diff options
Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 231 |
1 files changed, 142 insertions, 89 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c index 4340578..d344d41 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -65,6 +65,7 @@ static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space); static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset); static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id); +static herr_t H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags); /*********************/ @@ -567,7 +568,7 @@ done: static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) { - struct H5O_t *oh = NULL; /* Pointer to dataset's object header */ + H5O_t *oh = NULL; /* Pointer to dataset's object header */ size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ H5O_loc_t *oloc = NULL; /* Dataset's object location */ H5O_layout_t *layout; /* Dataset's layout information */ @@ -653,10 +654,10 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) /* Get a pointer to the object header itself */ if((oh = H5O_protect(oloc, dxpl_id)) == NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header") + HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect dataset object header") /* Write new fill value message */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) + if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message") /* If there is valid information for the old fill value struct, add it */ @@ -672,12 +673,12 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop); /* Write old fill value */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) + if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message") } /* end if */ /* Update the datatype and dataspace header messages */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) + if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") @@ -687,7 +688,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) H5O_pline_t *pline; /* Dataset's I/O pipeline information */ pline = &dset->shared->dcpl_cache.pline; - if(pline->nused > 0 && H5O_msg_append(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) + if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") } /* end if */ @@ -696,7 +697,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) * allocation until later. */ if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0) + if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") /* Update external storage message, if it's used */ @@ -716,7 +717,7 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) /* Pin the heap down in memory */ if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE))) - HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to protect EFL file name heap") + HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap") /* Insert "empty" name first */ if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) { @@ -741,18 +742,18 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) /* Release the heap */ if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to unprotect EFL file name heap") + HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap") heap = NULL; /* Insert EFL message into dataset object header */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) + if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") } /* end if */ /* Create layout message */ /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ /* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) + if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") #ifdef H5O_ENABLE_BOGUS @@ -778,15 +779,16 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) } #endif /* H5O_ENABLE_BOGUS */ - /* Add a modification time message. */ - if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") + /* Add a modification time message, if using older format. */ + if(!use_latest_format) + if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") done: /* Release pointer to object header itself */ if(oloc != NULL && oh != NULL) if(H5O_unprotect(oloc, oh) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header") + HDONE_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect dataset object header") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_update_oh_info() */ @@ -1428,7 +1430,7 @@ H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) && ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) && IS_H5FD_MPI(dataset->oloc.file)) { - if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, TRUE, FALSE) < 0) + if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") } /* end if */ @@ -1491,28 +1493,14 @@ H5D_close(H5D_t *dataset) dataset->shared->fo_count--; if(dataset->shared->fo_count == 0) { - /* Update the dataspace on disk, if it's been changed */ - if(dataset->shared->space_dirty) { - if(H5S_write(&(dataset->oloc), dataset->shared->space, TRUE, H5AC_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") - dataset->shared->space_dirty = FALSE; - } /* end if */ + /* Flush the dataset's information */ + if(H5D_flush_real(dataset, H5AC_dxpl_id, H5F_FLUSH_NONE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") /* Free the data sieve buffer, if it's been allocated */ if(dataset->shared->cache.contig.sieve_buf) { HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ - /* Flush the raw data buffer, if its dirty */ - if(dataset->shared->cache.contig.sieve_dirty) { - /* Write dirty data sieve buffer to file */ - if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, - dataset->shared->cache.contig.sieve_size, H5AC_dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") - - /* Reset sieve buffer dirty flag */ - dataset->shared->cache.contig.sieve_dirty = FALSE; - } /* end if */ - dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); } /* end if */ @@ -1522,19 +1510,19 @@ H5D_close(H5D_t *dataset) break; case H5D_CHUNKED: + /* Check for skip list for iterating over chunks during I/O to close */ + if(dataset->shared->cache.chunk.sel_chunks) { + HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0); + H5SL_close(dataset->shared->cache.chunk.sel_chunks); + dataset->shared->cache.chunk.sel_chunks = NULL; + } /* end if */ + /* Flush and destroy chunks in the cache */ - if(H5D_istore_dest(dataset,H5AC_dxpl_id) < 0) + if(H5D_istore_dest(dataset, H5AC_dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") break; case H5D_COMPACT: - /* Update header message of layout for compact dataset. */ - if(dataset->shared->layout.u.compact.dirty) { - if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), H5AC_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to update layout message") - dataset->shared->layout.u.compact.dirty = FALSE; - } /* end if */ - /* Free the buffer for the raw data for compact datasets */ dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf); break; @@ -1716,7 +1704,7 @@ H5D_get_file(const H5D_t *dset) */ herr_t H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, - hbool_t update_time, hbool_t full_overwrite) + hbool_t full_overwrite) { struct H5O_layout_t *layout; /* The dataset's layout information */ hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */ @@ -1833,12 +1821,15 @@ H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc } /* end else */ } /* end if */ - /* Also update header message for layout with new address, if we - * set the address. (this is improves forward compatibility). + /* If we set the address (and aren't in the middle of creating the + * dataset), mark the layout header message for later writing to + * the file. (this improves forward compatibility). + */ + /* (The layout message is already in the dataset's object header, this + * operation just sets the address and makes it constant) */ if(time_alloc != H5D_ALLOC_CREATE && addr_set) - if(H5O_msg_write(&dset->oloc, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_time, &dset->shared->layout, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") + dset->shared->layout_dirty = TRUE; } /* end if */ done: @@ -2309,7 +2300,7 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) + if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") @@ -2349,7 +2340,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_flush_cb + * Function: H5D_flush_real * * Purpose: Flush any dataset information cached in memory * @@ -2357,69 +2348,132 @@ done: * Failure: Negative * * Programmer: Quincey Koziol - * November 8, 2007 + * December 6, 2007 * *------------------------------------------------------------------------- */ -static int -H5D_flush_cb(void *_dataset, hid_t UNUSED id, void *_udata) +static herr_t +H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags) { - H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */ - H5D_flush_ud_t *udata = (H5D_flush_ud_t *)_udata; /* User data for callback */ - int ret_value = H5_ITER_CONT; /* Return value */ + H5O_t *oh = NULL; /* Pointer to dataset's object header */ + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT(H5D_flush_cb) + FUNC_ENTER_NOAPI_NOINIT(H5D_flush_real) /* Check args */ HDassert(dataset); - /* Check for dataset in same file */ - if(udata->f == dataset->oloc.file) { + /* Check for metadata changes that will require updating the object's modification time */ + if(dataset->shared->layout_dirty || dataset->shared->space_dirty) { + unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */ + + /* Get a pointer to the dataset's object header */ + if((oh = H5O_protect(&dataset->oloc, dxpl_id)) == NULL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect dataset object header") + + /* Update the layout on disk, if it's been changed */ + if(dataset->shared->layout_dirty) { + if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message") + dataset->shared->layout_dirty = FALSE; + + /* Reset the "update the modification time" flag, so we only do it once */ + update_flags = 0; + } /* end if */ + /* Update the dataspace on disk, if it's been changed */ if(dataset->shared->space_dirty) { - if(H5S_write(&(dataset->oloc), dataset->shared->space, TRUE, udata->dxpl_id) < 0) + if(H5S_write(dataset->oloc.file, dxpl_id, oh, update_flags, dataset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") dataset->shared->space_dirty = FALSE; + + /* Reset the "update the modification time" flag, so we only do it once */ + update_flags = 0; } /* end if */ - /* Flush the raw data buffer, if we have a dirty one */ - if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { - HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ + /* _Somebody_ should have update the modification time! */ + HDassert(update_flags == 0); + } /* end if */ - /* Write dirty data sieve buffer to file */ - if(H5F_block_write(udata->f, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, - dataset->shared->cache.contig.sieve_size, udata->dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") + /* Flush the raw data buffer, if we have a dirty one */ + if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { + HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ - /* Reset sieve buffer dirty flag */ - dataset->shared->cache.contig.sieve_dirty = FALSE; - } /* end if */ + /* Write dirty data sieve buffer to file */ + if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, + dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") - /* Flush cached information for each kind of dataset */ - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - break; + /* Reset sieve buffer dirty flag */ + dataset->shared->cache.contig.sieve_dirty = FALSE; + } /* end if */ - case H5D_CHUNKED: - /* Flush the raw data cache */ - if(H5D_istore_flush(dataset, udata->dxpl_id, udata->flags & H5F_FLUSH_INVALIDATE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache") - break; + /* Flush cached information for each kind of dataset */ + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + break; - case H5D_COMPACT: - if(dataset->shared->layout.u.compact.dirty) { - if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), udata->dxpl_id) < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") - dataset->shared->layout.u.compact.dirty = FALSE; - } /* end if */ - break; + case H5D_CHUNKED: + /* Flush the raw data cache */ + if(H5D_istore_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache") + break; - default: - HDassert("not implemented yet" && 0); + case H5D_COMPACT: + if(dataset->shared->layout.u.compact.dirty) { + if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") + dataset->shared->layout.u.compact.dirty = FALSE; + } /* end if */ + break; + + default: + HDassert("not implemented yet" && 0); #ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") #endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + +done: + /* Release pointer to object header */ + if(oh != NULL) + if(H5O_unprotect(&(dataset->oloc), oh) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect dataset object header") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_flush_real() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_flush_cb + * + * Purpose: Flush any dataset information cached in memory + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * November 8, 2007 + * + *------------------------------------------------------------------------- + */ +static int +H5D_flush_cb(void *_dataset, hid_t UNUSED id, void *_udata) +{ + H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */ + H5D_flush_ud_t *udata = (H5D_flush_ud_t *)_udata; /* User data for callback */ + int ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_flush_cb) + + /* Check args */ + HDassert(dataset); + + /* Check for dataset in same file */ + if(udata->f == dataset->oloc.file) { + /* Flush the dataset's information */ + if(H5D_flush_real(dataset, udata->dxpl_id, udata->flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to flush cached dataset info") } /* end if */ done: @@ -2460,7 +2514,6 @@ H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) H5I_search(H5I_DATASET, H5D_flush_cb, &udata); done: - FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_flush() */ |