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-rw-r--r--src/H5D.c568
-rw-r--r--src/H5Dcompact.c10
-rw-r--r--src/H5Dcontig.c193
-rw-r--r--src/H5Distore.c78
-rw-r--r--src/H5Dprivate.h2
-rw-r--r--src/H5Dpublic.h6
-rw-r--r--src/H5FDmpio.h9
-rw-r--r--src/H5FDmpiposix.h4
-rw-r--r--src/H5Farray.c64
-rw-r--r--src/H5Fcompact.c10
-rw-r--r--src/H5Fcontig.c193
-rw-r--r--src/H5Fistore.c78
-rw-r--r--src/H5Fpkg.h2
-rw-r--r--src/H5Fprivate.h9
-rw-r--r--src/H5Oefl.c2
-rw-r--r--src/H5Olayout.c1
-rw-r--r--src/H5S.c22
-rw-r--r--src/H5Smpio.c2
-rw-r--r--src/H5Sprivate.h10
-rw-r--r--src/H5Sselect.c4
20 files changed, 857 insertions, 410 deletions
diff --git a/src/H5D.c b/src/H5D.c
index 645e81b..577e25f 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -22,6 +22,7 @@
#include "H5Gprivate.h" /* Group headers */
#include "H5HLprivate.h" /* Name heap */
#include "H5Iprivate.h" /* IDs */
+#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
@@ -44,8 +45,11 @@
# include "H5Rpublic.h"
#endif /*H5_HAVE_PARALLEL*/
+/* Pablo information */
#define PABLO_MASK H5D_mask
+/* Local typedefs */
+
/*
* A dataset is the following struct.
*/
@@ -56,11 +60,22 @@ struct H5D_t {
H5O_layout_t layout; /* data layout */
};
+/* Enumerated type for allocating dataset's storage */
+typedef enum {
+ H5D_ALLOC_CREATE, /* Dataset is being created */
+ H5D_ALLOC_OPEN, /* Dataset is being opened */
+ H5D_ALLOC_EXTEND, /* Dataset's dataspace is being extended */
+ H5D_ALLOC_WRITE /* Dataset is being extended */
+} H5D_alloc_time_t;
+/* Interface initialization */
static int interface_initialize_g = 0;
#define INTERFACE_INIT H5D_init_interface
+
+/* Local functions */
static herr_t H5D_init_interface(void);
-static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space);
+static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset,H5D_alloc_time_t alloc_time);
+static herr_t H5D_init_storage(H5D_t *dataset);
H5D_t * H5D_new(hid_t dcpl_id);
static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf,
const H5T_t *buf_type, const H5S_t *space);
@@ -70,7 +85,7 @@ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation);
H5FL_DEFINE_STATIC(H5D_t);
/* Declare a free list to manage blocks of type conversion data */
-H5FL_BLK_DEFINE_STATIC(type_conv);
+H5FL_BLK_DEFINE(type_conv);
/* Declare a free list to manage blocks of single datatype element data */
H5FL_BLK_DEFINE(type_elem);
@@ -1533,22 +1548,46 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter");
if(H5P_get(plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout");
- if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout");
- if(dcpl_layout==H5D_COMPACT && space_time==H5D_SPACE_ALLOC_LATE)
+ if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
+
+ /* Check if the space_time is the default and set it accordingly */
+ if(space_time==H5D_SPACE_ALLOC_DEFAULT) {
+ switch(dcpl_layout) {
+ case H5D_COMPACT:
+ space_time=H5D_SPACE_ALLOC_EARLY;
+ break;
+
+ case H5D_CONTIGUOUS:
+ space_time=H5D_SPACE_ALLOC_LATE;
+ break;
+
+ case H5D_CHUNKED:
+ space_time=H5D_SPACE_ALLOC_INCR;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
+ } /* end switch */
+ } /* end if */
+
+ /* Don't allow compact datasets to allocate space later */
+ if(dcpl_layout==H5D_COMPACT && space_time!=H5D_SPACE_ALLOC_EARLY)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation");
/* What file is the dataset being added to? */
if (NULL==(f=H5G_insertion_file(loc, name)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point");
-#ifdef H5_HAVE_PARALLEL
/* If MPIO or MPIPOSIX is used, no filter support yet. */
if((IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) && dcpl_pline.nfilters > 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet");
-#endif /*H5_HAVE_PARALLEL*/
+
+ /* Check if this dataset is going into a parallel file and set space allocation time */
+ if(IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f))
+ space_time=H5D_SPACE_ALLOC_EARLY;
if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time");
@@ -1576,6 +1615,10 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
if (NULL == (new_plist = H5I_object(new_dset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list");
+ /* Set the space_time for the dataset, in case the default was used */
+ if(H5P_set(new_plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "can't set allocation time");
+
if(H5P_get(new_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout");
@@ -1588,6 +1631,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1;
assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim));
new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type);
+ new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */
switch (new_dset->layout.type) {
case H5D_CONTIGUOUS:
@@ -1741,34 +1785,11 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset");
/*
- * Allocate storage. We assume that external storage is already
- * allocated by the caller, or at least will be before I/O is performed.
- * For parallelization, space is always allocated now except using
- * external storage. For contiguous layout, space is allocated now if
- * space allocate time is early; otherwise delay allocation until H5Dwrite.
- * For compact dataset, space is allocated regardless of space allocation
- * time.
+ * Allocate storage if space allocate time is early; otherwise delay allocation until later.
*/
-#ifdef H5_HAVE_PARALLEL
- if (0==efl.nused) {
- if(H5F_arr_create(f, &(new_dset->layout))<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage");
- } /* end if */
- else
- new_dset->layout.addr = HADDR_UNDEF;
-#else /*H5_HAVE_PARALLEL*/
- if (0==efl.nused) {
- if(dcpl_layout==H5D_CHUNKED || dcpl_layout==H5D_COMPACT ||
- (dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY)) {
- if (H5F_arr_create(f, &(new_dset->layout))<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage");
- } /* end if */
- else
- new_dset->layout.addr = HADDR_UNDEF;
- } /* end if */
- else
- new_dset->layout.addr = HADDR_UNDEF;
-#endif /*H5_HAVE_PARALLEL*/
+ if(space_time==H5D_SPACE_ALLOC_EARLY)
+ if (H5D_alloc_storage(f, new_dset,H5D_ALLOC_CREATE)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage");
/* Update external storage message */
if (efl.nused>0) {
@@ -1791,34 +1812,9 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update external file list message");
} /* end if */
- /* Initialize the raw data when it's
- * 1. Parallel I/O
- * 2. layout is contiguous, space allocation time is early, fill value
- * writing time is upon allocation
- * 3. external space is treated the same as internal except it's always
- * assumed as early for space allocation time
- * 4. compact dataset and fill value writing time is upon allocation
- */
-#ifdef H5_HAVE_PARALLEL
- if (H5D_init_storage(new_dset, space)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage");
-#else /*H5_HAVE_PARALLEL*/
- if(fill_time==H5D_FILL_TIME_ALLOC) {
- if((dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY)
- || (dcpl_layout==H5D_CHUNKED && space_time==H5D_SPACE_ALLOC_EARLY)
- || dcpl_layout==H5D_COMPACT ) {
- if (H5D_init_storage(new_dset, space)<0) {
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage");
- }
- }
- }
-#endif /*H5_HAVE_PARALLEL*/
-
/* Update layout message */
if (H5D_COMPACT != new_dset->layout.type && H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0, &(new_dset->layout))<0)
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout");
- if (H5D_COMPACT == new_dset->layout.type)
- new_dset->layout.dirty = TRUE;
/* Success */
ret_value = new_dset;
@@ -1969,7 +1965,6 @@ H5D_open_oid(H5G_entry_t *ent)
{
H5D_t *dataset = NULL; /*new dataset struct */
H5D_t *ret_value = NULL; /*return value */
- H5S_t *space = NULL; /*data space */
H5O_fill_new_t fill = {NULL, 0, NULL, H5D_SPACE_ALLOC_LATE, H5D_FILL_TIME_ALLOC, TRUE};
H5O_fill_t fill_prop = {NULL, 0, NULL};
H5O_pline_t pline; /* I/O pipeline information */
@@ -1997,47 +1992,11 @@ H5D_open_oid(H5G_entry_t *ent)
/* Get the type and space */
if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type info from dataset header");
- if (NULL==(space=H5S_read (&(dataset->ent))))
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data space info from dataset header");
/* Get dataset creation property list object */
if (NULL == (plist = H5I_object(dataset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list");
- /* Retrieve & release the previous fill-value settings */
- if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value");
- H5O_reset(H5O_FILL, &fill_prop);
-
- /* Get the new fill value message */
- if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) {
- H5E_clear();
- HDmemset(&fill, 0, sizeof(fill));
- }
- if(fill.fill_defined) {
- if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value");
- } else {
- /* For compatibility with v1.4. Retrieve the old fill value message.
- * If size is 0, make it -1 for undefined. */
- if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) {
- H5E_clear();
- HDmemset(&fill_prop, 0, sizeof(fill_prop));
- }
- if(fill_prop.size == 0) {
- fill_prop.type = fill_prop.buf = NULL;
- fill_prop.size = (size_t)-1;
- }
- } /* end else */
-
- /* Set fill value properties */
- if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
- if(H5P_set(plist, H5D_CRT_SPACE_TIME_NAME, &fill.space_time) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
- if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
-
/* Get the optional filters message */
HDmemset(&pline,0,sizeof(H5O_pline_t));
if(NULL == H5O_read(&(dataset->ent), H5O_PLINE, 0, &pline)) {
@@ -2047,11 +2006,9 @@ H5D_open_oid(H5G_entry_t *ent)
if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set pipeline");
-#ifdef H5_HAVE_PARALLEL
/* If MPIO or MPIPOSIX is used, no filter support yet. */
if((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && pline.nfilters > 0)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet");
-#endif /*H5_HAVE_PARALLEL*/
/*
* Get the raw data layout info. It's actually stored in two locations:
@@ -2094,6 +2051,58 @@ H5D_open_oid(H5G_entry_t *ent)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
} /* end switch */
+ /* Retrieve & release the previous fill-value settings */
+ if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value");
+ H5O_reset(H5O_FILL, &fill_prop);
+
+ /* Get the new fill value message */
+ if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) {
+ H5E_clear();
+ HDmemset(&fill, 0, sizeof(fill));
+
+ /* Set the space allocation time appropriately, based on the type of dataset storage */
+ switch (dataset->layout.type) {
+ case H5D_COMPACT:
+ fill.space_time=H5D_SPACE_ALLOC_EARLY;
+ break;
+
+ case H5D_CONTIGUOUS:
+ fill.space_time=H5D_SPACE_ALLOC_LATE;
+ break;
+
+ case H5D_CHUNKED:
+ fill.space_time=H5D_SPACE_ALLOC_INCR;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
+ } /* end switch */
+ } /* end if */
+ if(fill.fill_defined) {
+ if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value");
+ } else {
+ /* For compatibility with v1.4. Retrieve the old fill value message.
+ * If size is 0, make it -1 for undefined. */
+ if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) {
+ H5E_clear();
+ HDmemset(&fill_prop, 0, sizeof(fill_prop));
+ }
+ if(fill_prop.size == 0) {
+ fill_prop.type = fill_prop.buf = NULL;
+ fill_prop.size = (size_t)-1;
+ }
+ } /* end else */
+
+ /* Set fill value properties */
+ if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
+ if(H5P_set(plist, H5D_CRT_SPACE_TIME_NAME, &fill.space_time) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
+ if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value");
+
/* Get the external file list message, which might not exist. Space is
* also undefined when space allocate time is H5D_SPACE_ALLOC_LATE. */
if( !H5F_addr_defined(dataset->layout.addr)) {
@@ -2103,12 +2112,14 @@ H5D_open_oid(H5G_entry_t *ent)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list");
}
/*
- * Make sure all storage is properly initialized for chunked datasets.
- * This is especially important for parallel I/O where the B-tree must
- * be fully populated before I/O can happen.
+ * Make sure all storage is properly initialized.
+ * This is important only for parallel I/O where the space must
+ * be fully allocated before I/O can happen.
*/
- if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) && H5D_CHUNKED==dataset->layout.type) {
- if (H5D_init_storage(dataset, space)<0)
+ if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)
+ && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF)
+ && (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) {
+ if (H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_OPEN)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage");
}
@@ -2116,8 +2127,6 @@ H5D_open_oid(H5G_entry_t *ent)
ret_value = dataset;
done:
- if (space)
- H5S_close(space);
if (ret_value==NULL && dataset) {
if (H5F_addr_defined(dataset->ent.header))
H5O_close(&(dataset->ent));
@@ -2360,7 +2369,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
* fill time is NEVER, there is no way to tell whether part of data
* has been overwritten. So just proceed in reading.
*/
- if(nelmts > 0 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS
+ if(nelmts > 0 && efl.nused==0 && dataset->layout.type!=H5D_COMPACT
&& dataset->layout.addr==HADDR_UNDEF) {
/* Should be impossible, but check anyway... */
@@ -2695,6 +2704,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5O_efl_t efl; /* External File List info */
H5O_fill_t fill; /* Fill value info */
H5D_fill_time_t fill_time; /* When to write the fill values */
+ H5D_space_time_t space_time; /* When to allocate raw data space */
H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */
H5P_genplist_t *dc_plist; /* Dataset creation roperty list */
unsigned sconv_flags=0; /* Flags for the space conversion */
@@ -2728,14 +2738,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
mem_space = file_space;
nelmts = (*mem_space->select.get_npoints)(mem_space);
-#ifdef H5_HAVE_PARALLEL
/* If MPIO or MPIPOSIX is used, no VL datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
if ( (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_VLEN)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet");
-#endif /*H5_HAVE_PARALLEL*/
-#ifdef H5_HAVE_PARALLEL
/* If MPIO or MPIPOSIX is used, no dataset region reference datatype support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
@@ -2743,7 +2750,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5T_get_class(mem_type)==H5T_REFERENCE &&
H5T_get_ref_type(mem_type)==H5R_DATASET_REGION)
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet");
-#endif /*H5_HAVE_PARALLEL*/
if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file");
@@ -2794,24 +2800,15 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill time");
if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list");
+ if(H5P_get(dc_plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
- /* Allocate data space and initialize it if it hasn't been. Also modify
- * header message for layout(this is only for forward compatibility). */
- if(nelmts > 0 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS &&
+ /* Allocate data space and initialize it if it hasn't been. */
+ if(nelmts > 0 && dataset->layout.type!=H5D_COMPACT &&
dataset->layout.addr==HADDR_UNDEF) {
/* Allocate storage */
- if(H5F_arr_create(dataset->ent.file, &(dataset->layout))<0)
+ if(H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_WRITE)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage");
-
- /* Initialize raw data */
- if(fill_time==H5D_FILL_TIME_ALLOC)
- if(H5D_init_storage(dataset, file_space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value");
-
- /* Update layout message */
- if (H5O_modify (&(dataset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT,
- &(dataset->layout)) < 0)
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message");
} /* end if */
/*
@@ -3084,10 +3081,11 @@ done:
herr_t
H5D_extend (H5D_t *dataset, const hsize_t *size)
{
- herr_t changed, ret_value=SUCCEED;
- H5S_t *space = NULL;
- H5O_fill_t fill;
- H5P_genplist_t *plist; /* Property list */
+ int changed; /* Flag to indicate that the dataspace was successfully extended */
+ H5S_t *space = NULL; /* Dataset's dataspace */
+ H5D_space_time_t space_time; /* When to allocate raw data space */
+ H5P_genplist_t *plist; /* Property list */
+ herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_extend, FAIL);
@@ -3095,6 +3093,12 @@ H5D_extend (H5D_t *dataset, const hsize_t *size)
assert (dataset);
assert (size);
+ /* Get the dataset creation property list */
+ if (NULL == (plist = H5I_object(dataset->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list");
+ if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
+
/*
* NOTE: Restrictions on extensions were checked when the dataset was
* created. All extensions are allowed here since none should be
@@ -3112,26 +3116,10 @@ H5D_extend (H5D_t *dataset, const hsize_t *size)
if (H5S_modify (&(dataset->ent), space)<0)
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace");
- /* Initialize the new parts of the dataset */
-#ifdef LATER
- if (H5S_select_all(space)<0 ||
- H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL, old_dims, NULL)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to select new extents for fill value");
-#else
- /*
- * We don't have the H5S_SELECT_DIFF operator yet. We really only
- * need it for contiguous datasets because the chunked datasets will
- * either fill on demand during I/O or attempt a fill of all chunks.
- */
- if (NULL == (plist = H5I_object(dataset->dcpl_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list");
- if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
- if(H5D_CONTIGUOUS == dataset->layout.type && fill.buf)
- HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to select fill value region");
-#endif
- if (H5D_init_storage(dataset, space)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value");
+ /* Allocate space for the new parts of the dataset, if appropriate */
+ if(space_time==H5D_SPACE_ALLOC_EARLY)
+ if (H5D_alloc_storage(dataset->ent.file, dataset, H5D_ALLOC_EXTEND)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value");
} /* end if */
done:
@@ -3226,6 +3214,128 @@ H5D_get_file (const H5D_t *dset)
/*-------------------------------------------------------------------------
+ * Function: H5D_alloc_storage
+ *
+ * Purpose: Allocate storage for the raw data of a dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Friday, January 16, 1998
+ *
+ * Modifications:
+ * Quincey Koziol
+ * Thursday, August 22, 2002
+ * Moved here from H5F_arr_create and moved more logic into
+ * this function from places where it was being called.
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_alloc_time_t alloc_time)
+{
+ H5P_genplist_t *plist; /* Dataset's creation property list */
+ H5O_efl_t efl; /* External File List info */
+ H5D_fill_time_t fill_time; /* When to write fill values */
+ H5D_space_time_t space_time; /* When to allocate raw data space */
+ struct H5O_layout_t *layout; /* The dataset's layout information */
+ hsize_t nbytes; /* The number of bytes in the dataset */
+ unsigned space_allocated=0; /* Flag to indicate that space was allocated */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOINIT(H5D_alloc_storage);
+
+ /* check args */
+ assert (f);
+ assert (dset);
+
+ /* Get external file list properties */
+ if (NULL == (plist = H5I_object(dset->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list");
+ if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list");
+
+ /* If the data is stored in external files, don't set an address for the layout
+ * We assume that external storage is already
+ * allocated by the caller, or at least will be before I/O is performed.
+ */
+ if(efl.nused==0) {
+ /* Get properties needed */
+ if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time");
+ if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
+
+ /* Get a pointer to the dataset's layout information */
+ layout=&(dset->layout);
+
+ switch (layout->type) {
+ case H5D_CONTIGUOUS:
+ if(layout->addr==HADDR_UNDEF) {
+ /* Reserve space in the file for the entire array */
+ for (u=0, nbytes=1; u<layout->ndims; u++)
+ nbytes *= layout->dim[u];
+ assert (nbytes>0);
+ if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes)))
+ HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space");
+
+ /* Indicate that we allocated space */
+ space_allocated=1;
+ } /* end if */
+ break;
+
+ case H5D_CHUNKED:
+ if(layout->addr==HADDR_UNDEF) {
+ /* Create the root of the B-tree that describes chunked storage */
+ if (H5F_istore_create (f, layout/*out*/)<0)
+ HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage");
+
+ /* Indicate that we allocated space */
+ space_allocated=1;
+ } /* end if */
+ break;
+
+ case H5D_COMPACT:
+ /* Check if space is already allocated */
+ if(layout->buf==NULL) {
+ /* Reserve space in layout header message for the entire array. */
+ assert(layout->size>0);
+ if (NULL==(layout->buf=H5MM_malloc(layout->size)))
+ HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset");
+ layout->dirty = TRUE;
+
+ /* Indicate that we allocated space */
+ space_allocated=1;
+ } /* end if */
+ break;
+
+ default:
+ assert ("not implemented yet" && 0);
+ HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
+ } /* end switch */
+
+ /* If we are filling the dataset on allocation, do that now */
+ if(fill_time==H5D_FILL_TIME_ALLOC
+ && !(space_time==H5D_SPACE_ALLOC_INCR && alloc_time==H5D_ALLOC_WRITE)) {
+ if(H5D_init_storage(dset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value");
+ } /* end if */
+
+ /* Also update header message for layout with new address
+ * (this is only for forward compatibility).
+ */
+ if(space_allocated && alloc_time!=H5D_ALLOC_CREATE)
+ if (H5O_modify (&(dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(dset->layout)) < 0)
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message");
+ } /* end if */
+
+done:
+ FUNC_LEAVE (ret_value);
+} /* end H5D_alloc_storage() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D_init_storage
*
* Purpose: Initialize the data for a new dataset. If a selection is
@@ -3247,32 +3357,31 @@ H5D_get_file (const H5D_t *dset)
*-------------------------------------------------------------------------
*/
static herr_t
-H5D_init_storage(H5D_t *dset, const H5S_t *space)
+H5D_init_storage(H5D_t *dset)
{
hssize_t snpoints; /* Number of points in space (for error checking) */
size_t npoints; /* Number of points in space */
- size_t ptsperbuf; /* Maximum # of points which fit in the buffer */
- size_t bufsize=64*1024; /* Size of buffer to write */
- size_t size; /* Current # of points to write */
- hsize_t addr; /* Offset in dataset */
- void *buf = NULL; /* Buffer for fill value writing */
+ H5S_t *space = NULL; /* Dataset's dataspace */
H5O_fill_t fill; /* Fill value information */
- H5D_space_time_t space_time; /* When to allocate space */
+ H5O_efl_t efl; /* External File List info */
H5P_genplist_t *plist; /* Property list */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOINIT(H5D_init_storage);
assert(dset);
- assert(space);
/* Get fill value, external file list, and data pipeline properties */
if (NULL == (plist = H5I_object(dset->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list");
if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
- if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time");
+ if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list");
+
+ /* Get the dataset's dataspace */
+ if (NULL==(space=H5S_read (&(dset->ent))))
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header");
/* Get the number of elements in the dataset's dataspace */
snpoints = H5S_get_simple_extent_npoints(space);
@@ -3290,54 +3399,17 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
break;
case H5D_CONTIGUOUS:
- /* If fill value is library default, get the dataset's type's size */
- if(!fill.buf) {
- fill.size=H5T_get_size(dset->type);
- assert(fill.size);
- } /* end if */
-
- /*
- * Fill the entire current extent with the fill value. We can do
- * this quite efficiently by making sure we copy the fill value
- * in relatively large pieces.
- */
- ptsperbuf = MAX(1, bufsize/fill.size);
- bufsize = ptsperbuf*fill.size;
-
- /* Allocate temporary buffer */
- if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL)
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer");
-
- /* Fill the buffer with the user's fill value */
- if(fill.buf)
- H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf);
- else /* Fill the buffer with the default fill value */
- HDmemset(buf,0,bufsize);
-
- /* Start at the beginning of the dataset */
- addr = 0;
-
- /* Loop through writing the fill value to the dataset */
- while (npoints>0) {
- size = MIN(ptsperbuf, npoints) * fill.size;
- if (H5F_seq_write(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
- &(dset->layout), plist, space, fill.size, size, addr, buf)<0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
- npoints -= MIN(ptsperbuf, npoints);
- addr += size;
- } /* end while */
+ if (H5F_contig_fill(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
+ &(dset->layout), plist, space, H5T_get_size(dset->type))<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset");
break;
case H5D_CHUNKED:
/*
- * If the dataset is accessed via parallel I/O, allocate file space
+ * Allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
- if (space_time==H5D_SPACE_ALLOC_EARLY
-#ifdef H5_HAVE_PARALLEL
- || (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file))
-#endif /*H5_HAVE_PARALLEL*/
- ) {
+ {
/* We only handle simple data spaces so far */
int ndims;
hsize_t dim[H5O_LAYOUT_NDIMS];
@@ -3345,7 +3417,6 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info");
dim[ndims] = dset->layout.dim[ndims];
- ndims++;
if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
&(dset->layout), dim, plist)<0)
@@ -3355,8 +3426,8 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
} /* end switch */
done:
- if (buf)
- H5FL_BLK_FREE(type_conv,buf);
+ if (space)
+ H5S_close(space);
FUNC_LEAVE(ret_value);
}
@@ -3430,23 +3501,29 @@ H5D_get_storage_size(H5D_t *dset)
switch(dset->layout.type) {
case H5D_CHUNKED:
- ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims,
+ if(dset->layout.addr == HADDR_UNDEF)
+ ret_value=0;
+ else
+ ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims,
dset->layout.addr);
break;
+
case H5D_CONTIGUOUS:
/* Datasets which are not allocated yet are using no space on disk */
if(dset->layout.addr == HADDR_UNDEF)
- ret_value=0;
+ ret_value=0;
else {
for (u=0, ret_value=1; u<dset->layout.ndims; u++)
ret_value *= dset->layout.dim[u];
} /* end else */
break;
+
case H5D_COMPACT:
ret_value = dset->layout.size;
break;
+
default:
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset type");
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type");
}
done:
@@ -4001,8 +4078,11 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size)
herr_t ret_value = SUCCEED; /* Return value */
H5S_t *space = NULL;
H5P_genplist_t *plist;
+ H5D_space_time_t space_time; /* When to allocate raw data space */
int u;
- int shrink = 0;
+ unsigned shrink = 0; /* Flag to indicate a dimension has shrank */
+ unsigned expand = 0; /* Flag to indicate a dimension has grown */
+ int changed = 0;
FUNC_ENTER_NOAPI(H5D_set_extent, FAIL);
@@ -4018,56 +4098,62 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dset header");
/*-------------------------------------------------------------------------
- * Check if we are shrinking in any of the dimensions
+ * Check if we are shrinking or expanding any of the dimensions
*-------------------------------------------------------------------------
*/
if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
for(u = 0; u < rank; u++) {
- if(size[u] < curr_dims[u]) {
+ if(size[u] < curr_dims[u])
shrink = 1;
- break;
- }
+ if(size[u] > curr_dims[u])
+ expand = 1;
}
/*-------------------------------------------------------------------------
* Modify the size of the data space
*-------------------------------------------------------------------------
*/
- if(H5S_set_extent(space, size) < 0)
+ if((changed=H5S_set_extent(space, size)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space");
- /*-------------------------------------------------------------------------
- * Modify the dataset storage
- *-------------------------------------------------------------------------
- */
- /* Save the new dataspace in the file if necessary */
- if(H5S_modify(&(dset->ent), space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace");
-
- /* Initialize the new parts of the dset */
- if(H5D_init_storage(dset, space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage");
-
-
- /*-------------------------------------------------------------------------
- * Remove chunk information in the case of chunked datasets
- * This removal takes place only in case we are shrinking the dateset
- *-------------------------------------------------------------------------
- */
- if(shrink && H5D_CHUNKED == dset->layout.type) {
- /* Remove excess chunks */
- if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ");
-
+ /* Don't bother updating things, unless they've changed */
+ if(changed) {
/* Get the dataset creation property list */
- if(NULL == (plist = H5I_object(dset->dcpl_id)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list");
-
- /* Reset the elements outsize the new dimensions, but in existing chunks */
- if(H5F_istore_initialize_by_extent(dset->ent.file, &dset->layout, plist, space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ");
+ if(NULL == (plist = H5I_object(dset->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list");
+ if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time");
+
+ /*-------------------------------------------------------------------------
+ * Modify the dataset storage
+ *-------------------------------------------------------------------------
+ */
+ /* Save the new dataspace in the file if necessary */
+ if(H5S_modify(&(dset->ent), space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace");
+
+ /* Allocate space for the new parts of the dataset, if appropriate */
+ if(expand && space_time==H5D_SPACE_ALLOC_EARLY)
+ if(H5D_alloc_storage(dset->ent.file, dset, H5D_ALLOC_EXTEND) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage");
+
+
+ /*-------------------------------------------------------------------------
+ * Remove chunk information in the case of chunked datasets
+ * This removal takes place only in case we are shrinking the dateset
+ *-------------------------------------------------------------------------
+ */
+ if(shrink && H5D_CHUNKED == dset->layout.type) {
+ /* Remove excess chunks */
+ if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ");
+
+ /* Reset the elements outsize the new dimensions, but in existing chunks */
+ if(H5F_istore_initialize_by_extent(dset->ent.file, &dset->layout, plist, space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ");
+ } /* end if */
} /* end if */
done:
diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index 3a36edb..0a21211 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -44,9 +44,9 @@ static int interface_initialize_g = 0;
*-------------------------------------------------------------------------
*/
herr_t
-H5F_compact_readv(H5F_t *f, const H5O_layout_t *layout, size_t nseq,
+H5F_compact_readv(H5F_t UNUSED *f, const H5O_layout_t *layout, size_t nseq,
size_t size_arr[], hsize_t offset_arr[],
- hid_t dxpl_id, void *_buf/*out*/)
+ hid_t UNUSED dxpl_id, void *_buf/*out*/)
{
unsigned char *buf=(unsigned char *)_buf;
size_t size;
@@ -93,11 +93,11 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5F_compact_writev(H5F_t *f, H5O_layout_t *layout, size_t nseq,
+H5F_compact_writev(H5F_t UNUSED *f, H5O_layout_t *layout, size_t nseq,
size_t size_arr[], hsize_t offset_arr[],
- hid_t dxpl_id, const void *_buf)
+ hid_t UNUSED dxpl_id, const void *_buf)
{
- unsigned char *buf=(unsigned char *)_buf;
+ const unsigned char *buf=(const unsigned char *)_buf;
size_t size;
haddr_t offset;
unsigned u;
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
index 89f9fc5..fce1ba9 100644
--- a/src/H5Dcontig.c
+++ b/src/H5Dcontig.c
@@ -14,11 +14,19 @@
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
-#include "H5private.h"
-#include "H5Eprivate.h"
+#include "H5private.h" /* Generic Functions */
+#include "H5Dprivate.h" /* Dataset functions */
+#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h"
#include "H5FDprivate.h" /*file driver */
#include "H5FLprivate.h" /*Free Lists */
+#include "H5Oprivate.h" /* Object headers */
+#include "H5Pprivate.h" /* Property lists */
+#include "H5Vprivate.h" /* Vector and array functions */
+
+/* MPIO & MPIPOSIX drivers needed for special checks */
+#include "H5FDmpio.h"
+#include "H5FDmpiposix.h"
/* Interface initialization */
#define PABLO_MASK H5Fcontig_mask
@@ -28,6 +36,187 @@ static int interface_initialize_g = 0;
/* Declare a PQ free list to manage the sieve buffer information */
H5FL_BLK_DEFINE(sieve_buf);
+/* Extern the free list to manage blocks of type conversion data */
+H5FL_BLK_EXTERN(type_conv);
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5F_contig_fill
+ *
+ * Purpose: Write fill values to a contiguously stored dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * August 22, 2002
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout,
+ struct H5P_genplist_t *dc_plist, const struct H5S_t *space,
+ size_t elmt_size)
+{
+ H5O_fill_t fill; /* Fill value information */
+ H5O_efl_t efl; /* External File List info */
+ hssize_t snpoints; /* Number of points in space (for error checking) */
+ size_t npoints; /* Number of points in space */
+ size_t ptsperbuf; /* Maximum # of points which fit in the buffer */
+ size_t bufsize=64*1024; /* Size of buffer to write */
+ size_t size; /* Current # of points to write */
+ hsize_t addr; /* Offset in dataset */
+ void *buf = NULL; /* Buffer for fill value writing */
+#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
+ int mpi_rank=(-1); /* This process's rank */
+ int mpi_size=(-1); /* Total # of processes */
+ int mpi_round=0; /* Current process responsible for I/O */
+ int mpi_code; /* MPI return code */
+ unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */
+ unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
+#endif /* H5_HAVE_PARALLEL */
+ herr_t ret_value=SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5F_contig_fill, FAIL);
+
+ /* Check args */
+ assert(f);
+ assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
+ assert(layout && H5D_CONTIGUOUS==layout->type);
+ assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
+ assert(H5F_addr_defined(layout->addr));
+ assert(dc_plist!=NULL);
+ assert(space);
+ assert(elmt_size>0);
+
+ /* Get necessary properties from dataset creation property list */
+ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+ HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value");
+ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list");
+
+#ifdef H5_HAVE_PARALLEL
+ /* Retrieve up MPI parameters */
+ if(IS_H5FD_MPIO(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
+ if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
+ if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size");
+
+ /* Set the MPI-capable file driver flag */
+ using_mpi=1;
+ } /* end if */
+ else {
+ if(IS_H5FD_MPIPOSIX(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
+ if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
+ if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size");
+
+ /* Set the MPI-capable file driver flag */
+ using_mpi=1;
+ } /* end if */
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+
+ /* Get the number of elements in the dataset's dataspace */
+ snpoints = H5S_get_simple_extent_npoints(space);
+ assert(snpoints>=0);
+ H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t);
+
+ /* Don't write default fill-values to external files */
+ if(efl.nused>0 && !fill.buf)
+ HGOTO_DONE(SUCCEED);
+
+ /* If fill value is library default, use the element size */
+ if(!fill.buf)
+ fill.size=elmt_size;
+
+ /*
+ * Fill the entire current extent with the fill value. We can do
+ * this quite efficiently by making sure we copy the fill value
+ * in relatively large pieces.
+ */
+ ptsperbuf = MAX(1, bufsize/fill.size);
+ bufsize = ptsperbuf*fill.size;
+
+ /* Allocate temporary buffer */
+ if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL)
+ HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer");
+
+ /* Fill the buffer with the user's fill value */
+ if(fill.buf)
+ H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf);
+ else /* Fill the buffer with the default fill value */
+ HDmemset(buf,0,bufsize);
+
+ /* Start at the beginning of the dataset */
+ addr = 0;
+
+ /* Loop through writing the fill value to the dataset */
+ while (npoints>0) {
+ size = MIN(ptsperbuf, npoints) * fill.size;
+
+#ifdef H5_HAVE_PARALLEL
+ /* Check if this file is accessed with an MPI-capable file driver */
+ if(using_mpi) {
+ /* Round-robin write the chunks out from only one process */
+ if(mpi_round==mpi_rank) {
+ if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space,
+ fill.size, size, addr, buf)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
+ } /* end if */
+ mpi_round=(++mpi_round)%mpi_size;
+
+ /* Indicate that blocks are being written */
+ blocks_written=1;
+ } /* end if */
+ else {
+#endif /* H5_HAVE_PARALLEL */
+ if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space,
+ fill.size, size, addr, buf)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
+#ifdef H5_HAVE_PARALLEL
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+
+ npoints -= MIN(ptsperbuf, npoints);
+ addr += size;
+ } /* end while */
+
+#ifdef H5_HAVE_PARALLEL
+ /* Only need to block at the barrier if we actually wrote fill values */
+ /* And if we are using an MPI-capable file driver */
+ if(using_mpi && blocks_written) {
+ /* Wait at barrier to avoid race conditions where some processes are
+ * still writing out fill values and other processes race ahead to data
+ * in, getting bogus data.
+ */
+ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
+ } /* end if */
+#endif /* H5_HAVE_PARALLEL */
+
+done:
+ /* Free the buffer for fill values */
+ if (buf)
+ H5FL_BLK_FREE(type_conv,buf);
+
+ FUNC_LEAVE(ret_value);
+}
+
/*-------------------------------------------------------------------------
* Function: H5F_contig_read
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 0bba74e..f36b6200 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used and file can be written to, we must bypass the
* chunk-cache scheme because other MPI processes could be writing to
@@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other
* MPI processes could be writing to other elements in the same chunk.
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
H5P_genplist_t *dx_plist; /* Data xfer property list */
double split_ratios[3];/* B-tree node splitting ratios */
#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank=(-1); /* This process's rank */
int mpi_size=(-1); /* Total # of processes */
int mpi_round=0; /* Current process responsible for I/O */
@@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
+ unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */
int i; /* Local index variable */
unsigned u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
@@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
#ifdef H5_HAVE_PARALLEL
/* Retrieve up MPI parameters */
if(IS_H5FD_MPIO(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
@@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end if */
else {
if(IS_H5FD_MPIPOSIX(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
/* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
@@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end else */
#endif /* H5_HAVE_PARALLEL */
-#ifdef H5_HAVE_PARALLEL
- /* Can't use data I/O pipeline in parallel (yet) */
- if (using_mpi && pline.nfilters>0)
- HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel");
-#endif /* H5_HAVE_PARALLEL */
-
/*
* Setup indice to go through all chunks. (Future improvement
* should allocate only chunks that have no file space assigned yet.
@@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
/* Loop over all chunks */
carry=0;
while (carry==0) {
- /* Check if the chunk exists yet */
+ /* Check if the chunk exists yet on disk */
+ chunk_exists=1;
if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) {
+ H5F_rdcc_t *rdcc = &(f->shared->rdcc); /*raw data chunk cache */
+ H5F_rdcc_ent_t *ent = NULL; /*cache entry */
+
+ /* Didn't find the chunk on disk */
+ chunk_exists = 0;
+
+ /* Look for chunk in cache */
+ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+
+ /* Assume a match */
+ chunk_exists = 1;
+ for(u = 0; u < layout->ndims && chunk_exists; u++) {
+ if(ent->offset[u] != chunk_offset[u])
+ chunk_exists = 0; /* Reset if no match */
+ } /* end for */
+ } /* end if */
+ } /* end for */
+ } /* end if */
+
+ if(!chunk_exists) {
/* Initialize the chunk information */
udata.mesg = *layout;
udata.key.filter_mask = 0;
@@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
- if(IS_H5FD_MPIO(f)) {
- if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end if */
- else {
- /* Sanity Check */
- assert(IS_H5FD_MPIPOSIX(f));
-
- if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end else */
+ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
} /* end if */
#endif /* H5_HAVE_PARALLEL */
@@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
- found = 0;
- for(u = 0; u < ent->layout->ndims - 1; u++) {
- if((hsize_t)ent->offset[u] > curr_dims[u]) {
- found = 1;
- break;
- }
- }
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+ found = 0;
+ for(u = 0; u < ent->layout->ndims - 1; u++) {
+ if((hsize_t)ent->offset[u] > curr_dims[u]) {
+ found = 1;
+ break;
+ }
+ }
+ } /* end if */
if(found) {
#if defined (H5F_ISTORE_DEBUG)
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index a60c041..d1d0a02 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -63,7 +63,7 @@
/* Definitions for space allocation time */
#define H5D_CRT_SPACE_TIME_NAME "space_time"
#define H5D_CRT_SPACE_TIME_SIZE sizeof(H5D_space_time_t)
-#define H5D_CRT_SPACE_TIME_DEF H5D_SPACE_ALLOC_LATE
+#define H5D_CRT_SPACE_TIME_DEF H5D_SPACE_ALLOC_DEFAULT
/* Definitions for time of fill value writing */
#define H5D_CRT_FILL_TIME_NAME "fill_time"
#define H5D_CRT_FILL_TIME_SIZE sizeof(H5D_fill_time_t)
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 855f05f..3cad621 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -33,8 +33,10 @@ typedef enum H5D_layout_t {
/* Values for the space allocation time property */
typedef enum H5D_space_time_t {
H5D_SPACE_ALLOC_ERROR =-1,
- H5D_SPACE_ALLOC_LATE =0,
- H5D_SPACE_ALLOC_EARLY =1
+ H5D_SPACE_ALLOC_DEFAULT =0,
+ H5D_SPACE_ALLOC_EARLY =1,
+ H5D_SPACE_ALLOC_LATE =2,
+ H5D_SPACE_ALLOC_INCR =3
} H5D_space_time_t;
/* Values for the status of space allocation */
diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h
index c5133f3..f1dd6f7 100644
--- a/src/H5FDmpio.h
+++ b/src/H5FDmpio.h
@@ -34,8 +34,12 @@ typedef struct H5FD_mpio_dxpl_t {
H5FD_mpio_xfer_t xfer_mode; /*collective or independent I/O */
} H5FD_mpio_dxpl_t;
-#ifdef H5_HAVE_PARALLEL
/* Macros */
+
+#define IS_H5FD_MPIO(f) /* (H5F_t *f) */ \
+ (H5FD_MPIO==H5F_get_driver_id(f))
+
+#ifdef H5_HAVE_PARALLEL
/*Turn on H5FDmpio_debug if H5F_DEBUG is on */
#ifdef H5F_DEBUG
#ifndef H5FDmpio_DEBUG
@@ -43,9 +47,6 @@ typedef struct H5FD_mpio_dxpl_t {
#endif
#endif
-#define IS_H5FD_MPIO(f) /* (H5F_t *f) */ \
- (H5FD_MPIO==H5F_get_driver_id(f))
-
/* Function prototypes */
#ifdef __cplusplus
extern "C" {
diff --git a/src/H5FDmpiposix.h b/src/H5FDmpiposix.h
index 81d05d4..3f262e1 100644
--- a/src/H5FDmpiposix.h
+++ b/src/H5FDmpiposix.h
@@ -31,13 +31,13 @@
# define H5FD_MPIPOSIX (-1)
#endif
-#ifdef H5_HAVE_PARALLEL
-
/* Macros */
#define IS_H5FD_MPIPOSIX(f) /* (H5F_t *f) */ \
(H5FD_MPIPOSIX==H5F_get_driver_id(f))
+#ifdef H5_HAVE_PARALLEL
+
/* Function prototypes */
#ifdef __cplusplus
extern "C" {
diff --git a/src/H5Farray.c b/src/H5Farray.c
index e3657d0..8e01099 100644
--- a/src/H5Farray.c
+++ b/src/H5Farray.c
@@ -20,7 +20,6 @@
#include "H5Fpkg.h"
#include "H5FDprivate.h" /*file driver */
#include "H5Iprivate.h"
-#include "H5MFprivate.h"
#include "H5MMprivate.h" /*memory management */
#include "H5Oprivate.h"
#include "H5Pprivate.h"
@@ -37,69 +36,6 @@ static int interface_initialize_g = 0;
/*-------------------------------------------------------------------------
- * Function: H5F_arr_create
- *
- * Purpose: Creates an array of bytes.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: Robb Matzke
- * Friday, January 16, 1998
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
-{
- unsigned u;
- hsize_t nbytes;
- herr_t ret_value = SUCCEED; /* Return value */
-
- FUNC_ENTER_NOAPI(H5F_arr_create, FAIL);
-
- /* check args */
- assert (f);
- assert (layout);
- layout->addr = HADDR_UNDEF; /*just in case we fail*/
-
- switch (layout->type) {
- case H5D_CONTIGUOUS:
- /* Reserve space in the file for the entire array */
- for (u=0, nbytes=1; u<layout->ndims; u++)
- nbytes *= layout->dim[u];
- assert (nbytes>0);
- if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes)))
- HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space");
- break;
-
- case H5D_CHUNKED:
- /* Create the root of the B-tree that describes chunked storage */
- if (H5F_istore_create (f, layout/*out*/)<0)
- HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage");
- break;
-
- case H5D_COMPACT:
- /* Reserve space in layout header message for the entire array. */
- assert(layout->size>0);
- if (NULL==(layout->buf=H5MM_malloc(layout->size)))
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset");
- layout->dirty = TRUE;
- break;
-
- default:
- assert ("not implemented yet" && 0);
- HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
- "unsupported storage layout");
- } /* end switch */
-
-done:
- FUNC_LEAVE (ret_value);
-}
-
-
-/*-------------------------------------------------------------------------
* Function: H5F_arr_read
*
* Purpose: Reads a hyperslab of a file byte array into a hyperslab of
diff --git a/src/H5Fcompact.c b/src/H5Fcompact.c
index 3a36edb..0a21211 100644
--- a/src/H5Fcompact.c
+++ b/src/H5Fcompact.c
@@ -44,9 +44,9 @@ static int interface_initialize_g = 0;
*-------------------------------------------------------------------------
*/
herr_t
-H5F_compact_readv(H5F_t *f, const H5O_layout_t *layout, size_t nseq,
+H5F_compact_readv(H5F_t UNUSED *f, const H5O_layout_t *layout, size_t nseq,
size_t size_arr[], hsize_t offset_arr[],
- hid_t dxpl_id, void *_buf/*out*/)
+ hid_t UNUSED dxpl_id, void *_buf/*out*/)
{
unsigned char *buf=(unsigned char *)_buf;
size_t size;
@@ -93,11 +93,11 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5F_compact_writev(H5F_t *f, H5O_layout_t *layout, size_t nseq,
+H5F_compact_writev(H5F_t UNUSED *f, H5O_layout_t *layout, size_t nseq,
size_t size_arr[], hsize_t offset_arr[],
- hid_t dxpl_id, const void *_buf)
+ hid_t UNUSED dxpl_id, const void *_buf)
{
- unsigned char *buf=(unsigned char *)_buf;
+ const unsigned char *buf=(const unsigned char *)_buf;
size_t size;
haddr_t offset;
unsigned u;
diff --git a/src/H5Fcontig.c b/src/H5Fcontig.c
index 89f9fc5..fce1ba9 100644
--- a/src/H5Fcontig.c
+++ b/src/H5Fcontig.c
@@ -14,11 +14,19 @@
#define H5F_PACKAGE /*suppress error about including H5Fpkg */
-#include "H5private.h"
-#include "H5Eprivate.h"
+#include "H5private.h" /* Generic Functions */
+#include "H5Dprivate.h" /* Dataset functions */
+#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h"
#include "H5FDprivate.h" /*file driver */
#include "H5FLprivate.h" /*Free Lists */
+#include "H5Oprivate.h" /* Object headers */
+#include "H5Pprivate.h" /* Property lists */
+#include "H5Vprivate.h" /* Vector and array functions */
+
+/* MPIO & MPIPOSIX drivers needed for special checks */
+#include "H5FDmpio.h"
+#include "H5FDmpiposix.h"
/* Interface initialization */
#define PABLO_MASK H5Fcontig_mask
@@ -28,6 +36,187 @@ static int interface_initialize_g = 0;
/* Declare a PQ free list to manage the sieve buffer information */
H5FL_BLK_DEFINE(sieve_buf);
+/* Extern the free list to manage blocks of type conversion data */
+H5FL_BLK_EXTERN(type_conv);
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5F_contig_fill
+ *
+ * Purpose: Write fill values to a contiguously stored dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * August 22, 2002
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout,
+ struct H5P_genplist_t *dc_plist, const struct H5S_t *space,
+ size_t elmt_size)
+{
+ H5O_fill_t fill; /* Fill value information */
+ H5O_efl_t efl; /* External File List info */
+ hssize_t snpoints; /* Number of points in space (for error checking) */
+ size_t npoints; /* Number of points in space */
+ size_t ptsperbuf; /* Maximum # of points which fit in the buffer */
+ size_t bufsize=64*1024; /* Size of buffer to write */
+ size_t size; /* Current # of points to write */
+ hsize_t addr; /* Offset in dataset */
+ void *buf = NULL; /* Buffer for fill value writing */
+#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
+ int mpi_rank=(-1); /* This process's rank */
+ int mpi_size=(-1); /* Total # of processes */
+ int mpi_round=0; /* Current process responsible for I/O */
+ int mpi_code; /* MPI return code */
+ unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */
+ unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
+#endif /* H5_HAVE_PARALLEL */
+ herr_t ret_value=SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5F_contig_fill, FAIL);
+
+ /* Check args */
+ assert(f);
+ assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
+ assert(layout && H5D_CONTIGUOUS==layout->type);
+ assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
+ assert(H5F_addr_defined(layout->addr));
+ assert(dc_plist!=NULL);
+ assert(space);
+ assert(elmt_size>0);
+
+ /* Get necessary properties from dataset creation property list */
+ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+ HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value");
+ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list");
+
+#ifdef H5_HAVE_PARALLEL
+ /* Retrieve up MPI parameters */
+ if(IS_H5FD_MPIO(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
+ if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
+ if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size");
+
+ /* Set the MPI-capable file driver flag */
+ using_mpi=1;
+ } /* end if */
+ else {
+ if(IS_H5FD_MPIPOSIX(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
+ if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
+ if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size");
+
+ /* Set the MPI-capable file driver flag */
+ using_mpi=1;
+ } /* end if */
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+
+ /* Get the number of elements in the dataset's dataspace */
+ snpoints = H5S_get_simple_extent_npoints(space);
+ assert(snpoints>=0);
+ H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t);
+
+ /* Don't write default fill-values to external files */
+ if(efl.nused>0 && !fill.buf)
+ HGOTO_DONE(SUCCEED);
+
+ /* If fill value is library default, use the element size */
+ if(!fill.buf)
+ fill.size=elmt_size;
+
+ /*
+ * Fill the entire current extent with the fill value. We can do
+ * this quite efficiently by making sure we copy the fill value
+ * in relatively large pieces.
+ */
+ ptsperbuf = MAX(1, bufsize/fill.size);
+ bufsize = ptsperbuf*fill.size;
+
+ /* Allocate temporary buffer */
+ if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL)
+ HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer");
+
+ /* Fill the buffer with the user's fill value */
+ if(fill.buf)
+ H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf);
+ else /* Fill the buffer with the default fill value */
+ HDmemset(buf,0,bufsize);
+
+ /* Start at the beginning of the dataset */
+ addr = 0;
+
+ /* Loop through writing the fill value to the dataset */
+ while (npoints>0) {
+ size = MIN(ptsperbuf, npoints) * fill.size;
+
+#ifdef H5_HAVE_PARALLEL
+ /* Check if this file is accessed with an MPI-capable file driver */
+ if(using_mpi) {
+ /* Round-robin write the chunks out from only one process */
+ if(mpi_round==mpi_rank) {
+ if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space,
+ fill.size, size, addr, buf)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
+ } /* end if */
+ mpi_round=(++mpi_round)%mpi_size;
+
+ /* Indicate that blocks are being written */
+ blocks_written=1;
+ } /* end if */
+ else {
+#endif /* H5_HAVE_PARALLEL */
+ if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space,
+ fill.size, size, addr, buf)<0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
+#ifdef H5_HAVE_PARALLEL
+ } /* end else */
+#endif /* H5_HAVE_PARALLEL */
+
+ npoints -= MIN(ptsperbuf, npoints);
+ addr += size;
+ } /* end while */
+
+#ifdef H5_HAVE_PARALLEL
+ /* Only need to block at the barrier if we actually wrote fill values */
+ /* And if we are using an MPI-capable file driver */
+ if(using_mpi && blocks_written) {
+ /* Wait at barrier to avoid race conditions where some processes are
+ * still writing out fill values and other processes race ahead to data
+ * in, getting bogus data.
+ */
+ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
+ } /* end if */
+#endif /* H5_HAVE_PARALLEL */
+
+done:
+ /* Free the buffer for fill values */
+ if (buf)
+ H5FL_BLK_FREE(type_conv,buf);
+
+ FUNC_LEAVE(ret_value);
+}
+
/*-------------------------------------------------------------------------
* Function: H5F_contig_read
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 0bba74e..f36b6200 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used and file can be written to, we must bypass the
* chunk-cache scheme because other MPI processes could be writing to
@@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other
* MPI processes could be writing to other elements in the same chunk.
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
H5P_genplist_t *dx_plist; /* Data xfer property list */
double split_ratios[3];/* B-tree node splitting ratios */
#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank=(-1); /* This process's rank */
int mpi_size=(-1); /* Total # of processes */
int mpi_round=0; /* Current process responsible for I/O */
@@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
+ unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */
int i; /* Local index variable */
unsigned u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
@@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
#ifdef H5_HAVE_PARALLEL
/* Retrieve up MPI parameters */
if(IS_H5FD_MPIO(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
@@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end if */
else {
if(IS_H5FD_MPIPOSIX(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
/* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
@@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end else */
#endif /* H5_HAVE_PARALLEL */
-#ifdef H5_HAVE_PARALLEL
- /* Can't use data I/O pipeline in parallel (yet) */
- if (using_mpi && pline.nfilters>0)
- HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel");
-#endif /* H5_HAVE_PARALLEL */
-
/*
* Setup indice to go through all chunks. (Future improvement
* should allocate only chunks that have no file space assigned yet.
@@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
/* Loop over all chunks */
carry=0;
while (carry==0) {
- /* Check if the chunk exists yet */
+ /* Check if the chunk exists yet on disk */
+ chunk_exists=1;
if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) {
+ H5F_rdcc_t *rdcc = &(f->shared->rdcc); /*raw data chunk cache */
+ H5F_rdcc_ent_t *ent = NULL; /*cache entry */
+
+ /* Didn't find the chunk on disk */
+ chunk_exists = 0;
+
+ /* Look for chunk in cache */
+ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+
+ /* Assume a match */
+ chunk_exists = 1;
+ for(u = 0; u < layout->ndims && chunk_exists; u++) {
+ if(ent->offset[u] != chunk_offset[u])
+ chunk_exists = 0; /* Reset if no match */
+ } /* end for */
+ } /* end if */
+ } /* end for */
+ } /* end if */
+
+ if(!chunk_exists) {
/* Initialize the chunk information */
udata.mesg = *layout;
udata.key.filter_mask = 0;
@@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
- if(IS_H5FD_MPIO(f)) {
- if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end if */
- else {
- /* Sanity Check */
- assert(IS_H5FD_MPIPOSIX(f));
-
- if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end else */
+ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
} /* end if */
#endif /* H5_HAVE_PARALLEL */
@@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
- found = 0;
- for(u = 0; u < ent->layout->ndims - 1; u++) {
- if((hsize_t)ent->offset[u] > curr_dims[u]) {
- found = 1;
- break;
- }
- }
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+ found = 0;
+ for(u = 0; u < ent->layout->ndims - 1; u++) {
+ if((hsize_t)ent->offset[u] > curr_dims[u]) {
+ found = 1;
+ break;
+ }
+ }
+ } /* end if */
if(found) {
#if defined (H5F_ISTORE_DEBUG)
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index 92e6a5b..fb2c58d 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -183,8 +183,6 @@ __DLL__ herr_t H5F_istore_init (H5F_t *f);
__DLL__ herr_t H5F_istore_flush (H5F_t *f, hbool_t preempt);
__DLL__ herr_t H5F_istore_dest (H5F_t *f);
__DLL__ herr_t H5F_istore_stats (H5F_t *f, hbool_t headers);
-__DLL__ herr_t H5F_istore_create(H5F_t *f,
- struct H5O_layout_t *layout/*in,out*/);
__DLL__ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
struct H5P_genplist_t *dc_plist,
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 15ef548..b3a48f3 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -345,8 +345,6 @@ __DLL__ herr_t H5F_get_obj_count(H5F_t *f, unsigned types,
__DLL__ herr_t H5F_get_obj_ids(H5F_t *f, unsigned types, hid_t *obj_id_list);
/* Functions that operate on array storage */
-__DLL__ herr_t H5F_arr_create(H5F_t *f,
- struct H5O_layout_t *layout /*in,out*/);
__DLL__ herr_t H5F_arr_read (H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
struct H5P_genplist_t *dc_plist,
@@ -393,7 +391,14 @@ __DLL__ herr_t H5F_seq_writev(H5F_t *f, hid_t dxpl_id,
size_t seq_len[], hsize_t file_offset[], const void *_buf);
+/* Functions that operate on contiguous storage */
+__DLL__ herr_t H5F_contig_fill(H5F_t *f, hid_t dxpl_id,
+ struct H5O_layout_t *layout, struct H5P_genplist_t *dc_plist,
+ const struct H5S_t *space, size_t elmt_size);
+
/* Functions that operate on indexed storage */
+__DLL__ herr_t H5F_istore_create(H5F_t *f,
+ struct H5O_layout_t *layout/*in,out*/);
__DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id,
const struct H5O_layout_t *layout,
const hsize_t *space_dim,
diff --git a/src/H5Oefl.c b/src/H5Oefl.c
index eacdeb3..388aa4a 100644
--- a/src/H5Oefl.c
+++ b/src/H5Oefl.c
@@ -532,7 +532,7 @@ H5O_efl_write (H5F_t UNUSED *f, const H5O_efl_t *efl, haddr_t addr,
HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "write past logical end of file");
if (H5F_OVERFLOW_HSIZET2OFFT (efl->slot[i].offset+skip))
HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed");
- if ((fd=HDopen (efl->slot[i].name, O_RDWR, 0))<0) {
+ if ((fd=HDopen (efl->slot[i].name, O_CREAT|O_RDWR, 0666))<0) {
if (HDaccess (efl->slot[i].name, F_OK)<0) {
HGOTO_ERROR (H5E_EFL, H5E_CANTOPENFILE, FAIL, "external raw data file does not exist");
} else {
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index 65f4cdb..33797c6 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -211,7 +211,6 @@ H5O_layout_encode(H5F_t *f, uint8_t *p, const void *_mesg)
if(mesg->type==H5D_COMPACT) {
UINT32ENCODE(p, mesg->size);
if(mesg->size>0 && mesg->buf) {
- H5_CHECK_OVERFLOW(mesg->size,ssize_t,size_t);
HDmemcpy(p, mesg->buf, mesg->size);
p += mesg->size;
}
diff --git a/src/H5S.c b/src/H5S.c
index 34eb4ea..6424ada 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -1899,11 +1899,11 @@ done:
*
*-------------------------------------------------------------------------
*/
-herr_t
+int
H5S_set_extent( H5S_t *space, const hsize_t *size )
{
unsigned u;
- herr_t ret_value=SUCCEED;
+ herr_t ret_value=0;
FUNC_ENTER_NOAPI( H5S_set_extent, FAIL );
@@ -1911,19 +1911,21 @@ H5S_set_extent( H5S_t *space, const hsize_t *size )
assert( space && H5S_SIMPLE==space->extent.type );
assert( size);
- /* Check for changing dimensions of a scalar dataspace */
- if(space->extent.u.simple.rank==0)
-
/* Verify that the dimensions being changed are allowed to change */
- for ( u = 0; u < space->extent.u.simple.rank; u++ )
+ for ( u = 0; u < space->extent.u.simple.rank; u++ ) {
if ( space->extent.u.simple.max &&
H5S_UNLIMITED != space->extent.u.simple.max[u] &&
- space->extent.u.simple.max[u]<size[u] )
+ space->extent.u.simple.max[u]!=size[u] )
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,"dimension cannot be modified");
+ ret_value++;
+ } /* end for */
- /* Update dimensions with new values */
- for ( u = 0; u < space->extent.u.simple.rank; u++ )
- space->extent.u.simple.size[u] = size[u];
+ /* Update */
+ if (ret_value) {
+ /* Update dimensions with new values */
+ for ( u = 0; u < space->extent.u.simple.rank; u++ )
+ space->extent.u.simple.size[u] = size[u];
+ } /* end if */
done:
FUNC_LEAVE( ret_value );
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index 61297bb..125c946 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -915,7 +915,7 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5S_mpio_spaces_write(H5F_t *f, const H5O_layout_t *layout,
+H5S_mpio_spaces_write(H5F_t *f, H5O_layout_t *layout,
H5P_genplist_t UNUSED *dc_plist, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf)
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 393f6bb..083847e 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -109,7 +109,7 @@ typedef struct H5S_conv_t {
/* Write directly from app buffer to file */
- herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
+ herr_t (*write)(H5F_t *f, struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf);
@@ -156,7 +156,7 @@ __DLL__ int H5S_cmp(const H5S_t *ds1, const H5S_t *ds2);
__DLL__ htri_t H5S_is_simple(const H5S_t *sdim);
__DLL__ herr_t H5S_extent_release(H5S_t *space);
__DLL__ int H5S_extend(H5S_t *space, const hsize_t *size);
-__DLL__ herr_t H5S_set_extent(H5S_t *space, const hsize_t *size);
+__DLL__ int H5S_set_extent(H5S_t *space, const hsize_t *size);
__DLL__ herr_t H5S_debug(H5F_t *f, const void *_mesg, FILE *stream,
int indent, int fwidth);
@@ -168,7 +168,7 @@ __DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);
__DLL__ herr_t H5S_select_fill(void *fill, size_t fill_size,
const H5S_t *space, void *buf);
-__DLL__ herr_t H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout,
+__DLL__ herr_t H5S_select_fscat (H5F_t *f, struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space,
H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id,
const void *_buf);
@@ -185,7 +185,7 @@ __DLL__ hsize_t H5S_select_mgath (const void *_buf, size_t elmt_size,
__DLL__ herr_t H5S_select_read(H5F_t *f, const struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/);
-__DLL__ herr_t H5S_select_write(H5F_t *f, const struct H5O_layout_t *layout,
+__DLL__ herr_t H5S_select_write(H5F_t *f, struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, const void *buf/*out*/);
@@ -206,7 +206,7 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
/* MPI-IO function to write directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
- const struct H5O_layout_t *layout,
+ struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 10ece00..70888e8 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -777,7 +777,7 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout,
+H5S_select_fscat (H5F_t *f, struct H5O_layout_t *layout,
H5P_genplist_t *dc_plist, size_t elmt_size,
const H5S_t *space, H5S_sel_iter_t *iter,
hsize_t nelmts, hid_t dxpl_id, const void *_buf)
@@ -1365,7 +1365,7 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5S_select_write(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist,
+H5S_select_write(H5F_t *f, H5O_layout_t *layout, H5P_genplist_t *dc_plist,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, const void *_buf/*out*/)
{