Date: 2021-03-03T22:26:20+00:00

Actual source code: sbaijfact.c
petsc-3.14.5 2021-03-03
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      2: #include <../src/mat/impls/baij/seq/baij.h>
      3: #include <../src/mat/impls/sbaij/seq/sbaij.h>
      4: #include <petsc/private/kernels/blockinvert.h>
      5: #include <petscis.h>

      7: PetscErrorCode MatGetInertia_SeqSBAIJ(Mat F,PetscInt *nneg,PetscInt *nzero,PetscInt *npos)
      8: {
      9:   Mat_SeqSBAIJ *fact=(Mat_SeqSBAIJ*)F->data;
     10:   MatScalar    *dd=fact->a;
     11:   PetscInt     mbs=fact->mbs,bs=F->rmap->bs,i,nneg_tmp,npos_tmp,*fi=fact->diag;

     14:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for bs: %D >1 yet",bs);
     15:   if (F->factorerrortype==MAT_FACTOR_NUMERIC_ZEROPIVOT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatFactor fails with numeric zeropivot");

     17:   nneg_tmp = 0; npos_tmp = 0;
     18:   for (i=0; i<mbs; i++) {
     19:     if (PetscRealPart(dd[*fi]) > 0.0) npos_tmp++;
     20:     else if (PetscRealPart(dd[*fi]) < 0.0) nneg_tmp++;
     21:     fi++;
     22:   }
     23:   if (nneg)  *nneg  = nneg_tmp;
     24:   if (npos)  *npos  = npos_tmp;
     25:   if (nzero) *nzero = mbs - nneg_tmp - npos_tmp;
     26:   return(0);
     27: }

     29: /*
     30:   Symbolic U^T*D*U factorization for SBAIJ format. Modified from SSF of YSMP.
     31:   Use Modified Sparse Row (MSR) storage for u and ju. See page 85, "Iterative Methods ..." by Saad.
     32: */
     33: PetscErrorCode MatCholeskyFactorSymbolic_SeqSBAIJ_MSR(Mat F,Mat A,IS perm,const MatFactorInfo *info)
     34: {
     35:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data,*b;
     37:   const PetscInt *rip,*ai,*aj;
     38:   PetscInt       i,mbs = a->mbs,*jutmp,bs = A->rmap->bs,bs2=a->bs2;
     39:   PetscInt       m,reallocs = 0,prow;
     40:   PetscInt       *jl,*q,jmin,jmax,juidx,nzk,qm,*iu,*ju,k,j,vj,umax,maxadd;
     41:   PetscReal      f = info->fill;
     42:   PetscBool      perm_identity;

     45:   /* check whether perm is the identity mapping */
     46:   ISIdentity(perm,&perm_identity);
     47:   ISGetIndices(perm,&rip);

     49:   if (perm_identity) { /* without permutation */
     50:     a->permute = PETSC_FALSE;

     52:     ai = a->i; aj = a->j;
     53:   } else {            /* non-trivial permutation */
     54:     a->permute = PETSC_TRUE;

     56:     MatReorderingSeqSBAIJ(A,perm);

     58:     ai = a->inew; aj = a->jnew;
     59:   }

     61:   /* initialization */
     62:   PetscMalloc1(mbs+1,&iu);
     63:   umax  = (PetscInt)(f*ai[mbs] + 1); umax += mbs + 1;
     64:   PetscMalloc1(umax,&ju);
     65:   iu[0] = mbs+1;
     66:   juidx = mbs + 1; /* index for ju */
     67:   /* jl linked list for pivot row -- linked list for col index */
     68:   PetscMalloc2(mbs,&jl,mbs,&q);
     69:   for (i=0; i<mbs; i++) {
     70:     jl[i] = mbs;
     71:     q[i]  = 0;
     72:   }

     74:   /* for each row k */
     75:   for (k=0; k<mbs; k++) {
     76:     for (i=0; i<mbs; i++) q[i] = 0;  /* to be removed! */
     77:     nzk  = 0; /* num. of nz blocks in k-th block row with diagonal block excluded */
     78:     q[k] = mbs;
     79:     /* initialize nonzero structure of k-th row to row rip[k] of A */
     80:     jmin = ai[rip[k]] +1; /* exclude diag[k] */
     81:     jmax = ai[rip[k]+1];
     82:     for (j=jmin; j<jmax; j++) {
     83:       vj = rip[aj[j]]; /* col. value */
     84:       if (vj > k) {
     85:         qm = k;
     86:         do {
     87:           m = qm; qm = q[m];
     88:         } while (qm < vj);
     89:         if (qm == vj) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Duplicate entry in A\n");
     90:         nzk++;
     91:         q[m]  = vj;
     92:         q[vj] = qm;
     93:       } /* if (vj > k) */
     94:     } /* for (j=jmin; j<jmax; j++) */

     96:     /* modify nonzero structure of k-th row by computing fill-in
     97:        for each row i to be merged in */
     98:     prow = k;
     99:     prow = jl[prow]; /* next pivot row (== mbs for symbolic factorization) */

    101:     while (prow < k) {
    102:       /* merge row prow into k-th row */
    103:       jmin = iu[prow] + 1; jmax = iu[prow+1];
    104:       qm   = k;
    105:       for (j=jmin; j<jmax; j++) {
    106:         vj = ju[j];
    107:         do {
    108:           m = qm; qm = q[m];
    109:         } while (qm < vj);
    110:         if (qm != vj) {
    111:           nzk++; q[m] = vj; q[vj] = qm; qm = vj;
    112:         }
    113:       }
    114:       prow = jl[prow]; /* next pivot row */
    115:     }

    117:     /* add k to row list for first nonzero element in k-th row */
    118:     if (nzk > 0) {
    119:       i     = q[k]; /* col value of first nonzero element in U(k, k+1:mbs-1) */
    120:       jl[k] = jl[i]; jl[i] = k;
    121:     }
    122:     iu[k+1] = iu[k] + nzk;

    124:     /* allocate more space to ju if needed */
    125:     if (iu[k+1] > umax) {
    126:       /* estimate how much additional space we will need */
    127:       /* use the strategy suggested by David Hysom <hysom@perch-t.icase.edu> */
    128:       /* just double the memory each time */
    129:       maxadd = umax;
    130:       if (maxadd < nzk) maxadd = (mbs-k)*(nzk+1)/2;
    131:       umax += maxadd;

    133:       /* allocate a longer ju */
    134:       PetscMalloc1(umax,&jutmp);
    135:       PetscArraycpy(jutmp,ju,iu[k]);
    136:       PetscFree(ju);
    137:       ju   = jutmp;
    138:       reallocs++; /* count how many times we realloc */
    139:     }

    141:     /* save nonzero structure of k-th row in ju */
    142:     i=k;
    143:     while (nzk--) {
    144:       i           = q[i];
    145:       ju[juidx++] = i;
    146:     }
    147:   }

    149: #if defined(PETSC_USE_INFO)
    150:   if (ai[mbs] != 0) {
    151:     PetscReal af = ((PetscReal)iu[mbs])/((PetscReal)ai[mbs]);
    152:     PetscInfo3(A,"Reallocs %D Fill ratio:given %g needed %g\n",reallocs,(double)f,(double)af);
    153:     PetscInfo1(A,"Run with -pc_factor_fill %g or use \n",(double)af);
    154:     PetscInfo1(A,"PCFactorSetFill(pc,%g);\n",(double)af);
    155:     PetscInfo(A,"for best performance.\n");
    156:   } else {
    157:     PetscInfo(A,"Empty matrix\n");
    158:   }
    159: #endif

    161:   ISRestoreIndices(perm,&rip);
    162:   PetscFree2(jl,q);

    164:   /* put together the new matrix */
    165:   MatSeqSBAIJSetPreallocation(F,bs,MAT_SKIP_ALLOCATION,NULL);

    167:   /* PetscLogObjectParent((PetscObject)B,(PetscObject)iperm); */
    168:   b                = (Mat_SeqSBAIJ*)(F)->data;
    169:   b->singlemalloc  = PETSC_FALSE;
    170:   b->free_a        = PETSC_TRUE;
    171:   b->free_ij       = PETSC_TRUE;

    173:   PetscMalloc1((iu[mbs]+1)*bs2,&b->a);
    174:   b->j    = ju;
    175:   b->i    = iu;
    176:   b->diag = NULL;
    177:   b->ilen = NULL;
    178:   b->imax = NULL;
    179:   b->row  = perm;

    181:   b->pivotinblocks = PETSC_FALSE; /* need to get from MatFactorInfo */

    183:   PetscObjectReference((PetscObject)perm);

    185:   b->icol = perm;
    186:   PetscObjectReference((PetscObject)perm);
    187:   PetscMalloc1(bs*mbs+bs,&b->solve_work);
    188:   /* In b structure:  Free imax, ilen, old a, old j.
    189:      Allocate idnew, solve_work, new a, new j */
    190:   PetscLogObjectMemory((PetscObject)F,(iu[mbs]-mbs)*(sizeof(PetscInt)+sizeof(MatScalar)));
    191:   b->maxnz = b->nz = iu[mbs];

    193:   (F)->info.factor_mallocs   = reallocs;
    194:   (F)->info.fill_ratio_given = f;
    195:   if (ai[mbs] != 0) {
    196:     (F)->info.fill_ratio_needed = ((PetscReal)iu[mbs])/((PetscReal)ai[mbs]);
    197:   } else {
    198:     (F)->info.fill_ratio_needed = 0.0;
    199:   }
    200:   MatSeqSBAIJSetNumericFactorization_inplace(F,perm_identity);
    201:   return(0);
    202: }
    203: /*
    204:     Symbolic U^T*D*U factorization for SBAIJ format.
    205:     See MatICCFactorSymbolic_SeqAIJ() for description of its data structure.
    206: */
    207: #include <petscbt.h>
    208: #include <../src/mat/utils/freespace.h>
    209: PetscErrorCode MatCholeskyFactorSymbolic_SeqSBAIJ(Mat fact,Mat A,IS perm,const MatFactorInfo *info)
    210: {
    211:   Mat_SeqSBAIJ       *a = (Mat_SeqSBAIJ*)A->data;
    212:   Mat_SeqSBAIJ       *b;
    213:   PetscErrorCode     ierr;
    214:   PetscBool          perm_identity,missing;
    215:   PetscReal          fill = info->fill;
    216:   const PetscInt     *rip,*ai=a->i,*aj=a->j;
    217:   PetscInt           i,mbs=a->mbs,bs=A->rmap->bs,reallocs=0,prow;
    218:   PetscInt           *jl,jmin,jmax,nzk,*ui,k,j,*il,nextprow;
    219:   PetscInt           nlnk,*lnk,ncols,*cols,*uj,**ui_ptr,*uj_ptr,*udiag;
    220:   PetscFreeSpaceList free_space=NULL,current_space=NULL;
    221:   PetscBT            lnkbt;

    224:   if (A->rmap->n != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Must be square matrix, rows %D columns %D",A->rmap->n,A->cmap->n);
    225:   MatMissingDiagonal(A,&missing,&i);
    226:   if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry %D",i);
    227:   if (bs > 1) {
    228:     MatCholeskyFactorSymbolic_SeqSBAIJ_inplace(fact,A,perm,info);
    229:     return(0);
    230:   }

    232:   /* check whether perm is the identity mapping */
    233:   ISIdentity(perm,&perm_identity);
    234:   if (!perm_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported for sbaij matrix. Use aij format");
    235:   a->permute = PETSC_FALSE;
    236:   ISGetIndices(perm,&rip);

    238:   /* initialization */
    239:   PetscMalloc1(mbs+1,&ui);
    240:   PetscMalloc1(mbs+1,&udiag);
    241:   ui[0] = 0;

    243:   /* jl: linked list for storing indices of the pivot rows
    244:      il: il[i] points to the 1st nonzero entry of U(i,k:mbs-1) */
    245:   PetscMalloc4(mbs,&ui_ptr,mbs,&il,mbs,&jl,mbs,&cols);
    246:   for (i=0; i<mbs; i++) {
    247:     jl[i] = mbs; il[i] = 0;
    248:   }

    250:   /* create and initialize a linked list for storing column indices of the active row k */
    251:   nlnk = mbs + 1;
    252:   PetscLLCreate(mbs,mbs,nlnk,lnk,lnkbt);

    254:   /* initial FreeSpace size is fill*(ai[mbs]+1) */
    255:   PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,ai[mbs]+1),&free_space);
    256:   current_space = free_space;

    258:   for (k=0; k<mbs; k++) {  /* for each active row k */
    259:     /* initialize lnk by the column indices of row rip[k] of A */
    260:     nzk   = 0;
    261:     ncols = ai[k+1] - ai[k];
    262:     if (!ncols) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_MAT_CH_ZRPVT,"Empty row %D in matrix ",k);
    263:     for (j=0; j<ncols; j++) {
    264:       i       = *(aj + ai[k] + j);
    265:       cols[j] = i;
    266:     }
    267:     PetscLLAdd(ncols,cols,mbs,nlnk,lnk,lnkbt);
    268:     nzk += nlnk;

    270:     /* update lnk by computing fill-in for each pivot row to be merged in */
    271:     prow = jl[k]; /* 1st pivot row */

    273:     while (prow < k) {
    274:       nextprow = jl[prow];
    275:       /* merge prow into k-th row */
    276:       jmin   = il[prow] + 1; /* index of the 2nd nzero entry in U(prow,k:mbs-1) */
    277:       jmax   = ui[prow+1];
    278:       ncols  = jmax-jmin;
    279:       uj_ptr = ui_ptr[prow] + jmin - ui[prow]; /* points to the 2nd nzero entry in U(prow,k:mbs-1) */
    280:       PetscLLAddSorted(ncols,uj_ptr,mbs,nlnk,lnk,lnkbt);
    281:       nzk   += nlnk;

    283:       /* update il and jl for prow */
    284:       if (jmin < jmax) {
    285:         il[prow] = jmin;
    286:         j        = *uj_ptr; jl[prow] = jl[j]; jl[j] = prow;
    287:       }
    288:       prow = nextprow;
    289:     }

    291:     /* if free space is not available, make more free space */
    292:     if (current_space->local_remaining<nzk) {
    293:       i    = mbs - k + 1; /* num of unfactored rows */
    294:       i    = PetscIntMultTruncate(i,PetscMin(nzk, i-1)); /* i*nzk, i*(i-1): estimated and max additional space needed */
    295:       PetscFreeSpaceGet(i,&current_space);
    296:       reallocs++;
    297:     }

    299:     /* copy data into free space, then initialize lnk */
    300:     PetscLLClean(mbs,mbs,nzk,lnk,current_space->array,lnkbt);

    302:     /* add the k-th row into il and jl */
    303:     if (nzk > 1) {
    304:       i     = current_space->array[1]; /* col value of the first nonzero element in U(k, k+1:mbs-1) */
    305:       jl[k] = jl[i]; jl[i] = k;
    306:       il[k] = ui[k] + 1;
    307:     }
    308:     ui_ptr[k] = current_space->array;

    310:     current_space->array           += nzk;
    311:     current_space->local_used      += nzk;
    312:     current_space->local_remaining -= nzk;

    314:     ui[k+1] = ui[k] + nzk;
    315:   }

    317:   ISRestoreIndices(perm,&rip);
    318:   PetscFree4(ui_ptr,il,jl,cols);

    320:   /* destroy list of free space and other temporary array(s) */
    321:   PetscMalloc1(ui[mbs]+1,&uj);
    322:   PetscFreeSpaceContiguous_Cholesky(&free_space,uj,mbs,ui,udiag); /* store matrix factor */
    323:   PetscLLDestroy(lnk,lnkbt);

    325:   /* put together the new matrix in MATSEQSBAIJ format */
    326:   MatSeqSBAIJSetPreallocation(fact,bs,MAT_SKIP_ALLOCATION,NULL);

    328:   b               = (Mat_SeqSBAIJ*)fact->data;
    329:   b->singlemalloc = PETSC_FALSE;
    330:   b->free_a       = PETSC_TRUE;
    331:   b->free_ij      = PETSC_TRUE;

    333:   PetscMalloc1(ui[mbs]+1,&b->a);

    335:   b->j         = uj;
    336:   b->i         = ui;
    337:   b->diag      = udiag;
    338:   b->free_diag = PETSC_TRUE;
    339:   b->ilen      = NULL;
    340:   b->imax      = NULL;
    341:   b->row       = perm;
    342:   b->icol      = perm;

    344:   PetscObjectReference((PetscObject)perm);
    345:   PetscObjectReference((PetscObject)perm);

    347:   b->pivotinblocks = PETSC_FALSE; /* need to get from MatFactorInfo */

    349:   PetscMalloc1(mbs+1,&b->solve_work);
    350:   PetscLogObjectMemory((PetscObject)fact,ui[mbs]*(sizeof(PetscInt)+sizeof(MatScalar)));

    352:   b->maxnz = b->nz = ui[mbs];

    354:   fact->info.factor_mallocs   = reallocs;
    355:   fact->info.fill_ratio_given = fill;
    356:   if (ai[mbs] != 0) {
    357:     fact->info.fill_ratio_needed = ((PetscReal)ui[mbs])/ai[mbs];
    358:   } else {
    359:     fact->info.fill_ratio_needed = 0.0;
    360:   }
    361: #if defined(PETSC_USE_INFO)
    362:   if (ai[mbs] != 0) {
    363:     PetscReal af = fact->info.fill_ratio_needed;
    364:     PetscInfo3(A,"Reallocs %D Fill ratio:given %g needed %g\n",reallocs,(double)fill,(double)af);
    365:     PetscInfo1(A,"Run with -pc_factor_fill %g or use \n",(double)af);
    366:     PetscInfo1(A,"PCFactorSetFill(pc,%g) for best performance.\n",(double)af);
    367:   } else {
    368:     PetscInfo(A,"Empty matrix\n");
    369:   }
    370: #endif
    371:   fact->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering;
    372:   return(0);
    373: }

    375: PetscErrorCode MatCholeskyFactorSymbolic_SeqSBAIJ_inplace(Mat fact,Mat A,IS perm,const MatFactorInfo *info)
    376: {
    377:   Mat_SeqSBAIJ       *a = (Mat_SeqSBAIJ*)A->data;
    378:   Mat_SeqSBAIJ       *b;
    379:   PetscErrorCode     ierr;
    380:   PetscBool          perm_identity,missing;
    381:   PetscReal          fill = info->fill;
    382:   const PetscInt     *rip,*ai,*aj;
    383:   PetscInt           i,mbs=a->mbs,bs=A->rmap->bs,reallocs=0,prow,d;
    384:   PetscInt           *jl,jmin,jmax,nzk,*ui,k,j,*il,nextprow;
    385:   PetscInt           nlnk,*lnk,ncols,*cols,*uj,**ui_ptr,*uj_ptr;
    386:   PetscFreeSpaceList free_space=NULL,current_space=NULL;
    387:   PetscBT            lnkbt;

    390:   MatMissingDiagonal(A,&missing,&d);
    391:   if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry %D",d);

    393:   /*
    394:    This code originally uses Modified Sparse Row (MSR) storage
    395:    (see page 85, "Iterative Methods ..." by Saad) for the output matrix B - bad choise!
    396:    Then it is rewritten so the factor B takes seqsbaij format. However the associated
    397:    MatCholeskyFactorNumeric_() have not been modified for the cases of bs>1 or !perm_identity,
    398:    thus the original code in MSR format is still used for these cases.
    399:    The code below should replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR() whenever
    400:    MatCholeskyFactorNumeric_() is modified for using sbaij symbolic factor.
    401:   */
    402:   if (bs > 1) {
    403:     MatCholeskyFactorSymbolic_SeqSBAIJ_MSR(fact,A,perm,info);
    404:     return(0);
    405:   }

    407:   /* check whether perm is the identity mapping */
    408:   ISIdentity(perm,&perm_identity);

    410:   if (perm_identity) {
    411:     a->permute = PETSC_FALSE;

    413:     ai = a->i; aj = a->j;
    414:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported for sbaij matrix. Use aij format");
    415:   ISGetIndices(perm,&rip);

    417:   /* initialization */
    418:   PetscMalloc1(mbs+1,&ui);
    419:   ui[0] = 0;

    421:   /* jl: linked list for storing indices of the pivot rows
    422:      il: il[i] points to the 1st nonzero entry of U(i,k:mbs-1) */
    423:   PetscMalloc4(mbs,&ui_ptr,mbs,&il,mbs,&jl,mbs,&cols);
    424:   for (i=0; i<mbs; i++) {
    425:     jl[i] = mbs; il[i] = 0;
    426:   }

    428:   /* create and initialize a linked list for storing column indices of the active row k */
    429:   nlnk = mbs + 1;
    430:   PetscLLCreate(mbs,mbs,nlnk,lnk,lnkbt);

    432:   /* initial FreeSpace size is fill*(ai[mbs]+1) */
    433:   PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,ai[mbs]+1),&free_space);
    434:   current_space = free_space;

    436:   for (k=0; k<mbs; k++) {  /* for each active row k */
    437:     /* initialize lnk by the column indices of row rip[k] of A */
    438:     nzk   = 0;
    439:     ncols = ai[rip[k]+1] - ai[rip[k]];
    440:     for (j=0; j<ncols; j++) {
    441:       i       = *(aj + ai[rip[k]] + j);
    442:       cols[j] = rip[i];
    443:     }
    444:     PetscLLAdd(ncols,cols,mbs,nlnk,lnk,lnkbt);
    445:     nzk += nlnk;

    447:     /* update lnk by computing fill-in for each pivot row to be merged in */
    448:     prow = jl[k]; /* 1st pivot row */

    450:     while (prow < k) {
    451:       nextprow = jl[prow];
    452:       /* merge prow into k-th row */
    453:       jmin   = il[prow] + 1; /* index of the 2nd nzero entry in U(prow,k:mbs-1) */
    454:       jmax   = ui[prow+1];
    455:       ncols  = jmax-jmin;
    456:       uj_ptr = ui_ptr[prow] + jmin - ui[prow]; /* points to the 2nd nzero entry in U(prow,k:mbs-1) */
    457:       PetscLLAddSorted(ncols,uj_ptr,mbs,nlnk,lnk,lnkbt);
    458:       nzk   += nlnk;

    460:       /* update il and jl for prow */
    461:       if (jmin < jmax) {
    462:         il[prow] = jmin;

    464:         j = *uj_ptr; jl[prow] = jl[j]; jl[j] = prow;
    465:       }
    466:       prow = nextprow;
    467:     }

    469:     /* if free space is not available, make more free space */
    470:     if (current_space->local_remaining<nzk) {
    471:       i    = mbs - k + 1; /* num of unfactored rows */
    472:       i    = PetscMin(PetscIntMultTruncate(i,nzk), PetscIntMultTruncate(i,i-1)); /* i*nzk, i*(i-1): estimated and max additional space needed */
    473:       PetscFreeSpaceGet(i,&current_space);
    474:       reallocs++;
    475:     }

    477:     /* copy data into free space, then initialize lnk */
    478:     PetscLLClean(mbs,mbs,nzk,lnk,current_space->array,lnkbt);

    480:     /* add the k-th row into il and jl */
    481:     if (nzk-1 > 0) {
    482:       i     = current_space->array[1]; /* col value of the first nonzero element in U(k, k+1:mbs-1) */
    483:       jl[k] = jl[i]; jl[i] = k;
    484:       il[k] = ui[k] + 1;
    485:     }
    486:     ui_ptr[k] = current_space->array;

    488:     current_space->array           += nzk;
    489:     current_space->local_used      += nzk;
    490:     current_space->local_remaining -= nzk;

    492:     ui[k+1] = ui[k] + nzk;
    493:   }

    495:   ISRestoreIndices(perm,&rip);
    496:   PetscFree4(ui_ptr,il,jl,cols);

    498:   /* destroy list of free space and other temporary array(s) */
    499:   PetscMalloc1(ui[mbs]+1,&uj);
    500:   PetscFreeSpaceContiguous(&free_space,uj);
    501:   PetscLLDestroy(lnk,lnkbt);

    503:   /* put together the new matrix in MATSEQSBAIJ format */
    504:   MatSeqSBAIJSetPreallocation(fact,bs,MAT_SKIP_ALLOCATION,NULL);

    506:   b               = (Mat_SeqSBAIJ*)fact->data;
    507:   b->singlemalloc = PETSC_FALSE;
    508:   b->free_a       = PETSC_TRUE;
    509:   b->free_ij      = PETSC_TRUE;

    511:   PetscMalloc1(ui[mbs]+1,&b->a);

    513:   b->j    = uj;
    514:   b->i    = ui;
    515:   b->diag = NULL;
    516:   b->ilen = NULL;
    517:   b->imax = NULL;
    518:   b->row  = perm;

    520:   b->pivotinblocks = PETSC_FALSE; /* need to get from MatFactorInfo */

    522:   PetscObjectReference((PetscObject)perm);
    523:   b->icol  = perm;
    524:   PetscObjectReference((PetscObject)perm);
    525:   PetscMalloc1(mbs+1,&b->solve_work);
    526:   PetscLogObjectMemory((PetscObject)fact,(ui[mbs]-mbs)*(sizeof(PetscInt)+sizeof(MatScalar)));
    527:   b->maxnz = b->nz = ui[mbs];

    529:   fact->info.factor_mallocs   = reallocs;
    530:   fact->info.fill_ratio_given = fill;
    531:   if (ai[mbs] != 0) {
    532:     fact->info.fill_ratio_needed = ((PetscReal)ui[mbs])/ai[mbs];
    533:   } else {
    534:     fact->info.fill_ratio_needed = 0.0;
    535:   }
    536: #if defined(PETSC_USE_INFO)
    537:   if (ai[mbs] != 0) {
    538:     PetscReal af = fact->info.fill_ratio_needed;
    539:     PetscInfo3(A,"Reallocs %D Fill ratio:given %g needed %g\n",reallocs,(double)fill,(double)af);
    540:     PetscInfo1(A,"Run with -pc_factor_fill %g or use \n",(double)af);
    541:     PetscInfo1(A,"PCFactorSetFill(pc,%g) for best performance.\n",(double)af);
    542:   } else {
    543:     PetscInfo(A,"Empty matrix\n");
    544:   }
    545: #endif
    546:   MatSeqSBAIJSetNumericFactorization_inplace(fact,perm_identity);
    547:   return(0);
    548: }

    550: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_N(Mat C,Mat A,const MatFactorInfo *info)
    551: {
    552:   Mat_SeqSBAIJ   *a   = (Mat_SeqSBAIJ*)A->data,*b = (Mat_SeqSBAIJ*)C->data;
    553:   IS             perm = b->row;
    555:   const PetscInt *ai,*aj,*perm_ptr,mbs=a->mbs,*bi=b->i,*bj=b->j;
    556:   PetscInt       i,j;
    557:   PetscInt       *a2anew,k,k1,jmin,jmax,*jl,*il,vj,nexti,ili;
    558:   PetscInt       bs  =A->rmap->bs,bs2 = a->bs2;
    559:   MatScalar      *ba = b->a,*aa,*ap,*dk,*uik;
    560:   MatScalar      *u,*diag,*rtmp,*rtmp_ptr;
    561:   MatScalar      *work;
    562:   PetscInt       *pivots;
    563:   PetscBool      allowzeropivot,zeropivotdetected;

    566:   /* initialization */
    567:   PetscCalloc1(bs2*mbs,&rtmp);
    568:   PetscMalloc2(mbs,&il,mbs,&jl);
    569:   allowzeropivot = PetscNot(A->erroriffailure);

    571:   il[0] = 0;
    572:   for (i=0; i<mbs; i++) jl[i] = mbs;

    574:   PetscMalloc3(bs2,&dk,bs2,&uik,bs,&work);
    575:   PetscMalloc1(bs,&pivots);

    577:   ISGetIndices(perm,&perm_ptr);

    579:   /* check permutation */
    580:   if (!a->permute) {
    581:     ai = a->i; aj = a->j; aa = a->a;
    582:   } else {
    583:     ai   = a->inew; aj = a->jnew;
    584:     PetscMalloc1(bs2*ai[mbs],&aa);
    585:     PetscArraycpy(aa,a->a,bs2*ai[mbs]);
    586:     PetscMalloc1(ai[mbs],&a2anew);
    587:     PetscArraycpy(a2anew,a->a2anew,ai[mbs]);

    589:     for (i=0; i<mbs; i++) {
    590:       jmin = ai[i]; jmax = ai[i+1];
    591:       for (j=jmin; j<jmax; j++) {
    592:         while (a2anew[j] != j) {
    593:           k = a2anew[j]; a2anew[j] = a2anew[k]; a2anew[k] = k;
    594:           for (k1=0; k1<bs2; k1++) {
    595:             dk[k1]       = aa[k*bs2+k1];
    596:             aa[k*bs2+k1] = aa[j*bs2+k1];
    597:             aa[j*bs2+k1] = dk[k1];
    598:           }
    599:         }
    600:         /* transform columnoriented blocks that lie in the lower triangle to roworiented blocks */
    601:         if (i > aj[j]) {
    602:           ap = aa + j*bs2;                     /* ptr to the beginning of j-th block of aa */
    603:           for (k=0; k<bs2; k++) dk[k] = ap[k]; /* dk <- j-th block of aa */
    604:           for (k=0; k<bs; k++) {               /* j-th block of aa <- dk^T */
    605:             for (k1=0; k1<bs; k1++) *ap++ = dk[k + bs*k1];
    606:           }
    607:         }
    608:       }
    609:     }
    610:     PetscFree(a2anew);
    611:   }

    613:   /* for each row k */
    614:   for (k = 0; k<mbs; k++) {

    616:     /*initialize k-th row with elements nonzero in row perm(k) of A */
    617:     jmin = ai[perm_ptr[k]]; jmax = ai[perm_ptr[k]+1];

    619:     ap = aa + jmin*bs2;
    620:     for (j = jmin; j < jmax; j++) {
    621:       vj       = perm_ptr[aj[j]];   /* block col. index */
    622:       rtmp_ptr = rtmp + vj*bs2;
    623:       for (i=0; i<bs2; i++) *rtmp_ptr++ = *ap++;
    624:     }

    626:     /* modify k-th row by adding in those rows i with U(i,k) != 0 */
    627:     PetscArraycpy(dk,rtmp+k*bs2,bs2);
    628:     i    = jl[k]; /* first row to be added to k_th row  */

    630:     while (i < k) {
    631:       nexti = jl[i]; /* next row to be added to k_th row */

    633:       /* compute multiplier */
    634:       ili = il[i];  /* index of first nonzero element in U(i,k:bms-1) */

    636:       /* uik = -inv(Di)*U_bar(i,k) */
    637:       diag = ba + i*bs2;
    638:       u    = ba + ili*bs2;
    639:       PetscArrayzero(uik,bs2);
    640:       PetscKernel_A_gets_A_minus_B_times_C(bs,uik,diag,u);

    642:       /* update D(k) += -U(i,k)^T * U_bar(i,k) */
    643:       PetscKernel_A_gets_A_plus_Btranspose_times_C(bs,dk,uik,u);
    644:       PetscLogFlops(4.0*bs*bs2);

    646:       /* update -U(i,k) */
    647:       PetscArraycpy(ba+ili*bs2,uik,bs2);

    649:       /* add multiple of row i to k-th row ... */
    650:       jmin = ili + 1; jmax = bi[i+1];
    651:       if (jmin < jmax) {
    652:         for (j=jmin; j<jmax; j++) {
    653:           /* rtmp += -U(i,k)^T * U_bar(i,j) */
    654:           rtmp_ptr = rtmp + bj[j]*bs2;
    655:           u        = ba + j*bs2;
    656:           PetscKernel_A_gets_A_plus_Btranspose_times_C(bs,rtmp_ptr,uik,u);
    657:         }
    658:         PetscLogFlops(2.0*bs*bs2*(jmax-jmin));

    660:         /* ... add i to row list for next nonzero entry */
    661:         il[i] = jmin;             /* update il(i) in column k+1, ... mbs-1 */
    662:         j     = bj[jmin];
    663:         jl[i] = jl[j]; jl[j] = i; /* update jl */
    664:       }
    665:       i = nexti;
    666:     }

    668:     /* save nonzero entries in k-th row of U ... */

    670:     /* invert diagonal block */
    671:     diag = ba+k*bs2;
    672:     PetscArraycpy(diag,dk,bs2);

    674:     PetscKernel_A_gets_inverse_A(bs,diag,pivots,work,allowzeropivot,&zeropivotdetected);
    675:     if (zeropivotdetected) C->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT;

    677:     jmin = bi[k]; jmax = bi[k+1];
    678:     if (jmin < jmax) {
    679:       for (j=jmin; j<jmax; j++) {
    680:         vj       = bj[j];      /* block col. index of U */
    681:         u        = ba + j*bs2;
    682:         rtmp_ptr = rtmp + vj*bs2;
    683:         for (k1=0; k1<bs2; k1++) {
    684:           *u++        = *rtmp_ptr;
    685:           *rtmp_ptr++ = 0.0;
    686:         }
    687:       }

    689:       /* ... add k to row list for first nonzero entry in k-th row */
    690:       il[k] = jmin;
    691:       i     = bj[jmin];
    692:       jl[k] = jl[i]; jl[i] = k;
    693:     }
    694:   }

    696:   PetscFree(rtmp);
    697:   PetscFree2(il,jl);
    698:   PetscFree3(dk,uik,work);
    699:   PetscFree(pivots);
    700:   if (a->permute) {
    701:     PetscFree(aa);
    702:   }

    704:   ISRestoreIndices(perm,&perm_ptr);

    706:   C->ops->solve          = MatSolve_SeqSBAIJ_N_inplace;
    707:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_N_inplace;
    708:   C->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_N_inplace;
    709:   C->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_N_inplace;

    711:   C->assembled    = PETSC_TRUE;
    712:   C->preallocated = PETSC_TRUE;

    714:   PetscLogFlops(1.3333*bs*bs2*b->mbs); /* from inverting diagonal blocks */
    715:   return(0);
    716: }

    718: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering(Mat C,Mat A,const MatFactorInfo *info)
    719: {
    720:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data,*b = (Mat_SeqSBAIJ*)C->data;
    722:   PetscInt       i,j,mbs=a->mbs,*bi=b->i,*bj=b->j;
    723:   PetscInt       *ai,*aj,k,k1,jmin,jmax,*jl,*il,vj,nexti,ili;
    724:   PetscInt       bs  =A->rmap->bs,bs2 = a->bs2;
    725:   MatScalar      *ba = b->a,*aa,*ap,*dk,*uik;
    726:   MatScalar      *u,*diag,*rtmp,*rtmp_ptr;
    727:   MatScalar      *work;
    728:   PetscInt       *pivots;
    729:   PetscBool      allowzeropivot,zeropivotdetected;

    732:   PetscCalloc1(bs2*mbs,&rtmp);
    733:   PetscMalloc2(mbs,&il,mbs,&jl);
    734:   il[0] = 0;
    735:   for (i=0; i<mbs; i++) jl[i] = mbs;

    737:   PetscMalloc3(bs2,&dk,bs2,&uik,bs,&work);
    738:   PetscMalloc1(bs,&pivots);
    739:   allowzeropivot = PetscNot(A->erroriffailure);

    741:   ai = a->i; aj = a->j; aa = a->a;

    743:   /* for each row k */
    744:   for (k = 0; k<mbs; k++) {

    746:     /*initialize k-th row with elements nonzero in row k of A */
    747:     jmin = ai[k]; jmax = ai[k+1];
    748:     ap   = aa + jmin*bs2;
    749:     for (j = jmin; j < jmax; j++) {
    750:       vj       = aj[j];   /* block col. index */
    751:       rtmp_ptr = rtmp + vj*bs2;
    752:       for (i=0; i<bs2; i++) *rtmp_ptr++ = *ap++;
    753:     }

    755:     /* modify k-th row by adding in those rows i with U(i,k) != 0 */
    756:     PetscArraycpy(dk,rtmp+k*bs2,bs2);
    757:     i    = jl[k]; /* first row to be added to k_th row  */

    759:     while (i < k) {
    760:       nexti = jl[i]; /* next row to be added to k_th row */

    762:       /* compute multiplier */
    763:       ili = il[i];  /* index of first nonzero element in U(i,k:bms-1) */

    765:       /* uik = -inv(Di)*U_bar(i,k) */
    766:       diag = ba + i*bs2;
    767:       u    = ba + ili*bs2;
    768:       PetscArrayzero(uik,bs2);
    769:       PetscKernel_A_gets_A_minus_B_times_C(bs,uik,diag,u);

    771:       /* update D(k) += -U(i,k)^T * U_bar(i,k) */
    772:       PetscKernel_A_gets_A_plus_Btranspose_times_C(bs,dk,uik,u);
    773:       PetscLogFlops(2.0*bs*bs2);

    775:       /* update -U(i,k) */
    776:       PetscArraycpy(ba+ili*bs2,uik,bs2);

    778:       /* add multiple of row i to k-th row ... */
    779:       jmin = ili + 1; jmax = bi[i+1];
    780:       if (jmin < jmax) {
    781:         for (j=jmin; j<jmax; j++) {
    782:           /* rtmp += -U(i,k)^T * U_bar(i,j) */
    783:           rtmp_ptr = rtmp + bj[j]*bs2;
    784:           u        = ba + j*bs2;
    785:           PetscKernel_A_gets_A_plus_Btranspose_times_C(bs,rtmp_ptr,uik,u);
    786:         }
    787:         PetscLogFlops(2.0*bs*bs2*(jmax-jmin));

    789:         /* ... add i to row list for next nonzero entry */
    790:         il[i] = jmin;             /* update il(i) in column k+1, ... mbs-1 */
    791:         j     = bj[jmin];
    792:         jl[i] = jl[j]; jl[j] = i; /* update jl */
    793:       }
    794:       i = nexti;
    795:     }

    797:     /* save nonzero entries in k-th row of U ... */

    799:     /* invert diagonal block */
    800:     diag = ba+k*bs2;
    801:     PetscArraycpy(diag,dk,bs2);

    803:     PetscKernel_A_gets_inverse_A(bs,diag,pivots,work,allowzeropivot,&zeropivotdetected);
    804:     if (zeropivotdetected) C->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT;

    806:     jmin = bi[k]; jmax = bi[k+1];
    807:     if (jmin < jmax) {
    808:       for (j=jmin; j<jmax; j++) {
    809:         vj       = bj[j];      /* block col. index of U */
    810:         u        = ba + j*bs2;
    811:         rtmp_ptr = rtmp + vj*bs2;
    812:         for (k1=0; k1<bs2; k1++) {
    813:           *u++        = *rtmp_ptr;
    814:           *rtmp_ptr++ = 0.0;
    815:         }
    816:       }

    818:       /* ... add k to row list for first nonzero entry in k-th row */
    819:       il[k] = jmin;
    820:       i     = bj[jmin];
    821:       jl[k] = jl[i]; jl[i] = k;
    822:     }
    823:   }

    825:   PetscFree(rtmp);
    826:   PetscFree2(il,jl);
    827:   PetscFree3(dk,uik,work);
    828:   PetscFree(pivots);

    830:   C->ops->solve          = MatSolve_SeqSBAIJ_N_NaturalOrdering_inplace;
    831:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_N_NaturalOrdering_inplace;
    832:   C->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_N_NaturalOrdering_inplace;
    833:   C->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_N_NaturalOrdering_inplace;
    834:   C->assembled           = PETSC_TRUE;
    835:   C->preallocated        = PETSC_TRUE;

    837:   PetscLogFlops(1.3333*bs*bs2*b->mbs); /* from inverting diagonal blocks */
    838:   return(0);
    839: }

    841: /*
    842:     Numeric U^T*D*U factorization for SBAIJ format. Modified from SNF of YSMP.
    843:     Version for blocks 2 by 2.
    844: */
    845: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_2(Mat C,Mat A,const MatFactorInfo *info)
    846: {
    847:   Mat_SeqSBAIJ   *a   = (Mat_SeqSBAIJ*)A->data,*b = (Mat_SeqSBAIJ*)C->data;
    848:   IS             perm = b->row;
    850:   const PetscInt *ai,*aj,*perm_ptr;
    851:   PetscInt       i,j,mbs=a->mbs,*bi=b->i,*bj=b->j;
    852:   PetscInt       *a2anew,k,k1,jmin,jmax,*jl,*il,vj,nexti,ili;
    853:   MatScalar      *ba = b->a,*aa,*ap;
    854:   MatScalar      *u,*diag,*rtmp,*rtmp_ptr,dk[4],uik[4];
    855:   PetscReal      shift = info->shiftamount;
    856:   PetscBool      allowzeropivot,zeropivotdetected;

    859:   allowzeropivot = PetscNot(A->erroriffailure);

    861:   /* initialization */
    862:   /* il and jl record the first nonzero element in each row of the accessing
    863:      window U(0:k, k:mbs-1).
    864:      jl:    list of rows to be added to uneliminated rows
    865:             i>= k: jl(i) is the first row to be added to row i
    866:             i<  k: jl(i) is the row following row i in some list of rows
    867:             jl(i) = mbs indicates the end of a list
    868:      il(i): points to the first nonzero element in columns k,...,mbs-1 of
    869:             row i of U */
    870:   PetscCalloc1(4*mbs,&rtmp);
    871:   PetscMalloc2(mbs,&il,mbs,&jl);
    872:   il[0] = 0;
    873:   for (i=0; i<mbs; i++) jl[i] = mbs;

    875:   ISGetIndices(perm,&perm_ptr);

    877:   /* check permutation */
    878:   if (!a->permute) {
    879:     ai = a->i; aj = a->j; aa = a->a;
    880:   } else {
    881:     ai   = a->inew; aj = a->jnew;
    882:     PetscMalloc1(4*ai[mbs],&aa);
    883:     PetscArraycpy(aa,a->a,4*ai[mbs]);
    884:     PetscMalloc1(ai[mbs],&a2anew);
    885:     PetscArraycpy(a2anew,a->a2anew,ai[mbs]);

    887:     for (i=0; i<mbs; i++) {
    888:       jmin = ai[i]; jmax = ai[i+1];
    889:       for (j=jmin; j<jmax; j++) {
    890:         while (a2anew[j] != j) {
    891:           k = a2anew[j]; a2anew[j] = a2anew[k]; a2anew[k] = k;
    892:           for (k1=0; k1<4; k1++) {
    893:             dk[k1]     = aa[k*4+k1];
    894:             aa[k*4+k1] = aa[j*4+k1];
    895:             aa[j*4+k1] = dk[k1];
    896:           }
    897:         }
    898:         /* transform columnoriented blocks that lie in the lower triangle to roworiented blocks */
    899:         if (i > aj[j]) {
    900:           ap    = aa + j*4;  /* ptr to the beginning of the block */
    901:           dk[1] = ap[1];     /* swap ap[1] and ap[2] */
    902:           ap[1] = ap[2];
    903:           ap[2] = dk[1];
    904:         }
    905:       }
    906:     }
    907:     PetscFree(a2anew);
    908:   }

    910:   /* for each row k */
    911:   for (k = 0; k<mbs; k++) {

    913:     /*initialize k-th row with elements nonzero in row perm(k) of A */
    914:     jmin = ai[perm_ptr[k]]; jmax = ai[perm_ptr[k]+1];
    915:     ap   = aa + jmin*4;
    916:     for (j = jmin; j < jmax; j++) {
    917:       vj       = perm_ptr[aj[j]];   /* block col. index */
    918:       rtmp_ptr = rtmp + vj*4;
    919:       for (i=0; i<4; i++) *rtmp_ptr++ = *ap++;
    920:     }

    922:     /* modify k-th row by adding in those rows i with U(i,k) != 0 */
    923:     PetscArraycpy(dk,rtmp+k*4,4);
    924:     i    = jl[k]; /* first row to be added to k_th row  */

    926:     while (i < k) {
    927:       nexti = jl[i]; /* next row to be added to k_th row */

    929:       /* compute multiplier */
    930:       ili = il[i];  /* index of first nonzero element in U(i,k:bms-1) */

    932:       /* uik = -inv(Di)*U_bar(i,k): - ba[ili]*ba[i] */
    933:       diag   = ba + i*4;
    934:       u      = ba + ili*4;
    935:       uik[0] = -(diag[0]*u[0] + diag[2]*u[1]);
    936:       uik[1] = -(diag[1]*u[0] + diag[3]*u[1]);
    937:       uik[2] = -(diag[0]*u[2] + diag[2]*u[3]);
    938:       uik[3] = -(diag[1]*u[2] + diag[3]*u[3]);

    940:       /* update D(k) += -U(i,k)^T * U_bar(i,k): dk += uik*ba[ili] */
    941:       dk[0] += uik[0]*u[0] + uik[1]*u[1];
    942:       dk[1] += uik[2]*u[0] + uik[3]*u[1];
    943:       dk[2] += uik[0]*u[2] + uik[1]*u[3];
    944:       dk[3] += uik[2]*u[2] + uik[3]*u[3];

    946:       PetscLogFlops(16.0*2.0);

    948:       /* update -U(i,k): ba[ili] = uik */
    949:       PetscArraycpy(ba+ili*4,uik,4);

    951:       /* add multiple of row i to k-th row ... */
    952:       jmin = ili + 1; jmax = bi[i+1];
    953:       if (jmin < jmax) {
    954:         for (j=jmin; j<jmax; j++) {
    955:           /* rtmp += -U(i,k)^T * U_bar(i,j): rtmp[bj[j]] += uik*ba[j]; */
    956:           rtmp_ptr     = rtmp + bj[j]*4;
    957:           u            = ba + j*4;
    958:           rtmp_ptr[0] += uik[0]*u[0] + uik[1]*u[1];
    959:           rtmp_ptr[1] += uik[2]*u[0] + uik[3]*u[1];
    960:           rtmp_ptr[2] += uik[0]*u[2] + uik[1]*u[3];
    961:           rtmp_ptr[3] += uik[2]*u[2] + uik[3]*u[3];
    962:         }
    963:         PetscLogFlops(16.0*(jmax-jmin));

    965:         /* ... add i to row list for next nonzero entry */
    966:         il[i] = jmin;             /* update il(i) in column k+1, ... mbs-1 */
    967:         j     = bj[jmin];
    968:         jl[i] = jl[j]; jl[j] = i; /* update jl */
    969:       }
    970:       i = nexti;
    971:     }

    973:     /* save nonzero entries in k-th row of U ... */

    975:     /* invert diagonal block */
    976:     diag = ba+k*4;
    977:     PetscArraycpy(diag,dk,4);
    978:     PetscKernel_A_gets_inverse_A_2(diag,shift,allowzeropivot,&zeropivotdetected);
    979:     if (zeropivotdetected) C->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT;

    981:     jmin = bi[k]; jmax = bi[k+1];
    982:     if (jmin < jmax) {
    983:       for (j=jmin; j<jmax; j++) {
    984:         vj       = bj[j];      /* block col. index of U */
    985:         u        = ba + j*4;
    986:         rtmp_ptr = rtmp + vj*4;
    987:         for (k1=0; k1<4; k1++) {
    988:           *u++        = *rtmp_ptr;
    989:           *rtmp_ptr++ = 0.0;
    990:         }
    991:       }

    993:       /* ... add k to row list for first nonzero entry in k-th row */
    994:       il[k] = jmin;
    995:       i     = bj[jmin];
    996:       jl[k] = jl[i]; jl[i] = k;
    997:     }
    998:   }

    1000:   PetscFree(rtmp);
    1001:   PetscFree2(il,jl);
    1002:   if (a->permute) {
    1003:     PetscFree(aa);
    1004:   }
    1005:   ISRestoreIndices(perm,&perm_ptr);

    1007:   C->ops->solve          = MatSolve_SeqSBAIJ_2_inplace;
    1008:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_2_inplace;
    1009:   C->assembled           = PETSC_TRUE;
    1010:   C->preallocated        = PETSC_TRUE;

    1012:   PetscLogFlops(1.3333*8*b->mbs); /* from inverting diagonal blocks */
    1013:   return(0);
    1014: }

    1016: /*
    1017:       Version for when blocks are 2 by 2 Using natural ordering
    1018: */
    1019: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering(Mat C,Mat A,const MatFactorInfo *info)
    1020: {
    1021:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data,*b = (Mat_SeqSBAIJ*)C->data;
    1023:   PetscInt       i,j,mbs=a->mbs,*bi=b->i,*bj=b->j;
    1024:   PetscInt       *ai,*aj,k,k1,jmin,jmax,*jl,*il,vj,nexti,ili;
    1025:   MatScalar      *ba = b->a,*aa,*ap,dk[8],uik[8];
    1026:   MatScalar      *u,*diag,*rtmp,*rtmp_ptr;
    1027:   PetscReal      shift = info->shiftamount;
    1028:   PetscBool      allowzeropivot,zeropivotdetected;

    1031:   allowzeropivot = PetscNot(A->erroriffailure);

    1033:   /* initialization */
    1034:   /* il and jl record the first nonzero element in each row of the accessing
    1035:      window U(0:k, k:mbs-1).
    1036:      jl:    list of rows to be added to uneliminated rows
    1037:             i>= k: jl(i) is the first row to be added to row i
    1038:             i<  k: jl(i) is the row following row i in some list of rows
    1039:             jl(i) = mbs indicates the end of a list
    1040:      il(i): points to the first nonzero element in columns k,...,mbs-1 of
    1041:             row i of U */
    1042:   PetscCalloc1(4*mbs,&rtmp);
    1043:   PetscMalloc2(mbs,&il,mbs,&jl);
    1044:   il[0] = 0;
    1045:   for (i=0; i<mbs; i++) jl[i] = mbs;

    1047:   ai = a->i; aj = a->j; aa = a->a;

    1049:   /* for each row k */
    1050:   for (k = 0; k<mbs; k++) {

    1052:     /*initialize k-th row with elements nonzero in row k of A */
    1053:     jmin = ai[k]; jmax = ai[k+1];
    1054:     ap   = aa + jmin*4;
    1055:     for (j = jmin; j < jmax; j++) {
    1056:       vj       = aj[j];   /* block col. index */
    1057:       rtmp_ptr = rtmp + vj*4;
    1058:       for (i=0; i<4; i++) *rtmp_ptr++ = *ap++;
    1059:     }

    1061:     /* modify k-th row by adding in those rows i with U(i,k) != 0 */
    1062:     PetscArraycpy(dk,rtmp+k*4,4);
    1063:     i    = jl[k]; /* first row to be added to k_th row  */

    1065:     while (i < k) {
    1066:       nexti = jl[i]; /* next row to be added to k_th row */

    1068:       /* compute multiplier */
    1069:       ili = il[i];  /* index of first nonzero element in U(i,k:bms-1) */

    1071:       /* uik = -inv(Di)*U_bar(i,k): - ba[ili]*ba[i] */
    1072:       diag   = ba + i*4;
    1073:       u      = ba + ili*4;
    1074:       uik[0] = -(diag[0]*u[0] + diag[2]*u[1]);
    1075:       uik[1] = -(diag[1]*u[0] + diag[3]*u[1]);
    1076:       uik[2] = -(diag[0]*u[2] + diag[2]*u[3]);
    1077:       uik[3] = -(diag[1]*u[2] + diag[3]*u[3]);

    1079:       /* update D(k) += -U(i,k)^T * U_bar(i,k): dk += uik*ba[ili] */
    1080:       dk[0] += uik[0]*u[0] + uik[1]*u[1];
    1081:       dk[1] += uik[2]*u[0] + uik[3]*u[1];
    1082:       dk[2] += uik[0]*u[2] + uik[1]*u[3];
    1083:       dk[3] += uik[2]*u[2] + uik[3]*u[3];

    1085:       PetscLogFlops(16.0*2.0);

    1087:       /* update -U(i,k): ba[ili] = uik */
    1088:       PetscArraycpy(ba+ili*4,uik,4);

    1090:       /* add multiple of row i to k-th row ... */
    1091:       jmin = ili + 1; jmax = bi[i+1];
    1092:       if (jmin < jmax) {
    1093:         for (j=jmin; j<jmax; j++) {
    1094:           /* rtmp += -U(i,k)^T * U_bar(i,j): rtmp[bj[j]] += uik*ba[j]; */
    1095:           rtmp_ptr     = rtmp + bj[j]*4;
    1096:           u            = ba + j*4;
    1097:           rtmp_ptr[0] += uik[0]*u[0] + uik[1]*u[1];
    1098:           rtmp_ptr[1] += uik[2]*u[0] + uik[3]*u[1];
    1099:           rtmp_ptr[2] += uik[0]*u[2] + uik[1]*u[3];
    1100:           rtmp_ptr[3] += uik[2]*u[2] + uik[3]*u[3];
    1101:         }
    1102:         PetscLogFlops(16.0*(jmax-jmin));

    1104:         /* ... add i to row list for next nonzero entry */
    1105:         il[i] = jmin;             /* update il(i) in column k+1, ... mbs-1 */
    1106:         j     = bj[jmin];
    1107:         jl[i] = jl[j]; jl[j] = i; /* update jl */
    1108:       }
    1109:       i = nexti;
    1110:     }

    1112:     /* save nonzero entries in k-th row of U ... */

    1114:     /* invert diagonal block */
    1115:     diag = ba+k*4;
    1116:     PetscArraycpy(diag,dk,4);
    1117:     PetscKernel_A_gets_inverse_A_2(diag,shift,allowzeropivot,&zeropivotdetected);
    1118:     if (zeropivotdetected) C->factorerrortype = MAT_FACTOR_NUMERIC_ZEROPIVOT;

    1120:     jmin = bi[k]; jmax = bi[k+1];
    1121:     if (jmin < jmax) {
    1122:       for (j=jmin; j<jmax; j++) {
    1123:         vj       = bj[j];      /* block col. index of U */
    1124:         u        = ba + j*4;
    1125:         rtmp_ptr = rtmp + vj*4;
    1126:         for (k1=0; k1<4; k1++) {
    1127:           *u++        = *rtmp_ptr;
    1128:           *rtmp_ptr++ = 0.0;
    1129:         }
    1130:       }

    1132:       /* ... add k to row list for first nonzero entry in k-th row */
    1133:       il[k] = jmin;
    1134:       i     = bj[jmin];
    1135:       jl[k] = jl[i]; jl[i] = k;
    1136:     }
    1137:   }

    1139:   PetscFree(rtmp);
    1140:   PetscFree2(il,jl);

    1142:   C->ops->solve          = MatSolve_SeqSBAIJ_2_NaturalOrdering_inplace;
    1143:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_2_NaturalOrdering_inplace;
    1144:   C->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_2_NaturalOrdering_inplace;
    1145:   C->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_2_NaturalOrdering_inplace;
    1146:   C->assembled           = PETSC_TRUE;
    1147:   C->preallocated        = PETSC_TRUE;

    1149:   PetscLogFlops(1.3333*8*b->mbs); /* from inverting diagonal blocks */
    1150:   return(0);
    1151: }

    1153: /*
    1154:     Numeric U^T*D*U factorization for SBAIJ format.
    1155:     Version for blocks are 1 by 1.
    1156: */
    1157: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace(Mat C,Mat A,const MatFactorInfo *info)
    1158: {
    1159:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data,*b=(Mat_SeqSBAIJ*)C->data;
    1160:   IS             ip=b->row;
    1162:   const PetscInt *ai,*aj,*rip;
    1163:   PetscInt       *a2anew,i,j,mbs=a->mbs,*bi=b->i,*bj=b->j,*bcol;
    1164:   PetscInt       k,jmin,jmax,*jl,*il,col,nexti,ili,nz;
    1165:   MatScalar      *rtmp,*ba=b->a,*bval,*aa,dk,uikdi;
    1166:   PetscReal      rs;
    1167:   FactorShiftCtx sctx;

    1170:   /* MatPivotSetUp(): initialize shift context sctx */
    1171:   PetscMemzero(&sctx,sizeof(FactorShiftCtx));

    1173:   ISGetIndices(ip,&rip);
    1174:   if (!a->permute) {
    1175:     ai = a->i; aj = a->j; aa = a->a;
    1176:   } else {
    1177:     ai     = a->inew; aj = a->jnew;
    1178:     nz     = ai[mbs];
    1179:     PetscMalloc1(nz,&aa);
    1180:     a2anew = a->a2anew;
    1181:     bval   = a->a;
    1182:     for (j=0; j<nz; j++) {
    1183:       aa[a2anew[j]] = *(bval++);
    1184:     }
    1185:   }

    1187:   /* initialization */
    1188:   /* il and jl record the first nonzero element in each row of the accessing
    1189:      window U(0:k, k:mbs-1).
    1190:      jl:    list of rows to be added to uneliminated rows
    1191:             i>= k: jl(i) is the first row to be added to row i
    1192:             i<  k: jl(i) is the row following row i in some list of rows
    1193:             jl(i) = mbs indicates the end of a list
    1194:      il(i): points to the first nonzero element in columns k,...,mbs-1 of
    1195:             row i of U */
    1196:   PetscMalloc3(mbs,&rtmp,mbs,&il,mbs,&jl);

    1198:   do {
    1199:     sctx.newshift = PETSC_FALSE;
    1200:     il[0] = 0;
    1201:     for (i=0; i<mbs; i++) {
    1202:       rtmp[i] = 0.0; jl[i] = mbs;
    1203:     }

    1205:     for (k = 0; k<mbs; k++) {
    1206:       /*initialize k-th row by the perm[k]-th row of A */
    1207:       jmin = ai[rip[k]]; jmax = ai[rip[k]+1];
    1208:       bval = ba + bi[k];
    1209:       for (j = jmin; j < jmax; j++) {
    1210:         col       = rip[aj[j]];
    1211:         rtmp[col] = aa[j];
    1212:         *bval++   = 0.0; /* for in-place factorization */
    1213:       }

    1215:       /* shift the diagonal of the matrix */
    1216:       if (sctx.nshift) rtmp[k] += sctx.shift_amount;

    1218:       /* modify k-th row by adding in those rows i with U(i,k)!=0 */
    1219:       dk = rtmp[k];
    1220:       i  = jl[k]; /* first row to be added to k_th row  */

    1222:       while (i < k) {
    1223:         nexti = jl[i]; /* next row to be added to k_th row */

    1225:         /* compute multiplier, update diag(k) and U(i,k) */
    1226:         ili     = il[i]; /* index of first nonzero element in U(i,k:bms-1) */
    1227:         uikdi   = -ba[ili]*ba[bi[i]]; /* diagonal(k) */
    1228:         dk     += uikdi*ba[ili];
    1229:         ba[ili] = uikdi; /* -U(i,k) */

    1231:         /* add multiple of row i to k-th row */
    1232:         jmin = ili + 1; jmax = bi[i+1];
    1233:         if (jmin < jmax) {
    1234:           for (j=jmin; j<jmax; j++) rtmp[bj[j]] += uikdi*ba[j];
    1235:           PetscLogFlops(2.0*(jmax-jmin));

    1237:           /* update il and jl for row i */
    1238:           il[i] = jmin;
    1239:           j     = bj[jmin]; jl[i] = jl[j]; jl[j] = i;
    1240:         }
    1241:         i = nexti;
    1242:       }

    1244:       /* shift the diagonals when zero pivot is detected */
    1245:       /* compute rs=sum of abs(off-diagonal) */
    1246:       rs   = 0.0;
    1247:       jmin = bi[k]+1;
    1248:       nz   = bi[k+1] - jmin;
    1249:       if (nz) {
    1250:         bcol = bj + jmin;
    1251:         while (nz--) {
    1252:           rs += PetscAbsScalar(rtmp[*bcol]);
    1253:           bcol++;
    1254:         }
    1255:       }

    1257:       sctx.rs = rs;
    1258:       sctx.pv = dk;
    1259:       MatPivotCheck(C,A,info,&sctx,k);
    1260:       if (sctx.newshift) break;    /* sctx.shift_amount is updated */
    1261:       dk = sctx.pv;

    1263:       /* copy data into U(k,:) */
    1264:       ba[bi[k]] = 1.0/dk; /* U(k,k) */
    1265:       jmin      = bi[k]+1; jmax = bi[k+1];
    1266:       if (jmin < jmax) {
    1267:         for (j=jmin; j<jmax; j++) {
    1268:           col = bj[j]; ba[j] = rtmp[col]; rtmp[col] = 0.0;
    1269:         }
    1270:         /* add the k-th row into il and jl */
    1271:         il[k] = jmin;
    1272:         i     = bj[jmin]; jl[k] = jl[i]; jl[i] = k;
    1273:       }
    1274:     }
    1275:   } while (sctx.newshift);
    1276:   PetscFree3(rtmp,il,jl);
    1277:   if (a->permute) {PetscFree(aa);}

    1279:   ISRestoreIndices(ip,&rip);

    1281:   C->ops->solve          = MatSolve_SeqSBAIJ_1_inplace;
    1282:   C->ops->solves         = MatSolves_SeqSBAIJ_1_inplace;
    1283:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_1_inplace;
    1284:   C->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_1_inplace;
    1285:   C->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_1_inplace;
    1286:   C->assembled           = PETSC_TRUE;
    1287:   C->preallocated        = PETSC_TRUE;

    1289:   PetscLogFlops(C->rmap->N);
    1290:   if (sctx.nshift) {
    1291:     if (info->shifttype == (PetscReal)MAT_SHIFT_NONZERO) {
    1292:       PetscInfo2(A,"number of shiftnz tries %D, shift_amount %g\n",sctx.nshift,(double)sctx.shift_amount);
    1293:     } else if (info->shifttype == (PetscReal)MAT_SHIFT_POSITIVE_DEFINITE) {
    1294:       PetscInfo2(A,"number of shiftpd tries %D, shift_amount %g\n",sctx.nshift,(double)sctx.shift_amount);
    1295:     }
    1296:   }
    1297:   return(0);
    1298: }

    1300: /*
    1301:   Version for when blocks are 1 by 1 Using natural ordering under new datastructure
    1302:   Modified from MatCholeskyFactorNumeric_SeqAIJ()
    1303: */
    1304: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering(Mat B,Mat A,const MatFactorInfo *info)
    1305: {
    1306:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
    1307:   Mat_SeqSBAIJ   *b=(Mat_SeqSBAIJ*)B->data;
    1309:   PetscInt       i,j,mbs=A->rmap->n,*bi=b->i,*bj=b->j,*bdiag=b->diag,*bjtmp;
    1310:   PetscInt       *ai=a->i,*aj=a->j,*ajtmp;
    1311:   PetscInt       k,jmin,jmax,*c2r,*il,col,nexti,ili,nz;
    1312:   MatScalar      *rtmp,*ba=b->a,*bval,*aa=a->a,dk,uikdi;
    1313:   FactorShiftCtx sctx;
    1314:   PetscReal      rs;
    1315:   MatScalar      d,*v;

    1318:   PetscMalloc3(mbs,&rtmp,mbs,&il,mbs,&c2r);

    1320:   /* MatPivotSetUp(): initialize shift context sctx */
    1321:   PetscMemzero(&sctx,sizeof(FactorShiftCtx));

    1323:   if (info->shifttype == (PetscReal)MAT_SHIFT_POSITIVE_DEFINITE) { /* set sctx.shift_top=max{rs} */
    1324:     sctx.shift_top = info->zeropivot;

    1326:     PetscArrayzero(rtmp,mbs);

    1328:     for (i=0; i<mbs; i++) {
    1329:       /* calculate sum(|aij|)-RealPart(aii), amt of shift needed for this row */
    1330:       d        = (aa)[a->diag[i]];
    1331:       rtmp[i] += -PetscRealPart(d);  /* diagonal entry */
    1332:       ajtmp    = aj + ai[i] + 1;     /* exclude diagonal */
    1333:       v        = aa + ai[i] + 1;
    1334:       nz       = ai[i+1] - ai[i] - 1;
    1335:       for (j=0; j<nz; j++) {
    1336:         rtmp[i]        += PetscAbsScalar(v[j]);
    1337:         rtmp[ajtmp[j]] += PetscAbsScalar(v[j]);
    1338:       }
    1339:       if (PetscRealPart(rtmp[i]) > sctx.shift_top) sctx.shift_top = PetscRealPart(rtmp[i]);
    1340:     }
    1341:     sctx.shift_top *= 1.1;
    1342:     sctx.nshift_max = 5;
    1343:     sctx.shift_lo   = 0.;
    1344:     sctx.shift_hi   = 1.;
    1345:   }

    1347:   /* allocate working arrays
    1348:      c2r: linked list, keep track of pivot rows for a given column. c2r[col]: head of the list for a given col
    1349:      il:  for active k row, il[i] gives the index of the 1st nonzero entry in U[i,k:n-1] in bj and ba arrays
    1350:   */
    1351:   do {
    1352:     sctx.newshift = PETSC_FALSE;

    1354:     for (i=0; i<mbs; i++) c2r[i] = mbs;
    1355:     if (mbs) il[0] = 0;

    1357:     for (k = 0; k<mbs; k++) {
    1358:       /* zero rtmp */
    1359:       nz    = bi[k+1] - bi[k];
    1360:       bjtmp = bj + bi[k];
    1361:       for (j=0; j<nz; j++) rtmp[bjtmp[j]] = 0.0;

    1363:       /* load in initial unfactored row */
    1364:       bval = ba + bi[k];
    1365:       jmin = ai[k]; jmax = ai[k+1];
    1366:       for (j = jmin; j < jmax; j++) {
    1367:         col       = aj[j];
    1368:         rtmp[col] = aa[j];
    1369:         *bval++   = 0.0; /* for in-place factorization */
    1370:       }
    1371:       /* shift the diagonal of the matrix: ZeropivotApply() */
    1372:       rtmp[k] += sctx.shift_amount;  /* shift the diagonal of the matrix */

    1374:       /* modify k-th row by adding in those rows i with U(i,k)!=0 */
    1375:       dk = rtmp[k];
    1376:       i  = c2r[k]; /* first row to be added to k_th row  */

    1378:       while (i < k) {
    1379:         nexti = c2r[i]; /* next row to be added to k_th row */

    1381:         /* compute multiplier, update diag(k) and U(i,k) */
    1382:         ili     = il[i]; /* index of first nonzero element in U(i,k:bms-1) */
    1383:         uikdi   = -ba[ili]*ba[bdiag[i]]; /* diagonal(k) */
    1384:         dk     += uikdi*ba[ili]; /* update diag[k] */
    1385:         ba[ili] = uikdi; /* -U(i,k) */

    1387:         /* add multiple of row i to k-th row */
    1388:         jmin = ili + 1; jmax = bi[i+1];
    1389:         if (jmin < jmax) {
    1390:           for (j=jmin; j<jmax; j++) rtmp[bj[j]] += uikdi*ba[j];
    1391:           /* update il and c2r for row i */
    1392:           il[i] = jmin;
    1393:           j     = bj[jmin]; c2r[i] = c2r[j]; c2r[j] = i;
    1394:         }
    1395:         i = nexti;
    1396:       }

    1398:       /* copy data into U(k,:) */
    1399:       rs   = 0.0;
    1400:       jmin = bi[k]; jmax = bi[k+1]-1;
    1401:       if (jmin < jmax) {
    1402:         for (j=jmin; j<jmax; j++) {
    1403:           col = bj[j]; ba[j] = rtmp[col]; rs += PetscAbsScalar(ba[j]);
    1404:         }
    1405:         /* add the k-th row into il and c2r */
    1406:         il[k] = jmin;
    1407:         i     = bj[jmin]; c2r[k] = c2r[i]; c2r[i] = k;
    1408:       }

    1410:       sctx.rs = rs;
    1411:       sctx.pv = dk;
    1412:       MatPivotCheck(B,A,info,&sctx,k);
    1413:       if (sctx.newshift) break;
    1414:       dk = sctx.pv;

    1416:       ba[bdiag[k]] = 1.0/dk; /* U(k,k) */
    1417:     }
    1418:   } while (sctx.newshift);

    1420:   PetscFree3(rtmp,il,c2r);

    1422:   B->ops->solve          = MatSolve_SeqSBAIJ_1_NaturalOrdering;
    1423:   B->ops->solves         = MatSolves_SeqSBAIJ_1;
    1424:   B->ops->solvetranspose = MatSolve_SeqSBAIJ_1_NaturalOrdering;
    1425:   B->ops->matsolve       = MatMatSolve_SeqSBAIJ_1_NaturalOrdering;
    1426:   B->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_1_NaturalOrdering;
    1427:   B->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_1_NaturalOrdering;

    1429:   B->assembled    = PETSC_TRUE;
    1430:   B->preallocated = PETSC_TRUE;

    1432:   PetscLogFlops(B->rmap->n);

    1434:   /* MatPivotView() */
    1435:   if (sctx.nshift) {
    1436:     if (info->shifttype == (PetscReal)MAT_SHIFT_POSITIVE_DEFINITE) {
    1437:       PetscInfo4(A,"number of shift_pd tries %D, shift_amount %g, diagonal shifted up by %e fraction top_value %e\n",sctx.nshift,(double)sctx.shift_amount,(double)sctx.shift_fraction,(double)sctx.shift_top);
    1438:     } else if (info->shifttype == (PetscReal)MAT_SHIFT_NONZERO) {
    1439:       PetscInfo2(A,"number of shift_nz tries %D, shift_amount %g\n",sctx.nshift,(double)sctx.shift_amount);
    1440:     } else if (info->shifttype == (PetscReal)MAT_SHIFT_INBLOCKS) {
    1441:       PetscInfo2(A,"number of shift_inblocks applied %D, each shift_amount %g\n",sctx.nshift,(double)info->shiftamount);
    1442:     }
    1443:   }
    1444:   return(0);
    1445: }

    1447: PetscErrorCode MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace(Mat C,Mat A,const MatFactorInfo *info)
    1448: {
    1449:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data,*b=(Mat_SeqSBAIJ*)C->data;
    1451:   PetscInt       i,j,mbs = a->mbs;
    1452:   PetscInt       *ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j;
    1453:   PetscInt       k,jmin,*jl,*il,nexti,ili,*acol,*bcol,nz;
    1454:   MatScalar      *rtmp,*ba=b->a,*aa=a->a,dk,uikdi,*aval,*bval;
    1455:   PetscReal      rs;
    1456:   FactorShiftCtx sctx;

    1459:   /* MatPivotSetUp(): initialize shift context sctx */
    1460:   PetscMemzero(&sctx,sizeof(FactorShiftCtx));

    1462:   /* initialization */
    1463:   /* il and jl record the first nonzero element in each row of the accessing
    1464:      window U(0:k, k:mbs-1).
    1465:      jl:    list of rows to be added to uneliminated rows
    1466:             i>= k: jl(i) is the first row to be added to row i
    1467:             i<  k: jl(i) is the row following row i in some list of rows
    1468:             jl(i) = mbs indicates the end of a list
    1469:      il(i): points to the first nonzero element in U(i,k:mbs-1)
    1470:   */
    1471:   PetscMalloc1(mbs,&rtmp);
    1472:   PetscMalloc2(mbs,&il,mbs,&jl);

    1474:   do {
    1475:     sctx.newshift = PETSC_FALSE;
    1476:     il[0] = 0;
    1477:     for (i=0; i<mbs; i++) {
    1478:       rtmp[i] = 0.0; jl[i] = mbs;
    1479:     }

    1481:     for (k = 0; k<mbs; k++) {
    1482:       /*initialize k-th row with elements nonzero in row perm(k) of A */
    1483:       nz   = ai[k+1] - ai[k];
    1484:       acol = aj + ai[k];
    1485:       aval = aa + ai[k];
    1486:       bval = ba + bi[k];
    1487:       while (nz--) {
    1488:         rtmp[*acol++] = *aval++;
    1489:         *bval++       = 0.0; /* for in-place factorization */
    1490:       }

    1492:       /* shift the diagonal of the matrix */
    1493:       if (sctx.nshift) rtmp[k] += sctx.shift_amount;

    1495:       /* modify k-th row by adding in those rows i with U(i,k)!=0 */
    1496:       dk = rtmp[k];
    1497:       i  = jl[k]; /* first row to be added to k_th row  */

    1499:       while (i < k) {
    1500:         nexti = jl[i]; /* next row to be added to k_th row */
    1501:         /* compute multiplier, update D(k) and U(i,k) */
    1502:         ili     = il[i]; /* index of first nonzero element in U(i,k:bms-1) */
    1503:         uikdi   = -ba[ili]*ba[bi[i]];
    1504:         dk     += uikdi*ba[ili];
    1505:         ba[ili] = uikdi; /* -U(i,k) */

    1507:         /* add multiple of row i to k-th row ... */
    1508:         jmin = ili + 1;
    1509:         nz   = bi[i+1] - jmin;
    1510:         if (nz > 0) {
    1511:           bcol = bj + jmin;
    1512:           bval = ba + jmin;
    1513:           PetscLogFlops(2.0*nz);
    1514:           while (nz--) rtmp[*bcol++] += uikdi*(*bval++);

    1516:           /* update il and jl for i-th row */
    1517:           il[i] = jmin;
    1518:           j     = bj[jmin]; jl[i] = jl[j]; jl[j] = i;
    1519:         }
    1520:         i = nexti;
    1521:       }

    1523:       /* shift the diagonals when zero pivot is detected */
    1524:       /* compute rs=sum of abs(off-diagonal) */
    1525:       rs   = 0.0;
    1526:       jmin = bi[k]+1;
    1527:       nz   = bi[k+1] - jmin;
    1528:       if (nz) {
    1529:         bcol = bj + jmin;
    1530:         while (nz--) {
    1531:           rs += PetscAbsScalar(rtmp[*bcol]);
    1532:           bcol++;
    1533:         }
    1534:       }

    1536:       sctx.rs = rs;
    1537:       sctx.pv = dk;
    1538:       MatPivotCheck(C,A,info,&sctx,k);
    1539:       if (sctx.newshift) break;    /* sctx.shift_amount is updated */
    1540:       dk = sctx.pv;

    1542:       /* copy data into U(k,:) */
    1543:       ba[bi[k]] = 1.0/dk;
    1544:       jmin      = bi[k]+1;
    1545:       nz        = bi[k+1] - jmin;
    1546:       if (nz) {
    1547:         bcol = bj + jmin;
    1548:         bval = ba + jmin;
    1549:         while (nz--) {
    1550:           *bval++       = rtmp[*bcol];
    1551:           rtmp[*bcol++] = 0.0;
    1552:         }
    1553:         /* add k-th row into il and jl */
    1554:         il[k] = jmin;
    1555:         i     = bj[jmin]; jl[k] = jl[i]; jl[i] = k;
    1556:       }
    1557:     } /* end of for (k = 0; k<mbs; k++) */
    1558:   } while (sctx.newshift);
    1559:   PetscFree(rtmp);
    1560:   PetscFree2(il,jl);

    1562:   C->ops->solve          = MatSolve_SeqSBAIJ_1_NaturalOrdering_inplace;
    1563:   C->ops->solves         = MatSolves_SeqSBAIJ_1_inplace;
    1564:   C->ops->solvetranspose = MatSolve_SeqSBAIJ_1_NaturalOrdering_inplace;
    1565:   C->ops->forwardsolve   = MatForwardSolve_SeqSBAIJ_1_NaturalOrdering_inplace;
    1566:   C->ops->backwardsolve  = MatBackwardSolve_SeqSBAIJ_1_NaturalOrdering_inplace;

    1568:   C->assembled    = PETSC_TRUE;
    1569:   C->preallocated = PETSC_TRUE;

    1571:   PetscLogFlops(C->rmap->N);
    1572:   if (sctx.nshift) {
    1573:     if (info->shifttype == (PetscReal)MAT_SHIFT_NONZERO) {
    1574:       PetscInfo2(A,"number of shiftnz tries %D, shift_amount %g\n",sctx.nshift,(double)sctx.shift_amount);
    1575:     } else if (info->shifttype == (PetscReal)MAT_SHIFT_POSITIVE_DEFINITE) {
    1576:       PetscInfo2(A,"number of shiftpd tries %D, shift_amount %g\n",sctx.nshift,(double)sctx.shift_amount);
    1577:     }
    1578:   }
    1579:   return(0);
    1580: }

    1582: PetscErrorCode MatCholeskyFactor_SeqSBAIJ(Mat A,IS perm,const MatFactorInfo *info)
    1583: {
    1585:   Mat            C;

    1588:   MatGetFactor(A,"petsc",MAT_FACTOR_CHOLESKY,&C);
    1589:   MatCholeskyFactorSymbolic(C,A,perm,info);
    1590:   MatCholeskyFactorNumeric(C,A,info);

    1592:   A->ops->solve          = C->ops->solve;
    1593:   A->ops->solvetranspose = C->ops->solvetranspose;

    1595:   MatHeaderMerge(A,&C);
    1596:   return(0);
    1597: }