diff options
| -rw-r--r-- | src/H5B.c | 9 | ||||
| -rw-r--r-- | src/H5D.c | 109 | ||||
| -rw-r--r-- | src/H5Distore.c | 5 | ||||
| -rw-r--r-- | src/H5Dprivate.h | 2 | ||||
| -rw-r--r-- | src/H5Dpublic.h | 5 | ||||
| -rw-r--r-- | src/H5F.c | 26 | ||||
| -rw-r--r-- | src/H5Farray.c | 36 | ||||
| -rw-r--r-- | src/H5Fcore.c | 8 | ||||
| -rw-r--r-- | src/H5Ffamily.c | 16 | ||||
| -rw-r--r-- | src/H5Fistore.c | 5 | ||||
| -rw-r--r-- | src/H5Flow.c | 20 | ||||
| -rw-r--r-- | src/H5Fmpio.c | 41 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 20 | ||||
| -rw-r--r-- | src/H5Fsec2.c | 8 | ||||
| -rw-r--r-- | src/H5Fsplit.c | 14 | ||||
| -rw-r--r-- | src/H5Fstdio.c | 8 | ||||
| -rw-r--r-- | src/H5Gnode.c | 4 | ||||
| -rw-r--r-- | src/H5HG.c | 8 | ||||
| -rw-r--r-- | src/H5HL.c | 10 | ||||
| -rw-r--r-- | src/H5O.c | 9 | ||||
| -rw-r--r-- | src/H5P.c | 6 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 20 | ||||
| -rw-r--r-- | src/H5Ssimp.c | 28 | ||||
| -rw-r--r-- | src/debug.c | 2 |
24 files changed, 218 insertions, 201 deletions
@@ -281,7 +281,7 @@ H5B_load(H5F_t *f, const haddr_t *addr, const void *_type, void *udata) bt->native = H5MM_xmalloc(total_nkey_size); bt->key = H5MM_xmalloc((2 * H5B_K(f, type) + 1) * sizeof(H5B_key_t)); bt->child = H5MM_xmalloc(2 * H5B_K(f, type) * sizeof(haddr_t)); - if (H5F_block_read(f, addr, (hsize_t)size, bt->page) < 0) { + if (H5F_block_read(f, addr, (hsize_t)size, H5D_XFER_DFLT, bt->page) < 0) { HRETURN_ERROR(H5E_BTREE, H5E_READERROR, NULL, "can't read B-tree node"); } @@ -424,7 +424,8 @@ H5B_flush(H5F_t *f, hbool_t destroy, const haddr_t *addr, H5B_t *bt) * bother writing data for the child entries that don't exist or * for the final unchanged children. */ - if (H5F_block_write(f, addr, (hsize_t)size, bt->page) < 0) { + if (H5F_block_write(f, addr, (hsize_t)size, H5D_XFER_DFLT, + bt->page) < 0) { HRETURN_ERROR(H5E_BTREE, H5E_CANTFLUSH, FAIL, "unable to save B-tree node to disk"); } @@ -828,11 +829,11 @@ H5B_insert(H5F_t *f, const H5B_class_t *type, const haddr_t *addr, HRETURN_ERROR(H5E_BTREE, H5E_CANTFLUSH, FAIL, "unable to flush B-tree root node"); } - if (H5F_block_read(f, addr, (hsize_t)size, buf) < 0) { + if (H5F_block_read(f, addr, (hsize_t)size, H5D_XFER_DFLT, buf) < 0) { HRETURN_ERROR(H5E_BTREE, H5E_READERROR, FAIL, "unable to read B-tree root node"); } - if (H5F_block_write(f, &old_root, (hsize_t)size, buf) < 0) { + if (H5F_block_write(f, &old_root, (hsize_t)size, H5D_XFER_DFLT, buf) < 0) { HRETURN_ERROR(H5E_BTREE, H5E_WRITEERROR, FAIL, "unable to move B-tree root node"); } @@ -76,7 +76,7 @@ const H5D_xfer_t H5D_xfer_dflt = { NULL, /* Background buffer or NULL */ H5T_BKG_NO, /* Type of background buffer needed */ #ifdef HAVE_PARALLEL - H5D_XFER_INDEPENDENT, /* Independent data transfer */ + H5D_XFER_DFLT, /* Independent data transfer */ #endif }; @@ -1155,9 +1155,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5T_DEBUG H5_timer_t timer; #endif -#ifdef HAVE_PARALLEL - int access_mode_saved = -1; -#endif FUNC_ENTER(H5D_read, FAIL); @@ -1180,29 +1177,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* can always be simulated by independent access. */ /* Nevertheless, must check driver is MPIO before using those */ /* access_mode which exists only for MPIO case. */ - if (dataset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO){ - /* - * -AKC- - * "plant" the collective access mode into the file information - * so that the lower level mpio routines know to use collective - * access. - * This is not thread-safe, is a klutch for now. - * Should change all the I/O routines to pass along the xfer - * property list to the low level I/O for proper execution. - * Make it to work now. Must fix it later. - * -AKC- - */ -#ifdef AKC - printf("%s: collective access requested\n", FUNC); -#endif - access_mode_saved = - dataset->ent.file->shared->access_parms->u.mpio.access_mode; - dataset->ent.file->shared->access_parms->u.mpio.access_mode = - H5D_XFER_COLLECTIVE; - }else{ + if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access not permissible"); - } } #endif /*HAVE_PARALLEL*/ @@ -1241,18 +1218,19 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * Check if collective data transfer requested. */ if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){ - /* Supports only no conversion, type or space, for now. */ - if (H5T_conv_noop==tconv_func && - NULL!=sconv_func->read) { - status = (sconv_func->read)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), - &(dataset->create_parms->efl), - H5T_get_size (dataset->type), file_space, - mem_space, buf/*out*/); - if (status>=0) goto succeed; - HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, - "collective read failed"); - } + /* Supports only no conversion, type or space, for now. */ + if (H5T_conv_noop==tconv_func && + NULL!=sconv_func->read) { + status = (sconv_func->read)(dataset->ent.file, &(dataset->layout), + &(dataset->create_parms->compress), + &(dataset->create_parms->efl), + H5T_get_size (dataset->type), file_space, + mem_space, xfer_parms->xfer_mode, + buf/*out*/); + if (status>=0) goto succeed; + HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, + "collective read failed"); + } } #endif /*HAVE_PARALLEL*/ @@ -1268,7 +1246,8 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->compress), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, - mem_space, buf/*out*/); + mem_space, xfer_parms->xfer_mode, + buf/*out*/); if (status>=0) goto succeed; #ifdef H5D_DEBUG fprintf (stderr, "H5D: data space conversion could not be optimized " @@ -1356,6 +1335,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, smine_start, smine_nelmts, + xfer_parms->xfer_mode, tconv_buf/*out*/)!=smine_nelmts) { HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); } @@ -1407,15 +1387,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (bkg_buf && NULL==xfer_parms->bkg_buf) { H5MM_xfree (bkg_buf); } -#ifdef HAVE_PARALLEL - /* - * Check if collective data transfer requested. - * If so, need to restore the access mode. Shouldnot needed. - */ - if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){ - dataset->ent.file->shared->access_parms->u.mpio.access_mode = access_mode_saved; - } -#endif /*HAVE_PARALLEL*/ FUNC_LEAVE(ret_value); } @@ -1461,9 +1432,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5T_DEBUG H5_timer_t timer; #endif -#ifdef HAVE_PARALLEL - int access_mode_saved = -1; -#endif FUNC_ENTER(H5D_write, FAIL); @@ -1486,30 +1454,9 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* can always be simulated by independent access. */ /* Nevertheless, must check driver is MPIO before using those */ /* access_mode which exists only for MPIO case. */ - if (dataset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO){ - /* - * -AKC- - * "plant" the collective access mode into the file information - * so that the lower level mpio routines know to use collective - * access. - * This is not thread-safe, is a klutch for now. - * Should change all the I/O routines to pass along the xfer - * property list to the low level I/O for proper execution. - * Make it to work now. Must fix it later. - * -AKC- - */ -#ifdef AKC - printf("%s: collective access requested\n", FUNC); -#endif - access_mode_saved = - dataset->ent.file->shared->access_parms->u.mpio.access_mode; - dataset->ent.file->shared->access_parms->u.mpio.access_mode = - H5D_XFER_COLLECTIVE; - } - else{ + if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access not permissible"); - } } #endif /*HAVE_PARALLEL*/ @@ -1543,7 +1490,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, "unable to convert from memory to file data space"); } -#ifdef NO #ifdef HAVE_PARALLEL /* * Check if collective data transfer requested. @@ -1556,14 +1502,13 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->compress), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, - mem_space, buf); + mem_space, xfer_parms->xfer_mode, buf); if (status>=0) goto succeed; HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "collective write failed"); } } #endif /*HAVE_PARALLEL*/ -#endif /* @@ -1577,7 +1522,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->compress), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, - mem_space, buf); + mem_space, xfer_parms->xfer_mode, buf); if (status>=0) goto succeed; #ifdef H5D_DEBUG fprintf (stderr, "H5D: data space conversion could not be optimized " @@ -1672,6 +1617,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, smine_start, smine_nelmts, + xfer_parms->xfer_mode, bkg_buf/*out*/)!=smine_nelmts) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); @@ -1703,7 +1649,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &numbering, smine_start, smine_nelmts, - tconv_buf)<0) { + xfer_parms->xfer_mode, tconv_buf)<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed"); } } @@ -1720,15 +1666,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (bkg_buf && NULL==xfer_parms->bkg_buf) { H5MM_xfree (bkg_buf); } -#ifdef HAVE_PARALLEL - /* - * Check if collective data transfer requested. - * If so, need to restore the access mode. Shouldnot needed. - */ - if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){ - dataset->ent.file->shared->access_parms->u.mpio.access_mode = access_mode_saved; - } -#endif /*HAVE_PARALLEL*/ FUNC_LEAVE(ret_value); } diff --git a/src/H5Distore.c b/src/H5Distore.c index 91c4e9d..54b797d 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -713,7 +713,7 @@ H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk"); } - if (H5F_block_write (f, &(udata.addr), nbytes, out_ptr)<0) { + if (H5F_block_write (f, &(udata.addr), nbytes, H5D_XFER_DFLT, out_ptr)<0) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } @@ -1026,7 +1026,8 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, * the entire chunk size -- it reduces strain on the malloc() * subsystem. */ - if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, chunk)<0) { + if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, + H5D_XFER_DFLT, chunk)<0) { HGOTO_ERROR (H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk"); } diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 3ed4e2f..12c95d6 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -55,9 +55,7 @@ typedef struct H5D_xfer_t { void *tconv_buf; /*type conversion buffer or null */ void *bkg_buf; /*background buffer or null */ H5T_bkg_t need_bkg; /*type of background buffer needed */ -#ifdef HAVE_PARALLEL H5D_transfer_t xfer_mode; /*independent or collective transfer */ -#endif } H5D_xfer_t; typedef struct H5D_t H5D_t; diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index d1d5c26..a86d865 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -31,13 +31,12 @@ typedef enum H5D_layout_t { H5D_NLAYOUTS = 3 /*this one must be last! */ } H5D_layout_t; -#ifdef HAVE_PARALLEL /* Values for the data transfer property */ typedef enum H5D_transfer_t { H5D_XFER_INDEPENDENT, /*Independent data transfer */ - H5D_XFER_COLLECTIVE /*Collective data transfer */ + H5D_XFER_COLLECTIVE, /*Collective data transfer */ + H5D_XFER_DFLT /*default data transfer mode */ } H5D_transfer_t; -#endif #ifdef __cplusplus @@ -153,7 +153,6 @@ H5F_init_interface(void) #elif (H5F_LOW_DFLT == H5F_LOW_CORE) H5F_access_dflt.u.core.increment = 10*1024; #elif (H5F_LOW_DFLT == H5F_LOW_MPIO) - H5F_access_dflt.u.mpio.access_mode = H5D_XFER_INDEPENDENT; H5F_access_dflt.u.mpio.comm = MPI_COMM_SELF; H5F_access_dflt.u.mpio.info = MPI_INFO_NULL; #elif (H5F_LOW_DFLT == H5F_LOW_SPLIT) @@ -393,7 +392,7 @@ H5F_locate_signature(H5F_low_t *f_handle, const H5F_access_t *access_parms, H5F_low_size(f_handle, &max_addr); H5F_addr_reset(addr); while (H5F_addr_lt(addr, &max_addr)) { - if (H5F_low_read(f_handle, access_parms, addr, + if (H5F_low_read(f_handle, access_parms, H5D_XFER_DFLT, addr, H5F_SIGNATURE_LEN, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "can't read file"); } @@ -892,8 +891,8 @@ H5F_open(const char *name, uintn flags, &(f->shared->boot_addr)) < 0) { HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, NULL, "can't find signature"); } - if (H5F_low_read(f->shared->lf, access_parms, &(f->shared->boot_addr), - fixed_size, buf) < 0) { + if (H5F_low_read(f->shared->lf, access_parms, H5D_XFER_DFLT, + &(f->shared->boot_addr), fixed_size, buf) < 0) { HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "can't read boot block"); } @@ -971,8 +970,8 @@ H5F_open(const char *name, uintn flags, assert(variable_size <= sizeof buf); addr1 = f->shared->boot_addr; H5F_addr_inc(&addr1, (hsize_t)fixed_size); - if (H5F_low_read(f->shared->lf, access_parms, &addr1, variable_size, - buf) < 0) { + if (H5F_low_read(f->shared->lf, access_parms, H5D_XFER_DFLT, + &addr1, variable_size, buf) < 0) { HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, NULL, "can't read boot block"); } @@ -1336,6 +1335,7 @@ H5F_flush(H5F_t *f, hbool_t invalidate) /* write the boot block to disk */ if (H5F_low_write(f->shared->lf, f->shared->access_parms, + H5D_XFER_DFLT, &(f->shared->boot_addr), (size_t)(p-buf), buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't write header"); } @@ -1506,11 +1506,14 @@ H5Fclose(hid_t fid) * Jul 10 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ herr_t -H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, void *buf) +H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, + const H5D_transfer_t xfer_mode, void *buf) { haddr_t abs_addr; @@ -1523,7 +1526,7 @@ H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, void *buf) H5F_addr_add(&abs_addr, addr); /* Read the data */ - if (H5F_low_read(f->shared->lf, f->shared->access_parms, + if (H5F_low_read(f->shared->lf, f->shared->access_parms, xfer_mode, &abs_addr, (size_t)size, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "low-level read failed"); } @@ -1550,11 +1553,14 @@ H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, void *buf) * Jul 10 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ herr_t -H5F_block_write(H5F_t *f, const haddr_t *addr, hsize_t size, const void *buf) +H5F_block_write(H5F_t *f, const haddr_t *addr, hsize_t size, + const H5D_transfer_t xfer_mode, const void *buf) { haddr_t abs_addr; @@ -1571,7 +1577,7 @@ H5F_block_write(H5F_t *f, const haddr_t *addr, hsize_t size, const void *buf) H5F_addr_add(&abs_addr, addr); /* Write the data */ - if (H5F_low_write(f->shared->lf, f->shared->access_parms, + if (H5F_low_write(f->shared->lf, f->shared->access_parms, xfer_mode, &abs_addr, (size_t)size, buf)) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "low-level write failed"); } diff --git a/src/H5Farray.c b/src/H5Farray.c index b74decb..85df727 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -107,6 +107,8 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) * Friday, January 16, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -115,7 +117,7 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, 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*/) + const H5D_transfer_t xfer_mode, void *_buf/*out*/) { uint8 *buf = (uint8 *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -130,9 +132,6 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, haddr_t addr; /*address in file */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ -#ifdef HAVE_PARALLEL - intn is_collective; /*collective access flag*/ -#endif FUNC_ENTER (H5F_arr_read, FAIL); @@ -149,12 +148,7 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size); #ifdef HAVE_PARALLEL - is_collective = (f->shared->access_parms->driver==H5F_LOW_MPIO - && f->shared->access_parms->u.mpio.access_mode==H5D_XFER_COLLECTIVE); - if (is_collective){ -#ifdef AKC - printf("%s: collective read requested\n", FUNC); -#endif + if (xfer_mode==H5D_XFER_COLLECTIVE){ if (layout->type != H5D_CONTIGUOUS) HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "collective access on non-contiguous datasets not " @@ -216,7 +210,7 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, * memory. */ #ifdef HAVE_PARALLEL - if (is_collective){ + if (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. @@ -247,7 +241,7 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "external data read failed"); } - } else if (H5F_block_read (f, &addr, elmt_size, buf)<0) { + } else if (H5F_block_read (f, &addr, elmt_size, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "block read failed"); } @@ -319,6 +313,8 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, * Friday, January 16, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -327,7 +323,7 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, 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 H5D_transfer_t xfer_mode, const void *_buf) { const uint8 *buf = (const uint8 *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -342,9 +338,6 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, haddr_t addr; /*address in file */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ -#ifdef HAVE_PARALLEL - intn is_collective; /*collective access flag*/ -#endif FUNC_ENTER (H5F_arr_write, FAIL); @@ -361,12 +354,7 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, H5V_vector_cpy (layout->ndims, hslab_size, _hslab_size); #ifdef HAVE_PARALLEL - is_collective = (f->shared->access_parms->driver==H5F_LOW_MPIO - && f->shared->access_parms->u.mpio.access_mode==H5D_XFER_COLLECTIVE); - if (is_collective){ -#ifdef AKC - printf("%s: collective write requested\n", FUNC); -#endif + if (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"); @@ -427,7 +415,7 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, * disk. */ #ifdef HAVE_PARALLEL - if (is_collective){ + if (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. @@ -457,7 +445,7 @@ printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "external data write failed"); } - } else if (H5F_block_write (f, &addr, elmt_size, buf)<0) { + } else if (H5F_block_write (f, &addr, elmt_size, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); } diff --git a/src/H5Fcore.c b/src/H5Fcore.c index 4f8e216..99f64fb 100644 --- a/src/H5Fcore.c +++ b/src/H5Fcore.c @@ -33,8 +33,10 @@ static H5F_low_t *H5F_core_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_core_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_core_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf); static herr_t H5F_core_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); @@ -177,11 +179,14 @@ H5F_core_close(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms) * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_core_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf) { size_t n; @@ -224,11 +229,14 @@ H5F_core_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_core_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { size_t need_more; diff --git a/src/H5Ffamily.c b/src/H5Ffamily.c index 73895b8..e887acc 100644 --- a/src/H5Ffamily.c +++ b/src/H5Ffamily.c @@ -43,8 +43,10 @@ static H5F_low_t *H5F_fam_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_fam_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_fam_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf); static herr_t H5F_fam_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); static herr_t H5F_fam_flush(H5F_low_t *lf, const H5F_access_t *access_parms); @@ -292,11 +294,14 @@ H5F_fam_close(H5F_low_t *lf, const H5F_access_t *access_parms) * Monday, November 10, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_fam_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf) { size_t nbytes; @@ -324,7 +329,7 @@ H5F_fam_read(H5F_low_t *lf, const H5F_access_t *access_parms, nbytes = MIN(size, member_size.offset-offset.offset); cur_addr = offset; if (H5F_low_read(lf->u.fam.memb[membno], - access_parms->u.fam.memb_access, + access_parms->u.fam.memb_access, xfer_mode, &cur_addr, nbytes, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "can't read from family member"); @@ -356,11 +361,14 @@ H5F_fam_read(H5F_low_t *lf, const H5F_access_t *access_parms, * Monday, November 10, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_fam_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { size_t nbytes; @@ -438,7 +446,7 @@ H5F_fam_write(H5F_low_t *lf, const H5F_access_t *access_parms, /* Write the data to the member */ if (H5F_low_write(lf->u.fam.memb[membno], - access_parms->u.fam.memb_access, + access_parms->u.fam.memb_access, xfer_mode, &cur_addr, nbytes, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't write to family member"); @@ -497,12 +505,12 @@ H5F_fam_flush(H5F_low_t *lf, const H5F_access_t *access_parms) H5F_addr_inc(&addr3, (hsize_t)1); H5F_low_seteof(lf->u.fam.memb[0], &addr3); /*prevent a warning */ if (H5F_low_read(lf->u.fam.memb[0], access_parms->u.fam.memb_access, - &addr1, 1, buf) < 0) { + H5D_XFER_DFLT, &addr1, 1, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "can't read from first family member"); } if (H5F_low_write(lf->u.fam.memb[0], access_parms->u.fam.memb_access, - &addr1, 1, buf) < 0) { + H5D_XFER_DFLT, &addr1, 1, buf) < 0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't write to first family member"); } diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 91c4e9d..54b797d 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -713,7 +713,7 @@ H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk"); } - if (H5F_block_write (f, &(udata.addr), nbytes, out_ptr)<0) { + if (H5F_block_write (f, &(udata.addr), nbytes, H5D_XFER_DFLT, out_ptr)<0) { HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } @@ -1026,7 +1026,8 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, * the entire chunk size -- it reduces strain on the malloc() * subsystem. */ - if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, chunk)<0) { + if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, + H5D_XFER_DFLT, chunk)<0) { HGOTO_ERROR (H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk"); } diff --git a/src/H5Flow.c b/src/H5Flow.c index faa2202..82e1f1a 100644 --- a/src/H5Flow.c +++ b/src/H5Flow.c @@ -214,11 +214,14 @@ H5F_low_close(H5F_low_t *lf, const H5F_access_t *access_parms) * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ herr_t H5F_low_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/) { herr_t ret_value = FAIL; @@ -230,8 +233,8 @@ H5F_low_read(H5F_low_t *lf, const H5F_access_t *access_parms, assert(buf); if (lf->type->read) { - if ((ret_value = (lf->type->read) (lf, access_parms, addr, size, - buf)) < 0) { + if ((ret_value = (lf->type->read) (lf, access_parms, xfer_mode, + addr, size, buf)) < 0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, ret_value, "read failed"); } } else { @@ -263,11 +266,14 @@ H5F_low_read(H5F_low_t *lf, const H5F_access_t *access_parms, * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ herr_t H5F_low_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { herr_t ret_value = FAIL; @@ -289,8 +295,8 @@ H5F_low_write(H5F_low_t *lf, const H5F_access_t *access_parms, /* Write the data */ if (lf->type->write) { - if ((ret_value = (lf->type->write) (lf, access_parms, addr, size, - buf)) < 0) { + if ((ret_value = (lf->type->write) (lf, access_parms, xfer_mode, + addr, size, buf)) < 0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, ret_value, "write failed"); } } else { @@ -340,8 +346,10 @@ H5F_low_flush(H5F_low_t *lf, const H5F_access_t *access_parms) if (addr_defined(&(lf->eof)) && H5F_addr_gt(&(lf->eof), &last_byte)) { last_byte = lf->eof; last_byte.offset -= 1; - if (H5F_low_read(lf, access_parms, &last_byte, 1, buf) >= 0) { - H5F_low_write(lf, access_parms, &last_byte, 1, buf); + if (H5F_low_read(lf, access_parms, H5D_XFER_DFLT, &last_byte, + 1, buf) >= 0) { + H5F_low_write(lf, access_parms, H5D_XFER_DFLT, &last_byte, + 1, buf); } } /* Invoke the subclass the flush method */ diff --git a/src/H5Fmpio.c b/src/H5Fmpio.c index d55716c..7b28698 100644 --- a/src/H5Fmpio.c +++ b/src/H5Fmpio.c @@ -68,11 +68,11 @@ static H5F_low_t *H5F_mpio_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_mpio_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_mpio_read(H5F_low_t *lf, const H5F_access_t *access_parms, - const haddr_t *addr, size_t size, - uint8 *buf/*out*/); + const H5D_transfer_t xfer_mode, + const haddr_t *addr, size_t size, uint8 *buf/*out*/); static herr_t H5F_mpio_write(H5F_low_t *lf, const H5F_access_t *access_parms, - const haddr_t *addr, size_t size, - const uint8 *buf); + const H5D_transfer_t xfer_mode, + const haddr_t *addr, size_t size, const uint8 *buf); static herr_t H5F_mpio_flush(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_MPIOff_to_haddr(MPI_Offset mpi_off, haddr_t *addr); static herr_t H5F_haddr_to_MPIOff(haddr_t addr, MPI_Offset *mpi_off); @@ -241,16 +241,6 @@ H5F_mpio_open(const char *name, const H5F_access_t *access_parms, uintn flags, fprintf(stdout, "Entering H5F_mpio_open name=%s flags=%x\n", name, flags ); #endif - switch (access_parms->u.mpio.access_mode){ - case H5D_XFER_INDEPENDENT: - case H5D_XFER_COLLECTIVE: - /*void*/ - break; - - default: - HRETURN_ERROR(H5E_IO, H5E_BADVALUE, NULL, "invalid file access mode"); - } - /* convert HDF5 flags to MPI-IO flags */ /* some combinations are illegal; let MPI-IO figure it out */ mpi_amode = (flags&H5F_ACC_RDWR) ? MPI_MODE_RDWR : MPI_MODE_RDONLY; @@ -385,10 +375,14 @@ H5F_mpio_close(H5F_low_t *lf, const H5F_access_t *access_parms) * rky, 10 Apr 1998 * Call independent or collective MPI read, based on ACCESS_PARMS. * + * Albert Cheng, June 1, 1998 + * Added xfer_mode to control independent or collective MPI read. + * *------------------------------------------------------------------------- */ static herr_t H5F_mpio_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/) { MPI_Offset mpi_off; @@ -415,13 +409,17 @@ H5F_mpio_read(H5F_low_t *lf, const H5F_access_t *access_parms, } /* Read the data. */ - switch (access_parms->u.mpio.access_mode){ + switch (xfer_mode){ case H5D_XFER_INDEPENDENT: + case H5D_XFER_DFLT: mpierr = MPI_File_read_at ( lf->u.mpio.f, mpi_off, (void*) buf, size_i, MPI_BYTE, &mpi_stat ); break; case H5D_XFER_COLLECTIVE: +#ifdef H5F_MPIO_DEBUG + printf("%s: using MPIO collective mode\n", FUNC); +#endif mpierr = MPI_File_read_at_all ( lf->u.mpio.f, mpi_off, (void*) buf, size_i, MPI_BYTE, &mpi_stat ); break; @@ -501,12 +499,15 @@ H5F_mpio_read(H5F_low_t *lf, const H5F_access_t *access_parms, * rky, 24 April * Removed redundant write from H5F_Mpio_write. * + * Albert Cheng, June 1, 1998 + * Added xfer_mode to control independent or collective MPI write. + * *------------------------------------------------------------------------- */ static herr_t H5F_mpio_write(H5F_low_t *lf, const H5F_access_t *access_parms, - const haddr_t *addr, size_t size, - const uint8 *buf) + const H5D_transfer_t xfer_mode, + const haddr_t *addr, size_t size, const uint8 *buf) { MPI_Offset mpi_off; MPI_Status mpi_stat; @@ -530,13 +531,17 @@ H5F_mpio_write(H5F_low_t *lf, const H5F_access_t *access_parms, } /* Write the data. */ - switch (access_parms->u.mpio.access_mode){ + switch (xfer_mode){ case H5D_XFER_INDEPENDENT: + case H5D_XFER_DFLT: mpierr = MPI_File_write_at ( lf->u.mpio.f, mpi_off, (void*) buf, size_i, MPI_BYTE, &mpi_stat ); break; case H5D_XFER_COLLECTIVE: +#ifdef H5F_MPIO_DEBUG + printf("%s: using MPIO collective mode\n", FUNC); +#endif mpierr = MPI_File_write_at_all( lf->u.mpio.f, mpi_off, (void*) buf, size_i, MPI_BYTE, &mpi_stat ); break; diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 26942ce..5b0ec5b 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -22,6 +22,7 @@ /* This is a near top-level header! Try not to include much! */ #include <H5private.h> +#include <H5Dpublic.h> /*for the H5D_transfer_t type */ /* * Feature: Define this constant to be non-zero if you want to enable code @@ -266,7 +267,6 @@ typedef struct H5F_access_t { #ifdef HAVE_PARALLEL /* Properties for parallel I/O */ struct { - uintn access_mode; /* independent or collective variety? */ MPI_Comm comm; /* communicator for file access */ MPI_Info info; /* optional info for MPI-IO */ } mpio; @@ -303,9 +303,10 @@ typedef struct H5F_low_class_t { herr_t (*close)(struct H5F_low_t *lf, const H5F_access_t *access_parms); herr_t (*read)(struct H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf); - herr_t (*write)(struct H5F_low_t *lf, - const H5F_access_t *access_parms, + herr_t (*write)(struct H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); herr_t (*flush)(struct H5F_low_t *lf, const H5F_access_t *access_parms); @@ -502,12 +503,14 @@ herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, 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*/); + const hssize_t file_offset[], + const H5D_transfer_t xfer_mode, void *_buf/*out*/); herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, 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 hssize_t file_offset[], + const H5D_transfer_t xfer_mode, const void *_buf); /* Functions that operate on indexed storage */ herr_t H5F_istore_init (H5F_t *f); @@ -525,9 +528,10 @@ herr_t H5F_istore_write(H5F_t *f, const struct H5O_layout_t *layout, const void *buf); /* Functions that operate on contiguous storage wrt boot block */ -herr_t H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, void *buf); +herr_t H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, + const H5D_transfer_t xfer_mode, void *buf); herr_t H5F_block_write(H5F_t *f, const haddr_t *addr, hsize_t size, - const void *buf); + const H5D_transfer_t xfer_mode, const void *buf); /* Functions that operate directly on low-level files */ const H5F_low_class_t *H5F_low_class (H5F_driver_t driver); @@ -543,8 +547,10 @@ H5F_low_t *H5F_low_open(const H5F_low_class_t *type, const char *name, H5F_low_t *H5F_low_close(H5F_low_t *lf, const H5F_access_t *access_parms); hsize_t H5F_low_size(H5F_low_t *lf, haddr_t *addr); herr_t H5F_low_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf); herr_t H5F_low_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); herr_t H5F_low_flush(H5F_low_t *lf, const H5F_access_t *access_parms); diff --git a/src/H5Fsec2.c b/src/H5Fsec2.c index 11f6b9c..b0be347 100644 --- a/src/H5Fsec2.c +++ b/src/H5Fsec2.c @@ -31,9 +31,11 @@ static H5F_low_t *H5F_sec2_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_sec2_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_sec2_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/); static herr_t H5F_sec2_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); @@ -152,11 +154,14 @@ H5F_sec2_close(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms) * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_sec2_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf) { ssize_t n; @@ -256,11 +261,14 @@ H5F_sec2_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_sec2_write(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { uint64 mask; diff --git a/src/H5Fsplit.c b/src/H5Fsplit.c index 1359816..bc57db3 100644 --- a/src/H5Fsplit.c +++ b/src/H5Fsplit.c @@ -33,9 +33,11 @@ static H5F_low_t *H5F_split_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_split_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_split_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/); static herr_t H5F_split_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); static herr_t H5F_split_flush(H5F_low_t *lf, const H5F_access_t *access_parms); @@ -200,11 +202,14 @@ H5F_split_close(H5F_low_t *lf, const H5F_access_t *access_parms) * Monday, November 13, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_split_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/) { haddr_t tmp_addr; @@ -217,6 +222,7 @@ H5F_split_read(H5F_low_t *lf, const H5F_access_t *access_parms, assert(lf); assert(addr && H5F_addr_defined(addr)); assert(buf); + assert(xfer_mode != H5D_XFER_COLLECTIVE); /* no collective support */ /* Which file to we actually read from? */ if (addr->offset & lf->u.split.mask) { @@ -230,7 +236,7 @@ H5F_split_read(H5F_low_t *lf, const H5F_access_t *access_parms, } /* Read the data */ - status = H5F_low_read(sub, sub_parms, &tmp_addr, size, buf/*out*/); + status = H5F_low_read(sub, sub_parms, xfer_mode, &tmp_addr, size, buf/*out*/); FUNC_LEAVE(status); } @@ -248,11 +254,14 @@ H5F_split_read(H5F_low_t *lf, const H5F_access_t *access_parms, * Monday, November 13, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_split_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { haddr_t tmp_addr; @@ -265,6 +274,7 @@ H5F_split_write(H5F_low_t *lf, const H5F_access_t *access_parms, assert(lf); assert(addr && H5F_addr_defined(addr)); assert(buf); + assert(xfer_mode != H5D_XFER_COLLECTIVE); /* no collective support */ /* Which file to we actually write to? */ if (addr->offset & lf->u.split.mask) { @@ -278,7 +288,7 @@ H5F_split_write(H5F_low_t *lf, const H5F_access_t *access_parms, } /* Write the data */ - status = H5F_low_write(sub, sub_parms, &tmp_addr, size, buf); + status = H5F_low_write(sub, sub_parms, xfer_mode, &tmp_addr, size, buf); FUNC_LEAVE(status); } diff --git a/src/H5Fstdio.c b/src/H5Fstdio.c index fbccc5e..3ba7653 100644 --- a/src/H5Fstdio.c +++ b/src/H5Fstdio.c @@ -25,9 +25,11 @@ static H5F_low_t *H5F_stdio_open(const char *name, H5F_search_t *key/*out*/); static herr_t H5F_stdio_close(H5F_low_t *lf, const H5F_access_t *access_parms); static herr_t H5F_stdio_read(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/); static herr_t H5F_stdio_write(H5F_low_t *lf, const H5F_access_t *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf); static herr_t H5F_stdio_flush(H5F_low_t *lf, const H5F_access_t *access_parms); @@ -177,11 +179,14 @@ H5F_stdio_close(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms) * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_stdio_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, uint8 *buf/*out*/) { size_t n; @@ -285,11 +290,14 @@ H5F_stdio_read(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, * Wednesday, October 22, 1997 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ static herr_t H5F_stdio_write(H5F_low_t *lf, const H5F_access_t __unused__ *access_parms, + const H5D_transfer_t xfer_mode, const haddr_t *addr, size_t size, const uint8 *buf) { uint64 mask; diff --git a/src/H5Gnode.c b/src/H5Gnode.c index 9b6b749..6603799 100644 --- a/src/H5Gnode.c +++ b/src/H5Gnode.c @@ -340,7 +340,7 @@ H5G_node_flush(H5F_t *f, hbool_t destroy, const haddr_t *addr, H5G_ent_encode_vec(f, &p, sym->entry, sym->nsyms); HDmemset(p, 0, size - (p - buf)); - status = H5F_block_write(f, addr, (hsize_t)size, buf); + status = H5F_block_write(f, addr, (hsize_t)size, H5D_XFER_DFLT, buf); buf = H5MM_xfree(buf); if (status < 0) HRETURN_ERROR(H5E_SYM, H5E_WRITEERROR, FAIL, @@ -404,7 +404,7 @@ H5G_node_load(H5F_t *f, const haddr_t *addr, const void __unused__ *_udata1, sym = H5MM_xcalloc(1, sizeof(H5G_node_t)); sym->entry = H5MM_xcalloc((intn)(2*H5G_NODE_K(f)), sizeof(H5G_entry_t)); - if (H5F_block_read(f, addr, (hsize_t)size, buf) < 0) { + if (H5F_block_read(f, addr, (hsize_t)size, H5D_XFER_DFLT, buf) < 0) { HGOTO_ERROR(H5E_SYM, H5E_READERROR, NULL, "unabel to read symbol table node"); } @@ -200,7 +200,8 @@ H5HG_load (H5F_t *f, const haddr_t *addr, const void __unused__ *udata1, heap = H5MM_xcalloc (1, sizeof(H5HG_heap_t)); heap->addr = *addr; heap->chunk = H5MM_xmalloc (H5HG_MINSIZE); - if (H5F_block_read (f, addr, (hsize_t)H5HG_MINSIZE, heap->chunk)<0) { + if (H5F_block_read (f, addr, (hsize_t)H5HG_MINSIZE, + H5D_XFER_DFLT, heap->chunk)<0) { HGOTO_ERROR (H5E_HEAP, H5E_READERROR, NULL, "unable to read global heap collection"); } @@ -234,7 +235,7 @@ H5HG_load (H5F_t *f, const haddr_t *addr, const void __unused__ *udata1, H5F_addr_inc (&next_addr, (hsize_t)H5HG_MINSIZE); heap->chunk = H5MM_xrealloc (heap->chunk, heap->size); if (H5F_block_read (f, &next_addr, (hsize_t)(heap->size-H5HG_MINSIZE), - heap->chunk+H5HG_MINSIZE)<0) { + H5D_XFER_DFLT, heap->chunk+H5HG_MINSIZE)<0) { HGOTO_ERROR (H5E_HEAP, H5E_READERROR, NULL, "unable to read global heap collection"); } @@ -338,7 +339,8 @@ H5HG_flush (H5F_t *f, hbool_t destroy, const haddr_t *addr, H5HG_heap_t *heap) assert (heap); if (heap->dirty) { - if (H5F_block_write (f, addr, (hsize_t)(heap->size), heap->chunk)<0) { + if (H5F_block_write (f, addr, (hsize_t)(heap->size), + H5D_XFER_DFLT, heap->chunk)<0) { HRETURN_ERROR (H5E_HEAP, H5E_WRITEERROR, FAIL, "unable to write global heap collection to file"); } @@ -181,7 +181,8 @@ H5HL_load(H5F_t *f, const haddr_t *addr, const void __unused__ *udata1, assert(!udata1); assert(!udata2); - if (H5F_block_read(f, addr, (hsize_t)H5HL_SIZEOF_HDR(f), hdr) < 0) { + if (H5F_block_read(f, addr, (hsize_t)H5HL_SIZEOF_HDR(f), + H5D_XFER_DFLT, hdr) < 0) { HRETURN_ERROR(H5E_HEAP, H5E_READERROR, NULL, "unable to read heap header"); } @@ -214,7 +215,7 @@ H5HL_load(H5F_t *f, const haddr_t *addr, const void __unused__ *udata1, heap->chunk = H5MM_xcalloc(1, H5HL_SIZEOF_HDR(f) + heap->mem_alloc); if (heap->disk_alloc && H5F_block_read(f, &(heap->addr), (hsize_t)(heap->disk_alloc), - heap->chunk + H5HL_SIZEOF_HDR(f)) < 0) { + H5D_XFER_DFLT, heap->chunk + H5HL_SIZEOF_HDR(f)) < 0) { HGOTO_ERROR(H5E_HEAP, H5E_CANTLOAD, NULL, "unable to read heap data"); } @@ -345,17 +346,18 @@ H5HL_flush(H5F_t *f, hbool_t destroy, const haddr_t *addr, H5HL_t *heap) /* The header and data are contiguous */ if (H5F_block_write(f, addr, (hsize_t)(H5HL_SIZEOF_HDR(f)+heap->disk_alloc), - heap->chunk) < 0) { + H5D_XFER_DFLT, heap->chunk) < 0) { HRETURN_ERROR(H5E_HEAP, H5E_WRITEERROR, FAIL, "unable to write heap header and data to file"); } } else { if (H5F_block_write(f, addr, (hsize_t)H5HL_SIZEOF_HDR(f), - heap->chunk)<0) { + H5D_XFER_DFLT, heap->chunk)<0) { HRETURN_ERROR(H5E_HEAP, H5E_WRITEERROR, FAIL, "unable to write heap header to file"); } if (H5F_block_write(f, &(heap->addr), (hsize_t)(heap->disk_alloc), + H5D_XFER_DFLT, heap->chunk + H5HL_SIZEOF_HDR(f)) < 0) { HRETURN_ERROR(H5E_HEAP, H5E_WRITEERROR, FAIL, "unable to write heap data to file"); @@ -335,7 +335,7 @@ H5O_load(H5F_t *f, const haddr_t *addr, const void __unused__ *_udata1, /* read fixed-lenth part of object header */ hdr_size = H5O_SIZEOF_HDR(f); - if (H5F_block_read(f, addr, (hsize_t)hdr_size, buf) < 0) { + if (H5F_block_read(f, addr, (hsize_t)hdr_size, H5D_XFER_DFLT, buf) < 0) { HGOTO_ERROR(H5E_OHDR, H5E_READERROR, NULL, "unable to read object header"); } @@ -382,7 +382,7 @@ H5O_load(H5F_t *f, const haddr_t *addr, const void __unused__ *_udata1, oh->chunk[chunkno].addr = chunk_addr; oh->chunk[chunkno].size = chunk_size; oh->chunk[chunkno].image = H5MM_xmalloc(chunk_size); - if (H5F_block_read(f, &chunk_addr, (hsize_t)chunk_size, + if (H5F_block_read(f, &chunk_addr, (hsize_t)chunk_size, H5D_XFER_DFLT, oh->chunk[chunkno].image) < 0) { HGOTO_ERROR(H5E_OHDR, H5E_READERROR, NULL, "unable to read object header data"); @@ -521,7 +521,8 @@ H5O_flush(H5F_t *f, hbool_t destroy, const haddr_t *addr, H5O_t *oh) HDmemset (p, 0, H5O_SIZEOF_HDR(f)-12); /* write the object header header */ - if (H5F_block_write(f, addr, (hsize_t)H5O_SIZEOF_HDR(f), buf) < 0) { + if (H5F_block_write(f, addr, (hsize_t)H5O_SIZEOF_HDR(f), + H5D_XFER_DFLT, buf) < 0) { HRETURN_ERROR(H5E_OHDR, H5E_WRITEERROR, FAIL, "unable to write object header hdr to disk"); } @@ -593,7 +594,7 @@ H5O_flush(H5F_t *f, hbool_t destroy, const haddr_t *addr, H5O_t *oh) if (oh->chunk[i].dirty) { assert(H5F_addr_defined(&(oh->chunk[i].addr))); if (H5F_block_write(f, &(oh->chunk[i].addr), - (hsize_t)(oh->chunk[i].size), + (hsize_t)(oh->chunk[i].size), H5D_XFER_DFLT, oh->chunk[i].image) < 0) { HRETURN_ERROR(H5E_OHDR, H5E_WRITEERROR, FAIL, "unable to write object header data to disk"); @@ -2230,7 +2230,6 @@ H5Pset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info) #endif tmpl->driver = H5F_LOW_MPIO; - tmpl->u.mpio.access_mode = H5D_XFER_INDEPENDENT; tmpl->u.mpio.comm = comm; tmpl->u.mpio.info = info; @@ -2309,6 +2308,10 @@ H5Pget_mpi (hid_t tid, MPI_Comm *comm, MPI_Info *info) * Use independent I/O access. * H5D_XFER_COLLECTIVE * Use MPI collective I/O access. + * H5D_XFER_DFLT + * Use default I/O access. Currently, + * independent is the default mode. + * * * Return: Success: SUCCEED * @@ -2338,6 +2341,7 @@ H5Pset_xfer (hid_t tid, H5D_transfer_t data_xfer_mode) switch (data_xfer_mode){ case H5D_XFER_INDEPENDENT: case H5D_XFER_COLLECTIVE: + case H5D_XFER_DFLT: plist->xfer_mode = data_xfer_mode; break; default: diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index a023f5d..06e9d0f 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -73,7 +73,8 @@ typedef struct H5S_tconv_t { const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t *numbering, - size_t start, size_t nelmts, void *tconv_buf/*out*/); + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, void *tconv_buf/*out*/); /* Scatter elements from type conversion buffer to application buffer */ herr_t (*mscat)(const void *tconv_buf, size_t elmt_size, @@ -90,21 +91,22 @@ typedef struct H5S_tconv_t { const struct H5O_compress_t *compress, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t *numbering, - size_t start, size_t nelmts, const void *tconv_buf); + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, const void *tconv_buf); /* Read from file to application w/o intermediate scratch buffer */ herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, - void *buf/*out*/); + const H5D_transfer_t xfer_mode, void *buf/*out*/); /* Write directly from app buffer to file */ herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, - const void *buf); + const H5D_transfer_t xfer_mode, const void *buf); } H5S_conv_t; H5S_t *H5S_copy (const H5S_t *src); @@ -133,7 +135,8 @@ size_t H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t *numbering, - size_t start, size_t nelmts, void *tconv_buf/*out*/); + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, void *tconv_buf/*out*/); herr_t H5S_simp_mscat (const void *tconv_buf, size_t elmt_size, const H5S_t *mem_space, const H5S_number_t *numbering, size_t start, size_t nelmts, void *buf/*out*/); @@ -144,15 +147,16 @@ herr_t H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t *numbering, - size_t start, size_t nelmts, const void *tconv_buf); + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, const void *tconv_buf); herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, - void *buf/*out*/); + const H5D_transfer_t xfer_mode, void *buf/*out*/); herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, - const void *buf); + const H5D_transfer_t xfer_mode, const void *buf); #endif diff --git a/src/H5Ssimp.c b/src/H5Ssimp.c index f8b3e0d..64be705 100644 --- a/src/H5Ssimp.c +++ b/src/H5Ssimp.c @@ -119,6 +119,8 @@ H5S_simp_init (const struct H5O_layout_t __unused__ *layout, * Wednesday, January 21, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -127,7 +129,8 @@ H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t __unused__ *numbering, - size_t start, size_t nelmts, void *buf/*out*/) + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, void *buf/*out*/) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -185,7 +188,7 @@ H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, * Gather from file. */ if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, file_offset, - buf/*out*/)<0) { + xfer_mode, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -403,6 +406,8 @@ H5S_simp_mgath (const void *buf, size_t elmt_size, * Wednesday, January 21, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -411,7 +416,8 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_number_t __unused__ *numbering, - size_t start, size_t nelmts, const void *buf) + size_t start, size_t nelmts, + const H5D_transfer_t xfer_mode, const void *buf) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -469,7 +475,7 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, * Scatter to file. */ if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero, - file_offset, buf)<0) { + file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } @@ -494,6 +500,8 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, * Thursday, March 12, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -501,7 +509,8 @@ herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, void *buf/*out*/) + const H5S_t *mem_space, const H5D_transfer_t xfer_mode, + void *buf/*out*/) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; hsize_t hslab_size[H5O_LAYOUT_NDIMS]; @@ -574,7 +583,7 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, /* Read the hyperslab */ if (H5F_arr_read (f, layout, comp, efl, hslab_size, - mem_size, mem_offset, file_offset, buf)<0) { + mem_size, mem_offset, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read dataset"); } @@ -599,6 +608,8 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, * Thursday, March 12, 1998 * * Modifications: + * June 2, 1998 Albert Cheng + * Added xfer_mode argument * *------------------------------------------------------------------------- */ @@ -606,7 +617,8 @@ herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, const void *buf) + const H5S_t *mem_space, const H5D_transfer_t xfer_mode, + const void *buf) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; hsize_t hslab_size[H5O_LAYOUT_NDIMS]; @@ -679,7 +691,7 @@ H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, /* Write the hyperslab */ if (H5F_arr_write (f, layout, comp, efl, hslab_size, - mem_size, mem_offset, file_offset, buf)<0) { + mem_size, mem_offset, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write dataset"); } diff --git a/src/debug.c b/src/debug.c index 4b8fdc3..fdf21d9 100644 --- a/src/debug.c +++ b/src/debug.c @@ -90,7 +90,7 @@ main(int argc, char *argv[]) printf("Reading signature at address "); H5F_addr_print(stdout, &addr); printf(" (rel)\n"); - if (H5F_block_read(f, &addr, (hsize_t)sizeof(sig), sig) < 0) { + if (H5F_block_read(f, &addr, (hsize_t)sizeof(sig), H5D_XFER_DFLT, sig) < 0) { fprintf(stderr, "cannot read signature\n"); HDexit(3); } |