diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 254 | ||||
| -rw-r--r-- | src/H5Distore.c | 16 | ||||
| -rw-r--r-- | src/H5Fistore.c | 16 | ||||
| -rw-r--r-- | src/H5Fmpio.c | 13 |
4 files changed, 176 insertions, 123 deletions
@@ -28,7 +28,8 @@ static char RcsId[] = "@(#)$Revision$"; #include <H5Oprivate.h> /* Object headers */ #include <H5Pprivate.h> /* Property lists */ #include <H5Sprivate.h> /* Dataspace functions rky 980813 */ -#include <H5TBprivate.h> /* Temporary buffers */ +#include <H5TBprivate.h> /* Temporary buffers */ +#include <H5Vprivate.h> /* Vector and array functions */ #include <H5Zprivate.h> /* Data filters */ #ifdef QAK @@ -98,9 +99,7 @@ static hbool_t interface_initialize_g = FALSE; #define INTERFACE_INIT H5D_init_interface static herr_t H5D_init_interface(void); static void H5D_term_interface(void); -#ifdef HAVE_PARALLEL -static herr_t H5D_allocate (H5D_t *dataset, const H5D_xfer_t *xfer); -#endif +static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space); /*-------------------------------------------------------------------------- @@ -932,7 +931,8 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ - if (new_dset->create_parms->chunk_ndims != H5S_get_simple_extent_ndims(space)) { + if (new_dset->create_parms->chunk_ndims != + H5S_get_simple_extent_ndims(space)) { HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space"); } @@ -1030,25 +1030,17 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, } } + /* Initialize the raw data */ + if (H5D_init_storage(new_dset, space)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, + "unable to initialize storage"); + } + /* Give the dataset a name */ if (H5G_insert(loc, name, &(new_dset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); } -#ifdef HAVE_PARALLEL - /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, allocate file space for all chunks now. - */ - if (new_dset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO && - new_dset->layout.type == H5D_CHUNKED){ - if (H5D_allocate(new_dset, &H5D_xfer_dflt)<0) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, - "fail in file space allocation for chunks"); - } - } -#endif /* HAVE_PARALLEL */ - /* Success */ ret_value = new_dset; @@ -1193,22 +1185,18 @@ H5D_open(H5G_entry_t *loc, const char *name) "storage address is undefined an no external file list"); } -#ifdef HAVE_PARALLEL /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, and file is open writable, - * allocate file space for chunks that have not been - * allocated in its "previous access". + * Make sure all storage is properly initialized for chunked datasets. + * This is especially important for parallel I/O where the B-tree must + * be fully populated before I/O can happen. */ - if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && - dataset->layout.type == H5D_CHUNKED && - (dataset->ent.file->intent & H5F_ACC_RDWR)){ - if (H5D_allocate(dataset, &H5D_xfer_dflt)<0) { + if ((dataset->ent.file->intent & H5F_ACC_RDWR) && + H5D_CHUNKED==dataset->layout.type) { + if (H5D_init_storage(dataset, space)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, - "fail in file space allocation dataset"); + "unable to initialize file storage"); } } -#endif /* HAVE_PARALLEL */ /* Success */ ret_value = dataset; @@ -1505,14 +1493,16 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { /* Allocate temporary buffer */ - if (FAIL==(tconv_id = H5TB_get_buf (target_size,1,(void **)&tconv_buf))) { + if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1, + (void **)&tconv_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { /* Allocate temporary buffer */ - if (FAIL==(bkg_id = H5TB_get_buf (request_nelmts*dst_type_size,1,(void **)&bkg_buf))) { + if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1, + (void **)&bkg_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } @@ -1873,14 +1863,16 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { /* Allocate temporary buffer */ - if (FAIL==(tconv_id = H5TB_get_buf (target_size,1,(void **)&tconv_buf))) { + if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1, + (void **)&tconv_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { /* Allocate temporary buffer */ - if (FAIL==(bkg_id = H5TB_get_buf (request_nelmts*dst_type_size,1,(void **)&bkg_buf))) { + if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1, + (void **)&bkg_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } @@ -2069,7 +2061,6 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) * able to muck things up. */ - /* Increase the size of the data space */ if (NULL==(space=H5S_read (&(dataset->ent)))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, @@ -2080,26 +2071,37 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) "unable to increase size of data space"); } - /* Save the new dataspace in the file if necessary */ if (changed>0){ + /* Save the new dataspace in the file if necessary */ if (H5S_modify (&(dataset->ent), space)<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); } -#ifdef HAVE_PARALLEL + + /* Initialize the new parts of the dataset */ +#ifdef LATER + if (H5S_select_all(space)<0 || + H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL, + old_dims, NULL)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to select new extents for fill value"); + } +#else /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, need to allocate file space for all extended - * chunks now. + * We don't have the H5S_SELECT_DIFF operator yet. We really only + * need it for contiguous datasets because the chunked datasets will + * either fill on demand during I/O or attempt a fill of all chunks. */ - if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && - dataset->layout.type==H5D_CHUNKED){ - if (H5D_allocate(dataset, &H5D_xfer_dflt)<0) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "fail in file space allocation for chunks"); - } + if (H5D_CONTIGUOUS==dataset->layout.type && + dataset->create_parms->fill.buf) { + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, + "unable to select fill value region"); + } +#endif + if (H5D_init_storage(dataset, space)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize dataset with fill value"); } -#endif /* HAVE_PARALLEL */ } @@ -2161,86 +2163,134 @@ H5D_typeof (H5D_t *dset) } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- - * Function: H5D_allocate + * Function: H5D_init_storage * - * Purpose: Allocate file space for the data storage of the dataset. - * Return SUCCEED if all needed allocation succeed, otherwise - * FAIL. + * Purpose: Initialize the data for a new dataset. If a selection is + * defined for SPACE then initialize only that part of the + * dataset. * * Return: Success: SUCCEED * * Failure: FAIL * - * Note: Current implementation allocates chunked dataset only. - * - * Programmer: Albert Cheng - * July 9, 1998 + * Programmer: Robb Matzke + * Monday, October 5, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t -H5D_allocate (H5D_t *dataset, const H5D_xfer_t *xfer) +H5D_init_storage(H5D_t *dset, const H5S_t *space) { - H5S_t *space = NULL; + intn ndims; + hsize_t dim[H5O_LAYOUT_NDIMS]; + hsize_t npoints, ptsperbuf; + size_t i, size, bufsize=8*1024; + hbool_t all_zero; + hid_t buf_id = -1; + haddr_t addr; herr_t ret_value = FAIL; - hsize_t space_dim[H5O_LAYOUT_NDIMS]; - intn space_ndims; - H5O_layout_t *layout; + void *buf = NULL; - FUNC_ENTER(H5D_allocate, FAIL); -#ifdef AKC - printf("Enter %s:\n", FUNC); -#endif - - /* Check args */ - assert(dataset); - assert(&(dataset->layout)); - layout = &(dataset->layout); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(&(layout->addr))); - + FUNC_ENTER(H5D_init_storage, FAIL); + assert(dset); + assert(space); - switch (layout->type) { + switch (dset->layout.type) { case H5D_CONTIGUOUS: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); - - case H5D_CHUNKED: - if (NULL==(space=H5S_read (&(dataset->ent)))) { - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to read data space info from dataset header"); + /* + * If the fill value is non-zero then write the fill value to the + * specified selection. + */ + for (i=0, all_zero=TRUE; i<dset->create_parms->fill.size; i++) { + if (((uint8*)(dset->create_parms->fill.buf))[i]) { + all_zero = FALSE; + break; + } } - /* get current dims of dataset */ - if ((space_ndims=H5S_get_simple_extent_dims(space, space_dim, - NULL)) <= 0 || - space_ndims+1 != layout->ndims){ - HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to allocate chunk storage"); + npoints = H5S_get_simple_extent_npoints(space); + + if (!all_zero && npoints==H5S_get_select_npoints(space)) { + /* + * Fill the entire current extent with the fill value. We can do + * this quite efficiently by making sure we copy the fill value + * in relatively large pieces. + */ + ptsperbuf = MAX(1, bufsize/dset->create_parms->fill.size); + bufsize = ptsperbuf * dset->create_parms->fill.size; + if ((buf_id=H5TB_get_buf(bufsize, TRUE, &buf))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to get buffer for fill value"); + } + H5V_array_fill(buf, dset->create_parms->fill.buf, + dset->create_parms->fill.size, ptsperbuf); + if (dset->create_parms->efl.nused) { + H5F_addr_reset(&addr); + } else { + addr = dset->layout.addr; + } + + while (npoints>0) { + size = MIN(ptsperbuf, npoints) * dset->create_parms->fill.size; + if (dset->create_parms->efl.nused) { + if (H5O_efl_write(dset->ent.file, + &(dset->create_parms->efl), + &addr, size, buf)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to write fill value to dataset"); + } + } else { + if (H5F_block_write(dset->ent.file, &addr, size, + H5D_XFER_DFLT, buf)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to write fill value to dataset"); + } + } + npoints -= MIN(ptsperbuf, npoints); + H5F_addr_inc(&addr, size); + } + } else if (!all_zero) { + /* + * Fill the specified selection with the fill value. + */ + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, + "unable to initialize dataset with fill value"); } - /* copy the element size over */ - space_dim[space_ndims] = layout->dim[space_ndims]; + break; - if (H5F_istore_allocate(dataset->ent.file, - (layout), space_dim, xfer->split_ratios, - &(dataset->create_parms->pline), - &(dataset->create_parms->fill))<0) { - HRETURN(FAIL); + case H5D_CHUNKED: + /* + * If the dataset is accessed via parallel I/O, allocate file space + * for all chunks now and initialize each chunk with the fill value. + */ + if (H5F_LOW_MPIO==dset->ent.file->shared->access_parms->driver) { + /* We only handle simple data spaces so far */ + if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to get simple data space info"); + } + dim[ndims] = dset->layout.dim[ndims]; + ndims++; + + if (H5F_istore_allocate(dset->ent.file, &(dset->layout), + dim, H5D_xfer_dflt.split_ratios, + &(dset->create_parms->pline), + &(dset->create_parms->fill))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to allocate all chunks of dataset"); + } } break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); } - ret_value = SUCCEED; - done: - if (space) - H5S_close(space); - + done: + if (buf_id>=0 && H5TB_release_buf(buf_id)<0) { + HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to release fill value temporary buffer"); + } FUNC_LEAVE(ret_value); } -#endif + diff --git a/src/H5Distore.c b/src/H5Distore.c index 8c9dd1b..ed0659e 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -2001,7 +2001,6 @@ H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent, } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5F_istore_get_addr * @@ -2172,20 +2171,21 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, if (carry) break; } +#ifdef HAVE_PARALLEL /* * rky 980923 - * The following barrier is a temporary fix to prevent overwriting - * real data caused by a race between one proc's call of H5F_istore_allocate - * (from H5D_allocate, ultimately from H5Dcreate and H5Dextend) - * and another proc's call of H5Dwrite. - * Eventually, this barrier should be removed, - * when H5D_allocate is changed to call H5MF_alloc directly + * + * The following barrier is a temporary fix to prevent overwriting real + * data caused by a race between one proc's call of H5F_istore_allocate + * (from H5D_init_storage, ultimately from H5Dcreate and H5Dextend) and + * another proc's call of H5Dwrite. Eventually, this barrier should be + * removed, when H5D_init_storage is changed to call H5MF_alloc directly * to allocate space, instead of calling H5F_istore_unlock. */ if (MPI_Barrier( f->shared->access_parms->u.mpio.comm )) { HRETURN_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_Barrier failed"); } +#endif FUNC_LEAVE(SUCCEED); } -#endif diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 8c9dd1b..ed0659e 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -2001,7 +2001,6 @@ H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent, } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5F_istore_get_addr * @@ -2172,20 +2171,21 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, if (carry) break; } +#ifdef HAVE_PARALLEL /* * rky 980923 - * The following barrier is a temporary fix to prevent overwriting - * real data caused by a race between one proc's call of H5F_istore_allocate - * (from H5D_allocate, ultimately from H5Dcreate and H5Dextend) - * and another proc's call of H5Dwrite. - * Eventually, this barrier should be removed, - * when H5D_allocate is changed to call H5MF_alloc directly + * + * The following barrier is a temporary fix to prevent overwriting real + * data caused by a race between one proc's call of H5F_istore_allocate + * (from H5D_init_storage, ultimately from H5Dcreate and H5Dextend) and + * another proc's call of H5Dwrite. Eventually, this barrier should be + * removed, when H5D_init_storage is changed to call H5MF_alloc directly * to allocate space, instead of calling H5F_istore_unlock. */ if (MPI_Barrier( f->shared->access_parms->u.mpio.comm )) { HRETURN_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_Barrier failed"); } +#endif FUNC_LEAVE(SUCCEED); } -#endif diff --git a/src/H5Fmpio.c b/src/H5Fmpio.c index 8ca50d8..2ebe5c8 100644 --- a/src/H5Fmpio.c +++ b/src/H5Fmpio.c @@ -335,7 +335,8 @@ H5F_mpio_open(const char *name, const H5F_access_t *access_parms, uintn flags, } #endif - mpierr = MPI_File_open(access_parms->u.mpio.comm, (char*)name, mpi_amode, access_parms->u.mpio.info, &fh); + mpierr = MPI_File_open(access_parms->u.mpio.comm, (char*)name, mpi_amode, + access_parms->u.mpio.info, &fh); if (MPI_SUCCESS != mpierr) { MPI_Error_string( mpierr, mpierrmsg, &msglen ); HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, mpierrmsg ); @@ -511,7 +512,7 @@ H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms, "couldn't convert addr to MPIOffset" ); } size_i = (int)size; - if (size_i != size) { /* check type conversion */ + if ((size_t)size_i != size) { /* check type conversion */ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert size to int" ); } @@ -764,7 +765,7 @@ H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms, "couldn't convert addr to MPIOffset" ); } size_i = (int)size; - if (size_i != size) { /* check type conversion */ + if ((size_t)size_i != size) { /* check type conversion */ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert size to int" ); } @@ -975,9 +976,11 @@ H5F_MPIOff_to_haddr( MPI_Offset mpi_off, haddr_t *addr ) * Problems and limitations: * * Return: Success: return value is SUCCEED - * and the MPIOffset contains the converted value + * and the MPIOffset contains the converted + * value. * - * Failure: return value is FAIL, the MPIOffset is undefined + * Failure: return value is FAIL, the MPIOffset is + * undefined. * * Programmer: * January 30, 1998 |