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-rw-r--r--MANIFEST10
-rw-r--r--config/depend.in4
-rw-r--r--config/gnu-flags7
-rw-r--r--config/linux-gnulibc13
-rw-r--r--src/H5B.c25
-rw-r--r--src/H5Bprivate.h7
-rw-r--r--src/H5D.c143
-rw-r--r--src/H5Distore.c78
-rw-r--r--src/H5Dprivate.h18
-rw-r--r--src/H5Dpublic.h1
-rw-r--r--src/H5F.c22
-rw-r--r--src/H5Farray.c6
-rw-r--r--src/H5Fistore.c78
-rw-r--r--src/H5Fmpio.c91
-rw-r--r--src/H5Fprivate.h24
-rw-r--r--src/H5Fpublic.h7
-rw-r--r--src/H5Gnode.c6
-rw-r--r--src/H5P.c26
-rw-r--r--src/H5RA.c14
-rw-r--r--src/H5S.c36
-rw-r--r--src/H5Sall.c147
-rw-r--r--src/H5Shyper.c10
-rw-r--r--src/H5Smpio.c34
-rw-r--r--src/H5Spoint.c8
-rw-r--r--src/H5Sprivate.h28
-rw-r--r--src/H5Tpublic.h7
-rw-r--r--test/istore.c8
-rw-r--r--tools/h5ls.c14
28 files changed, 649 insertions, 213 deletions
diff --git a/MANIFEST b/MANIFEST
index 00d5d53..5f9a089 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -81,7 +81,6 @@
./doc/html/Dataspaces.html
./doc/html/Datatypes.html
./doc/html/ddl.html
-./doc/html/DDL.html _DO_NOT_DISTRIBUTE_
./doc/html/Debugging.html
./doc/html/Environment.html
./doc/html/Errors.html
@@ -196,14 +195,17 @@
./examples/h5_select.c
./examples/h5_attribute.c
-./pablo/HDF5record_RT.h
-./pablo/HDFentries.txt
+./pablo/HDFIOTrace.h
+./pablo/HDFTrace.h
+./pablo/HDFmpioProtos.h
+./pablo/HDFrecord_RT.h
./pablo/Makefile.in
-./pablo/PabloHDF5.c
./pablo/PabloHDF_RT.c
./pablo/PabloHDF_SDDF.c
./pablo/ProcIDs.h
+./pablo/PabloSedscr
./pablo/ProcTrace.h
+./pablo/ProcTrace.inc
./src/.distdep
./src/.indent.pro _DO_NOT_DISTRIBUTE_
diff --git a/config/depend.in b/config/depend.in
index dc72d74..7c61f4f 100644
--- a/config/depend.in
+++ b/config/depend.in
@@ -32,10 +32,10 @@ dep depend: .distdep
@for dep in $? dummy; do \
if [ $$dep != "dummy" ]; then \
echo Building dependencies for $$dep; \
- obj=`echo $$dep | sed 's/\.c/\\\\.o/'`; \
+ obj=`echo $$dep | sed 's/\.c/\\\\.lo/'`; \
sed '\%$$obj%,\%[^\\]$$%d' <$@ >$@- && mv $@- $@; \
$(TRACE) $$dep; \
- $(CC) -M -MG $(CPPFLAGS) $$dep >>$@; \
+ $(CC) -M -MG $(CPPFLAGS) $$dep |sed 's/\.o/.lo/' >>$@; \
fi; \
done;
-perl -p $(top_srcdir)/bin/distdep .depend >.distdep
diff --git a/config/gnu-flags b/config/gnu-flags
index 83c0ed7..46a38f4 100644
--- a/config/gnu-flags
+++ b/config/gnu-flags
@@ -59,6 +59,13 @@ EOF
;;
esac
+# Architecture-specific flags
+case "$host_cpu" in
+ i686)
+ ARCH=${ARCH:="-mcpu=pentiumpro -march=pentiumpro -malign-double"}
+ ;;
+esac
+
# Compiler flags
case "$cc_vendor-$cc_version" in
gcc-2.7*)
diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
index 266cd3a..e22b82d 100644
--- a/config/linux-gnulibc1
+++ b/config/linux-gnulibc1
@@ -12,9 +12,6 @@ if test "X-" = "X-$CC"; then
CC_BASENAME=gcc
fi
-# Architecture-specific flags
-ARCH=${ARCH:="-mcpu=pentiumpro -march=pentiumpro -malign-double"}
-
# Omit frame pointer for optimized code?
NOFP=${NOFP:=-fomit-frame-pointer}
diff --git a/src/H5B.c b/src/H5B.c
index 09bb967..ffc829e 100644
--- a/src/H5B.c
+++ b/src/H5B.c
@@ -1482,6 +1482,8 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
* Jun 23 1997
*
* Modifications:
+ * Robb Matzke, 1999-04-21
+ * The key values are passed to the function which is called.
*
*-------------------------------------------------------------------------
*/
@@ -1493,6 +1495,7 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
haddr_t next_addr;
const haddr_t *cur_addr = NULL;
haddr_t *child = NULL;
+ uint8_t *key = NULL;
intn i, nchildren;
herr_t ret_value = FAIL;
@@ -1507,7 +1510,7 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
assert(addr && H5F_addr_defined(addr));
assert(udata);
- if (NULL == (bt = H5AC_find(f, H5AC_BT, addr, type, udata))) {
+ if (NULL == (bt=H5AC_find(f, H5AC_BT, addr, type, udata))) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTLOAD, FAIL,
"unable to load B-tree node");
}
@@ -1524,7 +1527,8 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
* We've reached the left-most leaf. Now follow the right-sibling
* pointer from leaf to leaf until we've processed all leaves.
*/
- if (NULL==(child = H5MM_malloc (2*H5B_K(f,type)*sizeof(haddr_t)))) {
+ if (NULL==(child=H5MM_malloc(2*H5B_K(f,type)*sizeof(haddr_t))) ||
+ NULL==(key=H5MM_malloc((2*H5B_K(f, type)+1)*type->sizeof_nkey))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed");
}
@@ -1533,8 +1537,9 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
cur_addr=&next_addr) {
/*
- * Save all the child addresses since we can't leave the B-tree
- * node protected during an application callback.
+ * Save all the child addresses and native keys since we can't
+ * leave the B-tree node protected during an application
+ * callback.
*/
if (NULL==(bt=H5AC_find (f, H5AC_BT, cur_addr, type, udata))) {
HGOTO_ERROR (H5E_BTREE, H5E_CANTLOAD, FAIL, "B-tree node");
@@ -1542,6 +1547,11 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
for (i=0; i<bt->nchildren; i++) {
child[i] = bt->child[i];
}
+ for (i=0; i<bt->nchildren+1; i++) {
+ H5B_decode_key(f, bt, i);
+ memcpy(key+i*type->sizeof_nkey, bt->key[i].nkey,
+ type->sizeof_nkey);
+ }
next_addr = bt->right;
nchildren = bt->nchildren;
bt = NULL;
@@ -1551,10 +1561,13 @@ H5B_iterate (H5F_t *f, const H5B_class_t *type, const haddr_t *addr,
* application callback.
*/
for (i=0, ret_value=0; i<nchildren && !ret_value; i++) {
- ret_value = (type->list)(f, child+i, udata);
+ ret_value = (type->list)(f, key+i*type->sizeof_nkey,
+ child+i, key+(i+1)*type->sizeof_nkey,
+ udata);
}
}
- H5MM_xfree (child);
+ H5MM_xfree(child);
+ H5MM_xfree(key);
}
done:
diff --git a/src/H5Bprivate.h b/src/H5Bprivate.h
index 4cdfd9e..8dcbaea 100644
--- a/src/H5Bprivate.h
+++ b/src/H5Bprivate.h
@@ -87,8 +87,11 @@ typedef struct H5B_class_t {
/* remove existing data */
H5B_ins_t (*remove)(H5F_t*, const haddr_t*, void*, hbool_t*,
void*, void*, hbool_t*);
-
- herr_t (*list)(H5F_t*, const haddr_t*, void*); /*walk leaf nodes*/
+
+ /* iterate through the leaf nodes */
+ herr_t (*list)(H5F_t*, void*, const haddr_t*, void*, void*);
+
+ /* encode, decode, debug key values */
herr_t (*decode)(H5F_t*, struct H5B_t*, uint8_t*, void*);
herr_t (*encode)(H5F_t*, struct H5B_t*, uint8_t*, void*);
herr_t (*debug_key)(FILE*, intn, intn, const void*, const void*);
diff --git a/src/H5D.c b/src/H5D.c
index 656b7a5..03fce3d 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -66,28 +66,6 @@ const H5D_create_t H5D_create_dflt = {
{0, 0, NULL} /* No filters in pipeline */
};
-/* Default dataset transfer property list */
-const H5D_xfer_t H5D_xfer_dflt = {
- 1024*1024, /* Temporary buffer size */
- NULL, /* Type conversion buffer or NULL */
- NULL, /* Background buffer or NULL */
- H5T_BKG_NO, /* Type of background buffer needed */
- {0.1, 0.5, 0.9}, /* B-tree node splitting ratios */
-#ifndef HAVE_PARALLEL
- 1, /* Cache the hyperslab blocks by default*/
-#else
- 0, /*
- * Don't cache the hyperslab blocks by
- * default (for parallel)
- */
-#endif /* HAVE_PARALLEL */
- 0, /*
- * Default to no upper limit on hyperslab
- * block size to cache
- */
- H5D_XFER_DFLT, /* Independent data transfer */
-};
-
/* Interface initialization? */
static intn interface_initialize_g = 0;
#define INTERFACE_INIT H5D_init_interface
@@ -604,7 +582,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
- const H5D_xfer_t *xfer_parms = NULL;
+ const H5F_xfer_t *xfer_parms = NULL;
FUNC_ENTER(H5Dread, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
@@ -643,7 +621,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
}
}
if (H5P_DEFAULT == plist_id) {
- xfer_parms = &H5D_xfer_dflt;
+ xfer_parms = &H5F_xfer_dflt;
} else if (H5P_DATASET_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
@@ -703,7 +681,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
- const H5D_xfer_t *xfer_parms = NULL;
+ const H5F_xfer_t *xfer_parms = NULL;
FUNC_ENTER(H5Dwrite, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
@@ -742,7 +720,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
}
}
if (H5P_DEFAULT == plist_id) {
- xfer_parms = &H5D_xfer_dflt;
+ xfer_parms = &H5F_xfer_dflt;
} else if (H5P_DATASET_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
@@ -784,9 +762,9 @@ H5Dextend(hid_t dset_id, const hsize_t *size)
H5TRACE2("e","i*h",dset_id,size);
/* Check args */
- if (H5I_DATASET!=H5I_get_type (dset_id) ||
- NULL==(dset=H5I_object (dset_id))) {
- HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+ if (H5I_DATASET!=H5I_get_type(dset_id) ||
+ NULL==(dset=H5I_object(dset_id))) {
+ HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (!size) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified");
@@ -846,7 +824,7 @@ H5D_new(const H5D_create_t *create_parms)
done:
FUNC_LEAVE(ret_value);
-} /* end H5D_new() */
+}
/*-------------------------------------------------------------------------
@@ -1211,7 +1189,7 @@ H5D_open(H5G_entry_t *loc, const char *name)
done:
FUNC_LEAVE(ret_value);
-} /* end H5D_open() */
+}
/*-------------------------------------------------------------------------
* Function: H5D_open_oid
@@ -1364,7 +1342,7 @@ done:
H5MM_xfree(dataset);
}
FUNC_LEAVE(ret_value);
-} /* end H5D_open_oid() */
+}
/*-------------------------------------------------------------------------
* Function: H5D_close
@@ -1451,7 +1429,7 @@ H5D_close(H5D_t *dataset)
*/
herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
+ const H5S_t *file_space, const H5F_xfer_t *xfer_parms,
void *buf/*out*/)
{
hssize_t nelmts; /*number of elements */
@@ -1570,8 +1548,8 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
- mem_space, xfer_parms->xfer_mode,
- buf/*out*/, &must_convert );
+ mem_space, xfer_parms, buf/*out*/,
+ &must_convert);
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
@@ -1655,7 +1633,10 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
#endif
/* Start strip mining... */
- for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
+ assert(nelmts==(hssize_t)(size_t)nelmts); /*check for overflow*/
+ for (smine_start=0;
+ smine_start<(size_t)nelmts;
+ smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
@@ -1803,7 +1784,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
*/
herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
- const H5S_t *file_space, const H5D_xfer_t *xfer_parms,
+ const H5S_t *file_space, const H5F_xfer_t *xfer_parms,
const void *buf)
{
hssize_t nelmts; /*total number of elmts */
@@ -1934,8 +1915,8 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
- mem_space, xfer_parms->xfer_mode, buf,
- &must_convert /*out*/ );
+ mem_space, xfer_parms, buf,
+ &must_convert/*out*/);
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
@@ -2020,7 +2001,10 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
#endif
/* Start strip mining... */
- for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) {
+ assert(nelmts==(hssize_t)(size_t)nelmts); /*check for overflow*/
+ for (smine_start=0;
+ smine_start<(size_t)nelmts;
+ smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
@@ -2422,7 +2406,7 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
ndims++;
if (H5F_istore_allocate(dset->ent.file, &(dset->layout),
- dim, H5D_xfer_dflt.split_ratios,
+ dim, H5F_xfer_dflt.split_ratios,
&(dset->create_parms->pline),
&(dset->create_parms->fill))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
@@ -2441,3 +2425,80 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
FUNC_LEAVE(ret_value);
}
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_storage_size
+ *
+ * Purpose: Returns the amount of storage that is required for the
+ * dataset. For chunked datasets this is the number of allocated
+ * chunks times the chunk size.
+ *
+ * Return: Success: The amount of storage space allocated for the
+ * dataset, not counting meta data. The return
+ * value may be zero if no data has been stored.
+ *
+ * Failure: Zero
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+H5Dget_storage_size(hid_t dset_id)
+{
+ H5D_t *dset=NULL;
+ hsize_t size;
+
+ FUNC_ENTER(H5Dget_storage_size, 0);
+ H5TRACE1("h","i",dset_id);
+
+ /* Check args */
+ if (H5I_DATASET!=H5I_get_type(dset_id) ||
+ NULL==(dset=H5I_object(dset_id))) {
+ HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+ }
+
+ size = H5D_get_storage_size(dset);
+ FUNC_LEAVE(size);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_get_storage_size
+ *
+ * Purpose: Determines how much space has been reserved to store the raw
+ * data of a dataset.
+ *
+ * Return: Success: Number of bytes reserved to hold raw data.
+ *
+ * Failure: 0
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+H5D_get_storage_size(H5D_t *dset)
+{
+ hsize_t size;
+ int i;
+
+ FUNC_ENTER(H5D_get_storage_size, 0);
+
+ if (H5D_CHUNKED==dset->layout.type) {
+ size = H5F_istore_allocated(dset->ent.file, dset->layout.ndims,
+ &(dset->layout.addr));
+ } else {
+ for (i=0, size=1; i<dset->layout.ndims; i++) {
+ size *= dset->layout.dim[i];
+ }
+ }
+
+ FUNC_LEAVE(size);
+}
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 89e262b..d3435a9 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -108,6 +108,9 @@ static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr,
void *_md_key, void *_udata,
void *_rt_key, hbool_t *rt_key_changed,
haddr_t *new_node/*out*/);
+static herr_t H5F_istore_iterate (H5F_t *f, void *left_key,
+ const haddr_t *addr, void *right_key,
+ void *_udata);
static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
void *_key);
static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
@@ -143,6 +146,7 @@ typedef struct H5F_istore_ud1_t {
H5F_istore_key_t key; /*key values */
haddr_t addr; /*file address of chunk */
H5O_layout_t mesg; /*layout message */
+ hsize_t total_storage; /*output from iterator */
} H5F_istore_ud1_t;
/* inherits B-tree like properties from H5B */
@@ -158,7 +162,7 @@ H5B_class_t H5B_ISTORE[1] = {{
FALSE, /*follow min branch? */
FALSE, /*follow max branch? */
NULL, /*remove */
- NULL, /*list */
+ H5F_istore_iterate, /*iterator */
H5F_istore_decode_key, /*decode */
H5F_istore_encode_key, /*encode */
H5F_istore_debug_key, /*debug */
@@ -718,6 +722,36 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
/*-------------------------------------------------------------------------
+ * Function: H5F_istore_iterate
+ *
+ * Purpose: Simply counts the number of chunks for a dataset.
+ *
+ * Return: Success: Non-negative
+ *
+ * Failure: Negative
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5F_istore_iterate (H5F_t UNUSED *f, void *_lt_key,
+ const haddr_t UNUSED *addr,
+ void UNUSED *_rt_key, void *_udata)
+{
+ H5F_istore_ud1_t *bt_udata = (H5F_istore_ud1_t *)_udata;
+ H5F_istore_key_t *lt_key = (H5F_istore_key_t *)_lt_key;
+
+ FUNC_ENTER(H5F_istore_iterate, FAIL);
+ bt_udata->total_storage += lt_key->nbytes;
+ FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
* Function: H5F_istore_init
*
* Purpose: Initialize the raw data chunk cache for a file. This is
@@ -1513,7 +1547,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
+H5F_istore_read(H5F_t *f, const H5F_xfer_t *xfer, const H5O_layout_t *layout,
const H5O_pline_t *pline, const H5O_fill_t *fill,
const hssize_t offset_f[], const hsize_t size[], void *buf)
{
@@ -1601,7 +1635,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
if (f->shared->access_parms->driver==H5F_LOW_MPIO){
H5F_istore_ud1_t udata;
H5O_layout_t l; /* temporary layout */
- H5D_xfer_t tmp_xfer = *xfer;
+ H5F_xfer_t tmp_xfer = *xfer;
if (H5F_istore_get_addr(f, layout, chunk_offset, &udata)<0){
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to locate raw data chunk");
@@ -1683,7 +1717,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
+H5F_istore_write(H5F_t *f, const H5F_xfer_t *xfer, const H5O_layout_t *layout,
const H5O_pline_t *pline, const H5O_fill_t *fill,
const hssize_t offset_f[], const hsize_t size[],
const void *buf)
@@ -1776,7 +1810,7 @@ H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
if (f->shared->access_parms->driver==H5F_LOW_MPIO){
H5F_istore_ud1_t udata;
H5O_layout_t l; /* temporary layout */
- H5D_xfer_t tmp_xfer = *xfer;
+ H5F_xfer_t tmp_xfer = *xfer;
if (H5F_istore_get_addr(f, layout, chunk_offset, &udata)<0){
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to locate raw data chunk");
@@ -1895,6 +1929,40 @@ H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
/*-------------------------------------------------------------------------
+ * Function: H5F_istore_allocated
+ *
+ * Purpose: Return the number of bytes allocated in the file for storage
+ * of raw data under the specified B-tree (ADDR is the address
+ * of the B-tree).
+ *
+ * Return: Success: Number of bytes stored in all chunks.
+ *
+ * Failure: 0
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+H5F_istore_allocated(H5F_t *f, int ndims, haddr_t *addr)
+{
+ H5F_istore_ud1_t udata;
+
+ FUNC_ENTER(H5F_istore_nchunks, 0);
+ udata.mesg.ndims = ndims;
+ udata.total_storage = 0;
+ if (H5B_iterate(f, H5B_ISTORE, addr, &udata)<0) {
+ HRETURN_ERROR(H5E_IO, H5E_INTERNAL, 0,
+ "unable to iterate over chunk B-tree");
+ }
+ FUNC_LEAVE(udata.total_storage);
+}
+
+
+/*-------------------------------------------------------------------------
* Function: H5F_istore_stats
*
* Purpose: Print raw data cache statistics to the debug stream. If
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 7ce4dbc..e420619 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -50,21 +50,8 @@ typedef struct H5D_create_t {
H5O_pline_t pline; /*data filter pipeline */
} H5D_create_t;
-/* Dataset transfer property list */
-typedef struct H5D_xfer_t {
- size_t buf_size; /*max temp buffer size */
- void *tconv_buf; /*type conversion buffer or null */
- void *bkg_buf; /*background buffer or null */
- H5T_bkg_t need_bkg; /*type of background buffer needed */
- double split_ratios[3];/*B-tree node splitting ratios */
- uintn cache_hyper; /*cache hyperslab blocks during I/O? */
- uintn block_limit; /*largest hyperslab block to cache */
- H5D_transfer_t xfer_mode; /*independent or collective transfer */
-} H5D_xfer_t;
-
typedef struct H5D_t H5D_t;
__DLLVAR__ const H5D_create_t H5D_create_dflt;
-__DLLVAR__ const H5D_xfer_t H5D_xfer_dflt;
/* Functions defined in H5D.c */
__DLL__ H5D_t *H5D_create(H5G_entry_t *loc, const char *name,
@@ -75,15 +62,16 @@ __DLL__ herr_t H5D_close(H5D_t *dataset);
__DLL__ htri_t H5D_isa(H5G_entry_t *ent);
__DLL__ herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
- const H5D_xfer_t *xfer_parms, void *buf/*out*/);
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/);
__DLL__ herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type,
const H5S_t *mem_space, const H5S_t *file_space,
- const H5D_xfer_t *xfer_parms, const void *buf);
+ const H5F_xfer_t *xfer_parms, const void *buf);
__DLL__ herr_t H5D_extend(H5D_t *dataset, const hsize_t *size);
__DLL__ H5G_entry_t *H5D_entof(H5D_t *dataset);
__DLL__ H5T_t *H5D_typeof(H5D_t *dset);
__DLL__ H5S_t *H5D_get_space(H5D_t *dset);
__DLL__ H5D_t * H5D_open_oid(H5G_entry_t *ent);
__DLL__ H5F_t * H5D_get_file(const H5D_t *dset);
+__DLL__ hsize_t H5D_get_storage_size(H5D_t *dset);
#endif
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 9e6cba3..6130715 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -50,6 +50,7 @@ __DLL__ herr_t H5Dclose (hid_t dset_id);
__DLL__ hid_t H5Dget_space (hid_t dset_id);
__DLL__ hid_t H5Dget_type (hid_t dset_id);
__DLL__ hid_t H5Dget_create_plist (hid_t dset_id);
+__DLL__ hsize_t H5Dget_storage_size(hid_t dset_id);
__DLL__ herr_t H5Dread (hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/);
__DLL__ herr_t H5Dwrite (hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
diff --git a/src/H5F.c b/src/H5F.c
index 42884cf..f74745a 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -65,6 +65,28 @@ const H5F_create_t H5F_create_dflt = {
*/
H5F_access_t H5F_access_dflt;
+/* Default data transfer property list */
+const H5F_xfer_t H5F_xfer_dflt = {
+ 1024*1024, /* Temporary buffer size */
+ NULL, /* Type conversion buffer or NULL */
+ NULL, /* Background buffer or NULL */
+ H5T_BKG_NO, /* Type of background buffer needed */
+ {0.1, 0.5, 0.9}, /* B-tree node splitting ratios */
+#ifndef HAVE_PARALLEL
+ 1, /* Cache the hyperslab blocks by default*/
+#else
+ 0, /*
+ * Don't cache the hyperslab blocks by
+ * default (for parallel)
+ */
+#endif /* HAVE_PARALLEL */
+ 0, /*
+ * Default to no upper limit on hyperslab
+ * block size to cache
+ */
+ H5D_XFER_DFLT, /* Independent data transfer */
+};
+
/*
* Define the default mount property list.
*/
diff --git a/src/H5Farray.c b/src/H5Farray.c
index 88423ca..3141007 100644
--- a/src/H5Farray.c
+++ b/src/H5Farray.c
@@ -113,7 +113,7 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
*-------------------------------------------------------------------------
*/
herr_t
-H5F_arr_read (H5F_t *f, const H5D_xfer_t *xfer,
+H5F_arr_read (H5F_t *f, const H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const H5O_fill_t *fill,
const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
@@ -330,12 +330,12 @@ H5F_arr_read (H5F_t *f, const H5D_xfer_t *xfer,
*
* Sep 28, 1998 Robb Matzke
* Added `xfer' argument, removed `xfer_mode' argument since it
- * is a member of H5D_xfer_t.
+ * is a member of H5F_xfer_t.
*
*-------------------------------------------------------------------------
*/
herr_t
-H5F_arr_write (H5F_t *f, const H5D_xfer_t *xfer,
+H5F_arr_write (H5F_t *f, const H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 89e262b..d3435a9 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -108,6 +108,9 @@ static H5B_ins_t H5F_istore_insert(H5F_t *f, const haddr_t *addr,
void *_md_key, void *_udata,
void *_rt_key, hbool_t *rt_key_changed,
haddr_t *new_node/*out*/);
+static herr_t H5F_istore_iterate (H5F_t *f, void *left_key,
+ const haddr_t *addr, void *right_key,
+ void *_udata);
static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
void *_key);
static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8_t *raw,
@@ -143,6 +146,7 @@ typedef struct H5F_istore_ud1_t {
H5F_istore_key_t key; /*key values */
haddr_t addr; /*file address of chunk */
H5O_layout_t mesg; /*layout message */
+ hsize_t total_storage; /*output from iterator */
} H5F_istore_ud1_t;
/* inherits B-tree like properties from H5B */
@@ -158,7 +162,7 @@ H5B_class_t H5B_ISTORE[1] = {{
FALSE, /*follow min branch? */
FALSE, /*follow max branch? */
NULL, /*remove */
- NULL, /*list */
+ H5F_istore_iterate, /*iterator */
H5F_istore_decode_key, /*decode */
H5F_istore_encode_key, /*encode */
H5F_istore_debug_key, /*debug */
@@ -718,6 +722,36 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
/*-------------------------------------------------------------------------
+ * Function: H5F_istore_iterate
+ *
+ * Purpose: Simply counts the number of chunks for a dataset.
+ *
+ * Return: Success: Non-negative
+ *
+ * Failure: Negative
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5F_istore_iterate (H5F_t UNUSED *f, void *_lt_key,
+ const haddr_t UNUSED *addr,
+ void UNUSED *_rt_key, void *_udata)
+{
+ H5F_istore_ud1_t *bt_udata = (H5F_istore_ud1_t *)_udata;
+ H5F_istore_key_t *lt_key = (H5F_istore_key_t *)_lt_key;
+
+ FUNC_ENTER(H5F_istore_iterate, FAIL);
+ bt_udata->total_storage += lt_key->nbytes;
+ FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
* Function: H5F_istore_init
*
* Purpose: Initialize the raw data chunk cache for a file. This is
@@ -1513,7 +1547,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
+H5F_istore_read(H5F_t *f, const H5F_xfer_t *xfer, const H5O_layout_t *layout,
const H5O_pline_t *pline, const H5O_fill_t *fill,
const hssize_t offset_f[], const hsize_t size[], void *buf)
{
@@ -1601,7 +1635,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
if (f->shared->access_parms->driver==H5F_LOW_MPIO){
H5F_istore_ud1_t udata;
H5O_layout_t l; /* temporary layout */
- H5D_xfer_t tmp_xfer = *xfer;
+ H5F_xfer_t tmp_xfer = *xfer;
if (H5F_istore_get_addr(f, layout, chunk_offset, &udata)<0){
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to locate raw data chunk");
@@ -1683,7 +1717,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
+H5F_istore_write(H5F_t *f, const H5F_xfer_t *xfer, const H5O_layout_t *layout,
const H5O_pline_t *pline, const H5O_fill_t *fill,
const hssize_t offset_f[], const hsize_t size[],
const void *buf)
@@ -1776,7 +1810,7 @@ H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout,
if (f->shared->access_parms->driver==H5F_LOW_MPIO){
H5F_istore_ud1_t udata;
H5O_layout_t l; /* temporary layout */
- H5D_xfer_t tmp_xfer = *xfer;
+ H5F_xfer_t tmp_xfer = *xfer;
if (H5F_istore_get_addr(f, layout, chunk_offset, &udata)<0){
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to locate raw data chunk");
@@ -1895,6 +1929,40 @@ H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
/*-------------------------------------------------------------------------
+ * Function: H5F_istore_allocated
+ *
+ * Purpose: Return the number of bytes allocated in the file for storage
+ * of raw data under the specified B-tree (ADDR is the address
+ * of the B-tree).
+ *
+ * Return: Success: Number of bytes stored in all chunks.
+ *
+ * Failure: 0
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+H5F_istore_allocated(H5F_t *f, int ndims, haddr_t *addr)
+{
+ H5F_istore_ud1_t udata;
+
+ FUNC_ENTER(H5F_istore_nchunks, 0);
+ udata.mesg.ndims = ndims;
+ udata.total_storage = 0;
+ if (H5B_iterate(f, H5B_ISTORE, addr, &udata)<0) {
+ HRETURN_ERROR(H5E_IO, H5E_INTERNAL, 0,
+ "unable to iterate over chunk B-tree");
+ }
+ FUNC_LEAVE(udata.total_storage);
+}
+
+
+/*-------------------------------------------------------------------------
* Function: H5F_istore_stats
*
* Purpose: Print raw data cache statistics to the debug stream. If
diff --git a/src/H5Fmpio.c b/src/H5Fmpio.c
index aba0200..91be471 100644
--- a/src/H5Fmpio.c
+++ b/src/H5Fmpio.c
@@ -106,17 +106,16 @@ static H5F_low_t *H5F_mpio_open(const char *name,
H5F_search_t *key/*out*/);
static herr_t H5F_mpio_close(H5F_low_t *lf, const H5F_access_t *access_parms);
static herr_t H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms,
- const H5D_transfer_t xfer_mode,
- const haddr_t *addr, size_t size,
- uint8_t *buf/*out*/);
+ const H5F_xfer_t *xfer_parms, const haddr_t *addr,
+ size_t size, uint8_t *buf/*out*/);
htri_t H5F_mpio_tas_allsame(H5F_low_t *lf, hbool_t newval );
static herr_t H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms,
- const H5D_transfer_t xfer_mode,
- const haddr_t *addr, size_t size,
- const uint8_t *buf);
+ const H5F_xfer_t *xfer_parms, const haddr_t *addr,
+ size_t size, const uint8_t *buf);
static herr_t H5F_mpio_flush(H5F_low_t *lf, const H5F_access_t *access_parms);
-static herr_t H5F_MPIOff_to_haddr(MPI_Offset mpi_off, haddr_t *addr);
-static herr_t H5F_haddr_to_MPIOff(haddr_t addr, MPI_Offset *mpi_off);
+static herr_t H5F_MPIOff_to_haddr(MPI_Offset mpi_off, haddr_t *addr/*out*/);
+static herr_t H5F_haddr_to_MPIOff(const haddr_t *addr,
+ MPI_Offset *mpi_off/*out*/);
const H5F_low_class_t H5F_LOW_MPIO_g[1] = {{
H5F_mpio_access, /*access method */
@@ -497,11 +496,14 @@ H5F_mpio_close(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms)
* The guts of H5F_mpio_read and H5F_mpio_write
* should be replaced by a single dual-purpose routine.
*
+ * Robb Matzke, 19990421
+ * Changed xfer_mode to xfer_parms for all H5F_*_read() callbacks.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms,
- const H5D_transfer_t xfer_mode,
+ const H5F_xfer_t *xfer_parms,
const haddr_t *addr, size_t size, uint8_t *buf/*out*/)
{
MPI_Offset mpi_off, mpi_disp;
@@ -518,7 +520,7 @@ H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms,
#endif
/* some numeric conversions */
- if (SUCCEED != H5F_haddr_to_MPIOff( *addr, &mpi_off )) {
+ if (SUCCEED != H5F_haddr_to_MPIOff(addr, &mpi_off)) {
HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
"couldn't convert addr to MPIOffset" );
}
@@ -545,8 +547,9 @@ H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms,
buf_type = access_parms->u.mpio.btype;
file_type = access_parms->u.mpio.ftype;
if (SUCCEED !=
- H5F_haddr_to_MPIOff( access_parms->u.mpio.disp, &mpi_disp)) {
- HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert addr to MPIOffset" );
+ H5F_haddr_to_MPIOff(&(access_parms->u.mpio.disp), &mpi_disp)) {
+ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
+ "couldn't convert addr to MPIOffset" );
}
} else {
/* Prepare for a simple xfer of a contiguous block of bytes.
@@ -576,7 +579,7 @@ H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms,
access_parms->u.mpio.use_types = 0;
/* Read the data. */
- switch (xfer_mode){
+ switch (xfer_parms->xfer_mode){
case H5D_XFER_INDEPENDENT:
case H5D_XFER_DFLT:
mpierr = MPI_File_read_at ( lf->u.mpio.f, mpi_off, (void*) buf,
@@ -744,11 +747,14 @@ H5F_mpio_tas_allsame(H5F_low_t *lf, hbool_t newval )
* rky, 980828
* Added allsame parameter to make all but proc 0 skip the actual write.
*
+ * Robb Matzke, 19990421
+ * Changed xfer_mode to xfer_parms for all H5F_*_write() callbacks.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms,
- const H5D_transfer_t xfer_mode,
+ const H5F_xfer_t *xfer_parms,
const haddr_t *addr, size_t size, const uint8_t *buf)
{
MPI_Offset mpi_off, mpi_disp;
@@ -766,18 +772,19 @@ H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms,
#endif
/* some numeric conversions */
- if (SUCCEED != H5F_haddr_to_MPIOff( *addr, &mpi_off )) {
+ if (SUCCEED != H5F_haddr_to_MPIOff(addr, &mpi_off)) {
HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
- "couldn't convert addr to MPIOffset" );
+ "couldn't convert addr to MPIOffset" );
}
- if (SUCCEED!=H5F_haddr_to_MPIOff( access_parms->u.mpio.disp, &mpi_disp)) {
+ if (SUCCEED!=H5F_haddr_to_MPIOff(&(access_parms->u.mpio.disp),
+ &mpi_disp)) {
HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
- "couldn't convert addr to MPIOffset" );
+ "couldn't convert addr to MPIOffset" );
}
size_i = (int)size;
if ((size_t)size_i != size) { /* check type conversion */
HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
- "couldn't convert size to int" );
+ "couldn't convert size to int" );
}
#ifdef H5Fmpio_DEBUG
@@ -813,8 +820,9 @@ H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms,
buf_type = access_parms->u.mpio.btype;
file_type = access_parms->u.mpio.ftype;
if (SUCCEED !=
- H5F_haddr_to_MPIOff( access_parms->u.mpio.disp, &mpi_disp)) {
- HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert addr to MPIOffset" );
+ H5F_haddr_to_MPIOff(&(access_parms->u.mpio.disp), &mpi_disp)) {
+ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL,
+ "couldn't convert addr to MPIOffset" );
}
} else {
/* Prepare for a simple xfer of a contiguous block of bytes.
@@ -844,7 +852,7 @@ H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms,
access_parms->u.mpio.use_types = 0;
/* Write the data. */
- switch (xfer_mode){
+ switch (xfer_parms->xfer_mode){
case H5D_XFER_INDEPENDENT:
case H5D_XFER_DFLT:
mpierr = MPI_File_write_at ( lf->u.mpio.f, mpi_off, (void*) buf,
@@ -959,20 +967,25 @@ H5F_mpio_flush(H5F_low_t *lf, const H5F_access_t UNUSED *access_parms)
* January 30, 1998
*
* Modifications:
+ * Robb Matzke, 1999-04-23
+ * An error is reported for address overflows. The ADDR output
+ * argument is optional.
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5F_MPIOff_to_haddr( MPI_Offset mpi_off, haddr_t *addr )
+H5F_MPIOff_to_haddr(MPI_Offset mpi_off, haddr_t *addr/*out*/)
{
- herr_t ret_val = FAIL;
-
- addr->offset = (uint64_t) mpi_off;
- if (addr->offset == mpi_off)
- ret_val = SUCCEED;
+ FUNC_ENTER(H5F_MPIOff_to_haddr, FAIL);
- return (ret_val);
+ if (addr) addr->offset = (uint64_t) mpi_off;
+ if (mpi_off != (MPI_Offset)(uint64_t)mpi_off) {
+ HRETURN_ERROR(H5E_IO, H5E_OVERFLOW, FAIL, "bad MPI address");
+ }
+
+ FUNC_LEAVE(SUCCEED);
}
+
/*-------------------------------------------------------------------------
* Function: H5F_haddr_to_MPIOff
@@ -988,20 +1001,26 @@ H5F_MPIOff_to_haddr( MPI_Offset mpi_off, haddr_t *addr )
* January 30, 1998
*
* Modifications:
+ * Robb Matzke, 1999-04-23
+ * An error is reported for address overflows. The ADDR output
+ * argument is optional.
*
*-------------------------------------------------------------------------
*/
static herr_t
-H5F_haddr_to_MPIOff( haddr_t addr, MPI_Offset *mpi_off )
+H5F_haddr_to_MPIOff(const haddr_t *addr, MPI_Offset *mpi_off/*out*/)
{
- herr_t ret_val = FAIL;
-
- *mpi_off = (MPI_Offset) addr.offset;
- if (*mpi_off == addr.offset)
- ret_val = SUCCEED;
+ FUNC_ENTER(H5F_haddr_to_MPIOff, FAIL);
- return (ret_val);
+ if (mpi_off) *mpi_off = (MPI_Offset)addr->offset;
+ if (addr->offset != (uint64_t)(MPI_Offset)(addr->offset)) {
+ HRETURN_ERROR(H5E_IO, H5E_OVERFLOW, FAIL,
+ "hdf5 address overflows MPI address");
+ }
+
+ FUNC_LEAVE(SUCCEED);
}
+
/*-------------------------------------------------------------------------
* Function: H5PC_Wait_for_left_neighbor
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 55048b3..0d46f07 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -512,6 +512,18 @@ typedef struct H5F_t {
H5F_mtab_t mtab; /* File mount table */
} H5F_t;
+/* Dataset transfer property list */
+typedef struct H5F_xfer_t {
+ size_t buf_size; /*max temp buffer size */
+ void *tconv_buf; /*type conversion buffer or null */
+ void *bkg_buf; /*background buffer or null */
+ H5T_bkg_t need_bkg; /*type of background buffer needed */
+ double split_ratios[3];/*B-tree node splitting ratios */
+ uintn cache_hyper; /*cache hyperslab blocks during I/O? */
+ uintn block_limit; /*largest hyperslab block to cache */
+ H5D_transfer_t xfer_mode; /*independent or collective transfer */
+} H5F_xfer_t;
+
#ifdef NOT_YET
#define H5F_ENCODE_OFFSET(f,p,o) (H5F_SIZEOF_ADDR(f)==4 ? UINT32ENCODE(p,o) \
: H5F_SIZEOF_ADDR(f)==8 ? UINT64ENCODE(p,o) \
@@ -556,13 +568,14 @@ typedef struct H5F_t {
struct H5O_layout_t;
struct H5O_efl_t;
struct H5O_pline_t;
-struct H5D_xfer_t;
+struct H5F_xfer_t;
struct H5O_fill_t;
struct H5G_entry_t;
/* library variables */
__DLLVAR__ const H5F_create_t H5F_create_dflt;
__DLLVAR__ H5F_access_t H5F_access_dflt;
+__DLLVAR__ const H5F_xfer_t H5F_xfer_dflt;
__DLLVAR__ const H5F_mprop_t H5F_mount_dflt;
#ifdef HAVE_PARALLEL
@@ -588,7 +601,7 @@ __DLL__ herr_t H5F_mountpoint(struct H5G_entry_t *find/*in,out*/);
/* 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, const struct H5D_xfer_t *xfer,
+__DLL__ herr_t H5F_arr_read (H5F_t *f, const struct H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
@@ -597,7 +610,7 @@ __DLL__ herr_t H5F_arr_read (H5F_t *f, const struct H5D_xfer_t *xfer,
const hsize_t mem_size[],
const hssize_t mem_offset[],
const hssize_t file_offset[], void *_buf/*out*/);
-__DLL__ herr_t H5F_arr_write (H5F_t *f, const struct H5D_xfer_t *xfer,
+__DLL__ herr_t H5F_arr_write (H5F_t *f, const struct H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
@@ -611,16 +624,17 @@ __DLL__ herr_t H5F_arr_write (H5F_t *f, const struct H5D_xfer_t *xfer,
__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__ hsize_t H5F_istore_allocated(H5F_t *f, int ndims, haddr_t *addr);
__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, const struct H5D_xfer_t *xfer,
+__DLL__ herr_t H5F_istore_read(H5F_t *f, const struct H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const hssize_t offset[], const hsize_t size[],
void *buf/*out*/);
-__DLL__ herr_t H5F_istore_write(H5F_t *f, const struct H5D_xfer_t *xfer,
+__DLL__ herr_t H5F_istore_write(H5F_t *f, const struct H5F_xfer_t *xfer,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index 8646f02..177a17b 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -78,6 +78,13 @@ typedef enum H5F_scope_t {
/* Unlimited file size for H5Pset_external() */
#define H5F_UNLIMITED ((hsize_t)(-1L))
+/* How is the `bkg' buffer used by the conversion function? */
+typedef enum H5T_bkg_t {
+ H5T_BKG_NO = 0, /*background buffer is not needed, send NULL */
+ H5T_BKG_TEMP = 1, /*bkg buffer used as temp storage only */
+ H5T_BKG_YES = 2 /*init bkg buf with data before conversion */
+} H5T_bkg_t;
+
#ifdef __cplusplus
extern "C" {
#endif
diff --git a/src/H5Gnode.c b/src/H5Gnode.c
index 7f95906..09cc40c 100644
--- a/src/H5Gnode.c
+++ b/src/H5Gnode.c
@@ -61,7 +61,8 @@ static H5B_ins_t H5G_node_insert(H5F_t *f, const haddr_t *addr,
static H5B_ins_t H5G_node_remove(H5F_t *f, const haddr_t *addr, void *lt_key,
hbool_t *lt_key_changed, void *udata,
void *rt_key, hbool_t *rt_key_changed);
-static herr_t H5G_node_iterate(H5F_t *f, const haddr_t *addr, void *_udata);
+static herr_t H5G_node_iterate(H5F_t *f, void *_lt_key, const haddr_t *addr,
+ void *_rt_key, void *_udata);
static size_t H5G_node_sizeof_rkey(H5F_t *f, const void *_udata);
/* H5G inherits cache-like properties from H5AC */
@@ -1034,7 +1035,8 @@ H5G_node_remove(H5F_t *f, const haddr_t *addr, void *_lt_key/*in,out*/,
*-------------------------------------------------------------------------
*/
static herr_t
-H5G_node_iterate (H5F_t *f, const haddr_t *addr, void *_udata)
+H5G_node_iterate (H5F_t *f, void UNUSED *_lt_key, const haddr_t *addr,
+ void UNUSED *_rt_key, void *_udata)
{
H5G_bt_ud2_t *bt_udata = (H5G_bt_ud2_t *)_udata;
H5G_node_t *sn = NULL;
diff --git a/src/H5P.c b/src/H5P.c
index 99bc563..2bbc54c 100644
--- a/src/H5P.c
+++ b/src/H5P.c
@@ -182,11 +182,11 @@ H5Pcreate(H5P_class_t type)
break;
case H5P_DATASET_XFER:
- if (NULL==(plist = H5MM_malloc(sizeof(H5D_xfer_t)))) {
+ if (NULL==(plist = H5MM_malloc(sizeof(H5F_xfer_t)))) {
HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed");
}
- HDmemcpy(plist, &H5D_xfer_dflt, sizeof(H5D_xfer_t));
+ HDmemcpy(plist, &H5F_xfer_dflt, sizeof(H5F_xfer_t));
break;
case H5P_MOUNT:
@@ -1979,7 +1979,7 @@ H5Pget_cache(hid_t plist_id, int *mdc_nelmts,
herr_t
H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_buffer, FAIL);
H5TRACE4("e","izxx",plist_id,size,tconv,bkg);
@@ -2023,7 +2023,7 @@ H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg)
size_t
H5Pget_buffer(hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_buffer, 0);
H5TRACE3("z","ixx",plist_id,tconv,bkg);
@@ -2069,7 +2069,7 @@ H5Pget_buffer(hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/)
herr_t
H5Pset_hyper_cache(hid_t plist_id, unsigned cache, unsigned limit)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_hyper_cache, FAIL);
H5TRACE3("e","iIuIu",plist_id,cache,limit);
@@ -2107,7 +2107,7 @@ herr_t
H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/,
unsigned *limit/*out*/)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_hyper_cache, 0);
H5TRACE3("e","ixx",plist_id,cache,limit);
@@ -2148,7 +2148,7 @@ H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/,
herr_t
H5Pset_preserve(hid_t plist_id, hbool_t status)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_preserve, FAIL);
H5TRACE2("e","ib",plist_id,status);
@@ -2186,7 +2186,7 @@ H5Pset_preserve(hid_t plist_id, hbool_t status)
int
H5Pget_preserve(hid_t plist_id)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pset_preserve, FAIL);
H5TRACE1("Is","i",plist_id);
@@ -2497,7 +2497,7 @@ herr_t
H5Pget_btree_ratios(hid_t plist_id, double *left/*out*/, double *middle/*out*/,
double *right/*out*/)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER(H5Pget_btree_ratios, FAIL);
H5TRACE4("e","ixxx",plist_id,left,middle,right);
@@ -2544,7 +2544,7 @@ herr_t
H5Pset_btree_ratios(hid_t plist_id, double left, double middle,
double right)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER(H5Pget_btree_ratios, FAIL);
H5TRACE4("e","iddd",plist_id,left,middle,right);
@@ -2903,7 +2903,7 @@ H5Pget_mpi(hid_t plist_id, MPI_Comm *comm, MPI_Info *info)
herr_t
H5Pset_xfer(hid_t plist_id, H5D_transfer_t data_xfer_mode)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER(H5Pset_xfer, FAIL);
H5TRACE2("e","iDt",plist_id,data_xfer_mode);
@@ -2951,7 +2951,7 @@ H5Pset_xfer(hid_t plist_id, H5D_transfer_t data_xfer_mode)
herr_t
H5Pget_xfer(hid_t plist_id, H5D_transfer_t *data_xfer_mode)
{
- H5D_xfer_t *plist = NULL;
+ H5F_xfer_t *plist = NULL;
FUNC_ENTER (H5Pget_xfer, FAIL);
H5TRACE2("e","i*Dt",plist_id,data_xfer_mode);
@@ -3151,7 +3151,7 @@ H5P_copy (H5P_class_t type, const void *src)
break;
case H5P_DATASET_XFER:
- size = sizeof(H5D_xfer_t);
+ size = sizeof(H5F_xfer_t);
break;
case H5P_MOUNT:
diff --git a/src/H5RA.c b/src/H5RA.c
index bf0f5ef..389e8dc 100644
--- a/src/H5RA.c
+++ b/src/H5RA.c
@@ -738,7 +738,7 @@ H5RA_write(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
"memory allocation failed for meta data");
}
if (H5D_read(ra->meta, H5RA_meta_type_g, mm_space, mf_space,
- &H5D_xfer_dflt, meta)<0) {
+ &H5F_xfer_dflt, meta)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
"unable to read meta data");
}
@@ -779,7 +779,7 @@ H5RA_write(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
"unable to set meta data selection");
}
- if (H5D_write(ra->raw, type, rm_space, rf_space, &H5D_xfer_dflt,
+ if (H5D_write(ra->raw, type, rm_space, rf_space, &H5F_xfer_dflt,
raw_buf)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
"unable to write raw data");
@@ -809,7 +809,7 @@ H5RA_write(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
"unable to set meta data selection");
}
if (H5D_write(ra->meta, H5RA_meta_type_g, mm_space, mf_space,
- &H5D_xfer_dflt, meta)<0) {
+ &H5F_xfer_dflt, meta)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
"unable to write meta data");
}
@@ -926,7 +926,7 @@ H5RA_fix_overflow(H5RA_t *ra, H5T_t *type, H5RA_meta_t *meta, hsize_t nelmts,
HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
"unable to set overflow selection");
}
- if (H5D_write(ra->over, type, om_space, of_space, &H5D_xfer_dflt,
+ if (H5D_write(ra->over, type, om_space, of_space, &H5F_xfer_dflt,
buf)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_WRITEERROR, FAIL,
"unable to write to overflow dataset");
@@ -1103,7 +1103,7 @@ H5RA_read(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for raw dataset");
}
- if (H5D_read(ra->raw, type, rm_space, rf_space, &H5D_xfer_dflt,
+ if (H5D_read(ra->raw, type, rm_space, rf_space, &H5F_xfer_dflt,
raw_buf)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
"unable to read raw dataset");
@@ -1134,7 +1134,7 @@ H5RA_read(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
"unable to set meta data selection");
}
if (H5D_read(ra->meta, H5RA_meta_type_g, mm_space, mf_space,
- &H5D_xfer_dflt, meta)<0) {
+ &H5F_xfer_dflt, meta)<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_READERROR, FAIL,
"unable to read meta data");
}
@@ -1182,7 +1182,7 @@ H5RA_read(H5RA_t *ra, hssize_t start_row, hsize_t nrows, H5T_t *type,
HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
"unable to set overflow selection");
}
- if (H5D_read(ra->over, type, om_space, of_space, &H5D_xfer_dflt,
+ if (H5D_read(ra->over, type, om_space, of_space, &H5F_xfer_dflt,
buf_out[i])<0) {
HGOTO_ERROR(H5E_RAGGED, H5E_CANTINIT, FAIL,
"unable to read overflow dataset");
diff --git a/src/H5S.c b/src/H5S.c
index ff0a31c..d9e5c49 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -1462,7 +1462,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space)
* We can't do conversion if the source and destination select a
* different number of data points.
*/
- if (H5S_get_select_npoints (mem_space) != H5S_get_select_npoints (file_space)) {
+ if (H5S_get_select_npoints(mem_space) !=
+ H5S_get_select_npoints (file_space)) {
HRETURN_ERROR (H5E_DATASPACE, H5E_BADRANGE, NULL,
"memory and file data spaces are different sizes");
}
@@ -1489,7 +1490,27 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space)
}
/*
- * Extend the table.
+ * Create a new path.
+ */
+ if (NULL==(path = H5MM_calloc(sizeof(*path)))) {
+ HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
+ "memory allocation failed for data space conversion "
+ "path");
+ }
+ path->f = H5S_fconv_g[file_space->select.type];
+ path->m = H5S_mconv_g[mem_space->select.type];
+
+ /*
+ * Initialize direct read/write functions
+ */
+ if (H5S_SEL_ALL==file_space->select.type &&
+ H5S_SEL_ALL==mem_space->select.type) {
+ path->read = H5S_all_read;
+ path->write = H5S_all_write;
+ }
+
+ /*
+ * Add the new path to the table.
*/
if (H5S_nconv_g>=H5S_aconv_g) {
size_t n = MAX(10, 2*H5S_aconv_g);
@@ -1502,17 +1523,6 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space)
H5S_aconv_g = n;
H5S_conv_g = p;
}
-
- /*
- * Create a new path and add it to the table.
- */
- if (NULL==(path = H5MM_calloc(sizeof(*path)))) {
- HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
- "memory allocation failed for data space conversion "
- "path");
- }
- path->f = H5S_fconv_g[file_space->select.type];
- path->m = H5S_mconv_g[mem_space->select.type];
H5S_conv_g[H5S_nconv_g++] = path;
FUNC_LEAVE(path);
diff --git a/src/H5Sall.c b/src/H5Sall.c
index 5e91b6f..6ebd241 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -28,14 +28,14 @@ static size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, void *buf/*out*/);
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/);
static herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, const void *buf);
+ const H5F_xfer_t *xfer_parms, const void *buf);
static size_t H5S_all_mgath (const void *_buf, size_t elmt_size,
const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
size_t nelmts, void *_tconv_buf/*out*/);
@@ -172,7 +172,7 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, void *_buf/*out*/)
+ const H5F_xfer_t *xfer_parms, void *_buf/*out*/)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/
hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */
@@ -260,7 +260,7 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline, const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
- size_t nelmts, const H5D_xfer_t *xfer_parms, const void *_buf)
+ size_t nelmts, const H5F_xfer_t *xfer_parms, const void *_buf)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */
hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */
@@ -499,7 +499,144 @@ H5S_all_mscat (const void *_tconv_buf, size_t elmt_size,
mem_iter->all.offset+=nelmts;
FUNC_LEAVE (SUCCEED);
-} /* H5S_all_mscat() */
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5S_all_read
+ *
+ * Purpose: Reads directly from file into application memory if possible.
+ *
+ * Return: Success: Non-negative. If data was read directly then
+ * MUST_CONVERT is set to zero, otherwise
+ * MUST_CONVERT is set to non-zero.
+ *
+ * Failure: Negative. Return value of MUST_CONVERT is
+ * undefined.
+ *
+ * Programmer: Robb Matzke
+ * Thursday, April 22, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_all_read(H5F_t *f, const H5O_layout_t *layout, const H5O_pline_t *pline,
+ const H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space,
+ const H5S_t *mem_space, const H5F_xfer_t *xfer_parms,
+ void *buf/*out*/, hbool_t *must_convert/*out*/)
+{
+ hsize_t size[H5S_MAX_RANK];
+ hssize_t offset[H5S_MAX_RANK];
+ int i;
+
+ FUNC_ENTER(H5S_all_read, FAIL);
+ *must_convert = TRUE;
+
+ /* Check whether we can handle this */
+ if (H5S_SIMPLE!=mem_space->extent.type) goto fall_through;
+ if (H5S_SIMPLE!=file_space->extent.type) goto fall_through;
+ if (mem_space->extent.u.simple.rank!=
+ file_space->extent.u.simple.rank) goto fall_through;
+
+ /* Get information about memory and file */
+ for (i=0; i<mem_space->extent.u.simple.rank; i++) {
+ if (mem_space->extent.u.simple.max &&
+ mem_space->extent.u.simple.size[i]!=
+ mem_space->extent.u.simple.max[i]) goto fall_through;
+ if (file_space->extent.u.simple.max &&
+ file_space->extent.u.simple.size[i]!=
+ file_space->extent.u.simple.max[i]) goto fall_through;
+ if (mem_space->extent.u.simple.size[i]!=
+ file_space->extent.u.simple.size[i]) goto fall_through;
+ size[i] = mem_space->extent.u.simple.size[i];
+ offset[i] = 0;
+ }
+ size[i] = elmt_size;
+ offset[i] = 0;
+
+ /* Read data from the file */
+ if (H5F_arr_read(f, xfer_parms, layout, pline, NULL, efl, size,
+ size, offset, offset, buf/*out*/)<0) {
+ HRETURN_ERROR(H5E_IO, H5E_INTERNAL, FAIL,
+ "unable to write data to the file");
+ }
+ *must_convert = FALSE;
+
+ fall_through:
+ FUNC_LEAVE(SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5S_all_write
+ *
+ * Purpose: Writes data directly to the file if possible.
+ *
+ * Return: Success: Non-negative. If data was written directly
+ * then MUST_CONVERT is set to zero, otherwise
+ * MUST_CONVERT is set to non-zero.
+ *
+ * Failure: Negative. Return value of MUST_CONVERT is
+ * undefined.
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
+ const H5O_pline_t *pline, const H5O_efl_t *efl,
+ size_t elmt_size, const H5S_t *file_space,
+ const H5S_t *mem_space, const H5F_xfer_t *xfer_parms,
+ const void *buf, hbool_t *must_convert/*out*/)
+{
+ hsize_t size[H5S_MAX_RANK];
+ hssize_t offset[H5S_MAX_RANK];
+ int i;
+
+ FUNC_ENTER(H5S_all_write, FAIL);
+ *must_convert = TRUE;
+
+ /* Check whether we can handle this */
+ if (H5S_SIMPLE!=mem_space->extent.type) goto fall_through;
+ if (H5S_SIMPLE!=file_space->extent.type) goto fall_through;
+ if (mem_space->extent.u.simple.rank!=
+ file_space->extent.u.simple.rank) goto fall_through;
+
+ /* Get information about memory and file */
+ for (i=0; i<mem_space->extent.u.simple.rank; i++) {
+ if (mem_space->extent.u.simple.max &&
+ mem_space->extent.u.simple.size[i]!=
+ mem_space->extent.u.simple.max[i]) goto fall_through;
+ if (file_space->extent.u.simple.max &&
+ file_space->extent.u.simple.size[i]!=
+ file_space->extent.u.simple.max[i]) goto fall_through;
+ if (mem_space->extent.u.simple.size[i]!=
+ file_space->extent.u.simple.size[i]) goto fall_through;
+ size[i] = mem_space->extent.u.simple.size[i];
+ offset[i] = 0;
+ }
+ size[i] = elmt_size;
+ offset[i] = 0;
+
+ /* Write data to the file */
+ if (H5F_arr_write(f, xfer_parms, layout, pline, NULL, efl, size,
+ size, offset, offset, buf)<0) {
+ HRETURN_ERROR(H5E_IO, H5E_INTERNAL, FAIL,
+ "unable to write data to the file");
+ }
+ *must_convert = FALSE;
+
+
+ fall_through:
+ FUNC_LEAVE(SUCCEED);
+}
+
/*--------------------------------------------------------------------------
NAME
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 082d033..2fba497 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -32,7 +32,7 @@ typedef struct {
const H5S_t *space;
H5S_sel_iter_t *iter;
size_t nelmts;
- const H5D_xfer_t *xfer_parms;
+ const H5F_xfer_t *xfer_parms;
const void *src;
void *dst;
H5S_hyper_bound_t **lo_bounds;
@@ -60,14 +60,14 @@ static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, void *buf/*out*/);
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/);
static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, const void *buf);
+ const H5F_xfer_t *xfer_parms, const void *buf);
static size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size,
const H5S_t *mem_space,
H5S_sel_iter_t *mem_iter, size_t nelmts,
@@ -809,7 +809,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
- size_t nelmts, const H5D_xfer_t *xfer_parms,
+ size_t nelmts, const H5F_xfer_t *xfer_parms,
void *_buf/*out*/)
{
H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */
@@ -1070,7 +1070,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
- size_t nelmts, const H5D_xfer_t *xfer_parms,
+ size_t nelmts, const H5F_xfer_t *xfer_parms,
const void *_buf)
{
H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index a4e090b..19cbbbf 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -50,13 +50,12 @@ H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size,
hsize_t *count,
hbool_t *is_derived_type );
static herr_t
-H5S_mpio_spaces_xfer (H5F_t *f, const struct H5O_layout_t *layout,
+H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t UNUSED *pline,
const struct H5O_efl_t UNUSED *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, void *buf /*out*/,
- hbool_t *must_convert /*out*/,
- const hbool_t do_write );
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/,
+ hbool_t *must_convert/*out*/, const hbool_t do_write);
/*-------------------------------------------------------------------------
* Function: H5S_mpio_all_type
@@ -448,7 +447,7 @@ H5S_mpio_spaces_xfer (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t UNUSED *pline,
const struct H5O_efl_t UNUSED *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, void *buf /*out*/,
+ const H5F_xfer_t *xfer_parms, void *buf /*out*/,
hbool_t *must_convert /*out*/,
const hbool_t do_write )
{
@@ -526,13 +525,13 @@ H5S_mpio_spaces_xfer (H5F_t *f, const struct H5O_layout_t *layout,
HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"transfer size overflows size_t");
if (do_write) {
err = H5F_low_write( f->shared->lf, f->shared->access_parms,
- xfer_mode, &addr, mpi_count, buf );
+ xfer_parms->xfer_mode, &addr, mpi_count, buf );
if (err) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed");
}
} else {
err = H5F_low_read ( f->shared->lf, f->shared->access_parms,
- xfer_mode, &addr, mpi_count, buf );
+ xfer_parms->xfer_mode, &addr, mpi_count, buf );
if (err) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed");
}
@@ -577,16 +576,16 @@ H5S_mpio_spaces_read (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, void *buf /*out*/,
- hbool_t *must_convert /*out*/ )
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/,
+ hbool_t *must_convert/*out*/)
{
herr_t ret_value = FAIL;
FUNC_ENTER (H5S_mpio_spaces_read, FAIL);
- ret_value = H5S_mpio_spaces_xfer( f, layout, pline, efl, elmt_size,
- file_space, mem_space, xfer_mode, (void*)buf,
- must_convert /*out*/, 0 /*read*/ );
+ ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
+ file_space, mem_space, xfer_parms,
+ buf, must_convert/*out*/, 0/*read*/);
FUNC_LEAVE (ret_value);
} /* H5S_mpio_spaces_read() */
@@ -612,16 +611,17 @@ H5S_mpio_spaces_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, const void *buf,
- hbool_t *must_convert /*out*/ )
+ const H5F_xfer_t *xfer_parms, const void *buf,
+ hbool_t *must_convert/*out*/)
{
herr_t ret_value = FAIL;
FUNC_ENTER (H5S_mpio_spaces_write, FAIL);
- ret_value = H5S_mpio_spaces_xfer( f, layout, pline, efl, elmt_size,
- file_space, mem_space, xfer_mode, (void*)buf,
- must_convert /*out*/, 1 /*write*/ );
+ ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
+ file_space, mem_space, xfer_parms,
+ (void*)buf, must_convert/*out*/,
+ 1/*write*/);
FUNC_LEAVE (ret_value);
} /* H5S_mpio_spaces_write() */
diff --git a/src/H5Spoint.c b/src/H5Spoint.c
index a4f4931..a58461b 100644
--- a/src/H5Spoint.c
+++ b/src/H5Spoint.c
@@ -29,7 +29,7 @@ static size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms,
+ const H5F_xfer_t *xfer_parms,
void *buf/*out*/);
static herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
@@ -37,7 +37,7 @@ static herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms,
+ const H5F_xfer_t *xfer_parms,
const void *buf);
static size_t H5S_point_mgath (const void *_buf, size_t elmt_size,
const H5S_t *mem_space,
@@ -270,7 +270,7 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, void *_buf/*out*/)
+ const H5F_xfer_t *xfer_parms, void *_buf/*out*/)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/
hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */
@@ -377,7 +377,7 @@ H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_fill_t *fill, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
H5S_sel_iter_t *file_iter, size_t nelmts,
- const H5D_xfer_t *xfer_parms, const void *_buf)
+ const H5F_xfer_t *xfer_parms, const void *_buf)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */
hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 2710d9d..ff0a021 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -194,7 +194,7 @@ typedef struct H5S_fconv_t {
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
- size_t nelmts, const struct H5D_xfer_t *xfer_parms,
+ size_t nelmts, const struct H5F_xfer_t *xfer_parms,
void *tconv_buf/*out*/);
/* Scatter elements from type conversion buffer to disk */
@@ -203,7 +203,7 @@ typedef struct H5S_fconv_t {
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
- size_t nelmts, const struct H5D_xfer_t *xfer_parms,
+ size_t nelmts, const struct H5F_xfer_t *xfer_parms,
const void *tconv_buf);
} H5S_fconv_t;
@@ -253,8 +253,8 @@ typedef struct H5S_conv_t {
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, void *buf/*out*/,
- hbool_t *must_convert/*out*/ );
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/,
+ hbool_t *must_convert/*out*/);
/* Write directly from app buffer to file */
@@ -262,8 +262,8 @@ typedef struct H5S_conv_t {
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode, const void *buf,
- hbool_t *must_convert/*out*/ );
+ const H5F_xfer_t *xfer_parms, const void *buf,
+ hbool_t *must_convert/*out*/);
#ifdef H5S_DEBUG
struct {
@@ -352,6 +352,18 @@ __DLL__ hsize_t H5S_all_npoints(const H5S_t *space);
__DLL__ herr_t H5S_all_select_serialize(const H5S_t *space, uint8_t *buf);
__DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
+__DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_pline_t *pline,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const H5F_xfer_t *xfer_parms, void *buf/*out*/,
+ hbool_t *must_convert/*out*/);
+__DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_pline_t *pline,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const H5F_xfer_t *xfer_parms, const void *buf,
+ hbool_t *must_convert/*out*/);
/* Hyperslab selection functions */
__DLL__ herr_t H5S_hyper_add(H5S_t *space, const hssize_t *start,
@@ -386,7 +398,7 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode,
+ const H5F_xfer_t *xfer_parms,
void *buf/*out*/,
hbool_t *must_convert /*out*/ );
@@ -397,7 +409,7 @@ __DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space,
- const H5D_transfer_t xfer_mode,
+ const H5F_xfer_t *xfer_parms,
const void *buf,
hbool_t *must_convert /*out*/ );
#ifndef _H5S_IN_H5S_C
diff --git a/src/H5Tpublic.h b/src/H5Tpublic.h
index 495c63a..e3b6248 100644
--- a/src/H5Tpublic.h
+++ b/src/H5Tpublic.h
@@ -126,13 +126,6 @@ typedef enum H5T_pad_t {
H5T_NPAD = 3 /*THIS MUST BE LAST */
} H5T_pad_t;
-/* How is the `bkg' buffer used by the conversion function? */
-typedef enum H5T_bkg_t {
- H5T_BKG_NO = 0, /*background buffer is not needed, send NULL */
- H5T_BKG_TEMP = 1, /*bkg buffer used as temp storage only */
- H5T_BKG_YES = 2 /*init bkg buf with data before conversion */
-} H5T_bkg_t;
-
/* Commands sent to conversion functions */
typedef enum H5T_cmd_t {
H5T_CONV_INIT = 0, /*query and/or initialize private data */
diff --git a/test/istore.c b/test/istore.c
index c840a1f..adf23b6 100644
--- a/test/istore.c
+++ b/test/istore.c
@@ -297,7 +297,7 @@ test_extend(H5F_t *f, const char *prefix,
memset(buf, (signed)(128+ctr), (size_t)nelmts);
/* Write to disk */
- if (H5F_arr_write(f, &H5D_xfer_dflt, &layout, NULL, NULL, NULL, size,
+ if (H5F_arr_write(f, &H5F_xfer_dflt, &layout, NULL, NULL, NULL, size,
size, zero, offset, buf)<0) {
FAILED();
printf(" Write failed: ctr=%lu\n", (unsigned long)ctr);
@@ -306,7 +306,7 @@ test_extend(H5F_t *f, const char *prefix,
/* Read from disk */
memset(check, 0xff, (size_t)nelmts);
- if (H5F_arr_read(f, &H5D_xfer_dflt, &layout, NULL, NULL, NULL, size,
+ if (H5F_arr_read(f, &H5F_xfer_dflt, &layout, NULL, NULL, NULL, size,
size, zero, offset, check)<0) {
FAILED();
printf(" Read failed: ctr=%lu\n", (unsigned long)ctr);
@@ -337,7 +337,7 @@ test_extend(H5F_t *f, const char *prefix,
/* Now read the entire array back out and check it */
memset(buf, 0xff, nx * ny * nz);
- if (H5F_arr_read(f, &H5D_xfer_dflt, &layout, NULL, NULL, NULL, whole_size,
+ if (H5F_arr_read(f, &H5F_xfer_dflt, &layout, NULL, NULL, NULL, whole_size,
whole_size, zero, zero, buf)<0) {
FAILED();
puts(" Read failed for whole array.");
@@ -450,7 +450,7 @@ test_sparse(H5F_t *f, const char *prefix, size_t nblocks,
memset(buf, (signed)(128+ctr), nx * ny * nz);
/* write to disk */
- if (H5F_arr_write(f, &H5D_xfer_dflt, &layout, NULL, NULL, NULL, size,
+ if (H5F_arr_write(f, &H5F_xfer_dflt, &layout, NULL, NULL, NULL, size,
size, zero, offset, buf)<0) {
FAILED();
printf(" Write failed: ctr=%lu\n", (unsigned long)ctr);
diff --git a/tools/h5ls.c b/tools/h5ls.c
index 43b579e..1e08711 100644
--- a/tools/h5ls.c
+++ b/tools/h5ls.c
@@ -1187,7 +1187,7 @@ dataset_list2(hid_t dset, const char UNUSED *name)
char s[64]; /*temporary string buffer */
off_t f_offset; /*offset in external file */
hsize_t f_size; /*bytes used in external file */
- hsize_t total; /*total size or offset */
+ hsize_t total, used; /*total size or offset */
hsize_t chsize[64]; /*chunk size in elements */
int ndims; /*dimensionality */
int n, max_len; /*max extern file name length */
@@ -1210,6 +1210,18 @@ dataset_list2(hid_t dset, const char UNUSED *name)
printf("} %lu bytes\n", (unsigned long)total);
}
+ /* Print total raw storage size */
+ used = H5Sget_simple_extent_npoints(space) * H5Tget_size(type);
+ total = H5Dget_storage_size(dset);
+ printf(" %-10s ", "Storage:");
+ printf("%lu logical byte%s, %lu allocated byte%s",
+ (unsigned long)used, 1==used?"":"s",
+ (unsigned long)total, 1==total?"":"s");
+ if (total>0) {
+ printf(", %1.2f%% utilization", (used*100.0)/total);
+ }
+ putchar('\n');
+
/* Print information about external strorage */
if ((nf = H5Pget_external_count(dcpl))>0) {
for (i=0, max_len=0; i<nf; i++) {
generated by cgit v0.12 at 2024-11-02 04:47:34 (GMT)