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 PetscMPIInt rank; 2084 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)C),&rank);CHKERRQ(ierr); 2085 printf("[%d] reuse %d, ismax %d, CN %d, nstages %d, nmax %d\n",rank,scall,ismax,C->cmap->N,nstages,nmax); 2086 for (i=0,pos=0; i<nstages; i++) { 2087 if (pos+nmax <= ismax) max_no = nmax; 2088 else if (pos == ismax) max_no = 0; 2089 else max_no = ismax-pos; 2090 if (!max_no) printf("[%d] max_no=0, %d-stage\n",rank,i); 2091 ierr = MatGetSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);CHKERRQ(ierr); 2092 pos += max_no; 2093 } 2094 2095 if (scall == MAT_INITIAL_MATRIX) { 2096 /* save nstages for reuse */ 2097 subc = (Mat_SeqAIJ*)((*submat)[0]->data); 2098 smat = subc->submatis1; 2099 if (!smat) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"smat does not exit"); 2100 smat->nstages = nstages; 2101 } 2102 PetscFunctionReturn(0); 2103 } 2104 2105 /* -------------------------------------------------------------------------*/ 2106 PetscErrorCode MatGetSubMatrices_MPIAIJ_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats) 2107 { 2108 Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data; 2109 Mat A = c->A; 2110 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*subc; 2111 const PetscInt **icol,**irow; 2112 PetscInt *nrow,*ncol,start; 2113 PetscErrorCode ierr; 2114 PetscMPIInt rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr; 2115 PetscInt **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1; 2116 PetscInt nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol; 2117 PetscInt **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2; 2118 PetscInt **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax; 2119 #if defined(PETSC_USE_CTABLE) 2120 PetscTable *cmap,cmap_i=NULL,*rmap,rmap_i; 2121 #else 2122 PetscInt **cmap,*cmap_i=NULL,**rmap,*rmap_i; 2123 #endif 2124 const PetscInt *irow_i; 2125 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i; 2126 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 2127 MPI_Request *r_waits4,*s_waits3,*s_waits4; 2128 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 2129 MPI_Status *r_status3,*r_status4,*s_status4; 2130 MPI_Comm comm; 2131 PetscScalar **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i; 2132 PetscMPIInt *onodes1,*olengths1,end; 2133 PetscInt **row2proc,*row2proc_i,ilen_row,*imat_ilen,*imat_j,*imat_i,old_row; 2134 Mat_SubMat **smats,*smat_i; 2135 PetscBool *issorted,*allcolumns,colflag,iscsorted=PETSC_TRUE; 2136 PetscInt *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen; 2137 2138 PetscFunctionBegin; 2139 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2140 size = c->size; 2141 rank = c->rank; 2142 2143 ierr = PetscMalloc5(ismax,&smats,ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns);CHKERRQ(ierr); 2144 ierr = PetscMalloc5(ismax,&irow,ismax,&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);CHKERRQ(ierr); 2145 2146 for (i=0; i<ismax; i++) { 2147 ierr = ISSorted(iscol[i],&issorted[i]);CHKERRQ(ierr); 2148 if (!issorted[i]) iscsorted = issorted[i]; 2149 2150 ierr = ISSorted(isrow[i],&issorted[i]);CHKERRQ(ierr); 2151 2152 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 2153 ierr = ISGetLocalSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 2154 2155 /* Check for special case: allcolumn */ 2156 ierr = ISIdentity(iscol[i],&colflag);CHKERRQ(ierr); 2157 ierr = ISGetLocalSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 2158 if (colflag && ncol[i] == C->cmap->N) { 2159 allcolumns[i] = PETSC_TRUE; 2160 icol[i] = NULL; 2161 } else { 2162 allcolumns[i] = PETSC_FALSE; 2163 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 2164 } 2165 } 2166 2167 if (scall == MAT_REUSE_MATRIX) { 2168 /* Assumes new rows are same length as the old rows */ 2169 for (i=0; i<ismax; i++) { 2170 if (!submats[i]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats[%D] is null, cannot reuse",i); 2171 subc = (Mat_SeqAIJ*)(submats[i]->data); 2172 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"); 2173 2174 /* Initial matrix as if empty */ 2175 ierr = PetscMemzero(subc->ilen,submats[i]->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2176 2177 /* Initial matrix as if empty */ 2178 submats[i]->factortype = C->factortype; 2179 2180 smat_i = subc->submatis1; 2181 smats[i] = smat_i; 2182 2183 nrqs = smat_i->nrqs; 2184 nrqr = smat_i->nrqr; 2185 rbuf1 = smat_i->rbuf1; 2186 rbuf2 = smat_i->rbuf2; 2187 rbuf3 = smat_i->rbuf3; 2188 req_source2 = smat_i->req_source2; 2189 2190 sbuf1 = smat_i->sbuf1; 2191 sbuf2 = smat_i->sbuf2; 2192 ptr = smat_i->ptr; 2193 tmp = smat_i->tmp; 2194 ctr = smat_i->ctr; 2195 2196 pa = smat_i->pa; 2197 req_size = smat_i->req_size; 2198 req_source1 = smat_i->req_source1; 2199 2200 allcolumns[i] = smat_i->allcolumns; 2201 row2proc[i] = smat_i->row2proc; 2202 rmap[i] = smat_i->rmap; 2203 cmap[i] = smat_i->cmap; 2204 } 2205 2206 if (!ismax){ 2207 i = 0; 2208 if (!submats[i]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats[%D] is null, cannot reuse",i); 2209 subc = (Mat_SeqAIJ*)(submats[i]->data); 2210 2211 /* Initial matrix as if empty */ 2212 ierr = PetscMemzero(subc->ilen,submats[i]->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 2213 2214 /* Initial matrix as if empty */ 2215 submats[i]->factortype = C->factortype; 2216 smat_i = subc->submatis1; 2217 2218 nrqs = smat_i->nrqs; 2219 nrqr = smat_i->nrqr; 2220 rbuf1 = smat_i->rbuf1; 2221 rbuf2 = smat_i->rbuf2; 2222 rbuf3 = smat_i->rbuf3; 2223 req_source2 = smat_i->req_source2; 2224 2225 sbuf1 = smat_i->sbuf1; 2226 sbuf2 = smat_i->sbuf2; 2227 ptr = smat_i->ptr; 2228 tmp = smat_i->tmp; 2229 ctr = smat_i->ctr; 2230 2231 pa = smat_i->pa; 2232 req_size = smat_i->req_size; 2233 req_source1 = smat_i->req_source1; 2234 2235 allcolumns[i] = PETSC_TRUE; 2236 } 2237 } else { /* scall == MAT_INITIAL_MATRIX */ 2238 /* Get some new tags to keep the communication clean */ 2239 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 2240 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 2241 2242 /* evaluate communication - mesg to who, length of mesg, and buffer space 2243 required. Based on this, buffers are allocated, and data copied into them*/ 2244 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); /* mesg size, initialize work vectors */ 2245 2246 for (i=0; i<ismax; i++) { 2247 jmax = nrow[i]; 2248 irow_i = irow[i]; 2249 2250 ierr = PetscMalloc1(jmax,&row2proc_i);CHKERRQ(ierr); 2251 row2proc[i] = row2proc_i; 2252 2253 if (issorted[i]) proc = 0; 2254 for (j=0; j<jmax; j++) { 2255 if (!issorted[i]) proc = 0; 2256 row = irow_i[j]; 2257 while (row >= C->rmap->range[proc+1]) proc++; 2258 w4[proc]++; 2259 row2proc_i[j] = proc; /* map row index to proc */ 2260 } 2261 for (j=0; j<size; j++) { 2262 if (w4[j]) { w1[j] += w4[j]; w3[j]++; w4[j] = 0;} 2263 } 2264 } 2265 2266 nrqs = 0; /* no of outgoing messages */ 2267 msz = 0; /* total mesg length (for all procs) */ 2268 w1[rank] = 0; /* no mesg sent to self */ 2269 w3[rank] = 0; 2270 for (i=0; i<size; i++) { 2271 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 2272 } 2273 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 2274 for (i=0,j=0; i<size; i++) { 2275 if (w1[i]) { pa[j] = i; j++; } 2276 } 2277 2278 /* Each message would have a header = 1 + 2*(no of IS) + data */ 2279 for (i=0; i<nrqs; i++) { 2280 j = pa[i]; 2281 w1[j] += w2[j] + 2* w3[j]; 2282 msz += w1[j]; 2283 } 2284 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 2285 2286 /* Determine the number of messages to expect, their lengths, from from-ids */ 2287 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 2288 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 2289 2290 /* Now post the Irecvs corresponding to these messages */ 2291 tag0 = ((PetscObject)C)->tag; 2292 ierr = PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 2293 2294 ierr = PetscFree(onodes1);CHKERRQ(ierr); 2295 ierr = PetscFree(olengths1);CHKERRQ(ierr); 2296 2297 /* Allocate Memory for outgoing messages */ 2298 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 2299 ierr = PetscMemzero(sbuf1,size*sizeof(PetscInt*));CHKERRQ(ierr); 2300 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 2301 2302 { 2303 PetscInt *iptr = tmp; 2304 k = 0; 2305 for (i=0; i<nrqs; i++) { 2306 j = pa[i]; 2307 iptr += k; 2308 sbuf1[j] = iptr; 2309 k = w1[j]; 2310 } 2311 } 2312 2313 /* Form the outgoing messages. Initialize the header space */ 2314 for (i=0; i<nrqs; i++) { 2315 j = pa[i]; 2316 sbuf1[j][0] = 0; 2317 ierr = PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 2318 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 2319 } 2320 2321 /* Parse the isrow and copy data into outbuf */ 2322 for (i=0; i<ismax; i++) { 2323 row2proc_i = row2proc[i]; 2324 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 2325 irow_i = irow[i]; 2326 jmax = nrow[i]; 2327 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 2328 proc = row2proc_i[j]; 2329 if (proc != rank) { /* copy to the outgoing buf*/ 2330 ctr[proc]++; 2331 *ptr[proc] = irow_i[j]; 2332 ptr[proc]++; 2333 } 2334 } 2335 /* Update the headers for the current IS */ 2336 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 2337 if ((ctr_j = ctr[j])) { 2338 sbuf1_j = sbuf1[j]; 2339 k = ++sbuf1_j[0]; 2340 sbuf1_j[2*k] = ctr_j; 2341 sbuf1_j[2*k-1] = i; 2342 } 2343 } 2344 } 2345 2346 /* Now post the sends */ 2347 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 2348 for (i=0; i<nrqs; ++i) { 2349 j = pa[i]; 2350 ierr = MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);CHKERRQ(ierr); 2351 } 2352 2353 /* Post Receives to capture the buffer size */ 2354 ierr = PetscMalloc1(nrqs+1,&r_waits2);CHKERRQ(ierr); 2355 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 2356 rbuf2[0] = tmp + msz; 2357 for (i=1; i<nrqs; ++i) { 2358 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 2359 } 2360 for (i=0; i<nrqs; ++i) { 2361 j = pa[i]; 2362 ierr = MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);CHKERRQ(ierr); 2363 } 2364 2365 /* Send to other procs the buf size they should allocate */ 2366 /* Receive messages*/ 2367 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 2368 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 2369 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 2370 { 2371 PetscInt *sAi = a->i,*sBi = b->i,id,rstart = C->rmap->rstart; 2372 PetscInt *sbuf2_i; 2373 2374 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRQ(ierr); 2375 for (i=0; i<nrqr; ++i) { 2376 req_size[i] = 0; 2377 rbuf1_i = rbuf1[i]; 2378 start = 2*rbuf1_i[0] + 1; 2379 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRQ(ierr); 2380 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 2381 sbuf2_i = sbuf2[i]; 2382 for (j=start; j<end; j++) { 2383 id = rbuf1_i[j] - rstart; 2384 ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id]; 2385 sbuf2_i[j] = ncols; 2386 req_size[i] += ncols; 2387 } 2388 req_source1[i] = r_status1[i].MPI_SOURCE; 2389 /* form the header */ 2390 sbuf2_i[0] = req_size[i]; 2391 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 2392 2393 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 2394 } 2395 } 2396 ierr = PetscFree(r_status1);CHKERRQ(ierr); 2397 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 2398 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 2399 2400 /* Receive messages*/ 2401 ierr = PetscMalloc1(nrqs+1,&r_waits3);CHKERRQ(ierr); 2402 ierr = PetscMalloc1(nrqs+1,&r_status2);CHKERRQ(ierr); 2403 2404 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRQ(ierr); 2405 for (i=0; i<nrqs; ++i) { 2406 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 2407 req_source2[i] = r_status2[i].MPI_SOURCE; 2408 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRQ(ierr); 2409 } 2410 ierr = PetscFree(r_status2);CHKERRQ(ierr); 2411 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 2412 2413 /* Wait on sends1 and sends2 */ 2414 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 2415 ierr = PetscMalloc1(nrqr+1,&s_status2);CHKERRQ(ierr); 2416 2417 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr);} 2418 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr);} 2419 ierr = PetscFree(s_status1);CHKERRQ(ierr); 2420 ierr = PetscFree(s_status2);CHKERRQ(ierr); 2421 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 2422 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 2423 2424 /* Now allocate sending buffers for a->j, and send them off */ 2425 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 2426 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2427 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 2428 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 2429 2430 ierr = PetscMalloc1(nrqr+1,&s_waits3);CHKERRQ(ierr); 2431 { 2432 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i,lwrite; 2433 PetscInt *cworkA,*cworkB,cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2434 PetscInt cend = C->cmap->rend; 2435 PetscInt *a_j = a->j,*b_j = b->j,ctmp; 2436 2437 for (i=0; i<nrqr; i++) { 2438 rbuf1_i = rbuf1[i]; 2439 sbuf_aj_i = sbuf_aj[i]; 2440 ct1 = 2*rbuf1_i[0] + 1; 2441 ct2 = 0; 2442 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2443 kmax = rbuf1[i][2*j]; 2444 for (k=0; k<kmax; k++,ct1++) { 2445 row = rbuf1_i[ct1] - rstart; 2446 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2447 ncols = nzA + nzB; 2448 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 2449 2450 /* load the column indices for this row into cols */ 2451 cols = sbuf_aj_i + ct2; 2452 2453 lwrite = 0; 2454 for (l=0; l<nzB; l++) { 2455 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[lwrite++] = ctmp; 2456 } 2457 for (l=0; l<nzA; l++) cols[lwrite++] = cstart + cworkA[l]; 2458 for (l=0; l<nzB; l++) { 2459 if ((ctmp = bmap[cworkB[l]]) >= cend) cols[lwrite++] = ctmp; 2460 } 2461 2462 ct2 += ncols; 2463 } 2464 } 2465 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 2466 } 2467 } 2468 ierr = PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 2469 2470 /* create col map: global col of C -> local col of submatrices */ 2471 { 2472 const PetscInt *icol_i; 2473 #if defined(PETSC_USE_CTABLE) 2474 for (i=0; i<ismax; i++) { 2475 if (!allcolumns[i]) { 2476 ierr = PetscTableCreate(ncol[i]+1,C->cmap->N+1,&cmap[i]);CHKERRQ(ierr); 2477 2478 jmax = ncol[i]; 2479 icol_i = icol[i]; 2480 cmap_i = cmap[i]; 2481 for (j=0; j<jmax; j++) { 2482 ierr = PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2483 } 2484 } else cmap[i] = NULL; 2485 } 2486 #else 2487 for (i=0; i<ismax; i++) { 2488 if (!allcolumns[i]) { 2489 ierr = PetscCalloc1(C->cmap->N,&cmap[i]);CHKERRQ(ierr); 2490 jmax = ncol[i]; 2491 icol_i = icol[i]; 2492 cmap_i = cmap[i]; 2493 for (j=0; j<jmax; j++) { 2494 cmap_i[icol_i[j]] = j+1; 2495 } 2496 } else cmap[i] = NULL; 2497 } 2498 #endif 2499 } 2500 2501 /* Create lens which is required for MatCreate... */ 2502 for (i=0,j=0; i<ismax; i++) j += nrow[i]; 2503 ierr = PetscMalloc1(ismax,&lens);CHKERRQ(ierr); 2504 2505 if (ismax) { 2506 ierr = PetscCalloc1(j,&lens[0]);CHKERRQ(ierr); 2507 } 2508 for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1]; 2509 2510 /* Update lens from local data */ 2511 for (i=0; i<ismax; i++) { 2512 row2proc_i = row2proc[i]; 2513 jmax = nrow[i]; 2514 if (!allcolumns[i]) cmap_i = cmap[i]; 2515 irow_i = irow[i]; 2516 lens_i = lens[i]; 2517 for (j=0; j<jmax; j++) { 2518 row = irow_i[j]; 2519 proc = row2proc_i[j]; 2520 if (proc == rank) { 2521 ierr = MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2522 if (!allcolumns[i]) { 2523 for (k=0; k<ncols; k++) { 2524 #if defined(PETSC_USE_CTABLE) 2525 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2526 #else 2527 tcol = cmap_i[cols[k]]; 2528 #endif 2529 if (tcol) lens_i[j]++; 2530 } 2531 } else { /* allcolumns */ 2532 lens_i[j] = ncols; 2533 } 2534 ierr = MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);CHKERRQ(ierr); 2535 } 2536 } 2537 } 2538 2539 /* Create row map: global row of C -> local row of submatrices */ 2540 #if defined(PETSC_USE_CTABLE) 2541 for (i=0; i<ismax; i++) { 2542 ierr = PetscTableCreate(nrow[i]+1,C->rmap->N+1,&rmap[i]);CHKERRQ(ierr); 2543 irow_i = irow[i]; 2544 jmax = nrow[i]; 2545 for (j=0; j<jmax; j++) { 2546 ierr = PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 2547 } 2548 } 2549 #else 2550 for (i=0; i<ismax; i++) { 2551 ierr = PetscCalloc1(C->rmap->N,&rmap[i]);CHKERRQ(ierr); 2552 rmap_i = rmap[i]; 2553 irow_i = irow[i]; 2554 jmax = nrow[i]; 2555 for (j=0; j<jmax; j++) { 2556 rmap_i[irow_i[j]] = j; 2557 } 2558 } 2559 #endif 2560 2561 /* Update lens from offproc data */ 2562 { 2563 PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i; 2564 2565 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRQ(ierr); 2566 for (tmp2=0; tmp2<nrqs; tmp2++) { 2567 sbuf1_i = sbuf1[pa[tmp2]]; 2568 jmax = sbuf1_i[0]; 2569 ct1 = 2*jmax+1; 2570 ct2 = 0; 2571 rbuf2_i = rbuf2[tmp2]; 2572 rbuf3_i = rbuf3[tmp2]; 2573 for (j=1; j<=jmax; j++) { 2574 is_no = sbuf1_i[2*j-1]; 2575 max1 = sbuf1_i[2*j]; 2576 lens_i = lens[is_no]; 2577 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2578 rmap_i = rmap[is_no]; 2579 for (k=0; k<max1; k++,ct1++) { 2580 #if defined(PETSC_USE_CTABLE) 2581 ierr = PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 2582 row--; 2583 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 2584 #else 2585 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 2586 #endif 2587 max2 = rbuf2_i[ct1]; 2588 for (l=0; l<max2; l++,ct2++) { 2589 if (!allcolumns[is_no]) { 2590 #if defined(PETSC_USE_CTABLE) 2591 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2592 #else 2593 tcol = cmap_i[rbuf3_i[ct2]]; 2594 #endif 2595 if (tcol) lens_i[row]++; 2596 } else { /* allcolumns */ 2597 lens_i[row]++; /* lens_i[row] += max2 ? */ 2598 } 2599 } 2600 } 2601 } 2602 } 2603 } 2604 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 2605 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr);} 2606 ierr = PetscFree2(r_status3,s_status3);CHKERRQ(ierr); 2607 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 2608 2609 /* Create the submatrices */ 2610 for (i=0; i<ismax; i++) { 2611 PetscInt rbs,cbs; 2612 2613 ierr = ISGetBlockSize(isrow[i],&rbs);CHKERRQ(ierr); 2614 ierr = ISGetBlockSize(iscol[i],&cbs);CHKERRQ(ierr); 2615 2616 ierr = MatCreate(PETSC_COMM_SELF,submats+i);CHKERRQ(ierr); 2617 ierr = MatSetSizes(submats[i],nrow[i],ncol[i],PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2618 2619 ierr = MatSetBlockSizes(submats[i],rbs,cbs);CHKERRQ(ierr); 2620 ierr = MatSetType(submats[i],((PetscObject)A)->type_name);CHKERRQ(ierr); 2621 ierr = MatSeqAIJSetPreallocation(submats[i],0,lens[i]);CHKERRQ(ierr); 2622 2623 /* create struct Mat_SubMat and attached it to submat */ 2624 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 2625 subc = (Mat_SeqAIJ*)submats[i]->data; 2626 subc->submatis1 = smat_i; 2627 smats[i] = smat_i; 2628 2629 smat_i->destroy = submats[i]->ops->destroy; 2630 submats[i]->ops->destroy = MatDestroy_MPIAIJ_MatGetSubmatrices; 2631 submats[i]->factortype = C->factortype; 2632 2633 smat_i->id = i; 2634 smat_i->nrqs = nrqs; 2635 smat_i->nrqr = nrqr; 2636 smat_i->rbuf1 = rbuf1; 2637 smat_i->rbuf2 = rbuf2; 2638 smat_i->rbuf3 = rbuf3; 2639 smat_i->sbuf2 = sbuf2; 2640 smat_i->req_source2 = req_source2; 2641 2642 smat_i->sbuf1 = sbuf1; 2643 smat_i->ptr = ptr; 2644 smat_i->tmp = tmp; 2645 smat_i->ctr = ctr; 2646 2647 smat_i->pa = pa; 2648 smat_i->req_size = req_size; 2649 smat_i->req_source1 = req_source1; 2650 2651 smat_i->allcolumns = allcolumns[i]; 2652 smat_i->singleis = PETSC_FALSE; 2653 smat_i->row2proc = row2proc[i]; 2654 smat_i->rmap = rmap[i]; 2655 smat_i->cmap = cmap[i]; 2656 } 2657 2658 if (!ismax) { /* Create an empty submats[0] for reuse struct subc */ 2659 ierr = MatCreate(PETSC_COMM_SELF,&submats[0]);CHKERRQ(ierr); 2660 ierr = MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2661 ierr = MatSetType(submats[0],((PetscObject)A)->type_name);CHKERRQ(ierr); 2662 ierr = MatSeqAIJSetPreallocation(submats[0],0,NULL);CHKERRQ(ierr); 2663 2664 i = 0; 2665 /* create struct Mat_SubMat and attached it to submat */ 2666 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 2667 subc = (Mat_SeqAIJ*)submats[i]->data; 2668 subc->submatis1 = smat_i; 2669 2670 smat_i->destroy = submats[i]->ops->destroy; 2671 submats[i]->ops->destroy = MatDestroy_MPIAIJ_MatGetSubmatrices; 2672 submats[i]->factortype = C->factortype; 2673 2674 smat_i->id = i; 2675 smat_i->nrqs = nrqs; 2676 smat_i->nrqr = nrqr; 2677 smat_i->rbuf1 = rbuf1; 2678 smat_i->rbuf2 = rbuf2; 2679 smat_i->rbuf3 = rbuf3; 2680 smat_i->sbuf2 = sbuf2; 2681 smat_i->req_source2 = req_source2; 2682 2683 smat_i->sbuf1 = sbuf1; 2684 smat_i->ptr = ptr; 2685 smat_i->tmp = tmp; 2686 smat_i->ctr = ctr; 2687 2688 smat_i->pa = pa; 2689 smat_i->req_size = req_size; 2690 smat_i->req_source1 = req_source1; 2691 2692 smat_i->allcolumns = PETSC_TRUE; 2693 smat_i->singleis = PETSC_FALSE; 2694 smat_i->row2proc = NULL; 2695 smat_i->rmap = NULL; 2696 smat_i->cmap = NULL; 2697 } 2698 2699 if (ismax) {ierr = PetscFree(lens[0]);CHKERRQ(ierr);} 2700 ierr = PetscFree(lens);CHKERRQ(ierr); 2701 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 2702 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 2703 2704 } /* endof scall == MAT_INITIAL_MATRIX */ 2705 2706 /* Post recv matrix values */ 2707 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 2708 ierr = PetscMalloc1(nrqs+1,&rbuf4);CHKERRQ(ierr); 2709 ierr = PetscMalloc1(nrqs+1,&r_waits4);CHKERRQ(ierr); 2710 ierr = PetscMalloc1(nrqs+1,&r_status4);CHKERRQ(ierr); 2711 ierr = PetscMalloc1(nrqr+1,&s_status4);CHKERRQ(ierr); 2712 for (i=0; i<nrqs; ++i) { 2713 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf4[i]);CHKERRQ(ierr); 2714 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0],MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRQ(ierr); 2715 } 2716 2717 /* Allocate sending buffers for a->a, and send them off */ 2718 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 2719 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 2720 ierr = PetscMalloc1(j+1,&sbuf_aa[0]);CHKERRQ(ierr); 2721 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]; 2722 2723 ierr = PetscMalloc1(nrqr+1,&s_waits4);CHKERRQ(ierr); 2724 { 2725 PetscInt nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,lwrite; 2726 PetscInt cstart = C->cmap->rstart,rstart = C->rmap->rstart,*bmap = c->garray; 2727 PetscInt cend = C->cmap->rend; 2728 PetscInt *b_j = b->j; 2729 PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a; 2730 2731 for (i=0; i<nrqr; i++) { 2732 rbuf1_i = rbuf1[i]; 2733 sbuf_aa_i = sbuf_aa[i]; 2734 ct1 = 2*rbuf1_i[0]+1; 2735 ct2 = 0; 2736 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 2737 kmax = rbuf1_i[2*j]; 2738 for (k=0; k<kmax; k++,ct1++) { 2739 row = rbuf1_i[ct1] - rstart; 2740 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 2741 ncols = nzA + nzB; 2742 cworkB = b_j + b_i[row]; 2743 vworkA = a_a + a_i[row]; 2744 vworkB = b_a + b_i[row]; 2745 2746 /* load the column values for this row into vals*/ 2747 vals = sbuf_aa_i+ct2; 2748 2749 lwrite = 0; 2750 for (l=0; l<nzB; l++) { 2751 if ((bmap[cworkB[l]]) < cstart) vals[lwrite++] = vworkB[l]; 2752 } 2753 for (l=0; l<nzA; l++) vals[lwrite++] = vworkA[l]; 2754 for (l=0; l<nzB; l++) { 2755 if ((bmap[cworkB[l]]) >= cend) vals[lwrite++] = vworkB[l]; 2756 } 2757 2758 ct2 += ncols; 2759 } 2760 } 2761 ierr = MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRQ(ierr); 2762 } 2763 } 2764 2765 /* Assemble the matrices */ 2766 /* First assemble the local rows */ 2767 for (i=0; i<ismax; i++) { 2768 row2proc_i = row2proc[i]; 2769 subc = (Mat_SeqAIJ*)submats[i]->data; 2770 imat_ilen = subc->ilen; 2771 imat_j = subc->j; 2772 imat_i = subc->i; 2773 imat_a = subc->a; 2774 2775 if (!allcolumns[i]) cmap_i = cmap[i]; 2776 rmap_i = rmap[i]; 2777 irow_i = irow[i]; 2778 jmax = nrow[i]; 2779 for (j=0; j<jmax; j++) { 2780 row = irow_i[j]; 2781 proc = row2proc_i[j]; 2782 if (proc == rank) { 2783 old_row = row; 2784 #if defined(PETSC_USE_CTABLE) 2785 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2786 row--; 2787 #else 2788 row = rmap_i[row]; 2789 #endif 2790 ilen_row = imat_ilen[row]; 2791 ierr = MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2792 mat_i = imat_i[row]; 2793 mat_a = imat_a + mat_i; 2794 mat_j = imat_j + mat_i; 2795 if (!allcolumns[i]) { 2796 for (k=0; k<ncols; k++) { 2797 #if defined(PETSC_USE_CTABLE) 2798 ierr = PetscTableFind(cmap_i,cols[k]+1,&tcol);CHKERRQ(ierr); 2799 #else 2800 tcol = cmap_i[cols[k]]; 2801 #endif 2802 if (tcol) { 2803 *mat_j++ = tcol - 1; 2804 *mat_a++ = vals[k]; 2805 ilen_row++; 2806 } 2807 } 2808 } else { /* allcolumns */ 2809 for (k=0; k<ncols; k++) { 2810 *mat_j++ = cols[k]; /* global col index! */ 2811 *mat_a++ = vals[k]; 2812 ilen_row++; 2813 } 2814 } 2815 ierr = MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);CHKERRQ(ierr); 2816 2817 imat_ilen[row] = ilen_row; 2818 } 2819 } 2820 } 2821 2822 /* Now assemble the off proc rows */ 2823 ierr = MPI_Waitall(nrqs,r_waits4,r_status4);CHKERRQ(ierr); 2824 for (tmp2=0; tmp2<nrqs; tmp2++) { 2825 sbuf1_i = sbuf1[pa[tmp2]]; 2826 jmax = sbuf1_i[0]; 2827 ct1 = 2*jmax + 1; 2828 ct2 = 0; 2829 rbuf2_i = rbuf2[tmp2]; 2830 rbuf3_i = rbuf3[tmp2]; 2831 rbuf4_i = rbuf4[tmp2]; 2832 for (j=1; j<=jmax; j++) { 2833 is_no = sbuf1_i[2*j-1]; 2834 rmap_i = rmap[is_no]; 2835 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 2836 subc = (Mat_SeqAIJ*)submats[is_no]->data; 2837 imat_ilen = subc->ilen; 2838 imat_j = subc->j; 2839 imat_i = subc->i; 2840 imat_a = subc->a; 2841 max1 = sbuf1_i[2*j]; 2842 for (k=0; k<max1; k++,ct1++) { 2843 row = sbuf1_i[ct1]; 2844 #if defined(PETSC_USE_CTABLE) 2845 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 2846 row--; 2847 #else 2848 row = rmap_i[row]; 2849 #endif 2850 ilen = imat_ilen[row]; 2851 mat_i = imat_i[row]; 2852 mat_a = imat_a + mat_i; 2853 mat_j = imat_j + mat_i; 2854 max2 = rbuf2_i[ct1]; 2855 if (!allcolumns[is_no]) { 2856 for (l=0; l<max2; l++,ct2++) { 2857 #if defined(PETSC_USE_CTABLE) 2858 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 2859 #else 2860 tcol = cmap_i[rbuf3_i[ct2]]; 2861 #endif 2862 if (tcol) { 2863 *mat_j++ = tcol - 1; 2864 *mat_a++ = rbuf4_i[ct2]; 2865 ilen++; 2866 } 2867 } 2868 } else { /* allcolumns */ 2869 for (l=0; l<max2; l++,ct2++) { 2870 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 2871 *mat_a++ = rbuf4_i[ct2]; 2872 ilen++; 2873 } 2874 } 2875 imat_ilen[row] = ilen; 2876 } 2877 } 2878 } 2879 2880 if (!iscsorted) { /* sort column indices of the rows */ 2881 for (i=0; i<ismax; i++) { 2882 subc = (Mat_SeqAIJ*)submats[i]->data; 2883 imat_j = subc->j; 2884 imat_i = subc->i; 2885 imat_a = subc->a; 2886 imat_ilen = subc->ilen; 2887 2888 if (allcolumns[i]) continue; 2889 jmax = nrow[i]; 2890 for (j=0; j<jmax; j++) { 2891 PetscInt ilen; 2892 2893 mat_i = imat_i[j]; 2894 mat_a = imat_a + mat_i; 2895 mat_j = imat_j + mat_i; 2896 ilen = imat_ilen[j]; 2897 ierr = PetscSortIntWithScalarArray(ilen,mat_j,mat_a);CHKERRQ(ierr); 2898 } 2899 } 2900 } 2901 2902 ierr = PetscFree(r_status4);CHKERRQ(ierr); 2903 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 2904 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr);} 2905 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 2906 ierr = PetscFree(s_status4);CHKERRQ(ierr); 2907 2908 /* Restore the indices */ 2909 for (i=0; i<ismax; i++) { 2910 ierr = ISRestoreIndices(isrow[i],irow+i);CHKERRQ(ierr); 2911 if (!allcolumns[i]) { 2912 ierr = ISRestoreIndices(iscol[i],icol+i);CHKERRQ(ierr); 2913 } 2914 } 2915 2916 for (i=0; i<ismax; i++) { 2917 ierr = MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2918 ierr = MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2919 } 2920 if (!ismax) { /* an empty matrix */ 2921 ierr = MatAssemblyBegin(submats[0],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2922 ierr = MatAssemblyEnd(submats[0],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2923 } 2924 2925 /* Destroy allocated memory */ 2926 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 2927 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 2928 ierr = PetscFree5(irow,icol,nrow,ncol,issorted);CHKERRQ(ierr); 2929 2930 for (i=0; i<nrqs; ++i) { 2931 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 2932 } 2933 ierr = PetscFree(rbuf4);CHKERRQ(ierr); 2934 2935 ierr = PetscFree5(smats,row2proc,cmap,rmap,allcolumns);CHKERRQ(ierr); 2936 PetscFunctionReturn(0); 2937 } 2938 2939 /* 2940 Permute A & B into C's *local* index space using rowemb,dcolemb for A and rowemb,ocolemb for B. 2941 Embeddings are supposed to be injections and the above implies that the range of rowemb is a subset 2942 of [0,m), dcolemb is in [0,n) and ocolemb is in [N-n). 2943 If pattern == DIFFERENT_NONZERO_PATTERN, C is preallocated according to A&B. 2944 After that B's columns are mapped into C's global column space, so that C is in the "disassembled" 2945 state, and needs to be "assembled" later by compressing B's column space. 2946 2947 This function may be called in lieu of preallocation, so C should not be expected to be preallocated. 2948 Following this call, C->A & C->B have been created, even if empty. 2949 */ 2950 PetscErrorCode MatSetSeqMats_MPIAIJ(Mat C,IS rowemb,IS dcolemb,IS ocolemb,MatStructure pattern,Mat A,Mat B) 2951 { 2952 /* If making this function public, change the error returned in this function away from _PLIB. */ 2953 PetscErrorCode ierr; 2954 Mat_MPIAIJ *aij; 2955 Mat_SeqAIJ *Baij; 2956 PetscBool seqaij,Bdisassembled; 2957 PetscInt m,n,*nz,i,j,ngcol,col,rstart,rend,shift,count; 2958 PetscScalar v; 2959 const PetscInt *rowindices,*colindices; 2960 2961 PetscFunctionBegin; 2962 /* Check to make sure the component matrices (and embeddings) are compatible with C. */ 2963 if (A) { 2964 ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2965 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diagonal matrix is of wrong type"); 2966 if (rowemb) { 2967 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2968 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); 2969 } else { 2970 if (C->rmap->n != A->rmap->n) { 2971 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2972 } 2973 } 2974 if (dcolemb) { 2975 ierr = ISGetLocalSize(dcolemb,&n);CHKERRQ(ierr); 2976 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); 2977 } else { 2978 if (C->cmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Diag seq matrix is col-incompatible with the MPIAIJ matrix"); 2979 } 2980 } 2981 if (B) { 2982 ierr = PetscObjectTypeCompare((PetscObject)B,MATSEQAIJ,&seqaij);CHKERRQ(ierr); 2983 if (!seqaij) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diagonal matrix is of wrong type"); 2984 if (rowemb) { 2985 ierr = ISGetLocalSize(rowemb,&m);CHKERRQ(ierr); 2986 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); 2987 } else { 2988 if (C->rmap->n != B->rmap->n) { 2989 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Off-diag seq matrix is row-incompatible with the MPIAIJ matrix"); 2990 } 2991 } 2992 if (ocolemb) { 2993 ierr = ISGetLocalSize(ocolemb,&n);CHKERRQ(ierr); 2994 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); 2995 } else { 2996 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"); 2997 } 2998 } 2999 3000 aij = (Mat_MPIAIJ*)(C->data); 3001 if (!aij->A) { 3002 /* Mimic parts of MatMPIAIJSetPreallocation() */ 3003 ierr = MatCreate(PETSC_COMM_SELF,&aij->A);CHKERRQ(ierr); 3004 ierr = MatSetSizes(aij->A,C->rmap->n,C->cmap->n,C->rmap->n,C->cmap->n);CHKERRQ(ierr); 3005 ierr = MatSetBlockSizesFromMats(aij->A,C,C);CHKERRQ(ierr); 3006 ierr = MatSetType(aij->A,MATSEQAIJ);CHKERRQ(ierr); 3007 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->A);CHKERRQ(ierr); 3008 } 3009 if (A) { 3010 ierr = MatSetSeqMat_SeqAIJ(aij->A,rowemb,dcolemb,pattern,A);CHKERRQ(ierr); 3011 } else { 3012 ierr = MatSetUp(aij->A);CHKERRQ(ierr); 3013 } 3014 if (B) { /* Destroy the old matrix or the column map, depending on the sparsity pattern. */ 3015 /* 3016 If pattern == DIFFERENT_NONZERO_PATTERN, we reallocate B and 3017 need to "disassemble" B -- convert it to using C's global indices. 3018 To insert the values we take the safer, albeit more expensive, route of MatSetValues(). 3019 3020 If pattern == SUBSET_NONZERO_PATTERN, we do not "disassemble" B and do not reallocate; 3021 we MatZeroValues(B) first, so there may be a bunch of zeros that, perhaps, could be compacted out. 3022 3023 TODO: Put B's values into aij->B's aij structure in place using the embedding ISs? 3024 At least avoid calling MatSetValues() and the implied searches? 3025 */ 3026 3027 if (B && pattern == DIFFERENT_NONZERO_PATTERN) { 3028 #if defined(PETSC_USE_CTABLE) 3029 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 3030 #else 3031 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 3032 /* A bit of a HACK: ideally we should deal with case aij->B all in one code block below. */ 3033 if (aij->B) { 3034 ierr = PetscLogObjectMemory((PetscObject)C,-aij->B->cmap->n*sizeof(PetscInt));CHKERRQ(ierr); 3035 } 3036 #endif 3037 ngcol = 0; 3038 if (aij->lvec) { 3039 ierr = VecGetSize(aij->lvec,&ngcol);CHKERRQ(ierr); 3040 } 3041 if (aij->garray) { 3042 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 3043 ierr = PetscLogObjectMemory((PetscObject)C,-ngcol*sizeof(PetscInt));CHKERRQ(ierr); 3044 } 3045 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 3046 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 3047 } 3048 if (aij->B && B && pattern == DIFFERENT_NONZERO_PATTERN) { 3049 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 3050 } 3051 if (aij->B && B && pattern == SUBSET_NONZERO_PATTERN) { 3052 ierr = MatZeroEntries(aij->B);CHKERRQ(ierr); 3053 } 3054 } 3055 Bdisassembled = PETSC_FALSE; 3056 if (!aij->B) { 3057 ierr = MatCreate(PETSC_COMM_SELF,&aij->B);CHKERRQ(ierr); 3058 ierr = PetscLogObjectParent((PetscObject)C,(PetscObject)aij->B);CHKERRQ(ierr); 3059 ierr = MatSetSizes(aij->B,C->rmap->n,C->cmap->N,C->rmap->n,C->cmap->N);CHKERRQ(ierr); 3060 ierr = MatSetBlockSizesFromMats(aij->B,B,B);CHKERRQ(ierr); 3061 ierr = MatSetType(aij->B,MATSEQAIJ);CHKERRQ(ierr); 3062 Bdisassembled = PETSC_TRUE; 3063 } 3064 if (B) { 3065 Baij = (Mat_SeqAIJ*)(B->data); 3066 if (pattern == DIFFERENT_NONZERO_PATTERN) { 3067 ierr = PetscMalloc1(B->rmap->n,&nz);CHKERRQ(ierr); 3068 for (i=0; i<B->rmap->n; i++) { 3069 nz[i] = Baij->i[i+1] - Baij->i[i]; 3070 } 3071 ierr = MatSeqAIJSetPreallocation(aij->B,0,nz);CHKERRQ(ierr); 3072 ierr = PetscFree(nz);CHKERRQ(ierr); 3073 } 3074 3075 ierr = PetscLayoutGetRange(C->rmap,&rstart,&rend);CHKERRQ(ierr); 3076 shift = rend-rstart; 3077 count = 0; 3078 rowindices = NULL; 3079 colindices = NULL; 3080 if (rowemb) { 3081 ierr = ISGetIndices(rowemb,&rowindices);CHKERRQ(ierr); 3082 } 3083 if (ocolemb) { 3084 ierr = ISGetIndices(ocolemb,&colindices);CHKERRQ(ierr); 3085 } 3086 for (i=0; i<B->rmap->n; i++) { 3087 PetscInt row; 3088 row = i; 3089 if (rowindices) row = rowindices[i]; 3090 for (j=Baij->i[i]; j<Baij->i[i+1]; j++) { 3091 col = Baij->j[count]; 3092 if (colindices) col = colindices[col]; 3093 if (Bdisassembled && col>=rstart) col += shift; 3094 v = Baij->a[count]; 3095 ierr = MatSetValues(aij->B,1,&row,1,&col,&v,INSERT_VALUES);CHKERRQ(ierr); 3096 ++count; 3097 } 3098 } 3099 /* No assembly for aij->B is necessary. */ 3100 /* FIXME: set aij->B's nonzerostate correctly. */ 3101 } else { 3102 ierr = MatSetUp(aij->B);CHKERRQ(ierr); 3103 } 3104 C->preallocated = PETSC_TRUE; 3105 C->was_assembled = PETSC_FALSE; 3106 C->assembled = PETSC_FALSE; 3107 /* 3108 C will need to be assembled so that aij->B can be compressed into local form in MatSetUpMultiply_MPIAIJ(). 3109 Furthermore, its nonzerostate will need to be based on that of aij->A's and aij->B's. 3110 */ 3111 PetscFunctionReturn(0); 3112 } 3113 3114 /* 3115 B uses local indices with column indices ranging between 0 and N-n; they must be interpreted using garray. 3116 */ 3117 PetscErrorCode MatGetSeqMats_MPIAIJ(Mat C,Mat *A,Mat *B) 3118 { 3119 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) (C->data); 3120 3121 PetscFunctionBegin; 3122 PetscValidPointer(A,2); 3123 PetscValidPointer(B,3); 3124 /* FIXME: make sure C is assembled */ 3125 *A = aij->A; 3126 *B = aij->B; 3127 /* Note that we don't incref *A and *B, so be careful! */ 3128 PetscFunctionReturn(0); 3129 } 3130 3131 /* 3132 Extract MPI submatrices encoded by pairs of IS that may live on subcomms of C. 3133 NOT SCALABLE due to the use of ISGetNonlocalIS() (see below). 3134 */ 3135 PetscErrorCode MatGetSubMatricesMPI_MPIXAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[], 3136 PetscErrorCode(*getsubmats_seq)(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat**), 3137 PetscErrorCode(*getlocalmats)(Mat,Mat*,Mat*), 3138 PetscErrorCode(*setseqmat)(Mat,IS,IS,MatStructure,Mat), 3139 PetscErrorCode(*setseqmats)(Mat,IS,IS,IS,MatStructure,Mat,Mat)) 3140 { 3141 PetscErrorCode ierr; 3142 PetscMPIInt isize,flag; 3143 PetscInt i,ii,cismax,ispar; 3144 Mat *A,*B; 3145 IS *isrow_p,*iscol_p,*cisrow,*ciscol,*ciscol_p; 3146 3147 PetscFunctionBegin; 3148 if (!ismax) PetscFunctionReturn(0); 3149 3150 for (i = 0, cismax = 0; i < ismax; ++i) { 3151 PetscMPIInt isize; 3152 ierr = MPI_Comm_compare(((PetscObject)isrow[i])->comm,((PetscObject)iscol[i])->comm,&flag);CHKERRQ(ierr); 3153 if (flag != MPI_IDENT) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row and column index sets must have the same communicator"); 3154 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm, &isize);CHKERRQ(ierr); 3155 if (isize > 1) ++cismax; 3156 } 3157 3158 /* 3159 If cismax is zero on all C's ranks, then and only then can we use purely sequential matrix extraction. 3160 ispar counts the number of parallel ISs across C's comm. 3161 */ 3162 ierr = MPIU_Allreduce(&cismax,&ispar,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 3163 if (!ispar) { /* Sequential ISs only across C's comm, so can call the sequential matrix extraction subroutine. */ 3164 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,scall,submat);CHKERRQ(ierr); 3165 PetscFunctionReturn(0); 3166 } 3167 3168 /* if (ispar) */ 3169 /* 3170 Construct the "complements" -- the off-processor indices -- of the iscol ISs for parallel ISs only. 3171 These are used to extract the off-diag portion of the resulting parallel matrix. 3172 The row IS for the off-diag portion is the same as for the diag portion, 3173 so we merely alias (without increfing) the row IS, while skipping those that are sequential. 3174 */ 3175 ierr = PetscMalloc2(cismax,&cisrow,cismax,&ciscol);CHKERRQ(ierr); 3176 ierr = PetscMalloc1(cismax,&ciscol_p);CHKERRQ(ierr); 3177 for (i = 0, ii = 0; i < ismax; ++i) { 3178 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3179 if (isize > 1) { 3180 /* 3181 TODO: This is the part that's ***NOT SCALABLE***. 3182 To fix this we need to extract just the indices of C's nonzero columns 3183 that lie on the intersection of isrow[i] and ciscol[ii] -- the nonlocal 3184 part of iscol[i] -- without actually computing ciscol[ii]. This also has 3185 to be done without serializing on the IS list, so, most likely, it is best 3186 done by rewriting MatGetSubMatrices_MPIAIJ() directly. 3187 */ 3188 ierr = ISGetNonlocalIS(iscol[i],&(ciscol[ii]));CHKERRQ(ierr); 3189 /* Now we have to 3190 (a) make sure ciscol[ii] is sorted, since, even if the off-proc indices 3191 were sorted on each rank, concatenated they might no longer be sorted; 3192 (b) Use ISSortPermutation() to construct ciscol_p, the mapping from the 3193 indices in the nondecreasing order to the original index positions. 3194 If ciscol[ii] is strictly increasing, the permutation IS is NULL. 3195 */ 3196 ierr = ISSortPermutation(ciscol[ii],PETSC_FALSE,ciscol_p+ii);CHKERRQ(ierr); 3197 ierr = ISSort(ciscol[ii]);CHKERRQ(ierr); 3198 ++ii; 3199 } 3200 } 3201 ierr = PetscMalloc2(ismax,&isrow_p,ismax,&iscol_p);CHKERRQ(ierr); 3202 for (i = 0, ii = 0; i < ismax; ++i) { 3203 PetscInt j,issize; 3204 const PetscInt *indices; 3205 3206 /* 3207 Permute the indices into a nondecreasing order. Reject row and col indices with duplicates. 3208 */ 3209 ierr = ISSortPermutation(isrow[i],PETSC_FALSE,isrow_p+i);CHKERRQ(ierr); 3210 ierr = ISSort(isrow[i]);CHKERRQ(ierr); 3211 ierr = ISGetLocalSize(isrow[i],&issize);CHKERRQ(ierr); 3212 ierr = ISGetIndices(isrow[i],&indices);CHKERRQ(ierr); 3213 for (j = 1; j < issize; ++j) { 3214 if (indices[j] == indices[j-1]) { 3215 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]); 3216 } 3217 } 3218 ierr = ISRestoreIndices(isrow[i],&indices);CHKERRQ(ierr); 3219 3220 3221 ierr = ISSortPermutation(iscol[i],PETSC_FALSE,iscol_p+i);CHKERRQ(ierr); 3222 ierr = ISSort(iscol[i]);CHKERRQ(ierr); 3223 ierr = ISGetLocalSize(iscol[i],&issize);CHKERRQ(ierr); 3224 ierr = ISGetIndices(iscol[i],&indices);CHKERRQ(ierr); 3225 for (j = 1; j < issize; ++j) { 3226 if (indices[j-1] == indices[j]) { 3227 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]); 3228 } 3229 } 3230 ierr = ISRestoreIndices(iscol[i],&indices);CHKERRQ(ierr); 3231 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3232 if (isize > 1) { 3233 cisrow[ii] = isrow[i]; 3234 ++ii; 3235 } 3236 } 3237 /* 3238 Allocate the necessary arrays to hold the resulting parallel matrices as well as the intermediate 3239 array of sequential matrices underlying the resulting parallel matrices. 3240 Which arrays to allocate is based on the value of MatReuse scall and whether ISs are sorted and/or 3241 contain duplicates. 3242 3243 There are as many diag matrices as there are original index sets. There are only as many parallel 3244 and off-diag matrices, as there are parallel (comm size > 1) index sets. 3245 3246 ARRAYS that can hold Seq matrices get allocated in any event -- either here or by getsubmats_seq(): 3247 - If the array of MPI matrices already exists and is being reused, we need to allocate the array 3248 and extract the underlying seq matrices into it to serve as placeholders, into which getsubmats_seq 3249 will deposite the extracted diag and off-diag parts. Thus, we allocate the A&B arrays and fill them 3250 with A[i] and B[ii] extracted from the corresponding MPI submat. 3251 - However, if the rows, A's column indices or B's column indices are not sorted, the extracted A[i] & B[ii] 3252 will have a different order from what getsubmats_seq expects. To handle this case -- indicated 3253 by a nonzero isrow_p[i], iscol_p[i], or ciscol_p[ii] -- we duplicate A[i] --> AA[i], B[ii] --> BB[ii] 3254 (retrieve composed AA[i] or BB[ii]) and reuse them here. AA[i] and BB[ii] are then used to permute its 3255 values into A[i] and B[ii] sitting inside the corresponding submat. 3256 - If no reuse is taking place then getsubmats_seq will allocate the A&B arrays and create the corresponding 3257 A[i], B[ii], AA[i] or BB[ii] matrices. 3258 */ 3259 /* Parallel matrix array is allocated here only if no reuse is taking place. If reused, it is passed in by the caller. */ 3260 if (scall == MAT_INITIAL_MATRIX) { 3261 ierr = PetscMalloc1(ismax,submat);CHKERRQ(ierr); 3262 } 3263 3264 /* Now obtain the sequential A and B submatrices separately. */ 3265 /* scall=MAT_REUSE_MATRIX is not handled yet, because getsubmats_seq() requires reuse of A and B */ 3266 ierr = (*getsubmats_seq)(C,ismax,isrow,iscol,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr); 3267 ierr = (*getsubmats_seq)(C,cismax,cisrow,ciscol,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 3268 3269 /* 3270 If scall == MAT_REUSE_MATRIX AND the permutations are NULL, we are done, since the sequential 3271 matrices A & B have been extracted directly into the parallel matrices containing them, or 3272 simply into the sequential matrix identical with the corresponding A (if isize == 1). 3273 Note that in that case colmap doesn't need to be rebuilt, since the matrices are expected 3274 to have the same sparsity pattern. 3275 Otherwise, A and/or B have to be properly embedded into C's index spaces and the correct colmap 3276 must be constructed for C. This is done by setseqmat(s). 3277 */ 3278 for (i = 0, ii = 0; i < ismax; ++i) { 3279 /* 3280 TODO: cache ciscol, permutation ISs and maybe cisrow? What about isrow & iscol? 3281 That way we can avoid sorting and computing permutations when reusing. 3282 To this end: 3283 - remove the old cache, if it exists, when extracting submatrices with MAT_INITIAL_MATRIX 3284 - if caching arrays to hold the ISs, make and compose a container for them so that it can 3285 be destroyed upon destruction of C (use PetscContainerUserDestroy() to clear out the contents). 3286 */ 3287 MatStructure pattern; 3288 pattern = DIFFERENT_NONZERO_PATTERN; 3289 3290 ierr = MPI_Comm_size(((PetscObject)isrow[i])->comm,&isize);CHKERRQ(ierr); 3291 /* Construct submat[i] from the Seq pieces A (and B, if necessary). */ 3292 if (isize > 1) { 3293 if (scall == MAT_INITIAL_MATRIX) { 3294 ierr = MatCreate(((PetscObject)isrow[i])->comm,(*submat)+i);CHKERRQ(ierr); 3295 ierr = MatSetSizes((*submat)[i],A[i]->rmap->n,A[i]->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3296 ierr = MatSetType((*submat)[i],MATMPIAIJ);CHKERRQ(ierr); 3297 ierr = PetscLayoutSetUp((*submat)[i]->rmap);CHKERRQ(ierr); 3298 ierr = PetscLayoutSetUp((*submat)[i]->cmap);CHKERRQ(ierr); 3299 } 3300 /* 3301 For each parallel isrow[i], insert the extracted sequential matrices into the parallel matrix. 3302 */ 3303 { 3304 Mat AA,BB; 3305 AA = A[i]; 3306 BB = B[ii]; 3307 if (AA || BB) { 3308 ierr = setseqmats((*submat)[i],isrow_p[i],iscol_p[i],ciscol_p[ii],pattern,AA,BB);CHKERRQ(ierr); 3309 ierr = MatAssemblyBegin((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3310 ierr = MatAssemblyEnd((*submat)[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3311 } 3312 3313 ierr = MatDestroy(&AA);CHKERRQ(ierr); 3314 ierr = MatDestroy(&BB);CHKERRQ(ierr); 3315 } 3316 ierr = ISDestroy(ciscol+ii);CHKERRQ(ierr); 3317 ierr = ISDestroy(ciscol_p+ii);CHKERRQ(ierr); 3318 ++ii; 3319 } else { /* if (isize == 1) */ 3320 if (scall == MAT_REUSE_MATRIX) { 3321 ierr = MatDestroy(&(*submat)[i]);CHKERRQ(ierr); 3322 } 3323 if (isrow_p[i] || iscol_p[i]) { 3324 ierr = MatDuplicate(A[i],MAT_DO_NOT_COPY_VALUES,(*submat)+i);CHKERRQ(ierr); 3325 ierr = setseqmat((*submat)[i],isrow_p[i],iscol_p[i],pattern,A[i]);CHKERRQ(ierr); 3326 /* Otherwise A is extracted straight into (*submats)[i]. */ 3327 /* TODO: Compose A[i] on (*submat([i] for future use, if ((isrow_p[i] || iscol_p[i]) && MAT_INITIAL_MATRIX). */ 3328 ierr = MatDestroy(A+i);CHKERRQ(ierr); 3329 } else (*submat)[i] = A[i]; 3330 } 3331 ierr = ISDestroy(&isrow_p[i]);CHKERRQ(ierr); 3332 ierr = ISDestroy(&iscol_p[i]);CHKERRQ(ierr); 3333 } 3334 ierr = PetscFree2(cisrow,ciscol);CHKERRQ(ierr); 3335 ierr = PetscFree2(isrow_p,iscol_p);CHKERRQ(ierr); 3336 ierr = PetscFree(ciscol_p);CHKERRQ(ierr); 3337 ierr = PetscFree(A);CHKERRQ(ierr); 3338 ierr = PetscFree(B);CHKERRQ(ierr); 3339 PetscFunctionReturn(0); 3340 } 3341 3342 PetscErrorCode MatGetSubMatricesMPI_MPIAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 3343 { 3344 PetscErrorCode ierr; 3345 3346 PetscFunctionBegin; 3347 ierr = MatGetSubMatricesMPI_MPIXAIJ(C,ismax,isrow,iscol,scall,submat,MatGetSubMatrices_MPIAIJ,MatGetSeqMats_MPIAIJ,MatSetSeqMat_SeqAIJ,MatSetSeqMats_MPIAIJ);CHKERRQ(ierr); 3348 PetscFunctionReturn(0); 3349 } 3350