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-rwxr-xr-xbin/trace1
-rw-r--r--src/H5D.c65
-rw-r--r--src/H5Dchunk.c98
-rw-r--r--src/H5Dpkg.h1
-rw-r--r--src/H5Dpublic.h53
-rw-r--r--src/H5VLconnector.h3
-rw-r--r--src/H5VLnative_dataset.c18
-rw-r--r--test/chunk_info.c113
8 files changed, 333 insertions, 19 deletions
diff --git a/bin/trace b/bin/trace
index 0611fa5..a2052ce 100755
--- a/bin/trace
+++ b/bin/trace
@@ -53,6 +53,7 @@ $Source = "";
"H5D_scatter_func_t" => "DS",
"H5FD_mpio_xfer_t" => "Dt",
"H5D_vds_view_t" => "Dv",
+ "H5D_chunk_iter_op_t" => "x",
"herr_t" => "e",
"H5E_auto1_t" => "Ea",
"H5E_auto2_t" => "EA",
diff --git a/src/H5D.c b/src/H5D.c
index 2f0daaf..aa09f5f 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -2142,3 +2142,68 @@ H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filte
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_chunk_info_by_coord() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dchunk_iter
+ *
+ * Purpose: Iterates over all chunks in dataset with given callback and user data.
+ *
+ * Parameters:
+ * hid_t dset_id; IN: Chunked dataset ID
+ * H5D_chunk_iter_op_t cb IN: User callback function, called for every chunk.
+ * void *op_data IN/OUT: Optional user data passed on to user callback.
+ *
+ * Callback information:
+ * H5D_chunk_iter_op_t is defined as:
+ *
+ * typedef int (*H5D_chunk_iter_op_t)(
+ * const hsize_t *offset,
+ * uint32_t filter_mask,
+ * haddr_t addr,
+ * uint32_t nbytes,
+ * void *op_data);
+ *
+ * H5D_chunk_iter_op_t parameters:
+ * hsize_t *offset; IN/OUT: Array of starting logical coordinates of chunk.
+ * uint32_t filter_mask; IN: Filter mask of chunk.
+ * haddr_t addr; IN: Offset in file of chunk data.
+ * uint32_t nbytes; IN: Size in number of bytes of chunk data in file.
+ * void *op_data; IN/OUT: Pointer to any user-defined data
+ * associated with the operation.
+ *
+ * The return values from an operator are:
+ * Zero (H5_ITER_CONT) causes the iterator to continue, returning zero when all
+ * elements have been processed.
+ * Positive (H5_ITER_STOP) causes the iterator to immediately return that positive
+ * value, indicating short-circuit success.
+ * Negative (H5_ITER_ERROR) causes the iterator to immediately return that value,
+ * indicating failure.
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Gaute Hope
+ * August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dchunk_iter(hid_t dset_id, H5D_chunk_iter_op_t cb, void *op_data)
+{
+ H5VL_object_t *vol_obj = NULL; /* Dataset for this operation */
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE3("e", "ix*x", dset_id, cb, op_data);
+
+ /* Check arguments */
+ if (NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset identifier")
+
+ /* Call private function to get the chunk info given the chunk's index */
+ if (H5VL_dataset_specific(vol_obj, H5VL_DATASET_CHUNK_ITER, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, cb,
+ op_data) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't iterate over chunks")
+
+done:
+ FUNC_LEAVE_API(ret_value)
+} /* end H5Dchunk_iter() */
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 25fb2f8..6be29fd 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -245,6 +245,11 @@ typedef struct H5D_chunk_coll_info_t {
} H5D_chunk_coll_info_t;
#endif /* H5_HAVE_PARALLEL */
+typedef struct H5D_chunk_iter_cb_data_t {
+ H5D_chunk_iter_op_t cb; /* User defined callback */
+ void * op_data; /* User data for user defined callback */
+} H5D_chunk_iter_cb_data_t;
+
/********************/
/* Local Prototypes */
/********************/
@@ -269,6 +274,7 @@ static herr_t H5D__chunk_dest(H5D_t *dset);
static int H5D__get_num_chunks_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
static int H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
static int H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+static int H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata);
/* "Nonexistent" layout operation callback */
static ssize_t H5D__nonexistent_readvv(const H5D_io_info_t *io_info, size_t chunk_max_nseq,
@@ -7451,3 +7457,95 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned
done:
FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__get_chunk_info_by_coord() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_iter
+ *
+ * Purpose: Iterate over all the chunks in the dataset with given callbak.
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Gaute Hope
+ * August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_iter(const H5D_t *dset, H5D_chunk_iter_op_t cb, void *op_data)
+{
+ const H5O_layout_t *layout = NULL; /* Dataset layout */
+ const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */
+ H5D_rdcc_ent_t * ent; /* Cache entry index */
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
+
+ /* Check args */
+ HDassert(dset);
+ HDassert(dset->shared);
+
+ /* Get dataset layout and raw data chunk cache */
+ layout = &(dset->shared->layout);
+ rdcc = &(dset->shared->cache.chunk);
+ HDassert(layout);
+ HDassert(rdcc);
+ HDassert(H5D_CHUNKED == layout->type);
+
+ /* Search for cached chunks that haven't been written out */
+ for (ent = rdcc->head; ent; ent = ent->next)
+ /* Flush the chunk out to disk, to make certain the size is correct later */
+ if (H5D__chunk_flush_entry(dset, ent, FALSE) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ 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;
+
+ /* If the dataset is not written, return without errors */
+ if (H5F_addr_defined(idx_info.storage->idx_addr)) {
+ H5D_chunk_iter_cb_data_t data;
+ data.cb = cb;
+ data.op_data = op_data;
+
+ /* Iterate over the allocated chunks calling the iterator callback */
+ if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_iter_cb, &data) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to iterate over chunks.")
+ } /* end if H5F_addr_defined */
+
+done:
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
+} /* end H5D__chunk_iter() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_iter_cb
+ *
+ * Purpose: Call the user-defined function with the chunk data. The iterator continues if
+ * the user-defined function returns H5_ITER_CONT, and stops if H5_ITER_STOP is
+ * returned.
+ *
+ * Return: Success: H5_ITER_CONT or H5_ITER_STOP
+ * Failure: Negative (H5_ITER_ERROR)
+ *
+ * Programmer: Gaute Hope
+ * August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
+{
+ int ret_value = 0;
+
+ FUNC_ENTER_STATIC_NOERR
+
+ const H5D_chunk_iter_cb_data_t *data = (H5D_chunk_iter_cb_data_t *)udata;
+
+ ret_value = (data->cb)(chunk_rec->scaled, chunk_rec->filter_mask, chunk_rec->chunk_addr,
+ chunk_rec->nbytes, data->op_data);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_iter_cb */
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 64f2c7a..28561c9 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -565,6 +565,7 @@ H5_DLL herr_t H5D__get_chunk_info(const H5D_t *dset, const H5S_t *space, hsize_
unsigned *filter_mask, haddr_t *offset, hsize_t *size);
H5_DLL herr_t H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *coord, unsigned *filter_mask,
haddr_t *addr, hsize_t *size);
+H5_DLL herr_t H5D__chunk_iter(const H5D_t *dset, H5D_chunk_iter_op_t cb, void *op_data);
H5_DLL haddr_t H5D__get_offset(const H5D_t *dset);
H5_DLL herr_t H5D__vlen_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, hsize_t *size);
H5_DLL herr_t H5D__vlen_get_buf_size_gen(H5VL_object_t *vol_obj, hid_t type_id, hid_t space_id,
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index e48b727..0b5fac6 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -160,6 +160,14 @@ typedef herr_t (*H5D_scatter_func_t)(const void **src_buf /*out*/, size_t *src_b
typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_used, void *op_data);
//! <!-- [H5D_gather_func_t_snip] -->
+//! <!-- [H5D_chunk_iter_op_t_snip] -->
+/**
+ * Define the operator function pointer for H5Dchunk_iter()
+ */
+//! <!-- [H5D_chunk_iter_op_t_snip] -->
+typedef int (*H5D_chunk_iter_op_t)(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t nbytes,
+ void *op_data);
+
/********************/
/* Public Variables */
/********************/
@@ -630,6 +638,51 @@ H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, u
* --------------------------------------------------------------------------
* \ingroup H5D
*
+ * \brief Iterate over all chunks
+ *
+ * \dset_id
+ * \param[in] cb User callback function, called for every chunk.
+ * \param[in] op_data User-defined pointer to data required by op
+ *
+ * \return \herr_t
+ *
+ * \details H5Dget_chunk_iter iterates over all chunks in the dataset, calling the
+ * user supplied callback with the details of the chunk and the supplied
+ * \p op_data.
+ *
+ * Callback information:
+ * H5D_chunk_iter_op_t is defined as:
+ *
+ * typedef int (*H5D_chunk_iter_op_t)(
+ * const hsize_t *offset,
+ * uint32_t filter_mask,
+ * haddr_t addr,
+ * uint32_t nbytes,
+ * void *op_data);
+ *
+ * H5D_chunk_iter_op_t parameters:
+ * hsize_t *offset; IN/OUT: Array of starting logical coordinates of chunk.
+ * uint32_t filter_mask; IN: Filter mask of chunk.
+ * haddr_t addr; IN: Offset in file of chunk data.
+ * uint32_t nbytes; IN: Size in number of bytes of chunk data in file.
+ * void *op_data; IN/OUT: Pointer to any user-defined data
+ * associated with the operation.
+ *
+ * The return values from an operator are:
+ * Zero (H5_ITER_CONT) causes the iterator to continue, returning zero when all
+ * elements have been processed.
+ * Positive (H5_ITER_STOP) causes the iterator to immediately return that positive
+ * value, indicating short-circuit success.
+ * Negative (H5_ITER_ERROR) causes the iterator to immediately return that value,
+ * indicating failure.
+ *
+ */
+H5_DLL herr_t H5Dchunk_iter(hid_t dset_id, H5D_chunk_iter_op_t cb, void *op_data);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
* \brief Retrieves information about a chunk specified by its index
*
* \dset_id
diff --git a/src/H5VLconnector.h b/src/H5VLconnector.h
index 2a8ef6e..63613bc 100644
--- a/src/H5VLconnector.h
+++ b/src/H5VLconnector.h
@@ -82,7 +82,8 @@ typedef enum H5VL_dataset_specific_t {
H5VL_DATASET_SET_EXTENT, /* H5Dset_extent */
H5VL_DATASET_FLUSH, /* H5Dflush */
H5VL_DATASET_REFRESH, /* H5Drefresh */
- H5VL_DATASET_WAIT /* H5Dwait */
+ H5VL_DATASET_WAIT, /* H5Dwait */
+ H5VL_DATASET_CHUNK_ITER /* H5Dchunk_iter */
} H5VL_dataset_specific_t;
/* Typedef for VOL connector dataset optional VOL operations */
diff --git a/src/H5VLnative_dataset.c b/src/H5VLnative_dataset.c
index d78388e..21491e7 100644
--- a/src/H5VLnative_dataset.c
+++ b/src/H5VLnative_dataset.c
@@ -353,6 +353,24 @@ H5VL__native_dataset_specific(void *obj, H5VL_dataset_specific_t specific_type,
break;
}
+ case H5VL_DATASET_CHUNK_ITER: { /* H5Dchunk_iter */
+ H5D_chunk_iter_op_t cb = HDva_arg(arguments, H5D_chunk_iter_op_t);
+ void * op_data = HDva_arg(arguments, void *);
+
+ HDassert(dset->shared);
+
+ /* Make sure the dataset is chunked */
+ if (H5D_CHUNKED != dset->shared->layout.type) {
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+ }
+
+ /* Call private function */
+ if (H5D__chunk_iter(dset, cb, op_data) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't iterate over chunks")
+
+ break;
+ }
+
default:
HGOTO_ERROR(H5E_VOL, H5E_UNSUPPORTED, FAIL, "invalid specific operation")
} /* end switch */
diff --git a/test/chunk_info.c b/test/chunk_info.c
index ada2d80..c84f500 100644
--- a/test/chunk_info.c
+++ b/test/chunk_info.c
@@ -1482,6 +1482,50 @@ error:
return FAIL;
} /* test_chunk_info_version2_btrees() */
+typedef struct chunk_iter_info_t {
+ hsize_t offset[2];
+ uint32_t filter_mask;
+ haddr_t addr;
+ uint32_t nbytes;
+} chunk_iter_info_t;
+
+static int
+iter_cb(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t nbytes, void *op_data)
+{
+ chunk_iter_info_t **chunk_info = (chunk_iter_info_t **)op_data;
+
+ (*chunk_info)->offset[0] = offset[0];
+ (*chunk_info)->offset[1] = offset[1];
+ (*chunk_info)->filter_mask = filter_mask;
+ (*chunk_info)->addr = addr;
+ (*chunk_info)->nbytes = nbytes;
+
+ /* printf("offset: [%lld, %lld], addr: %ld, size: %d, filter mask: %d\n", offset[0], offset[1], addr,
+ * nbytes, filter_mask); */
+
+ *chunk_info += 1;
+
+ return H5_ITER_CONT;
+}
+
+static int
+iter_cb_stop(const hsize_t H5_ATTR_UNUSED *offset, uint32_t H5_ATTR_UNUSED filter_mask,
+ haddr_t H5_ATTR_UNUSED addr, uint32_t H5_ATTR_UNUSED nbytes, void *op_data)
+{
+ chunk_iter_info_t **chunk_info = (chunk_iter_info_t **)op_data;
+ *chunk_info += 1;
+ return H5_ITER_STOP;
+}
+
+static int
+iter_cb_fail(const hsize_t H5_ATTR_UNUSED *offset, uint32_t H5_ATTR_UNUSED filter_mask,
+ haddr_t H5_ATTR_UNUSED addr, uint32_t H5_ATTR_UNUSED nbytes, void *op_data)
+{
+ chunk_iter_info_t **chunk_info = (chunk_iter_info_t **)op_data;
+ *chunk_info += 1;
+ return H5_ITER_ERROR;
+}
+
/*-------------------------------------------------------------------------
* Function: test_basic_query
*
@@ -1502,24 +1546,26 @@ error:
static herr_t
test_basic_query(hid_t fapl)
{
- char filename[FILENAME_BUF_SIZE]; /* File name */
- hid_t basicfile = H5I_INVALID_HID; /* File ID */
- hid_t dspace = H5I_INVALID_HID; /* Dataspace ID */
- hid_t dset = H5I_INVALID_HID; /* Dataset ID */
- hid_t cparms = H5I_INVALID_HID; /* Creation plist */
- hsize_t dims[2] = {NX, NY}; /* Dataset dimensions */
- hsize_t chunk_dims[2] = {CHUNK_NX, CHUNK_NY}; /* Chunk dimensions */
- int direct_buf[CHUNK_NX][CHUNK_NY]; /* Data in chunks */
- unsigned flt_msk = 0; /* Filter mask */
- unsigned read_flt_msk = 0; /* Filter mask after direct read */
- hsize_t offset[2]; /* Offset coordinates of a chunk */
- hsize_t out_offset[2] = {0, 0}; /* Buffer to get offset coordinates */
- hsize_t size = 0; /* Size of an allocated/written chunk */
- hsize_t nchunks = 0; /* Number of chunks */
- haddr_t addr = 0; /* Address of an allocated/written chunk */
- hsize_t chk_index = 0; /* Index of a chunk */
- hsize_t ii, jj; /* Array indices */
- herr_t ret; /* Temporary returned value for verifying failure */
+ char filename[FILENAME_BUF_SIZE]; /* File name */
+ hid_t basicfile = H5I_INVALID_HID; /* File ID */
+ hid_t dspace = H5I_INVALID_HID; /* Dataspace ID */
+ hid_t dset = H5I_INVALID_HID; /* Dataset ID */
+ hid_t cparms = H5I_INVALID_HID; /* Creation plist */
+ hsize_t dims[2] = {NX, NY}; /* Dataset dimensions */
+ hsize_t chunk_dims[2] = {CHUNK_NX, CHUNK_NY}; /* Chunk dimensions */
+ int direct_buf[CHUNK_NX][CHUNK_NY]; /* Data in chunks */
+ unsigned flt_msk = 0; /* Filter mask */
+ unsigned read_flt_msk = 0; /* Filter mask after direct read */
+ hsize_t offset[2]; /* Offset coordinates of a chunk */
+ hsize_t out_offset[2] = {0, 0}; /* Buffer to get offset coordinates */
+ hsize_t size = 0; /* Size of an allocated/written chunk */
+ hsize_t nchunks = 0; /* Number of chunks */
+ haddr_t addr = 0; /* Address of an allocated/written chunk */
+ hsize_t chk_index = 0; /* Index of a chunk */
+ hsize_t ii, jj; /* Array indices */
+ chunk_iter_info_t chunk_infos[2]; /* chunk infos filled up by iterator */
+ chunk_iter_info_t *cptr; /* pointer to array of chunks */
+ herr_t ret; /* Temporary returned value for verifying failure */
TESTING("basic operations");
@@ -1627,6 +1673,37 @@ test_basic_query(hid_t fapl)
if (verify_empty_chunk_info(dset, offset) == FAIL)
FAIL_PUTS_ERROR("Verification of H5Dget_chunk_info_by_coord on empty chunk failed\n");
+ /* iterate over all chunks */
+ cptr = &(chunk_infos[0]);
+ if (H5Dchunk_iter(dset, &iter_cb, &cptr) < 0)
+ TEST_ERROR;
+
+ VERIFY(cptr, &(chunk_infos[2]), "Iterator did not iterate all chunks");
+ VERIFY(chunk_infos[0].offset[0], 0, "Offset mismatch");
+ VERIFY(chunk_infos[0].offset[1], 0, "Offset mismatch");
+ VERIFY(chunk_infos[0].filter_mask, 0, "Filter mismatch");
+ VERIFY(chunk_infos[0].nbytes, 96, "Size mismatch");
+
+ VERIFY(chunk_infos[1].offset[0], 1, "Offset mismatch");
+ VERIFY(chunk_infos[1].offset[1], 1, "Offset mismatch");
+
+ /* iterate and stop after one iteration */
+ cptr = &(chunk_infos[0]);
+ if (H5Dchunk_iter(dset, &iter_cb_stop, &cptr) < 0)
+ TEST_ERROR;
+ VERIFY(cptr, &(chunk_infos[1]), "Verification of halted iterator failed\n");
+
+ /* iterate and fail after one iteration */
+ cptr = &(chunk_infos[0]);
+ H5E_BEGIN_TRY
+ {
+ ret = H5Dchunk_iter(dset, &iter_cb_fail, &cptr);
+ }
+ H5E_END_TRY;
+ if (ret >= 0)
+ TEST_ERROR;
+ VERIFY(cptr, &(chunk_infos[1]), "Verification of halted iterator failed\n");
+
/* Release resourse */
if (H5Dclose(dset) < 0)
TEST_ERROR