1 /* 2 GAMG geometric-algebric multiogrid PC - Mark Adams 2011 3 */ 4 #include <../src/ksp/pc/impls/gamg/gamg.h> 5 6 PetscLogEvent gamg_setup_stages[NUM_SET]; 7 8 /* Private context for the GAMG preconditioner */ 9 typedef struct gamg_TAG { 10 PetscInt m_dim; 11 PetscInt m_Nlevels; 12 PetscInt m_data_sz; 13 PetscInt m_data_rows; 14 PetscInt m_data_cols; 15 PetscBool m_useSA; 16 PetscReal *m_data; /* blocked vector of vertex data on fine grid (coordinates) */ 17 } PC_GAMG; 18 19 /* -------------------------------------------------------------------------- */ 20 /* 21 PCSetCoordinates_GAMG 22 23 Input Parameter: 24 . pc - the preconditioner context 25 */ 26 EXTERN_C_BEGIN 27 #undef __FUNCT__ 28 #define __FUNCT__ "PCSetCoordinates_GAMG" 29 PetscErrorCode PCSetCoordinates_GAMG( PC a_pc, PetscInt a_ndm, PetscReal *a_coords ) 30 { 31 PC_MG *mg = (PC_MG*)a_pc->data; 32 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 33 PetscErrorCode ierr; 34 PetscInt arrsz,bs,my0,kk,ii,jj,nloc,Iend; 35 Mat Amat = a_pc->pmat; 36 PetscBool flag; 37 char str[64]; 38 39 PetscFunctionBegin; 40 ierr = MatGetBlockSize( Amat, &bs ); CHKERRQ( ierr ); 41 ierr = MatGetOwnershipRange( Amat, &my0, &Iend ); CHKERRQ(ierr); 42 nloc = (Iend-my0)/bs; 43 if((Iend-my0)%bs!=0) SETERRQ1(((PetscObject)Amat)->comm,PETSC_ERR_ARG_WRONG, "Bad local size %d.",nloc); 44 45 ierr = PetscOptionsGetString(PETSC_NULL,"-pc_gamg_type",str,64,&flag); CHKERRQ( ierr ); 46 pc_gamg->m_useSA = (PetscBool)(flag && strcmp(str,"sa") == 0); 47 48 pc_gamg->m_data_rows = 1; 49 if(a_coords == 0) pc_gamg->m_useSA = PETSC_TRUE; /* use SA if no data */ 50 if( !pc_gamg->m_useSA ) pc_gamg->m_data_cols = a_ndm; /* coordinates */ 51 else{ /* SA: null space vectors */ 52 if(a_coords != 0 && bs==1 ) pc_gamg->m_data_cols = 1; /* scalar w/ coords and SA (not needed) */ 53 else if(a_coords != 0) pc_gamg->m_data_cols = (a_ndm==2 ? 3 : 6); /* elasticity */ 54 else pc_gamg->m_data_cols = bs; /* no data, force SA with constant null space vectors */ 55 pc_gamg->m_data_rows = bs; 56 } 57 arrsz = nloc*pc_gamg->m_data_rows*pc_gamg->m_data_cols; 58 59 /* create data - syntactic sugar that should be refactored at some point */ 60 if (!pc_gamg->m_data || (pc_gamg->m_data_sz != arrsz)) { 61 ierr = PetscFree( pc_gamg->m_data ); CHKERRQ(ierr); 62 ierr = PetscMalloc((arrsz+1)*sizeof(double), &pc_gamg->m_data ); CHKERRQ(ierr); 63 } 64 for(kk=0;kk<arrsz;kk++)pc_gamg->m_data[kk] = -999.; 65 pc_gamg->m_data[arrsz] = -99.; 66 /* copy data in - column oriented */ 67 if( pc_gamg->m_useSA ) { 68 const PetscInt M = Iend - my0; 69 for(kk=0;kk<nloc;kk++){ 70 PetscReal *data = &pc_gamg->m_data[kk*bs]; 71 if( pc_gamg->m_data_cols==1 ) *data = 1.0; 72 else { 73 for(ii=0;ii<bs;ii++) 74 for(jj=0;jj<bs;jj++) 75 if(ii==jj)data[ii*M + jj] = 1.0; /* translational modes */ 76 else data[ii*M + jj] = 0.0; 77 if( a_coords != 0 ) { 78 if( a_ndm == 2 ){ /* rotational modes */ 79 data += 2*M; 80 data[0] = -a_coords[2*kk+1]; 81 data[1] = a_coords[2*kk]; 82 } 83 else { 84 data += 3*M; 85 data[0] = 0.0; data[M+0] = a_coords[3*kk+2]; data[2*M+0] = -a_coords[3*kk+1]; 86 data[1] = -a_coords[3*kk+2]; data[M+1] = 0.0; data[2*M+1] = a_coords[3*kk]; 87 data[2] = a_coords[3*kk+1]; data[M+2] = -a_coords[3*kk]; data[2*M+2] = 0.0; 88 } 89 } 90 } 91 } 92 } 93 else { 94 for( kk = 0 ; kk < nloc ; kk++ ){ 95 for( ii = 0 ; ii < a_ndm ; ii++ ) { 96 pc_gamg->m_data[ii*nloc + kk] = a_coords[kk*a_ndm + ii]; 97 } 98 } 99 } 100 assert(pc_gamg->m_data[arrsz] == -99.); 101 102 pc_gamg->m_data_sz = arrsz; 103 pc_gamg->m_dim = a_ndm; 104 105 PetscFunctionReturn(0); 106 } 107 EXTERN_C_END 108 109 110 /* -----------------------------------------------------------------------------*/ 111 #undef __FUNCT__ 112 #define __FUNCT__ "PCReset_GAMG" 113 PetscErrorCode PCReset_GAMG(PC pc) 114 { 115 PetscErrorCode ierr; 116 PC_MG *mg = (PC_MG*)pc->data; 117 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 118 119 PetscFunctionBegin; 120 ierr = PetscFree(pc_gamg->m_data);CHKERRQ(ierr); 121 pc_gamg->m_data = 0; pc_gamg->m_data_sz = 0; 122 PetscFunctionReturn(0); 123 } 124 125 /* -------------------------------------------------------------------------- */ 126 /* 127 partitionLevel 128 129 Input Parameter: 130 . a_Amat_fine - matrix on this fine (k) level 131 . a_ndata_rows - size of data to move (coarse grid) 132 . a_ndata_cols - size of data to move (coarse grid) 133 In/Output Parameter: 134 . a_P_inout - prolongation operator to the next level (k-1) 135 . a_coarse_data - data that need to be moved 136 . a_active_proc - number of active procs 137 Output Parameter: 138 . a_Amat_crs - coarse matrix that is created (k-1) 139 */ 140 141 #undef __FUNCT__ 142 #define __FUNCT__ "partitionLevel" 143 PetscErrorCode partitionLevel( Mat a_Amat_fine, 144 PetscInt a_ndata_rows, 145 PetscInt a_ndata_cols, 146 PetscInt a_cbs, 147 Mat *a_P_inout, 148 PetscReal **a_coarse_data, 149 PetscMPIInt *a_active_proc, 150 Mat *a_Amat_crs 151 ) 152 { 153 PetscErrorCode ierr; 154 Mat Cmat,Pnew,Pold=*a_P_inout; 155 IS new_indices,isnum; 156 MPI_Comm wcomm = ((PetscObject)a_Amat_fine)->comm; 157 PetscMPIInt nactive_procs,mype,npe; 158 PetscInt Istart,Iend,Istart0,Iend0,ncrs0,ncrs_new,fbs; 159 PetscInt neq,NN; 160 PetscMPIInt new_npe,targ_npe; 161 PetscBool flag = PETSC_FALSE; 162 163 PetscFunctionBegin; 164 ierr = MPI_Comm_rank( wcomm, &mype ); CHKERRQ(ierr); 165 ierr = MPI_Comm_size( wcomm, &npe ); CHKERRQ(ierr); 166 ierr = MatGetBlockSize( a_Amat_fine, &fbs ); CHKERRQ(ierr); 167 /* RAP */ 168 ierr = MatPtAP( a_Amat_fine, Pold, MAT_INITIAL_MATRIX, 2.0, &Cmat ); CHKERRQ(ierr); 169 170 ierr = MatSetBlockSize( Cmat, a_cbs ); CHKERRQ(ierr); 171 172 ierr = MatGetOwnershipRange( Cmat, &Istart0, &Iend0 ); CHKERRQ(ierr); 173 ncrs0 = (Iend0-Istart0)/a_cbs; assert((Iend0-Istart0)%a_cbs == 0); 174 175 /* Repartition Cmat_{k} and move colums of P^{k}_{k-1} and coordinates accordingly */ 176 ierr = MatGetSize( Cmat, &neq, &NN );CHKERRQ(ierr); 177 #define MIN_EQ_PROC 2000 178 nactive_procs = *a_active_proc; 179 targ_npe = neq/MIN_EQ_PROC; /* hardwire min. number of eq/proc */ 180 #define TOP_GRID_LIM 2000 181 if( targ_npe == 0 || neq < TOP_GRID_LIM ) new_npe = 1; /* chop coarsest grid */ 182 else if (targ_npe >= nactive_procs ) new_npe = nactive_procs; /* no change */ 183 else { 184 PetscMPIInt factstart,fact; 185 new_npe = -9999; 186 factstart = nactive_procs; 187 for(fact=factstart;fact>0;fact--){ /* try to find a better number of procs */ 188 if( nactive_procs%fact==0 && neq/(nactive_procs/fact) > MIN_EQ_PROC ) { 189 new_npe = nactive_procs/fact; 190 } 191 } 192 if(new_npe == -9999) new_npe = nactive_procs; 193 } 194 195 ierr = PetscOptionsHasName(PETSC_NULL,"-pc_gamg_avoid_repartitioning",&flag); 196 CHKERRQ( ierr ); 197 if( !flag ) { /* re-partition */ 198 MatPartitioning mpart; 199 Mat adj; 200 const PetscInt *is_idx; 201 PetscInt is_sz,kk,jj,ii,old_fact=(npe/nactive_procs), *isnewproc_idx; 202 /* create sub communicator */ 203 MPI_Comm cm,new_comm; 204 PetscInt membershipKey = mype%old_fact, new_fact=(npe/new_npe),counts[npe]; 205 IS isnewproc; 206 207 *a_active_proc = new_npe; /* output for next level */ 208 ierr = MPI_Comm_split(wcomm, membershipKey, mype, &cm); CHKERRQ(ierr); 209 ierr = PetscCommDuplicate( cm, &new_comm, PETSC_NULL ); CHKERRQ(ierr); 210 ierr = MPI_Comm_free( &cm ); CHKERRQ(ierr); 211 212 /* MatPartitioningApply call MatConvert, which is collective */ 213 ierr = PetscLogEventBegin(gamg_setup_stages[SET12],0,0,0,0);CHKERRQ(ierr); 214 if( a_cbs==1) { 215 ierr = MatConvert( Cmat, MATMPIADJ, MAT_INITIAL_MATRIX, &adj ); CHKERRQ(ierr); 216 } 217 else { 218 /* make a scalar matrix to partition */ 219 Mat tMat; 220 PetscInt Ii,ncols; const PetscScalar *vals; const PetscInt *idx; 221 MatInfo info; 222 ierr = MatGetInfo(Cmat,MAT_LOCAL,&info); CHKERRQ(ierr); 223 ncols = (PetscInt)info.nz_used/((ncrs0+1)*a_cbs*a_cbs)+1; 224 225 ierr = MatCreateMPIAIJ( wcomm, ncrs0, ncrs0, 226 PETSC_DETERMINE, PETSC_DETERMINE, 227 2*ncols, PETSC_NULL, ncols, PETSC_NULL, 228 &tMat ); 229 CHKERRQ(ierr); 230 231 for ( Ii = Istart0; Ii < Iend0; Ii++ ) { 232 PetscInt dest_row = Ii/a_cbs; 233 ierr = MatGetRow(Cmat,Ii,&ncols,&idx,&vals); CHKERRQ(ierr); 234 for( jj = 0 ; jj < ncols ; jj++ ){ 235 PetscInt dest_col = idx[jj]/a_cbs; 236 PetscScalar v = 1.0; 237 ierr = MatSetValues(tMat,1,&dest_row,1,&dest_col,&v,ADD_VALUES); CHKERRQ(ierr); 238 } 239 ierr = MatRestoreRow(Cmat,Ii,&ncols,&idx,&vals); CHKERRQ(ierr); 240 } 241 ierr = MatAssemblyBegin(tMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 242 ierr = MatAssemblyEnd(tMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 243 244 ierr = MatConvert( tMat, MATMPIADJ, MAT_INITIAL_MATRIX, &adj ); CHKERRQ(ierr); 245 246 ierr = MatDestroy( &tMat ); CHKERRQ(ierr); 247 } 248 if( membershipKey == 0 ) { 249 if(ncrs0==0)SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"zero local nodes -- increase min"); 250 /* hack to fix global data that pmetis.c uses in 'adj' */ 251 for( kk=0 , jj=0 ; kk<=npe ; jj++, kk += old_fact ) { 252 adj->rmap->range[jj] = adj->rmap->range[kk]; 253 } 254 ierr = MatPartitioningCreate( new_comm, &mpart ); CHKERRQ(ierr); 255 ierr = MatPartitioningSetAdjacency( mpart, adj ); CHKERRQ(ierr); 256 ierr = MatPartitioningSetFromOptions( mpart ); CHKERRQ(ierr); 257 ierr = MatPartitioningSetNParts( mpart, new_npe ); CHKERRQ(ierr); 258 ierr = MatPartitioningApply( mpart, &isnewproc ); CHKERRQ(ierr); 259 ierr = MatPartitioningDestroy( &mpart ); CHKERRQ(ierr); 260 /* collect IS info */ 261 ierr = ISGetLocalSize( isnewproc, &is_sz ); CHKERRQ(ierr); 262 ierr = PetscMalloc( a_cbs*is_sz*sizeof(PetscInt), &isnewproc_idx ); CHKERRQ(ierr); 263 ierr = ISGetIndices( isnewproc, &is_idx ); CHKERRQ(ierr); 264 /* spread partitioning across machine - probably the right thing to do but machine spec. */ 265 for(kk=0,jj=0;kk<is_sz;kk++){ 266 for(ii=0 ; ii<a_cbs ; ii++, jj++ ) { /* expand for equation level by 'bs' */ 267 isnewproc_idx[jj] = is_idx[kk] * new_fact; 268 } 269 } 270 ierr = ISRestoreIndices( isnewproc, &is_idx ); CHKERRQ(ierr); 271 ierr = ISDestroy( &isnewproc ); CHKERRQ(ierr); 272 is_sz *= a_cbs; 273 } 274 else { 275 isnewproc_idx = 0; 276 is_sz = 0; 277 } 278 ierr = MatDestroy( &adj ); CHKERRQ(ierr); 279 ierr = MPI_Comm_free( &new_comm ); CHKERRQ(ierr); 280 ierr = ISCreateGeneral( wcomm, is_sz, isnewproc_idx, PETSC_COPY_VALUES, &isnewproc ); 281 if( membershipKey == 0 ) { 282 ierr = PetscFree( isnewproc_idx ); CHKERRQ(ierr); 283 } 284 285 /* 286 Create an index set from the isnewproc index set to indicate the mapping TO 287 */ 288 ierr = ISPartitioningToNumbering( isnewproc, &isnum ); CHKERRQ(ierr); 289 /* 290 Determine how many elements are assigned to each processor 291 */ 292 ierr = ISPartitioningCount( isnewproc, npe, counts ); CHKERRQ(ierr); 293 ierr = ISDestroy( &isnewproc ); CHKERRQ(ierr); 294 ncrs_new = counts[mype]/a_cbs; 295 ierr = PetscLogEventEnd(gamg_setup_stages[SET12],0,0,0,0); CHKERRQ(ierr); 296 297 { /* Create a vector to contain the newly ordered element information */ 298 const PetscInt *idx, data_sz=a_ndata_rows*a_ndata_cols; 299 const PetscInt stride0=ncrs0*a_ndata_rows,strideNew=ncrs_new*a_ndata_rows; 300 PetscInt ii,jj,kk; 301 IS isscat; 302 PetscScalar *array; 303 Vec src_crd, dest_crd; 304 PetscReal *data = *a_coarse_data; 305 VecScatter vecscat; 306 PetscInt tidx[ncrs0*data_sz]; 307 308 ierr = VecCreate( wcomm, &dest_crd ); 309 ierr = VecSetSizes( dest_crd, data_sz*ncrs_new, PETSC_DECIDE ); CHKERRQ(ierr); 310 ierr = VecSetFromOptions( dest_crd ); CHKERRQ(ierr); /*funny vector-get global options?*/ 311 /* 312 There are 'a_ndata_rows*a_ndata_cols' data items per node, (one can think of the vectors of having 313 a block size of ...). Note, ISs are expanded into equation space by 'a_cbs'. 314 */ 315 ierr = ISGetIndices( isnum, &idx ); CHKERRQ(ierr); 316 for(ii=0,jj=0; ii<ncrs0 ; ii++) { 317 PetscInt id = idx[ii*a_cbs]/a_cbs; /* get node back */ 318 for( kk=0; kk<data_sz ; kk++, jj++) tidx[jj] = id*data_sz + kk; 319 } 320 ierr = ISRestoreIndices( isnum, &idx ); CHKERRQ(ierr); 321 ierr = ISCreateGeneral( wcomm, data_sz*ncrs0, tidx, PETSC_COPY_VALUES, &isscat ); 322 CHKERRQ(ierr); 323 /* 324 Create a vector to contain the original vertex information for each element 325 */ 326 ierr = VecCreateSeq( PETSC_COMM_SELF, data_sz*ncrs0, &src_crd ); CHKERRQ(ierr); 327 for( jj=0; jj<a_ndata_cols ; jj++ ) { 328 for( ii=0 ; ii<ncrs0 ; ii++) { 329 for( kk=0; kk<a_ndata_rows ; kk++ ) { 330 PetscInt ix = ii*a_ndata_rows + kk + jj*stride0, jx = ii*data_sz + kk*a_ndata_cols + jj; 331 ierr = VecSetValues( src_crd, 1, &jx, &data[ix], INSERT_VALUES ); CHKERRQ(ierr); 332 } 333 } 334 } 335 ierr = VecAssemblyBegin(src_crd); CHKERRQ(ierr); 336 ierr = VecAssemblyEnd(src_crd); CHKERRQ(ierr); 337 /* 338 Scatter the element vertex information (still in the original vertex ordering) 339 to the correct processor 340 */ 341 ierr = VecScatterCreate( src_crd, PETSC_NULL, dest_crd, isscat, &vecscat); 342 CHKERRQ(ierr); 343 ierr = ISDestroy( &isscat ); CHKERRQ(ierr); 344 ierr = VecScatterBegin(vecscat,src_crd,dest_crd,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 345 ierr = VecScatterEnd(vecscat,src_crd,dest_crd,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 346 ierr = VecScatterDestroy( &vecscat ); CHKERRQ(ierr); 347 ierr = VecDestroy( &src_crd ); CHKERRQ(ierr); 348 /* 349 Put the element vertex data into a new allocation of the gdata->ele 350 */ 351 ierr = PetscFree( *a_coarse_data ); CHKERRQ(ierr); 352 ierr = PetscMalloc( data_sz*ncrs_new*sizeof(PetscReal), a_coarse_data ); CHKERRQ(ierr); 353 354 ierr = VecGetArray( dest_crd, &array ); CHKERRQ(ierr); 355 data = *a_coarse_data; 356 for( jj=0; jj<a_ndata_cols ; jj++ ) { 357 for( ii=0 ; ii<ncrs_new ; ii++) { 358 for( kk=0; kk<a_ndata_rows ; kk++ ) { 359 PetscInt ix = ii*a_ndata_rows + kk + jj*strideNew, jx = ii*data_sz + kk*a_ndata_cols + jj; 360 data[ix] = PetscRealPart(array[jx]); 361 array[jx] = 1.e300; 362 } 363 } 364 } 365 ierr = VecRestoreArray( dest_crd, &array ); CHKERRQ(ierr); 366 ierr = VecDestroy( &dest_crd ); CHKERRQ(ierr); 367 } 368 369 /* 370 Invert for MatGetSubMatrix 371 */ 372 ierr = ISInvertPermutation( isnum, ncrs_new*a_cbs, &new_indices ); CHKERRQ(ierr); 373 ierr = ISSort( new_indices ); CHKERRQ(ierr); /* is this needed? */ 374 ierr = ISDestroy( &isnum ); CHKERRQ(ierr); 375 /* A_crs output */ 376 ierr = MatGetSubMatrix( Cmat, new_indices, new_indices, MAT_INITIAL_MATRIX, a_Amat_crs ); 377 CHKERRQ(ierr); 378 379 ierr = MatDestroy( &Cmat ); CHKERRQ(ierr); 380 Cmat = *a_Amat_crs; /* output */ 381 ierr = MatSetBlockSize( Cmat, a_cbs ); CHKERRQ(ierr); 382 383 /* prolongator */ 384 ierr = MatGetOwnershipRange( Pold, &Istart, &Iend ); CHKERRQ(ierr); 385 { 386 IS findices; 387 ierr = ISCreateStride(wcomm,Iend-Istart,Istart,1,&findices); CHKERRQ(ierr); 388 ierr = MatGetSubMatrix( Pold, findices, new_indices, MAT_INITIAL_MATRIX, &Pnew ); 389 CHKERRQ(ierr); 390 ierr = ISDestroy( &findices ); CHKERRQ(ierr); 391 } 392 ierr = MatDestroy( a_P_inout ); CHKERRQ(ierr); 393 *a_P_inout = Pnew; /* output */ 394 ierr = ISDestroy( &new_indices ); CHKERRQ(ierr); 395 } 396 else { 397 *a_Amat_crs = Cmat; /* output */ 398 } 399 400 PetscFunctionReturn(0); 401 } 402 403 #define GAMG_MAXLEVELS 30 404 #if defined(PETSC_USE_LOG) 405 PetscLogStage gamg_stages[20]; 406 #endif 407 /* -------------------------------------------------------------------------- */ 408 /* 409 PCSetUp_GAMG - Prepares for the use of the GAMG preconditioner 410 by setting data structures and options. 411 412 Input Parameter: 413 . pc - the preconditioner context 414 415 Application Interface Routine: PCSetUp() 416 417 Notes: 418 The interface routine PCSetUp() is not usually called directly by 419 the user, but instead is called by PCApply() if necessary. 420 */ 421 #undef __FUNCT__ 422 #define __FUNCT__ "PCSetUp_GAMG" 423 PetscErrorCode PCSetUp_GAMG( PC a_pc ) 424 { 425 PetscErrorCode ierr; 426 PC_MG *mg = (PC_MG*)a_pc->data; 427 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 428 Mat Amat = a_pc->mat, Pmat = a_pc->pmat; 429 PetscInt fine_level, level, level1, M, N, bs, nloc, lidx, Istart, Iend; 430 MPI_Comm wcomm = ((PetscObject)a_pc)->comm; 431 PetscMPIInt mype,npe,nactivepe; 432 PetscBool isOK; 433 Mat Aarr[GAMG_MAXLEVELS], Parr[GAMG_MAXLEVELS]; 434 PetscReal *coarse_data = 0, *data, emaxs[GAMG_MAXLEVELS]; 435 MatInfo info; 436 437 PetscFunctionBegin; 438 if( a_pc->setupcalled ) { 439 /* no state data in GAMG to destroy */ 440 ierr = PCReset_MG( a_pc ); CHKERRQ(ierr); 441 } 442 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 443 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 444 /* GAMG requires input of fine-grid matrix. It determines nlevels. */ 445 ierr = MatGetBlockSize( Amat, &bs ); CHKERRQ(ierr); 446 ierr = MatGetSize( Amat, &M, &N );CHKERRQ(ierr); 447 ierr = MatGetOwnershipRange( Amat, &Istart, &Iend ); CHKERRQ(ierr); 448 nloc = (Iend-Istart)/bs; assert((Iend-Istart)%bs == 0); 449 450 /* get data of not around */ 451 if( pc_gamg->m_data == 0 && nloc > 0 ) { 452 ierr = PCSetCoordinates_GAMG( a_pc, -1, 0 ); CHKERRQ( ierr ); 453 } 454 data = pc_gamg->m_data; 455 456 /* Get A_i and R_i */ 457 ierr = MatGetInfo(Amat,MAT_GLOBAL_SUM,&info); CHKERRQ(ierr); 458 PetscPrintf(PETSC_COMM_WORLD,"\t[%d]%s level %d N=%d, n data rows=%d, n data cols=%d, nnz/row (ave)=%d, np=%d\n", 459 mype,__FUNCT__,0,N,pc_gamg->m_data_rows,pc_gamg->m_data_cols,(PetscInt)(info.nz_used/(PetscReal)N),npe); 460 for ( level=0, Aarr[0] = Pmat, nactivepe = npe; /* hard wired stopping logic */ 461 level < GAMG_MAXLEVELS-1 && (level==0 || M>TOP_GRID_LIM) && (npe==1 || nactivepe>1); 462 level++ ){ 463 level1 = level + 1; 464 ierr = PetscLogEventBegin(gamg_setup_stages[SET1],0,0,0,0);CHKERRQ(ierr); 465 ierr = createProlongation(Aarr[level], data, pc_gamg->m_dim, pc_gamg->m_data_cols, pc_gamg->m_useSA, 466 level, &bs, &Parr[level1], &coarse_data, &isOK, &emaxs[level] ); 467 CHKERRQ(ierr); 468 ierr = PetscFree( data ); CHKERRQ( ierr ); 469 ierr = PetscLogEventEnd(gamg_setup_stages[SET1],0,0,0,0);CHKERRQ(ierr); 470 471 if(level==0) Aarr[0] = Amat; /* use Pmat for finest level setup, but use mat for solver */ 472 473 if( isOK ) { 474 ierr = PetscLogEventBegin(gamg_setup_stages[SET2],0,0,0,0);CHKERRQ(ierr); 475 ierr = partitionLevel( Aarr[level], pc_gamg->m_useSA ? bs : 1, pc_gamg->m_data_cols, bs, 476 &Parr[level1], &coarse_data, &nactivepe, &Aarr[level1] ); 477 CHKERRQ(ierr); 478 ierr = PetscLogEventEnd(gamg_setup_stages[SET2],0,0,0,0);CHKERRQ(ierr); 479 ierr = MatGetSize( Aarr[level1], &M, &N );CHKERRQ(ierr); 480 ierr = MatGetInfo(Aarr[level1],MAT_GLOBAL_SUM,&info); CHKERRQ(ierr); 481 PetscPrintf(PETSC_COMM_WORLD,"\t\t[%d]%s %d) N=%d, bs=%d, n data cols=%d, nnz/row (ave)=%d, %d active pes\n", 482 mype,__FUNCT__,level1,N,bs,pc_gamg->m_data_cols,(PetscInt)(info.nz_used/(PetscReal)N),nactivepe); 483 /* coarse grids with SA can have zero row/cols from singleton aggregates */ 484 /* aggregation method can probably gaurrentee this does not happen! - be safe for now */ 485 486 if( PETSC_TRUE ){ 487 Vec diag; PetscScalar *data_arr,v; PetscInt Istart,Iend,kk,nloceq,id; 488 v = 1.e-10; /* LU factor has hard wired numbers for small diags so this needs to match (yuk) */ 489 ierr = MatGetOwnershipRange(Aarr[level1], &Istart, &Iend); CHKERRQ(ierr); 490 nloceq = Iend-Istart; 491 ierr = MatGetVecs( Aarr[level1], &diag, 0 ); CHKERRQ(ierr); 492 ierr = MatGetDiagonal( Aarr[level1], diag ); CHKERRQ(ierr); 493 ierr = VecGetArray( diag, &data_arr ); CHKERRQ(ierr); 494 for(kk=0;kk<nloceq;kk++){ 495 if(data_arr[kk]==0.0) { 496 id = kk + Istart; 497 ierr = MatSetValues(Aarr[level1],1,&id,1,&id,&v,INSERT_VALUES); 498 CHKERRQ(ierr); 499 PetscPrintf(PETSC_COMM_SELF,"\t[%d]%s warning: added diag to zero (%d) on level %d \n",mype,__FUNCT__,id,level); 500 } 501 } 502 ierr = VecRestoreArray( diag, &data_arr ); CHKERRQ(ierr); 503 ierr = VecDestroy( &diag ); CHKERRQ(ierr); 504 ierr = MatAssemblyBegin(Aarr[level1],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 505 ierr = MatAssemblyEnd(Aarr[level1],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 506 } 507 } 508 else{ 509 coarse_data = 0; 510 break; 511 } 512 data = coarse_data; 513 } 514 if( coarse_data ) { 515 ierr = PetscFree( coarse_data ); CHKERRQ( ierr ); 516 } 517 PetscPrintf(PETSC_COMM_WORLD,"\t[%d]%s %d levels\n",0,__FUNCT__,level + 1); 518 pc_gamg->m_data = 0; /* destroyed coordinate data */ 519 pc_gamg->m_Nlevels = level + 1; 520 fine_level = level; 521 ierr = PCMGSetLevels(a_pc,pc_gamg->m_Nlevels,PETSC_NULL);CHKERRQ(ierr); 522 523 /* set default smoothers */ 524 for ( lidx=1, level = pc_gamg->m_Nlevels-2; 525 lidx <= fine_level; 526 lidx++, level--) { 527 PetscReal emax, emin; 528 KSP smoother; PC subpc; 529 ierr = PCMGGetSmoother( a_pc, lidx, &smoother ); CHKERRQ(ierr); 530 ierr = KSPSetType( smoother, KSPCHEBYCHEV );CHKERRQ(ierr); 531 if( emaxs[level] > 0.0 ) emax=emaxs[level]; 532 else{ /* eigen estimate 'emax' */ 533 KSP eksp; Mat Lmat = Aarr[level]; 534 Vec bb, xx; PC pc; 535 536 ierr = MatGetVecs( Lmat, &bb, 0 ); CHKERRQ(ierr); 537 ierr = MatGetVecs( Lmat, &xx, 0 ); CHKERRQ(ierr); 538 { 539 PetscRandom rctx; 540 ierr = PetscRandomCreate(wcomm,&rctx);CHKERRQ(ierr); 541 ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); 542 ierr = VecSetRandom(bb,rctx);CHKERRQ(ierr); 543 ierr = PetscRandomDestroy( &rctx ); CHKERRQ(ierr); 544 } 545 ierr = KSPCreate(wcomm,&eksp);CHKERRQ(ierr); 546 ierr = KSPSetType( eksp, KSPCG ); CHKERRQ(ierr); 547 ierr = KSPSetInitialGuessNonzero( eksp, PETSC_FALSE ); CHKERRQ(ierr); 548 ierr = KSPSetOperators( eksp, Lmat, Lmat, DIFFERENT_NONZERO_PATTERN ); CHKERRQ( ierr ); 549 ierr = KSPGetPC( eksp, &pc );CHKERRQ( ierr ); 550 ierr = PCSetType( pc, PCPBJACOBI ); CHKERRQ(ierr); /* should be same as above */ 551 ierr = KSPSetTolerances( eksp, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT, 10 ); 552 CHKERRQ(ierr); 553 //ierr = KSPSetConvergenceTest( eksp, KSPSkipConverged, 0, 0 ); CHKERRQ(ierr); 554 ierr = KSPSetNormType( eksp, KSP_NORM_NONE ); CHKERRQ(ierr); 555 556 ierr = KSPSetComputeSingularValues( eksp,PETSC_TRUE ); CHKERRQ(ierr); 557 ierr = KSPSolve( eksp, bb, xx ); CHKERRQ(ierr); 558 ierr = KSPComputeExtremeSingularValues( eksp, &emax, &emin ); CHKERRQ(ierr); 559 ierr = VecDestroy( &xx ); CHKERRQ(ierr); 560 ierr = VecDestroy( &bb ); CHKERRQ(ierr); 561 ierr = KSPDestroy( &eksp ); CHKERRQ(ierr); 562 PetscPrintf(PETSC_COMM_WORLD,"\t\t\t%s max eigen=%e min=%e PC=%s\n",__FUNCT__,emax,emin,PETSC_GAMG_SMOOTHER); 563 } 564 { 565 PetscInt N1, N0, tt; 566 ierr = MatGetSize( Aarr[level], &N1, &tt ); CHKERRQ(ierr); 567 ierr = MatGetSize( Aarr[level+1], &N0, &tt ); CHKERRQ(ierr); 568 emin = 1.*emax/((PetscReal)N1/(PetscReal)N0); /* this should be about the coarsening rate */ 569 emax *= 1.05; 570 571 } 572 573 ierr = KSPSetOperators( smoother, Aarr[level], Aarr[level], DIFFERENT_NONZERO_PATTERN ); 574 ierr = KSPChebychevSetEigenvalues( smoother, emax, emin );CHKERRQ(ierr); 575 /*ierr = KSPSetTolerances(smoother,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,2); CHKERRQ(ierr);*/ 576 ierr = KSPGetPC( smoother, &subpc ); CHKERRQ(ierr); 577 ierr = PCSetType( subpc, PETSC_GAMG_SMOOTHER ); CHKERRQ(ierr); 578 ierr = KSPSetNormType( smoother, KSP_NORM_NONE ); CHKERRQ(ierr); 579 } 580 { 581 KSP smoother; /* coarse grid */ 582 Mat Lmat = Aarr[pc_gamg->m_Nlevels-1]; 583 ierr = PCMGGetSmoother( a_pc, 0, &smoother ); CHKERRQ(ierr); 584 ierr = KSPSetOperators( smoother, Lmat, Lmat, DIFFERENT_NONZERO_PATTERN ); 585 CHKERRQ(ierr); 586 ierr = KSPSetNormType( smoother, KSP_NORM_NONE ); CHKERRQ(ierr); 587 } 588 589 /* should be called in PCSetFromOptions_GAMG(), but cannot be called prior to PCMGSetLevels() */ 590 ierr = PCSetFromOptions_MG(a_pc); CHKERRQ(ierr); 591 { 592 PetscBool galerkin; 593 ierr = PCMGGetGalerkin( a_pc, &galerkin); CHKERRQ(ierr); 594 if(galerkin){ 595 SETERRQ(wcomm,PETSC_ERR_ARG_WRONG, "GAMG does galerkin manually so it must not be used in PC_MG."); 596 } 597 } 598 599 /* set interpolation between the levels, create timer stages, clean up */ 600 if( PETSC_FALSE ) { 601 char str[32]; 602 sprintf(str,"MG Level %d (%d)",0,pc_gamg->m_Nlevels-1); 603 PetscLogStageRegister(str, &gamg_stages[fine_level]); 604 } 605 for (lidx=0,level=pc_gamg->m_Nlevels-1; 606 lidx<fine_level; 607 lidx++, level--){ 608 ierr = PCMGSetInterpolation( a_pc, lidx+1, Parr[level] );CHKERRQ(ierr); 609 if( !PETSC_TRUE ) { 610 PetscViewer viewer; char fname[32]; 611 sprintf(fname,"Pmat_%d.m",level); 612 ierr = PetscViewerASCIIOpen( wcomm, fname, &viewer ); CHKERRQ(ierr); 613 ierr = PetscViewerSetFormat( viewer, PETSC_VIEWER_ASCII_MATLAB); CHKERRQ(ierr); 614 ierr = MatView( Parr[level], viewer ); CHKERRQ(ierr); 615 ierr = PetscViewerDestroy( &viewer ); 616 sprintf(fname,"Amat_%d.m",level); 617 ierr = PetscViewerASCIIOpen( wcomm, fname, &viewer ); CHKERRQ(ierr); 618 ierr = PetscViewerSetFormat( viewer, PETSC_VIEWER_ASCII_MATLAB); CHKERRQ(ierr); 619 ierr = MatView( Aarr[level], viewer ); CHKERRQ(ierr); 620 ierr = PetscViewerDestroy( &viewer ); 621 } 622 ierr = MatDestroy( &Parr[level] ); CHKERRQ(ierr); 623 ierr = MatDestroy( &Aarr[level] ); CHKERRQ(ierr); 624 if( PETSC_FALSE ) { 625 char str[32]; 626 sprintf(str,"MG Level %d (%d)",lidx+1,level-1); 627 PetscLogStageRegister(str, &gamg_stages[level-1]); 628 } 629 } 630 631 /* setupcalled is set to 0 so that MG is setup from scratch */ 632 a_pc->setupcalled = 0; 633 ierr = PCSetUp_MG(a_pc);CHKERRQ(ierr); 634 635 PetscFunctionReturn(0); 636 } 637 638 /* ------------------------------------------------------------------------- */ 639 /* 640 PCDestroy_GAMG - Destroys the private context for the GAMG preconditioner 641 that was created with PCCreate_GAMG(). 642 643 Input Parameter: 644 . pc - the preconditioner context 645 646 Application Interface Routine: PCDestroy() 647 */ 648 #undef __FUNCT__ 649 #define __FUNCT__ "PCDestroy_GAMG" 650 PetscErrorCode PCDestroy_GAMG(PC pc) 651 { 652 PetscErrorCode ierr; 653 PC_MG *mg = (PC_MG*)pc->data; 654 PC_GAMG *pc_gamg= (PC_GAMG*)mg->innerctx; 655 656 PetscFunctionBegin; 657 ierr = PCReset_GAMG(pc);CHKERRQ(ierr); 658 ierr = PetscFree(pc_gamg);CHKERRQ(ierr); 659 ierr = PCDestroy_MG(pc);CHKERRQ(ierr); 660 PetscFunctionReturn(0); 661 } 662 663 #undef __FUNCT__ 664 #define __FUNCT__ "PCSetFromOptions_GAMG" 665 PetscErrorCode PCSetFromOptions_GAMG(PC pc) 666 { 667 /* PetscErrorCode ierr; */ 668 /* PC_MG *mg = (PC_MG*)pc->data; */ 669 /* PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; */ 670 /* MPI_Comm comm = ((PetscObject)pc)->comm; */ 671 672 PetscFunctionBegin; 673 PetscFunctionReturn(0); 674 } 675 676 /* -------------------------------------------------------------------------- */ 677 /* 678 PCCreate_GAMG - Creates a GAMG preconditioner context, PC_GAMG 679 680 Input Parameter: 681 . pc - the preconditioner context 682 683 Application Interface Routine: PCCreate() 684 685 */ 686 /* MC 687 PCGAMG - Use algebraic multigrid preconditioning. This preconditioner requires you provide 688 fine grid discretization matrix and coordinates on the fine grid. 689 690 Options Database Key: 691 Multigrid options(inherited) 692 + -pc_mg_cycles <1>: 1 for V cycle, 2 for W-cycle (MGSetCycles) 693 . -pc_mg_smoothup <1>: Number of post-smoothing steps (MGSetNumberSmoothUp) 694 . -pc_mg_smoothdown <1>: Number of pre-smoothing steps (MGSetNumberSmoothDown) 695 -pc_mg_type <multiplicative>: (one of) additive multiplicative full cascade kascade 696 GAMG options: 697 698 Level: intermediate 699 Concepts: multigrid 700 701 .seealso: PCCreate(), PCSetType(), PCType (for list of available types), PC, PCMGType, 702 PCMGSetLevels(), PCMGGetLevels(), PCMGSetType(), MPSetCycles(), PCMGSetNumberSmoothDown(), 703 PCMGSetNumberSmoothUp(), PCMGGetCoarseSolve(), PCMGSetResidual(), PCMGSetInterpolation(), 704 PCMGSetRestriction(), PCMGGetSmoother(), PCMGGetSmootherUp(), PCMGGetSmootherDown(), 705 PCMGSetCyclesOnLevel(), PCMGSetRhs(), PCMGSetX(), PCMGSetR() 706 M */ 707 708 EXTERN_C_BEGIN 709 #undef __FUNCT__ 710 #define __FUNCT__ "PCCreate_GAMG" 711 PetscErrorCode PCCreate_GAMG(PC pc) 712 { 713 PetscErrorCode ierr; 714 PC_GAMG *pc_gamg; 715 PC_MG *mg; 716 PetscClassId cookie; 717 718 PetscFunctionBegin; 719 /* PCGAMG is an inherited class of PCMG. Initialize pc as PCMG */ 720 ierr = PCSetType(pc,PCMG);CHKERRQ(ierr); /* calls PCCreate_MG() and MGCreate_Private() */ 721 ierr = PetscObjectChangeTypeName((PetscObject)pc,PCGAMG);CHKERRQ(ierr); 722 723 /* create a supporting struct and attach it to pc */ 724 ierr = PetscNewLog(pc,PC_GAMG,&pc_gamg);CHKERRQ(ierr); 725 mg = (PC_MG*)pc->data; 726 mg->innerctx = pc_gamg; 727 728 pc_gamg->m_Nlevels = -1; 729 730 /* overwrite the pointers of PCMG by the functions of PCGAMG */ 731 pc->ops->setfromoptions = PCSetFromOptions_GAMG; 732 pc->ops->setup = PCSetUp_GAMG; 733 pc->ops->reset = PCReset_GAMG; 734 pc->ops->destroy = PCDestroy_GAMG; 735 736 ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc, 737 "PCSetCoordinates_C", 738 "PCSetCoordinates_GAMG", 739 PCSetCoordinates_GAMG);CHKERRQ(ierr); 740 static int count = 0; 741 if( count++ == 0 ) { 742 PetscClassIdRegister("GAMG Setup",&cookie); 743 PetscLogEventRegister("GAMG: createProl", cookie, &gamg_setup_stages[SET1]); 744 PetscLogEventRegister(" make graph", cookie, &gamg_setup_stages[SET3]); 745 PetscLogEventRegister(" MIS/Agg", cookie, &gamg_setup_stages[SET4]); 746 PetscLogEventRegister(" geo: growSupp", cookie, &gamg_setup_stages[SET5]); 747 PetscLogEventRegister(" geo: triangle", cookie, &gamg_setup_stages[SET6]); 748 PetscLogEventRegister(" search & set", cookie, &gamg_setup_stages[FIND_V]); 749 PetscLogEventRegister(" SA: init", cookie, &gamg_setup_stages[SET7]); 750 /* PetscLogEventRegister(" SA: frmProl0", cookie, &gamg_setup_stages[SET8]); */ 751 PetscLogEventRegister(" SA: smooth", cookie, &gamg_setup_stages[SET9]); 752 PetscLogEventRegister("GAMG: partLevel", cookie, &gamg_setup_stages[SET2]); 753 PetscLogEventRegister(" PL repartition", cookie, &gamg_setup_stages[SET12]); 754 /* PetscLogEventRegister(" PL move data", cookie, &gamg_setup_stages[SET13]); */ 755 /* PetscLogEventRegister("GAMG: fix", cookie, &gamg_setup_stages[SET10]); */ 756 /* PetscLogEventRegister("GAMG: set levels", cookie, &gamg_setup_stages[SET11]); */ 757 } 758 759 PetscFunctionReturn(0); 760 } 761 EXTERN_C_END 762