Actual source code: hdf5io.c

      1: #include <petsc/private/viewerimpl.h>
      2: #include <petsc/private/viewerhdf5impl.h>
      3: #include <petsclayouthdf5.h>
      4: #include <petscis.h>

      6: #if defined(PETSC_HAVE_HDF5)

      8: struct _n_HDF5ReadCtx {
      9:   hid_t file, group, dataset, dataspace;
     10:   PetscInt timestep;
     11:   int lenInd, bsInd, rdim;
     12:   hsize_t *dims;
     13:   PetscBool complexVal, dim2, horizontal;
     14: };
     15: typedef struct _n_HDF5ReadCtx* HDF5ReadCtx;

     17: static PetscErrorCode PetscViewerHDF5ReadInitialize_Private(PetscViewer viewer, const char name[], HDF5ReadCtx *ctx)
     18: {
     19:   HDF5ReadCtx    h=NULL;

     23:   PetscNew(&h);
     24:   PetscViewerHDF5OpenGroup(viewer, &h->file, &h->group);
     25:   PetscStackCallHDF5Return(h->dataset,H5Dopen2,(h->group, name, H5P_DEFAULT));
     26:   PetscStackCallHDF5Return(h->dataspace,H5Dget_space,(h->dataset));
     27:   PetscViewerHDF5GetTimestep(viewer, &h->timestep);
     28:   PetscViewerHDF5HasAttribute(viewer,name,"complex",&h->complexVal);
     29:   if (h->complexVal) {PetscViewerHDF5ReadAttribute(viewer,name,"complex",PETSC_BOOL,&h->complexVal);}
     30:   /* MATLAB stores column vectors horizontally */
     31:   PetscViewerHDF5HasAttribute(viewer,name,"MATLAB_class",&h->horizontal);
     32:   *ctx = h;
     33:   return(0);
     34: }

     36: static PetscErrorCode PetscViewerHDF5ReadFinalize_Private(PetscViewer viewer, HDF5ReadCtx *ctx)
     37: {
     38:   HDF5ReadCtx    h;

     42:   h = *ctx;
     43:   PetscStackCallHDF5(H5Gclose,(h->group));
     44:   PetscStackCallHDF5(H5Sclose,(h->dataspace));
     45:   PetscStackCallHDF5(H5Dclose,(h->dataset));
     46:   PetscFree((*ctx)->dims);
     47:   PetscFree(*ctx);
     48:   return(0);
     49: }

     51: static PetscErrorCode PetscViewerHDF5ReadSizes_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscBool setup, PetscLayout *map_)
     52: {
     53:   PetscInt       bs, len, N;
     54:   PetscLayout    map;

     58:   if (!(*map_)) {
     59:     PetscLayoutCreate(PetscObjectComm((PetscObject)viewer),map_);
     60:   }
     61:   map = *map_;

     63:   /* Get actual number of dimensions in dataset */
     64:   PetscStackCallHDF5Return(ctx->rdim,H5Sget_simple_extent_dims,(ctx->dataspace, NULL, NULL));
     65:   PetscMalloc1(ctx->rdim, &ctx->dims);
     66:   PetscStackCallHDF5Return(ctx->rdim,H5Sget_simple_extent_dims,(ctx->dataspace, ctx->dims, NULL));

     68:   /*
     69:      Dimensions are in this order:
     70:      [0]        timesteps (optional)
     71:      [lenInd]   entries (numbers or blocks)
     72:      ...
     73:      [bsInd]    entries of blocks (optional)
     74:      [bsInd+1]  real & imaginary part (optional)
     75:       = rdim-1
     76:    */

     78:   /* Get entries dimension index */
     79:   ctx->lenInd = 0;
     80:   if (ctx->timestep >= 0) ++ctx->lenInd;

     82:   /* Get block dimension index */
     83:   ctx->bsInd = ctx->rdim-1;
     84:   if (ctx->complexVal) --ctx->bsInd;
     85:   if (ctx->lenInd > ctx->bsInd) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_PLIB, "Calculated block dimension index = %D < %D = length dimension index.",ctx->bsInd,ctx->lenInd);
     86:   if (ctx->bsInd > ctx->rdim - 1) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Calculated block dimension index = %D > %D = total number of dimensions - 1.",ctx->bsInd,ctx->rdim-1);

     88:   /* Get block size */
     89:   ctx->dim2 = PETSC_FALSE;
     90:   if (ctx->lenInd == ctx->bsInd) {
     91:     bs = 1; /* support vectors stored as 1D array */
     92:   } else {
     93:     bs = (PetscInt) ctx->dims[ctx->bsInd];
     94:     if (bs == 1) ctx->dim2 = PETSC_TRUE; /* vector with blocksize of 1, still stored as 2D array */
     95:   }

     97:   /* Get global size */
     98:   len = ctx->dims[ctx->lenInd];
     99:   if (ctx->horizontal) {
    100:     PetscInt t;
    101:     /* support horizontal 1D arrays (MATLAB vectors) - swap meaning of blocks and entries */
    102:     if (ctx->complexVal) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Complex and horizontal at the same time not allowed.");
    103:     t = len; len = bs; bs = t;
    104:     t = ctx->lenInd; ctx->lenInd = ctx->bsInd; ctx->bsInd = t;
    105:   }
    106:   N = (PetscInt) len*bs;

    108:   /* Set global size, blocksize and type if not yet set */
    109:   if (map->bs < 0) {
    110:     PetscLayoutSetBlockSize(map, bs);
    111:   } else if (map->bs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Block size of array in file is %D, not %D as expected",bs,map->bs);
    112:   if (map->N < 0) {
    113:     PetscLayoutSetSize(map, N);
    114:   } else if (map->N != N) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED, "Global size of array in file is %D, not %D as expected",N,map->N);
    115:   if (setup) {PetscLayoutSetUp(map);}
    116:   return(0);
    117: }

    119: static PetscErrorCode PetscViewerHDF5ReadSelectHyperslab_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscLayout map, hid_t *memspace)
    120: {
    121:   hsize_t        *count, *offset;
    122:   PetscInt       bs, n, low;
    123:   int            i;

    127:   /* Compute local size and ownership range */
    128:   PetscLayoutSetUp(map);
    129:   PetscLayoutGetBlockSize(map, &bs);
    130:   PetscLayoutGetLocalSize(map, &n);
    131:   PetscLayoutGetRange(map, &low, NULL);

    133:   /* Each process defines a dataset and reads it from the hyperslab in the file */
    134:   PetscMalloc2(ctx->rdim, &count, ctx->rdim, &offset);
    135:   for (i=0; i<ctx->rdim; i++) {
    136:     /* By default, select all entries with no offset */
    137:     offset[i] = 0;
    138:     count[i] = ctx->dims[i];
    139:   }
    140:   if (ctx->timestep >= 0) {
    141:     count[0]  = 1;
    142:     offset[0] = ctx->timestep;
    143:   }
    144:   {
    145:     PetscHDF5IntCast(n/bs, &count[ctx->lenInd]);
    146:     PetscHDF5IntCast(low/bs, &offset[ctx->lenInd]);
    147:   }
    148:   if (ctx->complexVal && count[ctx->bsInd+1] != 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Complex numbers must have exactly 2 parts (%D)",count[ctx->bsInd+1]);
    149:   PetscStackCallHDF5Return(*memspace,H5Screate_simple,(ctx->rdim, count, NULL));
    150:   PetscStackCallHDF5(H5Sselect_hyperslab,(ctx->dataspace, H5S_SELECT_SET, offset, NULL, count, NULL));
    151:   PetscFree2(count, offset);
    152:   return(0);
    153: }

    155: static PetscErrorCode PetscViewerHDF5ReadArray_Private(PetscViewer viewer, HDF5ReadCtx h, hid_t datatype, hid_t memspace, void *arr)
    156: {
    157:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

    160:   PetscStackCallHDF5(H5Dread,(h->dataset, datatype, memspace, h->dataspace, hdf5->dxpl_id, arr));
    161:   return(0);
    162: }

    164: /*@C
    165:   PetscViewerHDF5Load - Read a raw array from the HDF5 dataset.

    167:   Input Parameters:
    168: + viewer   - The HDF5 viewer
    169: . name     - The dataset name
    170: . map      - The layout which specifies array partitioning
    171: - datatype - The HDF5 datatype of the items in the dataset

    173:   Output Parameter:
    174: + map      - The set up layout (with global size and blocksize according to dataset)
    175: - newarr   - The partitioned array, a memory image of the given dataset

    177:   Level: developer

    179:   Notes:
    180:   This is intended mainly for internal use; users should use higher level routines such as ISLoad(), VecLoad(), DMLoad().
    181:   The array is partitioned according to the given PetscLayout which is converted to an HDF5 hyperslab.
    182:   This name is relative to the current group returned by PetscViewerHDF5OpenGroup().

    184:   Fortran Notes:
    185:   This routine is not available in Fortran.

    187: .seealso PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5OpenGroup(), PetscViewerHDF5ReadSizes(), VecLoad(), ISLoad()
    188: @*/
    189: PetscErrorCode PetscViewerHDF5Load(PetscViewer viewer, const char *name, PetscLayout map, hid_t datatype, void **newarr)
    190: {
    191:   HDF5ReadCtx     h=NULL;
    192:   hid_t           memspace=0;
    193:   size_t          unitsize;
    194:   void            *arr;
    195:   PetscErrorCode  ierr;

    198:   PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);
    199: #if defined(PETSC_USE_COMPLEX)
    200:   if (!h->complexVal) {
    201:     H5T_class_t clazz = H5Tget_class(datatype);
    202:     if (clazz == H5T_FLOAT) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"File contains real numbers but PETSc is configured for complex. The conversion is not yet implemented. Configure with --with-scalar-type=real.");
    203:   }
    204: #else
    205:   if (h->complexVal) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"File contains complex numbers but PETSc not configured for them. Configure with --with-scalar-type=complex.");
    206: #endif

    208:   PetscViewerHDF5ReadSizes_Private(viewer, h, PETSC_TRUE, &map);
    209:   PetscViewerHDF5ReadSelectHyperslab_Private(viewer, h, map, &memspace);

    211:   unitsize = H5Tget_size(datatype);
    212:   if (h->complexVal) unitsize *= 2;
    213:   if (unitsize <= 0 || unitsize > PetscMax(sizeof(PetscInt),sizeof(PetscScalar))) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Sanity check failed: HDF5 function H5Tget_size(datatype) returned suspicious value %D",unitsize);
    214:   PetscMalloc(map->n*unitsize, &arr);

    216:   PetscViewerHDF5ReadArray_Private(viewer, h, datatype, memspace, arr);
    217:   PetscStackCallHDF5(H5Sclose,(memspace));
    218:   PetscViewerHDF5ReadFinalize_Private(viewer, &h);
    219:   *newarr = arr;
    220:   return(0);
    221: }

    223: /*@C
    224:  PetscViewerHDF5ReadSizes - Read block size and global size of a vector (Vec or IS) stored in an HDF5 file.

    226:   Input Parameters:
    227: + viewer - The HDF5 viewer
    228: - name   - The dataset name

    230:   Output Parameter:
    231: + bs     - block size
    232: - N      - global size

    234:   Notes:
    235:   The dataset is stored as an HDF5 dataspace with 1-4 dimensions in the order
    236:   1) # timesteps (optional), 2) # blocks, 3) # elements per block (optional), 4) real and imaginary part (only for complex).

    238:   The dataset can be stored as a 2D dataspace even if its blocksize is 1; see PetscViewerHDF5SetBaseDimension2().

    240:   Level: advanced

    242: .seealso: PetscViewerHDF5Open(), VecLoad(), ISLoad(), VecGetSize(), ISGetSize(), PetscViewerHDF5SetBaseDimension2()
    243: @*/
    244: PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
    245: {
    246:   HDF5ReadCtx    h=NULL;
    247:   PetscLayout    map=NULL;

    252:   PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);
    253:   PetscViewerHDF5ReadSizes_Private(viewer, h, PETSC_FALSE, &map);
    254:   PetscViewerHDF5ReadFinalize_Private(viewer, &h);
    255:   if (bs) *bs = map->bs;
    256:   if (N) *N = map->N;
    257:   PetscLayoutDestroy(&map);
    258:   return(0);
    259: }

    261: #endif /* defined(PETSC_HAVE_HDF5) */