Actual source code: aomapping.c
petsc-3.13.6 2020-09-29
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      2: /*
      3:   These AO Section 1.5 Writing Application Codes with PETSc ordering routines do not require that the input
      4:   be a permutation, but merely a 1-1 mapping. This implementation still
      5:   keeps the entire ordering on each processor.
      6: */

      8:  #include <../src/vec/is/ao/aoimpl.h>

     10: typedef struct {
     11:   PetscInt N;
     12:   PetscInt *app;       /* app[i] is the partner for petsc[appPerm[i]] */
     13:   PetscInt *appPerm;
     14:   PetscInt *petsc;     /* petsc[j] is the partner for app[petscPerm[j]] */
     15:   PetscInt *petscPerm;
     16: } AO_Mapping;

     18: PetscErrorCode AODestroy_Mapping(AO ao)
     19: {
     20:   AO_Mapping     *aomap = (AO_Mapping*) ao->data;

     24:   PetscFree4(aomap->app,aomap->appPerm,aomap->petsc,aomap->petscPerm);
     25:   PetscFree(aomap);
     26:   return(0);
     27: }

     29: PetscErrorCode AOView_Mapping(AO ao, PetscViewer viewer)
     30: {
     31:   AO_Mapping     *aomap = (AO_Mapping*) ao->data;
     32:   PetscMPIInt    rank;
     33:   PetscInt       i;
     34:   PetscBool      iascii;

     38:   MPI_Comm_rank(PetscObjectComm((PetscObject)ao), &rank);
     39:   if (rank) return(0);
     40:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
     41:   if (iascii) {
     42:     PetscViewerASCIIPrintf(viewer, "Number of elements in ordering %D\n", aomap->N);
     43:     PetscViewerASCIIPrintf(viewer, "   App.   PETSc\n");
     44:     for (i = 0; i < aomap->N; i++) {
     45:       PetscViewerASCIIPrintf(viewer, "%D   %D    %D\n", i, aomap->app[i], aomap->petsc[aomap->appPerm[i]]);
     46:     }
     47:   }
     48:   return(0);
     49: }

     51: PetscErrorCode AOPetscToApplication_Mapping(AO ao, PetscInt n, PetscInt *ia)
     52: {
     53:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
     54:   PetscInt   *app   = aomap->app;
     55:   PetscInt   *petsc = aomap->petsc;
     56:   PetscInt   *perm  = aomap->petscPerm;
     57:   PetscInt   N      = aomap->N;
     58:   PetscInt   low, high, mid=0;
     59:   PetscInt   idex;
     60:   PetscInt   i;

     62:   /* It would be possible to use a single bisection search, which
     63:      recursively divided the indices to be converted, and searched
     64:      partitions which contained an index. This would result in
     65:      better running times if indices are clustered.
     66:   */
     68:   for (i = 0; i < n; i++) {
     69:     idex = ia[i];
     70:     if (idex < 0) continue;
     71:     /* Use bisection since the array is sorted */
     72:     low  = 0;
     73:     high = N - 1;
     74:     while (low <= high) {
     75:       mid = (low + high)/2;
     76:       if (idex == petsc[mid]) break;
     77:       else if (idex < petsc[mid]) high = mid - 1;
     78:       else low = mid + 1;
     79:     }
     80:     if (low > high) ia[i] = -1;
     81:     else            ia[i] = app[perm[mid]];
     82:   }
     83:   return(0);
     84: }

     86: PetscErrorCode AOApplicationToPetsc_Mapping(AO ao, PetscInt n, PetscInt *ia)
     87: {
     88:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
     89:   PetscInt   *app   = aomap->app;
     90:   PetscInt   *petsc = aomap->petsc;
     91:   PetscInt   *perm  = aomap->appPerm;
     92:   PetscInt   N      = aomap->N;
     93:   PetscInt   low, high, mid=0;
     94:   PetscInt   idex;
     95:   PetscInt   i;

     97:   /* It would be possible to use a single bisection search, which
     98:      recursively divided the indices to be converted, and searched
     99:      partitions which contained an index. This would result in
    100:      better running times if indices are clustered.
    101:   */
    103:   for (i = 0; i < n; i++) {
    104:     idex = ia[i];
    105:     if (idex < 0) continue;
    106:     /* Use bisection since the array is sorted */
    107:     low  = 0;
    108:     high = N - 1;
    109:     while (low <= high) {
    110:       mid = (low + high)/2;
    111:       if (idex == app[mid]) break;
    112:       else if (idex < app[mid]) high = mid - 1;
    113:       else low = mid + 1;
    114:     }
    115:     if (low > high) ia[i] = -1;
    116:     else            ia[i] = petsc[perm[mid]];
    117:   }
    118:   return(0);
    119: }

    121: static struct _AOOps AOps = {AOView_Mapping,
    122:                              AODestroy_Mapping,
    123:                              AOPetscToApplication_Mapping,
    124:                              AOApplicationToPetsc_Mapping,
    125:                              NULL,
    126:                              NULL,
    127:                              NULL,
    128:                              NULL};

    130: /*@C
    131:   AOMappingHasApplicationIndex - Searches for the supplied Section 1.5 Writing Application Codes with PETSc index.

    133:   Input Parameters:
    134: + ao       - The AOMapping
    135: - index    - The Section 1.5 Writing Application Codes with PETSc index

    137:   Output Parameter:
    138: . hasIndex - Flag is PETSC_TRUE if the index exists

    140:   Level: intermediate

    142: .seealso: AOMappingHasPetscIndex(), AOCreateMapping()
    143: @*/
    144: PetscErrorCode  AOMappingHasApplicationIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
    145: {
    146:   AO_Mapping *aomap;
    147:   PetscInt   *app;
    148:   PetscInt   low, high, mid;

    153:   aomap = (AO_Mapping*) ao->data;
    154:   app   = aomap->app;
    155:   /* Use bisection since the array is sorted */
    156:   low  = 0;
    157:   high = aomap->N - 1;
    158:   while (low <= high) {
    159:     mid = (low + high)/2;
    160:     if (idex == app[mid]) break;
    161:     else if (idex < app[mid]) high = mid - 1;
    162:     else low = mid + 1;
    163:   }
    164:   if (low > high) *hasIndex = PETSC_FALSE;
    165:   else *hasIndex = PETSC_TRUE;
    166:   return(0);
    167: }

    169: /*@
    170:   AOMappingHasPetscIndex - Searches for the supplied petsc index.

    172:   Input Parameters:
    173: + ao       - The AOMapping
    174: - index    - The petsc index

    176:   Output Parameter:
    177: . hasIndex - Flag is PETSC_TRUE if the index exists

    179:   Level: intermediate

    181: .seealso: AOMappingHasApplicationIndex(), AOCreateMapping()
    182: @*/
    183: PetscErrorCode  AOMappingHasPetscIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
    184: {
    185:   AO_Mapping *aomap;
    186:   PetscInt   *petsc;
    187:   PetscInt   low, high, mid;

    192:   aomap = (AO_Mapping*) ao->data;
    193:   petsc = aomap->petsc;
    194:   /* Use bisection since the array is sorted */
    195:   low  = 0;
    196:   high = aomap->N - 1;
    197:   while (low <= high) {
    198:     mid = (low + high)/2;
    199:     if (idex == petsc[mid]) break;
    200:     else if (idex < petsc[mid]) high = mid - 1;
    201:     else low = mid + 1;
    202:   }
    203:   if (low > high) *hasIndex = PETSC_FALSE;
    204:   else *hasIndex = PETSC_TRUE;
    205:   return(0);
    206: }

    208: /*@C
    209:   AOCreateMapping - Creates a basic Section 1.5 Writing Application Codes with PETSc mapping using two integer arrays.

    211:   Input Parameters:
    212: + comm    - MPI communicator that is to share AO
    213: . napp    - size of integer arrays
    214: . myapp   - integer array that defines an ordering
    215: - mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)

    217:   Output Parameter:
    218: . aoout   - the new Section 1.5 Writing Application Codes with PETSc mapping

    220:   Options Database Key:
    221: . -ao_view : call AOView() at the conclusion of AOCreateMapping()

    223:   Level: beginner

    225:     Notes:
    226:     the arrays myapp and mypetsc need NOT contain the all the integers 0 to napp-1, that is there CAN be "holes"  in the indices.
    227:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

    229: .seealso: AOCreateBasic(), AOCreateBasic(), AOCreateMappingIS(), AODestroy()
    230: @*/
    231: PetscErrorCode  AOCreateMapping(MPI_Comm comm,PetscInt napp,const PetscInt myapp[],const PetscInt mypetsc[],AO *aoout)
    232: {
    233:   AO             ao;
    234:   AO_Mapping     *aomap;
    235:   PetscInt       *allpetsc,  *allapp;
    236:   PetscInt       *petscPerm, *appPerm;
    237:   PetscInt       *petsc;
    238:   PetscMPIInt    size, rank,*lens, *disp,nnapp;
    239:   PetscInt       N, start;
    240:   PetscInt       i;

    245:   *aoout = 0;
    246:   AOInitializePackage();

    248:   PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);
    249:   PetscNewLog(ao,&aomap);
    250:   PetscMemcpy(ao->ops, &AOps, sizeof(AOps));
    251:   ao->data = (void*) aomap;

    253:   /* transmit all lengths to all processors */
    254:   MPI_Comm_size(comm, &size);
    255:   MPI_Comm_rank(comm, &rank);
    256:   PetscMalloc2(size, &lens,size,&disp);
    257:   nnapp = napp;
    258:   MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);
    259:   N     = 0;
    260:   for (i = 0; i < size; i++) {
    261:     disp[i] = N;
    262:     N      += lens[i];
    263:   }
    264:   aomap->N = N;
    265:   ao->N    = N;
    266:   ao->n    = N;

    268:   /* If mypetsc is 0 then use "natural" numbering */
    269:   if (!mypetsc) {
    270:     start = disp[rank];
    271:     PetscMalloc1(napp+1, &petsc);
    272:     for (i = 0; i < napp; i++) petsc[i] = start + i;
    273:   } else {
    274:     petsc = (PetscInt*)mypetsc;
    275:   }

    277:   /* get all indices on all processors */
    278:   PetscMalloc4(N, &allapp,N,&appPerm,N,&allpetsc,N,&petscPerm);
    279:   MPI_Allgatherv((void*)myapp, napp, MPIU_INT, allapp,   lens, disp, MPIU_INT, comm);
    280:   MPI_Allgatherv((void*)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);
    281:   PetscFree2(lens,disp);

    283:   /* generate a list of Section 1.5 Writing Application Codes with PETSc and PETSc node numbers */
    284:   PetscMalloc4(N, &aomap->app,N,&aomap->appPerm,N,&aomap->petsc,N,&aomap->petscPerm);
    285:   PetscLogObjectMemory((PetscObject)ao, 4*N * sizeof(PetscInt));
    286:   for (i = 0; i < N; i++) {
    287:     appPerm[i]   = i;
    288:     petscPerm[i] = i;
    289:   }
    290:   PetscSortIntWithPermutation(N, allpetsc, petscPerm);
    291:   PetscSortIntWithPermutation(N, allapp,   appPerm);
    292:   /* Form sorted arrays of indices */
    293:   for (i = 0; i < N; i++) {
    294:     aomap->app[i]   = allapp[appPerm[i]];
    295:     aomap->petsc[i] = allpetsc[petscPerm[i]];
    296:   }
    297:   /* Invert petscPerm[] into aomap->petscPerm[] */
    298:   for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;

    300:   /* Form map between aomap->app[] and aomap->petsc[] */
    301:   for (i = 0; i < N; i++) aomap->appPerm[i] = aomap->petscPerm[appPerm[i]];

    303:   /* Invert appPerm[] into allapp[] */
    304:   for (i = 0; i < N; i++) allapp[appPerm[i]] = i;

    306:   /* Form map between aomap->petsc[] and aomap->app[] */
    307:   for (i = 0; i < N; i++) aomap->petscPerm[i] = allapp[petscPerm[i]];

    309: #if defined(PETSC_USE_DEBUG)
    310:   /* Check that the permutations are complementary */
    311:   for (i = 0; i < N; i++) {
    312:     if (i != aomap->appPerm[aomap->petscPerm[i]]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid ordering");
    313:   }
    314: #endif
    315:   /* Cleanup */
    316:   if (!mypetsc) {
    317:     PetscFree(petsc);
    318:   }
    319:   PetscFree4(allapp,appPerm,allpetsc,petscPerm);

    321:   AOViewFromOptions(ao,NULL,"-ao_view");

    323:   *aoout = ao;
    324:   return(0);
    325: }

    327: /*@
    328:   AOCreateMappingIS - Creates a basic Section 1.5 Writing Application Codes with PETSc ordering using two index sets.

    330:   Input Parameters:
    331: + comm    - MPI communicator that is to share AO
    332: . isapp   - index set that defines an ordering
    333: - ispetsc - index set that defines another ordering, maybe NULL for identity IS

    335:   Output Parameter:
    336: . aoout   - the new Section 1.5 Writing Application Codes with PETSc ordering

    338:   Options Database Key:
    339: . -ao_view : call AOView() at the conclusion of AOCreateMappingIS()

    341:   Level: beginner

    343:     Notes:
    344:     the index sets isapp and ispetsc need NOT contain the all the integers 0 to N-1, that is there CAN be "holes"  in the indices.
    345:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

    347: .seealso: AOCreateBasic(), AOCreateMapping(), AODestroy()
    348: @*/
    349: PetscErrorCode  AOCreateMappingIS(IS isapp, IS ispetsc, AO *aoout)
    350: {
    351:   MPI_Comm       comm;
    352:   const PetscInt *mypetsc, *myapp;
    353:   PetscInt       napp, npetsc;

    357:   PetscObjectGetComm((PetscObject) isapp, &comm);
    358:   ISGetLocalSize(isapp, &napp);
    359:   if (ispetsc) {
    360:     ISGetLocalSize(ispetsc, &npetsc);
    361:     if (napp != npetsc) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "Local IS lengths must match");
    362:     ISGetIndices(ispetsc, &mypetsc);
    363:   } else {
    364:     mypetsc = NULL;
    365:   }
    366:   ISGetIndices(isapp, &myapp);

    368:   AOCreateMapping(comm, napp, myapp, mypetsc, aoout);

    370:   ISRestoreIndices(isapp, &myapp);
    371:   if (ispetsc) {
    372:     ISRestoreIndices(ispetsc, &mypetsc);
    373:   }
    374:   return(0);
    375: }