diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5Dchunk.c | 104 | ||||
| -rw-r--r-- | src/H5Dio.c | 84 | ||||
| -rw-r--r-- | src/H5Dprivate.h | 3 | ||||
| -rw-r--r-- | src/H5Dpublic.h | 2 | ||||
| -rw-r--r-- | src/H5F.c | 6 | ||||
| -rw-r--r-- | src/H5FDsec2.c | 2 | ||||
| -rw-r--r-- | src/H5Fpkg.h | 3 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 1 | ||||
| -rw-r--r-- | src/H5Fpublic.h | 1 |
9 files changed, 202 insertions, 4 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 7a06477..da7d809 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -281,6 +281,110 @@ H5FL_DEFINE(H5D_chunk_info_t); /* Declare a free list to manage the chunk sequence information */ H5FL_BLK_DEFINE_STATIC(chunk); + +/*------------------------------------------------------------------------- + * Function: H5D__direct_write + * + * Purpose: Internal routine for H5PSIdirect_write to write a chunk + * directly into the file. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 30 July 2012 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, unsigned filters, hsize_t *offset, + size_t data_size, const void *buf) +{ + const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ + H5D_chunk_ud_t udata; /* User data for querying chunk info */ + hsize_t chunk_idx; + H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ + H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ + const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ + int space_ndims; /* Dataset's space rank */ + hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ + H5FD_t *lf; + herr_t ret_value = SUCCEED; /* Return value */ + + /*FUNC_ENTER_PACKAGE*/ + FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL) + + /* Allocate data space and initialize it if it hasn't been. */ + if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { + /* Allocate storage */ + if(H5D__alloc_storage(dset, dxpl_id, H5D_ALLOC_WRITE, FALSE, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") + } /* end if */ + + + /* Retrieve the dataset dimensions */ + if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info") + + /* Calculate the index of this chunk */ + if(H5V_chunk_index((unsigned)space_ndims, offset, + layout->u.chunk.dim, layout->u.chunk.down_chunks, &chunk_idx) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") + + /* Find out the file address of the chunk */ + if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx, + &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") + + udata.filter_mask = filters; + + /* Check if the chunk needs to be 'inserted' (could exist already and + * the 'insert' operation could resize it) + */ + { + H5D_chk_idx_info_t idx_info; /* Chunked index info */ + + /* Compose chunked index info struct */ + idx_info.f = dset->oloc.file; + idx_info.dxpl_id = dxpl_id; + idx_info.pline = &(dset->shared->dcpl_cache.pline); + idx_info.layout = &(dset->shared->layout.u.chunk); + idx_info.storage = &(dset->shared->layout.storage.u.chunk); + + /* Set up the size of chunk for user data */ + udata.nbytes = data_size; + + /* Create the chunk it if it doesn't exist, or reallocate the chunk + * if its size changed. + */ + if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk") + + /* Make sure the address of the chunk is returned. */ + if(!H5F_addr_defined(udata.addr)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") + } /* end if */ + + /* Fill the DXPL cache values for later use */ + if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + + /* Evict the entry from the cache if present, but do not flush + * it to disk */ + if(UINT_MAX != udata.idx_hint) { + if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, + rdcc->slot[udata.idx_hint], FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk") + } /* end if */ + + /* Write the data to the file */ + if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, data_size, dxpl_id, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file") + + +done: + /*FUNC_LEAVE_NOAPI(ret_value)*/ + FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) +} /*------------------------------------------------------------------------- diff --git a/src/H5Dio.c b/src/H5Dio.c index 1bd6dae..7852b3e 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -28,6 +28,8 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Sprivate.h" /* Dataspace */ #ifdef H5_HAVE_PARALLEL /* Remove this if H5R_DATASET_REGION is no longer used in this file */ @@ -271,6 +273,88 @@ done: /*------------------------------------------------------------------------- + * Function: H5PSIdirect_write + * + * Purpose: Temporary name for the DECTRIS project. It writes an entire + * chunk to the file directly. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 30 July 2012 + * + *------------------------------------------------------------------------- + */ +herr_t +H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, unsigned filters, hsize_t *offset, + size_t data_size, const void *buf) +{ + H5D_t *dset = NULL; + int ndims; + hsize_t *dims = NULL; + hsize_t *internal_offset = NULL; + int i; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + + /* check arguments */ + if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if(NULL == dset->oloc.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + if(H5D_CHUNKED != dset->shared->layout.type) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") + + /* Get the default dataset transfer property list if the user didn't provide one */ + if(H5P_DEFAULT == dxpl_id) + dxpl_id= H5P_DATASET_XFER_DEFAULT; + else + if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + + if(!buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") + + ndims = (int)H5S_GET_EXTENT_NDIMS(dset->shared->space); + if(NULL == (dims = (hsize_t *)H5MM_malloc(ndims*sizeof(hsize_t)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for dimensions") + + if(NULL == (internal_offset = (hsize_t *)H5MM_malloc((ndims+1)*sizeof(hsize_t)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for offset") + + if(H5S_get_simple_extent_dims(dset->shared->space, dims, NULL) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims") + + for(i=0; i<ndims; i++) { + /* Make sure the offset doesn't exceed the dataset's dimensions */ + if(offset[i] > dims[i]) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset") + + /* Make sure the offset fall right on a chunk's boundary */ + if(offset[i] % dset->shared->layout.u.chunk.dim[i]) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary") + + internal_offset[i] = offset[i]; + } + + /* The library's chunking code requires the offset terminates with a zero */ + internal_offset[ndims] = 0; + + /* write raw data */ + if(H5D__chunk_direct_write(dset, dxpl_id, filters, internal_offset, data_size, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + +done: + if(dims) + H5MM_free(dims); + + FUNC_LEAVE_API(ret_value) +} /* end H5PSIdirect_write() */ + + +/*------------------------------------------------------------------------- * Function: H5D__read * * Purpose: Reads (part of) a DATASET into application memory BUF. See diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 85051c3..48c6ddd 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -178,5 +178,8 @@ H5_DLL herr_t H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_ad H5_DLL herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, unsigned ndims); +H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, unsigned filters, + hsize_t *offset, size_t data_size, const void *buf); + #endif /* _H5Dprivate_H */ diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index c878d4a..58c2a2b 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -118,6 +118,8 @@ H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf/*out*/); H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, const void *buf); +H5_DLL herr_t H5PSIdirect_write(hid_t dset_id, hid_t dxpl_id, unsigned filters, hsize_t *offset, + size_t data_size, const void *buf); H5_DLL herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op, void *operator_data); H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf); @@ -1261,7 +1261,7 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id, * way for us to detect it here anyway). */ if(drvr->cmp) - tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL); + tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL|H5F_ACC_SYNC); else tent_flags = flags; @@ -1464,9 +1464,9 @@ H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id) if(!filename || !*filename) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid file name") /* In this routine, we only accept the following flags: - * H5F_ACC_EXCL, H5F_ACC_TRUNC and H5F_ACC_DEBUG + * H5F_ACC_SYNC, H5F_ACC_EXCL, H5F_ACC_TRUNC and H5F_ACC_DEBUG */ - if(flags & ~(H5F_ACC_EXCL | H5F_ACC_TRUNC | H5F_ACC_DEBUG)) + if(flags & ~(H5F_ACC_SYNC | H5F_ACC_EXCL | H5F_ACC_TRUNC | H5F_ACC_DEBUG)) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid flags") /* The H5F_ACC_EXCL and H5F_ACC_TRUNC flags are mutually exclusive */ if((flags & H5F_ACC_EXCL) && (flags & H5F_ACC_TRUNC)) diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c index 241609d..b65fee9 100644 --- a/src/H5FDsec2.c +++ b/src/H5FDsec2.c @@ -357,6 +357,8 @@ H5FD_sec2_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr) o_flags |= O_CREAT; if(H5F_ACC_EXCL & flags) o_flags |= O_EXCL; + if(H5F_ACC_SYNC & flags) + o_flags |= O_SYNC; /* Open the file */ if((fd = HDopen(name, o_flags, 0666)) < 0) { diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h index 334879c..2d4678b 100644 --- a/src/H5Fpkg.h +++ b/src/H5Fpkg.h @@ -63,7 +63,8 @@ #define H5F_SUPER_ALL_FLAGS (H5F_SUPER_WRITE_ACCESS | H5F_SUPER_FILE_OK) /* Mask for removing private file access flags */ -#define H5F_ACC_PUBLIC_FLAGS 0x001fu +/* #define H5F_ACC_PUBLIC_FLAGS 0x001fu */ +#define H5F_ACC_PUBLIC_FLAGS 0x003fu /* Free space section+aggregator merge flags */ #define H5F_FS_MERGE_METADATA 0x01 /* Section can merge with metadata aggregator */ diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 7c6fae8..1ef40b0 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -547,6 +547,7 @@ H5_DLL hbool_t H5F_use_tmp_space(const H5F_t *f); H5_DLL hbool_t H5F_is_tmp_addr(const H5F_t *f, haddr_t addr); /* Functions that retrieve values from VFD layer */ +H5_DLL H5FD_t* H5F_get_driver(const H5F_t *f); H5_DLL hid_t H5F_get_driver_id(const H5F_t *f); H5_DLL herr_t H5F_get_fileno(const H5F_t *f, unsigned long *filenum); H5_DLL hbool_t H5F_has_feature(const H5F_t *f, unsigned feature); diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index f32b3e0..7b7acb4 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -48,6 +48,7 @@ #define H5F_ACC_EXCL (H5CHECK 0x0004u) /*fail if file already exists*/ #define H5F_ACC_DEBUG (H5CHECK 0x0008u) /*print debug info */ #define H5F_ACC_CREAT (H5CHECK 0x0010u) /*create non-existing files */ +#define H5F_ACC_SYNC (H5CHECK 0x0020u) /*no filesystem caching */ /* Value passed to H5Pset_elink_acc_flags to cause flags to be taken from the * parent file. */ |