Date: 2016-07-24T16:51:08+00:00

Actual source code: aomapping.c
petsc-3.7.3 2016-07-24
Report Typos and Errors

      2: /*
      3:   These AO application 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>          /*I  "petscao.h" I*/

     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;

     20: PetscErrorCode AODestroy_Mapping(AO ao)
     21: {
     22:   AO_Mapping     *aomap = (AO_Mapping*) ao->data;

     26:   PetscFree4(aomap->app,aomap->appPerm,aomap->petsc,aomap->petscPerm);
     27:   PetscFree(aomap);
     28:   return(0);
     29: }

     33: PetscErrorCode AOView_Mapping(AO ao, PetscViewer viewer)
     34: {
     35:   AO_Mapping     *aomap = (AO_Mapping*) ao->data;
     36:   PetscMPIInt    rank;
     37:   PetscInt       i;
     38:   PetscBool      iascii;

     42:   MPI_Comm_rank(PetscObjectComm((PetscObject)ao), &rank);
     43:   if (rank) return(0);
     44:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
     45:   if (iascii) {
     46:     PetscViewerASCIIPrintf(viewer, "Number of elements in ordering %D\n", aomap->N);
     47:     PetscViewerASCIIPrintf(viewer, "   App.   PETSc\n");
     48:     for (i = 0; i < aomap->N; i++) {
     49:       PetscViewerASCIIPrintf(viewer, "%D   %D    %D\n", i, aomap->app[i], aomap->petsc[aomap->appPerm[i]]);
     50:     }
     51:   }
     52:   return(0);
     53: }

     57: PetscErrorCode AOPetscToApplication_Mapping(AO ao, PetscInt n, PetscInt *ia)
     58: {
     59:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
     60:   PetscInt   *app   = aomap->app;
     61:   PetscInt   *petsc = aomap->petsc;
     62:   PetscInt   *perm  = aomap->petscPerm;
     63:   PetscInt   N      = aomap->N;
     64:   PetscInt   low, high, mid=0;
     65:   PetscInt   idex;
     66:   PetscInt   i;

     68:   /* It would be possible to use a single bisection search, which
     69:      recursively divided the indices to be converted, and searched
     70:      partitions which contained an index. This would result in
     71:      better running times if indices are clustered.
     72:   */
     74:   for (i = 0; i < n; i++) {
     75:     idex = ia[i];
     76:     if (idex < 0) continue;
     77:     /* Use bisection since the array is sorted */
     78:     low  = 0;
     79:     high = N - 1;
     80:     while (low <= high) {
     81:       mid = (low + high)/2;
     82:       if (idex == petsc[mid]) break;
     83:       else if (idex < petsc[mid]) high = mid - 1;
     84:       else low = mid + 1;
     85:     }
     86:     if (low > high) ia[i] = -1;
     87:     else            ia[i] = app[perm[mid]];
     88:   }
     89:   return(0);
     90: }

     94: PetscErrorCode AOApplicationToPetsc_Mapping(AO ao, PetscInt n, PetscInt *ia)
     95: {
     96:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
     97:   PetscInt   *app   = aomap->app;
     98:   PetscInt   *petsc = aomap->petsc;
     99:   PetscInt   *perm  = aomap->appPerm;
    100:   PetscInt   N      = aomap->N;
    101:   PetscInt   low, high, mid=0;
    102:   PetscInt   idex;
    103:   PetscInt   i;

    105:   /* It would be possible to use a single bisection search, which
    106:      recursively divided the indices to be converted, and searched
    107:      partitions which contained an index. This would result in
    108:      better running times if indices are clustered.
    109:   */
    111:   for (i = 0; i < n; i++) {
    112:     idex = ia[i];
    113:     if (idex < 0) continue;
    114:     /* Use bisection since the array is sorted */
    115:     low  = 0;
    116:     high = N - 1;
    117:     while (low <= high) {
    118:       mid = (low + high)/2;
    119:       if (idex == app[mid]) break;
    120:       else if (idex < app[mid]) high = mid - 1;
    121:       else low = mid + 1;
    122:     }
    123:     if (low > high) ia[i] = -1;
    124:     else            ia[i] = petsc[perm[mid]];
    125:   }
    126:   return(0);
    127: }

    129: static struct _AOOps AOps = {AOView_Mapping,
    130:                              AODestroy_Mapping,
    131:                              AOPetscToApplication_Mapping,
    132:                              AOApplicationToPetsc_Mapping,
    133:                              NULL,
    134:                              NULL,
    135:                              NULL,
    136:                              NULL};

    140: /*@C
    141:   AOMappingHasApplicationIndex - Searches for the supplied application index.

    143:   Input Parameters:
    144: + ao       - The AOMapping
    145: - index    - The application index

    147:   Output Parameter:
    148: . hasIndex - Flag is PETSC_TRUE if the index exists

    150:   Level: intermediate

    152: .keywords: AO, index
    153: .seealso: AOMappingHasPetscIndex(), AOCreateMapping()
    154: @*/
    155: PetscErrorCode  AOMappingHasApplicationIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
    156: {
    157:   AO_Mapping *aomap;
    158:   PetscInt   *app;
    159:   PetscInt   low, high, mid;

    164:   aomap = (AO_Mapping*) ao->data;
    165:   app   = aomap->app;
    166:   /* Use bisection since the array is sorted */
    167:   low  = 0;
    168:   high = aomap->N - 1;
    169:   while (low <= high) {
    170:     mid = (low + high)/2;
    171:     if (idex == app[mid]) break;
    172:     else if (idex < app[mid]) high = mid - 1;
    173:     else low = mid + 1;
    174:   }
    175:   if (low > high) *hasIndex = PETSC_FALSE;
    176:   else *hasIndex = PETSC_TRUE;
    177:   return(0);
    178: }

    182: /*@
    183:   AOMappingHasPetscIndex - Searches for the supplied petsc index.

    185:   Input Parameters:
    186: + ao       - The AOMapping
    187: - index    - The petsc index

    189:   Output Parameter:
    190: . hasIndex - Flag is PETSC_TRUE if the index exists

    192:   Level: intermediate

    194: .keywords: AO, index
    195: .seealso: AOMappingHasApplicationIndex(), AOCreateMapping()
    196: @*/
    197: PetscErrorCode  AOMappingHasPetscIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
    198: {
    199:   AO_Mapping *aomap;
    200:   PetscInt   *petsc;
    201:   PetscInt   low, high, mid;

    206:   aomap = (AO_Mapping*) ao->data;
    207:   petsc = aomap->petsc;
    208:   /* Use bisection since the array is sorted */
    209:   low  = 0;
    210:   high = aomap->N - 1;
    211:   while (low <= high) {
    212:     mid = (low + high)/2;
    213:     if (idex == petsc[mid]) break;
    214:     else if (idex < petsc[mid]) high = mid - 1;
    215:     else low = mid + 1;
    216:   }
    217:   if (low > high) *hasIndex = PETSC_FALSE;
    218:   else *hasIndex = PETSC_TRUE;
    219:   return(0);
    220: }

    224: /*@C
    225:   AOCreateMapping - Creates a basic application mapping using two integer arrays.

    227:   Input Parameters:
    228: + comm    - MPI communicator that is to share AO
    229: . napp    - size of integer arrays
    230: . myapp   - integer array that defines an ordering
    231: - mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)

    233:   Output Parameter:
    234: . aoout   - the new application mapping

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

    239:   Level: beginner

    241:     Notes: 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.
    242:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

    244: .keywords: AO, create
    245: .seealso: AOCreateBasic(), AOCreateBasic(), AOCreateMappingIS(), AODestroy()
    246: @*/
    247: PetscErrorCode  AOCreateMapping(MPI_Comm comm,PetscInt napp,const PetscInt myapp[],const PetscInt mypetsc[],AO *aoout)
    248: {
    249:   AO             ao;
    250:   AO_Mapping     *aomap;
    251:   PetscInt       *allpetsc,  *allapp;
    252:   PetscInt       *petscPerm, *appPerm;
    253:   PetscInt       *petsc;
    254:   PetscMPIInt    size, rank,*lens, *disp,nnapp;
    255:   PetscInt       N, start;
    256:   PetscInt       i;

    261:   *aoout = 0;
    262:   AOInitializePackage();

    264:   PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);
    265:   PetscNewLog(ao,&aomap);
    266:   PetscMemcpy(ao->ops, &AOps, sizeof(AOps));
    267:   ao->data = (void*) aomap;

    269:   /* transmit all lengths to all processors */
    270:   MPI_Comm_size(comm, &size);
    271:   MPI_Comm_rank(comm, &rank);
    272:   PetscMalloc2(size, &lens,size,&disp);
    273:   nnapp = napp;
    274:   MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);
    275:   N     = 0;
    276:   for (i = 0; i < size; i++) {
    277:     disp[i] = N;
    278:     N      += lens[i];
    279:   }
    280:   aomap->N = N;
    281:   ao->N    = N;
    282:   ao->n    = N;

    284:   /* If mypetsc is 0 then use "natural" numbering */
    285:   if (!mypetsc) {
    286:     start = disp[rank];
    287:     PetscMalloc1(napp+1, &petsc);
    288:     for (i = 0; i < napp; i++) petsc[i] = start + i;
    289:   } else {
    290:     petsc = (PetscInt*)mypetsc;
    291:   }

    293:   /* get all indices on all processors */
    294:   PetscMalloc4(N, &allapp,N,&appPerm,N,&allpetsc,N,&petscPerm);
    295:   MPI_Allgatherv((void*)myapp, napp, MPIU_INT, allapp,   lens, disp, MPIU_INT, comm);
    296:   MPI_Allgatherv((void*)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);
    297:   PetscFree2(lens,disp);

    299:   /* generate a list of application and PETSc node numbers */
    300:   PetscMalloc4(N, &aomap->app,N,&aomap->appPerm,N,&aomap->petsc,N,&aomap->petscPerm);
    301:   PetscLogObjectMemory((PetscObject)ao, 4*N * sizeof(PetscInt));
    302:   for (i = 0; i < N; i++) {
    303:     appPerm[i]   = i;
    304:     petscPerm[i] = i;
    305:   }
    306:   PetscSortIntWithPermutation(N, allpetsc, petscPerm);
    307:   PetscSortIntWithPermutation(N, allapp,   appPerm);
    308:   /* Form sorted arrays of indices */
    309:   for (i = 0; i < N; i++) {
    310:     aomap->app[i]   = allapp[appPerm[i]];
    311:     aomap->petsc[i] = allpetsc[petscPerm[i]];
    312:   }
    313:   /* Invert petscPerm[] into aomap->petscPerm[] */
    314:   for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;

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

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

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

    325: #if defined(PETSC_USE_DEBUG)
    326:   /* Check that the permutations are complementary */
    327:   for (i = 0; i < N; i++) {
    328:     if (i != aomap->appPerm[aomap->petscPerm[i]]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid ordering");
    329:   }
    330: #endif
    331:   /* Cleanup */
    332:   if (!mypetsc) {
    333:     PetscFree(petsc);
    334:   }
    335:   PetscFree4(allapp,appPerm,allpetsc,petscPerm);

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

    339:   *aoout = ao;
    340:   return(0);
    341: }

    345: /*@C
    346:   AOCreateMappingIS - Creates a basic application ordering using two index sets.

    348:   Input Parameters:
    349: + comm    - MPI communicator that is to share AO
    350: . isapp   - index set that defines an ordering
    351: - ispetsc - index set that defines another ordering, maybe NULL for identity IS

    353:   Output Parameter:
    354: . aoout   - the new application ordering

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

    359:   Level: beginner

    361:     Notes: 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.
    362:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

    364: .keywords: AO, create
    365: .seealso: AOCreateBasic(), AOCreateMapping(), AODestroy()
    366: @*/
    367: PetscErrorCode  AOCreateMappingIS(IS isapp, IS ispetsc, AO *aoout)
    368: {
    369:   MPI_Comm       comm;
    370:   const PetscInt *mypetsc, *myapp;
    371:   PetscInt       napp, npetsc;

    375:   PetscObjectGetComm((PetscObject) isapp, &comm);
    376:   ISGetLocalSize(isapp, &napp);
    377:   if (ispetsc) {
    378:     ISGetLocalSize(ispetsc, &npetsc);
    379:     if (napp != npetsc) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "Local IS lengths must match");
    380:     ISGetIndices(ispetsc, &mypetsc);
    381:   } else {
    382:     mypetsc = NULL;
    383:   }
    384:   ISGetIndices(isapp, &myapp);

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

    388:   ISRestoreIndices(isapp, &myapp);
    389:   if (ispetsc) {
    390:     ISRestoreIndices(ispetsc, &mypetsc);
    391:   }
    392:   return(0);
    393: }