Date: 2022-03-04T17:37:39+00:00

Actual source code: hdf5io.c

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

      5: #if defined(PETSC_HAVE_HDF5)

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

     15: PetscErrorCode PetscViewerHDF5CheckTimestepping_Internal(PetscViewer viewer, const char name[])
     16: {
     17:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
     18:   PetscBool        timestepping=PETSC_FALSE;
     19:   const char       *group;
     20:   PetscErrorCode   ierr;

     23:   PetscViewerHDF5GetGroup(viewer, &group);
     24:   PetscViewerHDF5ReadAttribute(viewer,name,"timestepping",PETSC_BOOL,&timestepping,&timestepping);
     25:   if (timestepping != hdf5->timestepping) SETERRQ4(PetscObjectComm((PetscObject)viewer),PETSC_ERR_FILE_UNEXPECTED,"Dataset %s/%s stored with timesteps? %s Timestepping pushed? %s", group, name, PetscBools[timestepping], PetscBools[hdf5->timestepping]);
     26:   return(0);
     27: }

     29: static PetscErrorCode PetscViewerHDF5ReadInitialize_Private(PetscViewer viewer, const char name[], HDF5ReadCtx *ctx)
     30: {
     31:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
     32:   HDF5ReadCtx      h=NULL;
     33:   PetscErrorCode   ierr;

     36:   PetscViewerHDF5CheckTimestepping_Internal(viewer, name);
     37:   PetscNew(&h);
     38:   PetscViewerHDF5OpenGroup(viewer, &h->file, &h->group);
     39:   PetscStackCallHDF5Return(h->dataset,H5Dopen2,(h->group, name, H5P_DEFAULT));
     40:   PetscStackCallHDF5Return(h->dataspace,H5Dget_space,(h->dataset));
     41:   PetscViewerHDF5ReadAttribute(viewer,name,"complex",PETSC_BOOL,&h->complexVal,&h->complexVal);
     42:   if (!hdf5->horizontal) {
     43:     /* MATLAB stores column vectors horizontally */
     44:     PetscViewerHDF5HasAttribute(viewer,name,"MATLAB_class",&hdf5->horizontal);
     45:   }
     46:   *ctx = h;
     47:   return(0);
     48: }

     50: static PetscErrorCode PetscViewerHDF5ReadFinalize_Private(PetscViewer viewer, HDF5ReadCtx *ctx)
     51: {
     52:   HDF5ReadCtx    h;

     56:   h = *ctx;
     57:   PetscStackCallHDF5(H5Gclose,(h->group));
     58:   PetscStackCallHDF5(H5Sclose,(h->dataspace));
     59:   PetscStackCallHDF5(H5Dclose,(h->dataset));
     60:   PetscFree((*ctx)->dims);
     61:   PetscFree(*ctx);
     62:   return(0);
     63: }

     65: static PetscErrorCode PetscViewerHDF5ReadSizes_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscBool setup, PetscLayout *map_)
     66: {
     67:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
     68:   PetscInt         bs, len, N;
     69:   PetscLayout      map;
     70:   PetscErrorCode   ierr;

     73:   if (!(*map_)) {
     74:     PetscLayoutCreate(PetscObjectComm((PetscObject)viewer),map_);
     75:   }
     76:   map = *map_;

     78:   /* Get actual number of dimensions in dataset */
     79:   PetscStackCallHDF5Return(ctx->rdim,H5Sget_simple_extent_dims,(ctx->dataspace, NULL, NULL));
     80:   PetscMalloc1(ctx->rdim, &ctx->dims);
     81:   PetscStackCallHDF5Return(ctx->rdim,H5Sget_simple_extent_dims,(ctx->dataspace, ctx->dims, NULL));

     83:   /*
     84:      Dimensions are in this order:
     85:      [0]        timesteps (optional)
     86:      [lenInd]   entries (numbers or blocks)
     87:      ...
     88:      [bsInd]    entries of blocks (optional)
     89:      [bsInd+1]  real & imaginary part (optional)
     90:       = rdim-1
     91:    */

     93:   /* Get entries dimension index */
     94:   ctx->lenInd = 0;
     95:   if (hdf5->timestepping) ++ctx->lenInd;

     97:   /* Get block dimension index */
     98:   if (ctx->complexVal) {
     99:     ctx->bsInd = ctx->rdim-2;
    100:     ctx->complexInd = ctx->rdim-1;
    101:   } else {
    102:     ctx->bsInd = ctx->rdim-1;
    103:     ctx->complexInd = -1;
    104:   }
    105:   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);
    106:   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);
    107:   if (ctx->complexVal && ctx->dims[ctx->complexInd] != 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Complex numbers must have exactly 2 parts (%D)",ctx->dims[ctx->complexInd]);

    109:   if (hdf5->horizontal) {
    110:     PetscInt t;
    111:     /* support horizontal 1D arrays (MATLAB vectors) - swap meaning of blocks and entries */
    112:     t = ctx->lenInd; ctx->lenInd = ctx->bsInd; ctx->bsInd = t;
    113:   }

    115:   /* Get block size */
    116:   ctx->dim2 = PETSC_FALSE;
    117:   if (ctx->lenInd == ctx->bsInd) {
    118:     bs = 1; /* support vectors stored as 1D array */
    119:   } else {
    120:     bs = (PetscInt) ctx->dims[ctx->bsInd];
    121:     if (bs == 1) ctx->dim2 = PETSC_TRUE; /* vector with blocksize of 1, still stored as 2D array */
    122:   }

    124:   /* Get global size */
    125:   len = ctx->dims[ctx->lenInd];
    126:   N = (PetscInt) len*bs;

    128:   /* Set global size, blocksize and type if not yet set */
    129:   if (map->bs < 0) {
    130:     PetscLayoutSetBlockSize(map, bs);
    131:   } 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);
    132:   if (map->N < 0) {
    133:     PetscLayoutSetSize(map, N);
    134:   } 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);
    135:   if (setup) {PetscLayoutSetUp(map);}
    136:   return(0);
    137: }

    139: static PetscErrorCode PetscViewerHDF5ReadSelectHyperslab_Private(PetscViewer viewer, HDF5ReadCtx ctx, PetscLayout map, hid_t *memspace)
    140: {
    141:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
    142:   hsize_t          *count, *offset;
    143:   PetscInt         bs, n, low;
    144:   int              i;
    145:   PetscErrorCode   ierr;

    148:   /* Compute local size and ownership range */
    149:   PetscLayoutSetUp(map);
    150:   PetscLayoutGetBlockSize(map, &bs);
    151:   PetscLayoutGetLocalSize(map, &n);
    152:   PetscLayoutGetRange(map, &low, NULL);

    154:   /* Each process defines a dataset and reads it from the hyperslab in the file */
    155:   PetscMalloc2(ctx->rdim, &count, ctx->rdim, &offset);
    156:   for (i=0; i<ctx->rdim; i++) {
    157:     /* By default, select all entries with no offset */
    158:     offset[i] = 0;
    159:     count[i] = ctx->dims[i];
    160:   }
    161:   if (hdf5->timestepping) {
    162:     count[0]  = 1;
    163:     offset[0] = hdf5->timestep;
    164:   }
    165:   {
    166:     PetscHDF5IntCast(n/bs, &count[ctx->lenInd]);
    167:     PetscHDF5IntCast(low/bs, &offset[ctx->lenInd]);
    168:   }
    169:   PetscStackCallHDF5Return(*memspace,H5Screate_simple,(ctx->rdim, count, NULL));
    170:   PetscStackCallHDF5(H5Sselect_hyperslab,(ctx->dataspace, H5S_SELECT_SET, offset, NULL, count, NULL));
    171:   PetscFree2(count, offset);
    172:   return(0);
    173: }

    175: static PetscErrorCode PetscViewerHDF5ReadArray_Private(PetscViewer viewer, HDF5ReadCtx h, hid_t datatype, hid_t memspace, void *arr)
    176: {
    177:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

    180:   PetscStackCallHDF5(H5Dread,(h->dataset, datatype, memspace, h->dataspace, hdf5->dxpl_id, arr));
    181:   return(0);
    182: }

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

    187:   Input Parameters:
    188: + viewer   - The HDF5 viewer
    189: . name     - The dataset name
    190: - datatype - The HDF5 datatype of the items in the dataset

    192:   Input/Output Parameter:
    193: . map      - The layout which specifies array partitioning, on output the
    194:              set up layout (with global size and blocksize according to dataset)

    196:   Output Parameter:
    197: . newarr   - The partitioned array, a memory image of the given dataset

    199:   Level: developer

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

    206:   Fortran Notes:
    207:   This routine is not available in Fortran.

    209: .seealso PetscViewerHDF5Open(), PetscViewerHDF5PushGroup(), PetscViewerHDF5OpenGroup(), PetscViewerHDF5ReadSizes(), VecLoad(), ISLoad()
    210: @*/
    211: PetscErrorCode PetscViewerHDF5Load(PetscViewer viewer, const char *name, PetscLayout map, hid_t datatype, void **newarr)
    212: {
    213:   PetscBool       has;
    214:   const char      *group;
    215:   HDF5ReadCtx     h=NULL;
    216:   hid_t           memspace=0;
    217:   size_t          unitsize;
    218:   void            *arr;
    219:   PetscErrorCode  ierr;

    222:   PetscViewerHDF5GetGroup(viewer, &group);
    223:   PetscViewerHDF5HasDataset(viewer, name, &has);
    224:   if (!has) SETERRQ2(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", name, group ? group : "/");
    225:   PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);
    226: #if defined(PETSC_USE_COMPLEX)
    227:   if (!h->complexVal) {
    228:     H5T_class_t clazz = H5Tget_class(datatype);
    229:     if (clazz == H5T_FLOAT) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Dataset %s/%s is marked as real but PETSc is configured for complex scalars. The conversion is not yet implemented. Configure with --with-scalar-type=real to read this dataset", group ? group : "",name);
    230:   }
    231: #else
    232:   if (h->complexVal) SETERRQ2(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Dataset %s/%s is marked as complex but PETSc is configured for real scalars. Configure with --with-scalar-type=complex to read this dataset", group ? group : "",name);
    233: #endif

    235:   PetscViewerHDF5ReadSizes_Private(viewer, h, PETSC_TRUE, &map);
    236:   PetscViewerHDF5ReadSelectHyperslab_Private(viewer, h, map, &memspace);

    238:   unitsize = H5Tget_size(datatype);
    239:   if (h->complexVal) unitsize *= 2;
    240:   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);
    241:   PetscMalloc(map->n*unitsize, &arr);

    243:   PetscViewerHDF5ReadArray_Private(viewer, h, datatype, memspace, arr);
    244:   PetscStackCallHDF5(H5Sclose,(memspace));
    245:   PetscViewerHDF5ReadFinalize_Private(viewer, &h);
    246:   *newarr = arr;
    247:   return(0);
    248: }

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

    253:   Input Parameters:
    254: + viewer - The HDF5 viewer
    255: - name   - The dataset name

    257:   Output Parameters:
    258: + bs     - block size
    259: - N      - global size

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

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

    267:   Level: advanced

    269: .seealso: PetscViewerHDF5Open(), VecLoad(), ISLoad(), VecGetSize(), ISGetSize(), PetscViewerHDF5SetBaseDimension2()
    270: @*/
    271: PetscErrorCode PetscViewerHDF5ReadSizes(PetscViewer viewer, const char name[], PetscInt *bs, PetscInt *N)
    272: {
    273:   HDF5ReadCtx    h=NULL;
    274:   PetscLayout    map=NULL;

    279:   PetscViewerHDF5ReadInitialize_Private(viewer, name, &h);
    280:   PetscViewerHDF5ReadSizes_Private(viewer, h, PETSC_FALSE, &map);
    281:   PetscViewerHDF5ReadFinalize_Private(viewer, &h);
    282:   if (bs) *bs = map->bs;
    283:   if (N) *N = map->N;
    284:   PetscLayoutDestroy(&map);
    285:   return(0);
    286: }

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