diff options
Diffstat (limited to 'src/H5Farray.c')
| -rw-r--r-- | src/H5Farray.c | 266 |
1 files changed, 153 insertions, 113 deletions
diff --git a/src/H5Farray.c b/src/H5Farray.c index 67c0446..6019f1e 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -15,10 +15,15 @@ #include <H5Dprivate.h> #include <H5Eprivate.h> #include <H5Fprivate.h> +#include <H5Iprivate.h> #include <H5MFprivate.h> #include <H5Oprivate.h> +#include <H5Pprivate.h> #include <H5Vprivate.h> +/* MPIO driver functions are needed for some special checks */ +#include <H5FDmpio.h> + /* Interface initialization */ #define PABLO_MASK H5Farray_mask #define INTERFACE_INIT NULL @@ -51,14 +56,14 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) /* check args */ assert (f); assert (layout); - layout->addr = H5F_ADDR_UNDEF; /*just in case we fail*/ + layout->addr = HADDR_UNDEF; /*just in case we fail*/ switch (layout->type) { case H5D_CONTIGUOUS: /* Reserve space in the file for the entire array */ for (i=0, nbytes=1; i<layout->ndims; i++) nbytes *= layout->dim[i]; assert (nbytes>0); - if (H5MF_alloc (f, H5MF_RAW, nbytes, &(layout->addr)/*out*/)<0) { + if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes))) { HRETURN_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); } @@ -103,22 +108,24 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) * Friday, January 16, 1998 * * Modifications: - * June 2, 1998 Albert Cheng + * Albert Cheng, 1998-06-02 * Added xfer_mode argument * - * Sep 28, 1998 Robb Matzke + * Robb Matzke, 1998-09-28 * Added the `xfer' argument and removed the `xfer_mode' * argument since it's a field of `xfer'. * + * Robb Matzke, 1999-08-02 + * Data transfer properties are passed by ID since that's how + * the virtual file layer wants them. *------------------------------------------------------------------------- */ herr_t -H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, - const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, const H5O_fill_t *fill, - const struct H5O_efl_t *efl, const hsize_t _hslab_size[], - const hsize_t mem_size[], const hssize_t mem_offset[], - const hssize_t file_offset[], void *_buf/*out*/) +H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, + const struct H5O_pline_t *pline, const H5O_fill_t *fill, + const struct H5O_efl_t *efl, const hsize_t _hslab_size[], + const hsize_t mem_size[], const hssize_t mem_offset[], + const hssize_t file_offset[], void *_buf/*out*/) { uint8_t *buf = (uint8_t*)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -133,27 +140,43 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, haddr_t addr; /*address in file */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ +#ifdef HAVE_PARALLEL + H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; +#endif - FUNC_ENTER (H5F_arr_read, FAIL); + FUNC_ENTER(H5F_arr_read, FAIL); /* Check args */ - assert (f); - assert (layout); - assert (_hslab_size); - assert (file_offset); - assert (mem_offset); - assert (mem_size); - assert (buf); + assert(f); + assert(layout); + assert(_hslab_size); + assert(file_offset); + assert(mem_offset); + assert(mem_size); + assert(buf); /* Make a local copy of size so we can modify it */ - H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size); + H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size); #ifdef HAVE_PARALLEL - if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){ - if (layout->type != H5D_CONTIGUOUS) - HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL, - "collective access on non-contiguous datasets not " - "supported yet"); + { + /* Get the transfer mode */ + H5F_xfer_t *dxpl; + H5FD_mpio_dxpl_t *dx; + if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) && + H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) && + H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) { + xfer_mode = dx->xfer_mode; + } + } +#endif + +#ifdef HAVE_PARALLEL + /* Collective MPIO access is unsupported for non-contiguous datasets */ + if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) { + HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL, + "collective access on non-contiguous datasets not " + "supported yet"); } #endif #ifdef QAK @@ -177,8 +200,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, */ for (i=0; i<ndims; i++) { if (mem_offset[i]<0 || file_offset[i]<0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "negative offsets are not valid"); + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "negative offsets are not valid"); } } @@ -186,8 +209,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * Filters cannot be used for contiguous data. */ if (pline && pline->nfilters>0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "filters are not allowed for contiguous data"); + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "filters are not allowed for contiguous data"); } /* @@ -195,12 +218,12 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * and memory. Optimize the strides to result in the fewest number of * I/O requests. */ - mem_start = H5V_hyper_stride (ndims, hslab_size, mem_size, - mem_offset, mem_stride/*out*/); - file_start = H5V_hyper_stride (ndims, hslab_size, layout->dim, - file_offset, file_stride/*out*/); - H5V_stride_optimize2 (&ndims, &elmt_size, hslab_size, - mem_stride, file_stride); + mem_start = H5V_hyper_stride(ndims, hslab_size, mem_size, + mem_offset, mem_stride/*out*/); + file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim, + file_offset, file_stride/*out*/); + H5V_stride_optimize2(&ndims, &elmt_size, hslab_size, + mem_stride, file_stride); /* * Initialize loop variables. The loop is a multi-dimensional loop @@ -208,8 +231,8 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * element of IDX is treated as a digit with IDX[0] being the least * significant digit. */ - H5V_vector_cpy (ndims, idx, hslab_size); - nelmts = H5V_vector_reduce_product (ndims, hslab_size); + H5V_vector_cpy(ndims, idx, hslab_size); + nelmts = H5V_vector_reduce_product(ndims, hslab_size); if (efl && efl->nused>0) { addr = 0; } else { @@ -223,19 +246,20 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * memory. */ #ifdef HAVE_PARALLEL - if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){ - /* Currently supports same number of collective access. - * Need to be changed LATER to combine all reads into one - * collective MPIO call. + if (H5FD_MPIO_COLLECTIVE==xfer_mode){ + /* + * Currently supports same number of collective access. Need to + * be changed LATER to combine all reads into one collective MPIO + * call. */ unsigned long max, min, temp; temp = nelmts; assert(temp==nelmts); /* verify no overflow */ MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX, - f->shared->access_parms->u.mpio.comm); + H5FD_mpio_communicator(f->shared->lf)); MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, - f->shared->access_parms->u.mpio.comm); + H5FD_mpio_communicator(f->shared->lf)); #ifdef AKC printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); #endif @@ -250,18 +274,17 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, /* Read from file */ if (efl && efl->nused>0) { - if (H5O_efl_read (f, efl, addr, elmt_size, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "external data read failed"); + if (H5O_efl_read(f, efl, addr, elmt_size, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "external data read failed"); } - } else if (H5F_block_read (f, addr, elmt_size, xfer, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "block read failed"); + } else if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); } /* Decrement indices and advance pointers */ for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { - addr += file_stride[j]; buf += mem_stride[j]; @@ -277,29 +300,29 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * into a proper hyperslab. */ if (efl && efl->nused>0) { - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "chunking and external files are mutually " - "exclusive"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "chunking and external files are mutually " + "exclusive"); } for (i=0; i<layout->ndims; i++) { if (0!=mem_offset[i] || hslab_size[i]!=mem_size[i]) { - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "unable to copy into a proper hyperslab"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "unable to copy into a proper hyperslab"); } } - if (H5F_istore_read (f, xfer, layout, pline, fill, file_offset, + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, file_offset, hslab_size, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } break; default: - assert ("not implemented yet" && 0); - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "unsupported storage layout"); + assert("not implemented yet" && 0); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "unsupported storage layout"); } - FUNC_LEAVE (SUCCEED); + FUNC_LEAVE(SUCCEED); } @@ -324,23 +347,25 @@ H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer, * Friday, January 16, 1998 * * Modifications: - * June 2, 1998 Albert Cheng + * Albert Cheng, 1998-06-02 * Added xfer_mode argument * - * Sep 28, 1998 Robb Matzke + * Robb Matzke, 1998-09-28 * Added `xfer' argument, removed `xfer_mode' argument since it * is a member of H5F_xfer_t. * + * Robb Matzke, 1999-08-02 + * Data transfer properties are passed by ID since that's how + * the virtual file layer wants them. *------------------------------------------------------------------------- */ herr_t -H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, - const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, - const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, - const hsize_t _hslab_size[], const hsize_t mem_size[], - const hssize_t mem_offset[], const hssize_t file_offset[], - const void *_buf) +H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, + const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, + const hsize_t _hslab_size[], const hsize_t mem_size[], + const hssize_t mem_offset[], const hssize_t file_offset[], + const void *_buf) { const uint8_t *buf = (const uint8_t *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -355,8 +380,11 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, haddr_t addr; /*address in file */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ +#ifdef HAVE_PARALLEL + H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; +#endif - FUNC_ENTER (H5F_arr_write, FAIL); + FUNC_ENTER(H5F_arr_write, FAIL); /* Check args */ assert(f); @@ -368,17 +396,29 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, assert(buf); /* Make a local copy of _size so we can modify it */ - H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size); + H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size); #ifdef HAVE_PARALLEL - if (xfer->xfer_mode==H5D_XFER_COLLECTIVE) { - if (layout->type != H5D_CONTIGUOUS) { - HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, - "collective access on non-contiguous datasets not " - "supported yet"); + { + /* Get the transfer mode */ + H5F_xfer_t *dxpl; + H5FD_mpio_dxpl_t *dx; + if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) && + H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) && + H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) { + xfer_mode = dx->xfer_mode; } } #endif + +#ifdef HAVE_PARALLEL + if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) { + HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, + "collective access on non-contiguous datasets not " + "supported yet"); + } +#endif + #ifdef QAK { extern int qak_debug; @@ -403,8 +443,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, */ for (i=0; i<ndims; i++) { if (mem_offset[i]<0 || file_offset[i]<0) { - HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "negative offsets are not valid"); + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "negative offsets are not valid"); } } @@ -412,8 +452,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, * Filters cannot be used for contiguous data */ if (pline && pline->nfilters>0) { - HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "filters are not allowed for contiguous data"); + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "filters are not allowed for contiguous data"); } /* @@ -421,12 +461,12 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, * Optimize the strides to result in the fewest number of I/O * requests. */ - mem_start = H5V_hyper_stride (ndims, hslab_size, mem_size, - mem_offset, mem_stride/*out*/); - file_start = H5V_hyper_stride (ndims, hslab_size, layout->dim, - file_offset, file_stride/*out*/); - H5V_stride_optimize2 (&ndims, &elmt_size, hslab_size, - mem_stride, file_stride); + mem_start = H5V_hyper_stride(ndims, hslab_size, mem_size, + mem_offset, mem_stride/*out*/); + file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim, + file_offset, file_stride/*out*/); + H5V_stride_optimize2(&ndims, &elmt_size, hslab_size, + mem_stride, file_stride); /* * Initialize loop variables. The loop is a multi-dimensional loop @@ -434,8 +474,8 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, * element of IDX is treated as a digit with IDX[0] being the least * significant digit. */ - H5V_vector_cpy (ndims, idx, hslab_size); - nelmts = H5V_vector_reduce_product (ndims, hslab_size); + H5V_vector_cpy(ndims, idx, hslab_size); + nelmts = H5V_vector_reduce_product(ndims, hslab_size); if (efl && efl->nused>0) { addr = 0; } else { @@ -449,19 +489,20 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, * disk. */ #ifdef HAVE_PARALLEL - if (xfer->xfer_mode==H5D_XFER_COLLECTIVE){ - /* Currently supports same number of collective access. - * Need to be changed LATER to combine all writes into one - * collective MPIO call. + if (H5FD_MPIO_COLLECTIVE==xfer_mode){ + /* + * Currently supports same number of collective access. Need to + * be changed LATER to combine all writes into one collective + * MPIO call. */ unsigned long max, min, temp; temp = nelmts; assert(temp==nelmts); /* verify no overflow */ MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX, - f->shared->access_parms->u.mpio.comm); + H5FD_mpio_communicator(f->shared->lf)); MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, - f->shared->access_parms->u.mpio.comm); + H5FD_mpio_communicator(f->shared->lf)); #ifdef AKC printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); #endif @@ -477,18 +518,17 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, /* Write to file */ if (efl && efl->nused>0) { - if (H5O_efl_write (f, efl, addr, elmt_size, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "external data write failed"); + if (H5O_efl_write(f, efl, addr, elmt_size, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "external data write failed"); } - } else if (H5F_block_write(f, addr, elmt_size, xfer, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "block write failed"); + } else if (H5F_block_write(f, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); } /* Decrement indices and advance pointers */ for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { - addr += file_stride[j]; buf += mem_stride[j]; @@ -505,27 +545,27 @@ H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer, * from a proper hyperslab. */ if (efl && efl->nused>0) { - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "chunking and external files are mutually " - "exclusive"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "chunking and external files are mutually " + "exclusive"); } for (i=0; i<layout->ndims; i++) { if (0!=mem_offset[i] || hslab_size[i]!=mem_size[i]) { - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "unable to copy from a proper hyperslab"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "unable to copy from a proper hyperslab"); } } - if (H5F_istore_write (f, xfer, layout, pline, fill, file_offset, - hslab_size, buf)<0) { - HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "chunked write failed"); + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, file_offset, + hslab_size, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "chunked write failed"); } break; default: - assert ("not implemented yet" && 0); - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "unsupported storage layout"); + assert("not implemented yet" && 0); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, + "unsupported storage layout"); } FUNC_LEAVE (SUCCEED); |