diff options
Diffstat (limited to 'src/H5Dcontig.c')
| -rw-r--r-- | src/H5Dcontig.c | 193 |
1 files changed, 191 insertions, 2 deletions
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 89f9fc5..fce1ba9 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -14,11 +14,19 @@ #define H5F_PACKAGE /*suppress error about including H5Fpkg */ -#include "H5private.h" -#include "H5Eprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Dprivate.h" /* Dataset functions */ +#include "H5Eprivate.h" /* Error handling */ #include "H5Fpkg.h" #include "H5FDprivate.h" /*file driver */ #include "H5FLprivate.h" /*Free Lists */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Pprivate.h" /* Property lists */ +#include "H5Vprivate.h" /* Vector and array functions */ + +/* MPIO & MPIPOSIX drivers needed for special checks */ +#include "H5FDmpio.h" +#include "H5FDmpiposix.h" /* Interface initialization */ #define PABLO_MASK H5Fcontig_mask @@ -28,6 +36,187 @@ static int interface_initialize_g = 0; /* Declare a PQ free list to manage the sieve buffer information */ H5FL_BLK_DEFINE(sieve_buf); +/* Extern the free list to manage blocks of type conversion data */ +H5FL_BLK_EXTERN(type_conv); + + +/*------------------------------------------------------------------------- + * Function: H5F_contig_fill + * + * Purpose: Write fill values to a contiguously stored dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * August 22, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, + struct H5P_genplist_t *dc_plist, const struct H5S_t *space, + size_t elmt_size) +{ + H5O_fill_t fill; /* Fill value information */ + H5O_efl_t efl; /* External File List info */ + hssize_t snpoints; /* Number of points in space (for error checking) */ + size_t npoints; /* Number of points in space */ + size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ + size_t bufsize=64*1024; /* Size of buffer to write */ + size_t size; /* Current # of points to write */ + hsize_t addr; /* Offset in dataset */ + void *buf = NULL; /* Buffer for fill value writing */ +#ifdef H5_HAVE_PARALLEL + MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ + int mpi_rank=(-1); /* This process's rank */ + int mpi_size=(-1); /* Total # of processes */ + int mpi_round=0; /* Current process responsible for I/O */ + int mpi_code; /* MPI return code */ + unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ + unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ +#endif /* H5_HAVE_PARALLEL */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5F_contig_fill, FAIL); + + /* Check args */ + assert(f); + assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); + assert(layout && H5D_CONTIGUOUS==layout->type); + assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->addr)); + assert(dc_plist!=NULL); + assert(space); + assert(elmt_size>0); + + /* Get necessary properties from dataset creation property list */ + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value"); + if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + +#ifdef H5_HAVE_PARALLEL + /* Retrieve up MPI parameters */ + if(IS_H5FD_MPIO(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + else { + if(IS_H5FD_MPIPOSIX(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + /* Get the number of elements in the dataset's dataspace */ + snpoints = H5S_get_simple_extent_npoints(space); + assert(snpoints>=0); + H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); + + /* Don't write default fill-values to external files */ + if(efl.nused>0 && !fill.buf) + HGOTO_DONE(SUCCEED); + + /* If fill value is library default, use the element size */ + if(!fill.buf) + fill.size=elmt_size; + + /* + * 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/fill.size); + bufsize = ptsperbuf*fill.size; + + /* Allocate temporary buffer */ + if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); + + /* Fill the buffer with the user's fill value */ + if(fill.buf) + H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf); + else /* Fill the buffer with the default fill value */ + HDmemset(buf,0,bufsize); + + /* Start at the beginning of the dataset */ + addr = 0; + + /* Loop through writing the fill value to the dataset */ + while (npoints>0) { + size = MIN(ptsperbuf, npoints) * fill.size; + +#ifdef H5_HAVE_PARALLEL + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Round-robin write the chunks out from only one process */ + if(mpi_round==mpi_rank) { + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); + } /* end if */ + mpi_round=(++mpi_round)%mpi_size; + + /* Indicate that blocks are being written */ + blocks_written=1; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); +#ifdef H5_HAVE_PARALLEL + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + npoints -= MIN(ptsperbuf, npoints); + addr += size; + } /* end while */ + +#ifdef H5_HAVE_PARALLEL + /* Only need to block at the barrier if we actually wrote fill values */ + /* And if we are using an MPI-capable file driver */ + if(using_mpi && blocks_written) { + /* Wait at barrier to avoid race conditions where some processes are + * still writing out fill values and other processes race ahead to data + * in, getting bogus data. + */ + if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ + +done: + /* Free the buffer for fill values */ + if (buf) + H5FL_BLK_FREE(type_conv,buf); + + FUNC_LEAVE(ret_value); +} + /*------------------------------------------------------------------------- * Function: H5F_contig_read |