 Mat *A,*B; 3083 IS *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p; 3084 3085 PetscFunctionBegin; 3086 if (!ismax) PetscFunctionReturn(0); 3087 3088 for (i = 0, cismax = 0; i < ismax; ++i) { 3089 PetscMPIInt isize; 3090 ierr = MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);CHKERRQ(ierr); 3091 if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator"); 3092 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm, &isize);CHKERRQ(ierr); 3093 if (isize > 1) ++cismax; 3094 } 3095 3096 /* 3097 If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction. 3098 ispar counts the number of parallel ISs across C's comm. 3099 */ 3100 ierr = MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 3101 if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */ 3102 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 3103 PetscFunctionReturn(0); 3104 } 3105 3106 /* if (ispar) */ 3107 /* 3108 Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only. 3109 These are used to extract the off-diag portion of the resulting parallel matrix. 3110 The row IS for the off-diag portion is the same as for the diag portion, 3111 so we merely alias (without increfing) the row IS, while skipping those that are sequential. 3112 */ 3113 ierr = PetscMalloc2(cismax,&cisrow,cismax,&ciscol);CHKERRQ(ierr); 3114 ierr = PetscMalloc1(cismax,&ciscol_p);CHKERRQ(ierr); 3115 for (i = 0, ii = 0; i < ismax; ++i) { 3116 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3117 if (isize > 1) { 3118 /* 3119 TODO: This is the part that's ***NOT SCALABLE***. 3120 To fix this we need to extract just the indices of C's nonzero columns 3121 that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal 3122 part of iscol[i] -- without actually computing ciscol[ii]. This also has 3123 to be done without serializing on the IS list, so, most likely, it is best 3124 done by rewriting MatGetSubMatrices_MPIAIJ() directly. 3125 */ 3126 ierr = ISGetNonlocalIS(iscol[i],&(ciscol[ii]));CHKERRQ(ierr); 3127 /* Now we have to 3128 (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices 3129 were sorted on each rank, concatenated they might no longer be sorted; 3130 (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the 3131 indices in the nondecreasing order to the original index positions. 3132 If ciscol[ii] is strictly increasing, the permutation IS is NULL. 3133 */ 3134 ierr = ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);CHKERRQ(ierr); 3135 ierr = ISSort(ciscol[ii]);CHKERRQ(ierr); 3136 ++ii; 3137 } 3138 } 3139 ierr = PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);CHKERRQ(ierr); 3140 for (i = 0, ii = 0; i < ismax; ++i) { 3141 PetscInt j,issize; 3142 const PetscInt *indices; 3143 3144 /* 3145 Permute the indices into a nondecreasing order. Reject row and col indices with duplicates. 3146 */ 3147 ierr = ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);CHKERRQ(ierr); 3148 ierr = ISSort(isrow[i]);CHKERRQ(ierr); 3149 ierr = ISGetLocalSize(isrow[i],&issize);CHKERRQ(ierr); 3150 ierr = ISGetIndices(isrow[i],&indices);CHKERRQ(ierr); 3151 for (j = 1; j < issize; ++j) { 3152 if (indices[j] == indices[j-1]) { 3153 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]); 3154 } 3155 } 3156 ierr = ISRestoreIndices(isrow[i],&indices);CHKERRQ(ierr); 3157 3158 3159 ierr = ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);CHKERRQ(ierr); 3160 ierr = ISSort(iscol[i]);CHKERRQ(ierr); 3161 ierr = ISGetLocalSize(iscol[i],&issize);CHKERRQ(ierr); 3162 ierr = ISGetIndices(iscol[i],&indices);CHKERRQ(ierr); 3163 for (j = 1; j < issize; ++j) { 3164 if (indices[j-1] == indices[j]) { 3165 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]); 3166 } 3167 } 3168 ierr = ISRestoreIndices(iscol[i],&indices);CHKERRQ(ierr); 3169 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3170 if (isize > 1) { 3171 cisrow[ii] = isrow[i]; 3172 ++ii; 3173 } 3174 } 3175 /* 3176 Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate 3177 array of sequential matrices underlying the resulting parallel matrices. 3178 Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or 3179 contain duplicates. 3180 3181 There are as many diag matrices as there are original index sets. There are only as many parallel 3182 and off-diag matrices, as there are parallel (comm size > 1) index sets. 3183 3184 ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq(): 3185 - If the array of MPI matrices already exists and is being reused, we need to allocate the array 3186 and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq 3187 will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them 3188 with A[i] and B[ii] extracted from the corresponding MPI submat. 3189 - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii] 3190 will have a different order from what getsubmats_seq expects. To handle this case -- indicated 3191 by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii] 3192 (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its 3193 values into A[i] and B[ii] sitting inside the corresponding submat. 3194 - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding 3195 A[i], B[ii], AA[i] or BB[ii] matrices. 3196 */ 3197 /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */ 3198 if (scall == MAT_INITIAL_MATRIX) { 3199 ierr = PetscMalloc1(ismax,submat);CHKERRQ(ierr); 3200 } 3201 3202 /* Now obtain the sequential A and B submatrices separately. */ 3203 /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */ 3204 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr); 3205 ierr = (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 3206 3207 /* 3208 If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential 3209 matrices A & B have been extracted directly into the parallel matrices containing them, or 3210 simply into the sequential matrix identical with the corresponding A (if isize == 1). 3211 Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected 3212 to have the same sparsity pattern. 3213 Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap 3214 must be constructed for C. This is done by setseqmat(s). 3215 */ 3216 for (i = 0, ii = 0; i < ismax; ++i) { 3217 /* 3218 TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol? 3219 That way we can avoid sorting and computing permutations when reusing. 3220 To this end: 3221 - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX 3222 - if caching arrays to hold the ISs, make and compose a container for them so that it can 3223 be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents). 3224 */ 3225 MatStructure pattern; 3226 pattern = DIFFERENT_NONZERO_PATTERN; 3227 3228 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3229 /* Construct submat[i] from the Seq pieces A (and B, if necessary). */ 3230 if (isize > 1) { 3231 if (scall == MAT_INITIAL_MATRIX) { 3232 ierr = MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);CHKERRQ(ierr); 3233 ierr = MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3234 ierr = MatSetType((*submat)[i],MATMPIAIJ);CHKERRQ(ierr); 3235 ierr = PetscLayoutSetUp((*submat)[i]->rmap);CHKERRQ(ierr); 3236 ierr = PetscLayoutSetUp((*submat)[i]->cmap);CHKERRQ(ierr); 3237 } 3238 /* 3239 For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix. 3240 */ 3241 { 3242 Mat AA,BB; 3243 AA = A[i]; 3244 BB = B[ii]; 3245 if (AA || BB) { 3246 ierr = setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);CHKERRQ(ierr); 3247 ierr = MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3248 ierr = MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3249 } 3250 3251 ierr = MatDestroy(&AA);CHKERRQ(ierr); 3252 ierr = MatDestroy(&BB);CHKERRQ(ierr); 3253 } 3254 ierr = ISDestroy(ciscol+ii);CHKERRQ(ierr); 3255 ierr = ISDestroy(ciscol_p+ii);CHKERRQ(ierr); 3256 ++ii; 3257 } else { /* if (isize == 1) */ 3258 if (scall == MAT_REUSE_MATRIX) { 3259 ierr = MatDestroy(&(*submat)[i]);CHKERRQ(ierr); 3260 } 3261 if (isrow_p[i] || iscol_p[i]) { 3262 ierr = MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);CHKERRQ(ierr); 3263 ierr = setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);CHKERRQ(ierr); 3264 /* Otherwise A is extracted straight into (*submats)[i]. */ 3265 /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */ 3266 ierr = MatDestroy(A+i);CHKERRQ(ierr); 3267 } else (*submat)[i] = A[i]; 3268 } 3269 ierr = ISDestroy(&isrow_p[i]);CHKERRQ(ierr); 3270 ierr = ISDestroy(&iscol_p[i]);CHKERRQ(ierr); 3271 } 3272 ierr = PetscFree2(cisrow,ciscol);CHKERRQ(ierr); 3273 ierr = PetscFree2(isrow_p,iscol_p);CHKERRQ(ierr); 3274 ierr = PetscFree(ciscol_p);CHKERRQ(ierr); 3275 ierr = PetscFree(A);CHKERRQ(ierr); 3276 ierr = PetscFree(B);CHKERRQ(ierr); 3277 PetscFunctionReturn(0); 3278 } 3279 3280 PetscErrorCode MatGetSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 3281 { 3282 PetscErrorCode ierr; 3283 3284 PetscFunctionBegin; 3285 ierr = MatGetSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatGetSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);CHKERRQ(ierr); 3286 PetscFunctionReturn(0); 3287 } 3288