xref: /petsc/src/vec/is/utils/isio.c (revision de8a3bf87eaa666847d4d614ad9bc31a1e65bf10)

#include <petscis.h>         /*I  "petscis.h"  I*/
#include <petsc/private/isimpl.h>
#include <petscviewerhdf5.h>

#if defined(PETSC_HAVE_HDF5)
/*
     This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with
   checks back and forth between the two types of variables.
*/
PetscErrorCode ISLoad_HDF5(IS is, PetscViewer viewer)
{
  hid_t           inttype;    /* int type (H5T_NATIVE_INT or H5T_NATIVE_LLONG) */
  hid_t           file_id, group, dset_id, filespace, memspace, plist_id;
  int             rdim, dim;
  hsize_t         dims[3], count[3], offset[3];
  PetscInt        n, N, bs, bsInd, lenInd, low, timestep;
  const PetscInt *ind;
  const char     *isname;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  if (!((PetscObject)is)->name) SETERRQ(PetscObjectComm((PetscObject)is), PETSC_ERR_SUP, "Since HDF5 format gives ASCII name for each object in file; must use ISLoad() after setting name of Vec with PetscObjectSetName()");
  ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
  ierr = PetscViewerHDF5GetTimestep(viewer, &timestep);CHKERRQ(ierr);
  ierr = ISGetBlockSize(is, &bs);CHKERRQ(ierr);
  /* Create the dataset with default properties and close filespace */
  ierr = PetscObjectGetName((PetscObject) is, &isname);CHKERRQ(ierr);
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
  PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, isname, H5P_DEFAULT));
#else
  PetscStackCallHDF5Return(dset_id,H5Dopen,(group, isname));
#endif
  /* Retrieve the dataspace for the dataset */
  PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id));
  dim = 0;
  if (timestep >= 0) ++dim;
  ++dim;
  ++dim;
  PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL));
  bsInd = rdim-1;
  lenInd = timestep >= 0 ? 1 : 0;
  if (rdim != dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected",rdim,dim);
  else if (bs != (PetscInt) dims[bsInd]) {
    ierr = ISSetBlockSize(is, dims[bsInd]);
    if (ierr) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Block size %d specified for IS does not match blocksize in file %d",bs,dims[bsInd]);
    bs = dims[bsInd];
  }

  /* Set Vec sizes,blocksize,and type if not already set */
  ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr);
  ierr = ISGetSize(is, &N);CHKERRQ(ierr);
  if (n < 0 && N < 0) {ierr = PetscLayoutSetSize(is->map, dims[lenInd]*bs);CHKERRQ(ierr);}
  ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
  /* If sizes and type already set,check if the vector global size is correct */
  ierr = ISGetSize(is, &N);CHKERRQ(ierr);
  if (N/bs != (PetscInt) dims[lenInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "IS in file different length (%d) then input vector (%d)", (PetscInt) dims[lenInd], N/bs);

  /* Each process defines a dataset and reads it from the hyperslab in the file */
  ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr);
  dim  = 0;
  if (timestep >= 0) {
    count[dim] = 1;
    ++dim;
  }
  ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    count[dim] = bs;
    ++dim;
  }
  PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL));

  /* Select hyperslab in the file */
  ierr = PetscLayoutGetRange(is->map, &low, NULL);CHKERRQ(ierr);
  dim  = 0;
  if (timestep >= 0) {
    offset[dim] = timestep;
    ++dim;
  }
  ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr);
  ++dim;
  if (bs >= 1) {
    offset[dim] = 0;
    ++dim;
  }
  PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL));

  /* Create property list for collective dataset read */
  PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
#endif
  /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */

#if defined(PETSC_USE_64BIT_INDICES)
  inttype = H5T_NATIVE_LLONG;
#else
  inttype = H5T_NATIVE_INT;
#endif
  ierr   = PetscMalloc1(n,&ind);CHKERRQ(ierr);
  PetscStackCallHDF5(H5Dread,(dset_id, inttype, memspace, filespace, plist_id, (void *) ind));
  ierr   = ISGeneralSetIndices(is, n, ind, PETSC_OWN_POINTER);CHKERRQ(ierr);

  /* Close/release resources */
  if (group != file_id) PetscStackCallHDF5(H5Gclose,(group));
  PetscStackCallHDF5(H5Pclose,(plist_id));
  PetscStackCallHDF5(H5Sclose,(filespace));
  PetscStackCallHDF5(H5Sclose,(memspace));
  PetscStackCallHDF5(H5Dclose,(dset_id));
  PetscFunctionReturn(0);
}
#endif

PetscErrorCode ISLoad_Binary(IS is, PetscViewer viewer)
{
  PetscErrorCode ierr;
  PetscBool      isgeneral,skipHeader,useMPIIO;
  int            fd;
  PetscInt       tr[2],N,ln,*idx;
  MPI_Request    request;
  MPI_Status     status;
  MPI_Comm       comm;
  PetscMPIInt    rank,size,tag;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)is,&comm);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)is,ISGENERAL,&isgeneral);CHKERRQ(ierr);
  if (!isgeneral) SETERRQ(comm,PETSC_ERR_ARG_INCOMP,"IS must be of type ISGENERAL to load into it");
  ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipHeader);CHKERRQ(ierr);
  if (skipHeader) SETERRQ(comm,PETSC_ERR_USER, "Currently no support for binary files without headers");
  /* force binary viewer to load .info file if it has not yet done so */
  ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr);

  ierr = PetscViewerBinaryRead(viewer,tr,2,NULL,PETSC_INT);CHKERRQ(ierr);
  if (tr[0] != IS_FILE_CLASSID) SETERRQ(comm,PETSC_ERR_ARG_WRONG,"Not an IS next in file");

  /* Has IS already had its layout defined */
  /* ierr = ISGetLayout(is,&map);CHKERRQ(ierr); */
  ierr = PetscLayoutGetSize(is->map,&N);CHKERRQ(ierr);
  if (N > -1 && N != tr[1]) SETERRQ2(comm,PETSC_ERR_ARG_SIZ,"Size of IS in file %D does not match size of IS provided",tr[1],N);
  if (N == -1) {
    N = tr[1];
    ierr = PetscLayoutSetSize(is->map,N);CHKERRQ(ierr);
    ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr);
  }
  ierr = PetscLayoutGetLocalSize(is->map,&ln);CHKERRQ(ierr);
  ierr = PetscMalloc1(ln,&idx);CHKERRQ(ierr);

  ierr = PetscViewerBinaryGetUseMPIIO(viewer,&useMPIIO);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MPIIO)
  if (useMPIIO) {
    MPI_File    mfdes;
    MPI_Offset  off;
    PetscMPIInt lsize;
    PetscInt    rstart;

    ierr = PetscMPIIntCast(ln,&lsize);CHKERRQ(ierr);
    ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr);
    ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr);
    ierr = PetscLayoutGetRange(is->map,&rstart,NULL);CHKERRQ(ierr);
    off += rstart*(MPI_Offset)sizeof(PetscInt);
    ierr = MPI_File_set_view(mfdes,off,MPIU_INT,MPIU_INT,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr);
    ierr = MPIU_File_read_all(mfdes,idx,lsize,MPIU_INT,MPI_STATUS_IGNORE);CHKERRQ(ierr);
    ierr = PetscViewerBinaryAddMPIIOOffset(viewer,N*(MPI_Offset)sizeof(PetscInt));CHKERRQ(ierr);
    ierr = ISGeneralSetIndices(is,ln,idx,PETSC_OWN_POINTER);CHKERRQ(ierr);
    PetscFunctionReturn(0);
  }
#endif

  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
  ierr = PetscObjectGetNewTag((PetscObject)viewer,&tag);CHKERRQ(ierr);
  ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr);

  if (!rank) {
    ierr = PetscBinaryRead(fd,idx,ln,PETSC_INT);CHKERRQ(ierr);

    if (size > 1) {
      PetscInt *range,n,i,*idxwork;

      /* read in other chuncks and send to other processors */
      /* determine maximum chunck owned by other */
      range = is->map->range;
      n = 1;
      for (i=1; i<size; i++) n = PetscMax(n,range[i+1] - range[i]);

      ierr = PetscMalloc1(n,&idxwork);CHKERRQ(ierr);
      for (i=1; i<size; i++) {
        n    = range[i+1] - range[i];
        ierr = PetscBinaryRead(fd,idxwork,n,PETSC_INT);CHKERRQ(ierr);
        ierr = MPI_Isend(idxwork,n,MPIU_INT,i,tag,comm,&request);CHKERRQ(ierr);
        ierr = MPI_Wait(&request,&status);CHKERRQ(ierr);
      }
      ierr = PetscFree(idxwork);CHKERRQ(ierr);
    }
  } else {
    ierr = MPI_Recv(idx,ln,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr);
  }
  ierr = ISGeneralSetIndices(is,ln,idx,PETSC_OWN_POINTER);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PetscErrorCode ISLoad_Default(IS is, PetscViewer viewer)
{
  PetscBool      isbinary;
#if defined(PETSC_HAVE_HDF5)
  PetscBool      ishdf5;
#endif
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HDF5)
  ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr);
#endif
  if (isbinary) {
    ierr = ISLoad_Binary(is, viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HDF5)
  } else if (ishdf5) {
    ierr = ISLoad_HDF5(is, viewer);CHKERRQ(ierr);
#endif
  }
  PetscFunctionReturn(0);
}