Actual source code: aijhdf5.c

      1: #include <../src/mat/impls/aij/seq/aij.h>
      2: #include <petsc/private/isimpl.h>
      3: #include <petsc/private/vecimpl.h>
      4: #include <petsclayouthdf5.h>

      6: PetscErrorCode MatLoad_AIJ_HDF5(Mat mat, PetscViewer viewer)
      7: {
      8:   PetscViewerFormat  format;
      9:   const PetscInt    *i_glob = NULL;
     10:   PetscInt          *i      = NULL;
     11:   const PetscInt    *j      = NULL;
     12:   const PetscScalar *a      = NULL;
     13:   char              *a_name = NULL, *i_name = NULL, *j_name = NULL, *c_name = NULL;
     14:   const char        *mat_name = NULL;
     15:   PetscInt           p, m, M, N;
     16:   PetscInt           bs = mat->rmap->bs;
     17:   PetscInt          *range;
     18:   PetscBool          flg;
     19:   IS                 is_i = NULL, is_j = NULL;
     20:   Vec                vec_a = NULL;
     21:   PetscLayout        jmap  = NULL;
     22:   MPI_Comm           comm;
     23:   PetscMPIInt        rank, size;

     25:   PetscFunctionBegin;
     26:   PetscCall(PetscViewerGetFormat(viewer, &format));
     27:   switch (format) {
     28:   case PETSC_VIEWER_HDF5_PETSC:
     29:   case PETSC_VIEWER_DEFAULT:
     30:   case PETSC_VIEWER_NATIVE:
     31:   case PETSC_VIEWER_HDF5_MAT:
     32:     break;
     33:   default:
     34:     SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
     35:   }

     37:   PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
     38:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
     39:   PetscCallMPI(MPI_Comm_size(comm, &size));
     40:   PetscCall(PetscObjectGetName((PetscObject)mat, &mat_name));
     41:   if (format == PETSC_VIEWER_HDF5_MAT) {
     42:     PetscCall(PetscStrallocpy("jc", &i_name));
     43:     PetscCall(PetscStrallocpy("ir", &j_name));
     44:     PetscCall(PetscStrallocpy("data", &a_name));
     45:     PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
     46:   } else {
     47:     /* TODO Once corresponding MatView is implemented, change the names to i,j,a */
     48:     /* TODO Maybe there could be both namings in the file, using "symbolic link" features of HDF5. */
     49:     PetscCall(PetscStrallocpy("jc", &i_name));
     50:     PetscCall(PetscStrallocpy("ir", &j_name));
     51:     PetscCall(PetscStrallocpy("data", &a_name));
     52:     PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
     53:   }

     55:   PetscOptionsBegin(comm, NULL, "Options for loading matrix from HDF5", "Mat");
     56:   PetscCall(PetscOptionsInt("-matload_block_size", "Set the blocksize used to store the matrix", "MatLoad", bs, &bs, &flg));
     57:   PetscOptionsEnd();
     58:   if (flg) PetscCall(MatSetBlockSize(mat, bs));

     60:   PetscCall(PetscViewerHDF5PushGroup(viewer, mat_name));
     61:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, c_name, PETSC_INT, NULL, &N));
     62:   PetscCall(PetscViewerHDF5ReadSizes(viewer, i_name, NULL, &M));
     63:   --M; /* i has size M+1 as there is global number of nonzeros stored at the end */

     65:   if (format == PETSC_VIEWER_HDF5_MAT && mat->symmetric != PETSC_BOOL3_TRUE) {
     66:     /* Swap row and columns layout for unallocated matrix. I want to avoid calling MatTranspose() just to transpose sparsity pattern and layout. */
     67:     PetscLayout tmp;
     68:     PetscCheck(!mat->preallocated, comm, PETSC_ERR_SUP, "Not for preallocated matrix - we would need to transpose it here which we want to avoid");
     69:     tmp       = mat->rmap;
     70:     mat->rmap = mat->cmap;
     71:     mat->cmap = tmp;
     72:   }

     74:   /* If global sizes are set, check if they are consistent with that given in the file */
     75:   PetscCheck(mat->rmap->N < 0 || mat->rmap->N == M, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows: Matrix in file has (%" PetscInt_FMT ") and input matrix has (%" PetscInt_FMT ")", mat->rmap->N, M);
     76:   PetscCheck(mat->cmap->N < 0 || mat->cmap->N == N, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of cols: Matrix in file has (%" PetscInt_FMT ") and input matrix has (%" PetscInt_FMT ")", mat->cmap->N, N);

     78:   /* Determine ownership of all (block) rows and columns */
     79:   mat->rmap->N = M;
     80:   mat->cmap->N = N;
     81:   PetscCall(PetscLayoutSetUp(mat->rmap));
     82:   PetscCall(PetscLayoutSetUp(mat->cmap));
     83:   m = mat->rmap->n;

     85:   /* Read array i (array of row indices) */
     86:   PetscCall(PetscMalloc1(m + 1, &i)); /* allocate i with one more position for local number of nonzeros on each rank */
     87:   i[0] = i[m] = 0;                    /* make the last entry always defined - the code block below overwrites it just on last rank */
     88:   if (rank == size - 1) m++;          /* in the loaded array i_glob, only the last rank has one more position with the global number of nonzeros */
     89:   M++;
     90:   PetscCall(ISCreate(comm, &is_i));
     91:   PetscCall(PetscObjectSetName((PetscObject)is_i, i_name));
     92:   PetscCall(PetscLayoutSetLocalSize(is_i->map, m));
     93:   PetscCall(PetscLayoutSetSize(is_i->map, M));
     94:   PetscCall(ISLoad(is_i, viewer));
     95:   PetscCall(ISGetIndices(is_i, &i_glob));
     96:   PetscCall(PetscArraycpy(i, i_glob, m));

     98:   /* Reset m and M to the matrix sizes */
     99:   m = mat->rmap->n;
    100:   M--;

    102:   /* Create PetscLayout for j and a vectors; construct ranges first */
    103:   PetscCall(PetscMalloc1(size + 1, &range));
    104:   PetscCallMPI(MPI_Allgather(i, 1, MPIU_INT, range, 1, MPIU_INT, comm));
    105:   /* Last rank has global number of nonzeros (= length of j and a arrays) in i[m] (last i entry) so broadcast it */
    106:   range[size] = i[m];
    107:   PetscCallMPI(MPI_Bcast(&range[size], 1, MPIU_INT, size - 1, comm));
    108:   for (p = size - 1; p > 0; p--) {
    109:     if (!range[p]) range[p] = range[p + 1]; /* for ranks with 0 rows, take the value from the next processor */
    110:   }
    111:   i[m] = range[rank + 1]; /* i[m] (last i entry) is equal to next rank's offset */
    112:   /* Deduce rstart, rend, n and N from the ranges */
    113:   PetscCall(PetscLayoutCreateFromRanges(comm, range, PETSC_OWN_POINTER, 1, &jmap));

    115:   /* Convert global to local indexing of rows */
    116:   for (p = 1; p < m + 1; ++p) i[p] -= i[0];
    117:   i[0] = 0;

    119:   /* Read array j (array of column indices) */
    120:   PetscCall(ISCreate(comm, &is_j));
    121:   PetscCall(PetscObjectSetName((PetscObject)is_j, j_name));
    122:   PetscCall(PetscLayoutDuplicate(jmap, &is_j->map));
    123:   PetscCall(ISLoad(is_j, viewer));
    124:   PetscCall(ISGetIndices(is_j, &j));

    126:   /* Read array a (array of values) */
    127:   PetscCall(VecCreate(comm, &vec_a));
    128:   PetscCall(PetscObjectSetName((PetscObject)vec_a, a_name));
    129:   PetscCall(PetscLayoutDuplicate(jmap, &vec_a->map));
    130:   PetscCall(VecLoad(vec_a, viewer));
    131:   PetscCall(VecGetArrayRead(vec_a, &a));

    133:   /* populate matrix */
    134:   if (!((PetscObject)mat)->type_name) PetscCall(MatSetType(mat, MATAIJ));
    135:   PetscCall(MatSeqAIJSetPreallocationCSR(mat, i, j, a));
    136:   PetscCall(MatMPIAIJSetPreallocationCSR(mat, i, j, a));
    137:   /*
    138:   PetscCall(MatSeqBAIJSetPreallocationCSR(mat,bs,i,j,a));
    139:   PetscCall(MatMPIBAIJSetPreallocationCSR(mat,bs,i,j,a));
    140:   */

    142:   if (format == PETSC_VIEWER_HDF5_MAT && mat->symmetric != PETSC_BOOL3_TRUE) {
    143:     /* Transpose the input matrix back */
    144:     PetscCall(MatTranspose(mat, MAT_INPLACE_MATRIX, &mat));
    145:   }

    147:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    148:   PetscCall(PetscFree(i_name));
    149:   PetscCall(PetscFree(j_name));
    150:   PetscCall(PetscFree(a_name));
    151:   PetscCall(PetscFree(c_name));
    152:   PetscCall(PetscLayoutDestroy(&jmap));
    153:   PetscCall(PetscFree(i));
    154:   PetscCall(ISRestoreIndices(is_i, &i_glob));
    155:   PetscCall(ISRestoreIndices(is_j, &j));
    156:   PetscCall(VecRestoreArrayRead(vec_a, &a));
    157:   PetscCall(ISDestroy(&is_i));
    158:   PetscCall(ISDestroy(&is_j));
    159:   PetscCall(VecDestroy(&vec_a));
    160:   PetscFunctionReturn(PETSC_SUCCESS);
    161: }