xref: /petsc/src/mat/impls/aij/seq/hdf5/aijhdf5.c (revision 2e1d0745e031e9eda42a183866b5a94ccb2b4e44)

#include <../src/mat/impls/aij/seq/aij.h>
#include <petsc/private/isimpl.h>
#include <petsc/private/vecimpl.h>
#include <petsclayouthdf5.h>

PetscErrorCode MatLoad_AIJ_HDF5(Mat mat, PetscViewer viewer)
{
  PetscViewerFormat  format;
  const PetscInt    *i_glob = NULL;
  PetscInt          *i      = NULL;
  const PetscInt    *j      = NULL;
  const PetscScalar *a      = NULL;
  char              *a_name = NULL, *i_name = NULL, *j_name = NULL, *c_name = NULL;
  const char        *mat_name = NULL;
  PetscInt           p, m, M, N;
  PetscInt           bs = mat->rmap->bs;
  PetscInt          *range;
  PetscBool          flg;
  IS                 is_i = NULL, is_j = NULL;
  Vec                vec_a = NULL;
  PetscLayout        jmap  = NULL;
  MPI_Comm           comm;
  PetscMPIInt        rank, size;

  PetscFunctionBegin;
  PetscCall(PetscViewerGetFormat(viewer, &format));
  switch (format) {
  case PETSC_VIEWER_HDF5_PETSC:
  case PETSC_VIEWER_DEFAULT:
  case PETSC_VIEWER_NATIVE:
  case PETSC_VIEWER_HDF5_MAT:
    break;
  default:
    SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]);
  }

  PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
  PetscCallMPI(MPI_Comm_rank(comm, &rank));
  PetscCallMPI(MPI_Comm_size(comm, &size));
  PetscCall(PetscObjectGetName((PetscObject)mat, &mat_name));
  if (format == PETSC_VIEWER_HDF5_MAT) {
    PetscCall(PetscStrallocpy("jc", &i_name));
    PetscCall(PetscStrallocpy("ir", &j_name));
    PetscCall(PetscStrallocpy("data", &a_name));
    PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
  } else {
    /* TODO Once corresponding MatView is implemented, change the names to i,j,a */
    /* TODO Maybe there could be both namings in the file, using "symbolic link" features of HDF5. */
    PetscCall(PetscStrallocpy("jc", &i_name));
    PetscCall(PetscStrallocpy("ir", &j_name));
    PetscCall(PetscStrallocpy("data", &a_name));
    PetscCall(PetscStrallocpy("MATLAB_sparse", &c_name));
  }

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

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

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

  /* If global sizes are set, check if they are consistent with that given in the file */
  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);
  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);

  /* Determine ownership of all (block) rows and columns */
  mat->rmap->N = M;
  mat->cmap->N = N;
  PetscCall(PetscLayoutSetUp(mat->rmap));
  PetscCall(PetscLayoutSetUp(mat->cmap));
  m = mat->rmap->n;

  /* Read array i (array of row indices) */
  PetscCall(PetscMalloc1(m + 1, &i)); /* allocate i with one more position for local number of nonzeros on each rank */
  i[0] = i[m] = 0;                    /* make the last entry always defined - the code block below overwrites it just on last rank */
  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 */
  M++;
  PetscCall(ISCreate(comm, &is_i));
  PetscCall(PetscObjectSetName((PetscObject)is_i, i_name));
  PetscCall(PetscLayoutSetLocalSize(is_i->map, m));
  PetscCall(PetscLayoutSetSize(is_i->map, M));
  PetscCall(ISLoad(is_i, viewer));
  PetscCall(ISGetIndices(is_i, &i_glob));
  PetscCall(PetscArraycpy(i, i_glob, m));

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

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

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

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

  /* Read array a (array of values) */
  PetscCall(VecCreate(comm, &vec_a));
  PetscCall(PetscObjectSetName((PetscObject)vec_a, a_name));
  PetscCall(PetscLayoutDuplicate(jmap, &vec_a->map));
  PetscCall(VecLoad(vec_a, viewer));
  PetscCall(VecGetArrayRead(vec_a, &a));

  /* populate matrix */
  if (!((PetscObject)mat)->type_name) PetscCall(MatSetType(mat, MATAIJ));
  PetscCall(MatSeqAIJSetPreallocationCSR(mat, i, j, a));
  PetscCall(MatMPIAIJSetPreallocationCSR(mat, i, j, a));
  /*
  PetscCall(MatSeqBAIJSetPreallocationCSR(mat,bs,i,j,a));
  PetscCall(MatMPIBAIJSetPreallocationCSR(mat,bs,i,j,a));
  */

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

  PetscCall(PetscViewerHDF5PopGroup(viewer));
  PetscCall(PetscFree(i_name));
  PetscCall(PetscFree(j_name));
  PetscCall(PetscFree(a_name));
  PetscCall(PetscFree(c_name));
  PetscCall(PetscLayoutDestroy(&jmap));
  PetscCall(PetscFree(i));
  PetscCall(ISRestoreIndices(is_i, &i_glob));
  PetscCall(ISRestoreIndices(is_j, &j));
  PetscCall(VecRestoreArrayRead(vec_a, &a));
  PetscCall(ISDestroy(&is_i));
  PetscCall(ISDestroy(&is_j));
  PetscCall(VecDestroy(&vec_a));
  PetscFunctionReturn(PETSC_SUCCESS);
}