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-rw-r--r--src/H5D.c77
-rw-r--r--src/H5Distore.c2
-rw-r--r--src/H5Fistore.c2
-rw-r--r--src/H5Oefl.c4
-rw-r--r--src/H5S.c3
-rw-r--r--src/H5Sprivate.h20
-rw-r--r--src/H5Ssimp.c215
-rw-r--r--src/H5Tpkg.h2
-rw-r--r--src/H5Tprivate.h7
-rw-r--r--src/H5V.c29
10 files changed, 338 insertions, 23 deletions
diff --git a/src/H5D.c b/src/H5D.c
index ead898f..b417ca7 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -31,6 +31,12 @@ static char RcsId[] = "@(#)$Revision$";
#define PABLO_MASK H5D_mask
/*
+ * Define this to be zero or one depending on whether the I/O pipeline should
+ * be optimized.
+ */
+#define H5D_OPTIMIZE_PIPE 1
+
+/*
* A dataset is the following struct.
*/
struct H5D_t {
@@ -807,7 +813,7 @@ H5D_create(H5F_t *f, const char *name, const H5T_t *type, const H5S_t *space,
}
/* Create (open for write access) an object header */
- if (H5O_create(f, 0, &(new_dset->ent)) < 0) {
+ if (H5O_create(f, 80, &(new_dset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to create dataset object header");
}
@@ -1090,6 +1096,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5S_number_t numbering; /*element numbering info*/
H5T_cdata_t *cdata = NULL; /*type conversion data */
herr_t ret_value = FAIL;
+ herr_t status;
FUNC_ENTER(H5D_read, FAIL);
@@ -1140,10 +1147,36 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
* Compute the size of the request and allocate scratch buffers.
*/
nelmts = H5S_get_npoints(mem_space);
+
+ /*
+ * If there is no type conversion then try reading directly into the
+ * application's buffer.
+ */
+ if (H5D_OPTIMIZE_PIPE &&
+ H5T_conv_noop==tconv_func &&
+ NULL!=sconv_func->read) {
+#ifndef NDEBUG
+ fprintf (stderr, "HDF5-DIAG: Trying I/O pipe optimization...\n");
+#endif
+ status = (sconv_func->read)(dataset->ent.file, &(dataset->layout),
+ &(dataset->create_parms->efl),
+ H5T_get_size (dataset->type), file_space,
+ mem_space, buf/*out*/);
+ if (status>=0) goto succeed;
+#ifndef NDEBUG
+ fprintf (stderr, "HDF5-DIAG: I/O pipe optimization failed\n");
+#endif
+ H5E_clear ();
+ }
+
+
+ /*
+ * This is the general case.
+ */
#ifndef LATER
/*
* Note: this prototype version allocates a buffer large enough to
- * satisfy the entire request; strip mining is not implemented.
+ * satisfy the entire request; strip mining is not implemented.
*/
{
size_t src_size = nelmts * H5T_get_size(dataset->type);
@@ -1152,7 +1185,6 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size);
}
#endif
-
/*
* Gather the data from disk into the data type conversion buffer. Also
* gather data from application to background buffer (this step is not
@@ -1192,9 +1224,12 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
&numbering, 0, nelmts, buf/*out*/)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed");
}
+
+
+ succeed:
ret_value = SUCCEED;
- done:
+ done:
if (src_id >= 0) H5A_dec_ref(src_id);
if (dst_id >= 0) H5A_dec_ref(dst_id);
tconv_buf = H5MM_xfree(tconv_buf);
@@ -1233,7 +1268,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_conv_t *sconv_func = NULL; /*space conversion funcs*/
H5S_number_t numbering; /*element numbering info*/
H5T_cdata_t *cdata = NULL; /*type conversion data */
- herr_t ret_value = FAIL;
+ herr_t ret_value = FAIL, status;
FUNC_ENTER(H5D_write, FAIL);
@@ -1284,6 +1319,32 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
* Compute the size of the request and allocate scratch buffers.
*/
nelmts = H5S_get_npoints(mem_space);
+
+ /*
+ * If there is no type conversion then try writing directly from
+ * application buffer to file.
+ */
+ if (H5D_OPTIMIZE_PIPE &&
+ H5T_conv_noop==tconv_func &&
+ NULL!=sconv_func->write) {
+#ifndef NDEBUG
+ fprintf (stderr, "HDF5-DIAG: Trying I/O pipe optimization...\n");
+#endif
+ status = (sconv_func->write)(dataset->ent.file, &(dataset->layout),
+ &(dataset->create_parms->efl),
+ H5T_get_size (dataset->type), file_space,
+ mem_space, buf);
+ if (status>=0) goto succeed;
+#ifndef NDEBUG
+ fprintf (stderr, "HDF5-DIAG: I/O pipe optimization failed\n");
+#endif
+ H5E_clear ();
+ }
+
+
+ /*
+ * This is the general case.
+ */
#ifndef LATER
/*
* Note: This prototype version allocates a buffer large enough to
@@ -1296,8 +1357,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if (cdata->need_bkg) bkg_buf = H5MM_xmalloc (dst_size);
}
#endif
-
-
/*
* Gather data from application buffer into the data type conversion
* buffer. Also gather data from the file into the background buffer
@@ -1338,9 +1397,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
&numbering, 0, nelmts, tconv_buf)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed");
}
+
+ succeed:
ret_value = SUCCEED;
- done:
+ done:
if (src_id >= 0) H5A_dec_ref(src_id);
if (dst_id >= 0) H5A_dec_ref(dst_id);
tconv_buf = H5MM_xfree(tconv_buf);
diff --git a/src/H5Distore.c b/src/H5Distore.c
index eeed99c..25b81b2 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -835,7 +835,9 @@ herr_t
H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
{
H5F_istore_ud1_t udata;
+#ifndef NDEBUG
int i;
+#endif
FUNC_ENTER(H5F_istore_create, FAIL);
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index eeed99c..25b81b2 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -835,7 +835,9 @@ herr_t
H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
{
H5F_istore_ud1_t udata;
+#ifndef NDEBUG
int i;
+#endif
FUNC_ENTER(H5F_istore_create, FAIL);
diff --git a/src/H5Oefl.c b/src/H5Oefl.c
index 1b3fa6a..5f2db2a 100644
--- a/src/H5Oefl.c
+++ b/src/H5Oefl.c
@@ -373,7 +373,7 @@ H5O_efl_read (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, size_t size,
uint8 *buf)
{
int i, fd=-1;
- size_t to_read, cur, skip;
+ size_t to_read, cur, skip=0;
ssize_t n;
herr_t ret_value = FAIL;
@@ -458,7 +458,7 @@ H5O_efl_write (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, size_t size,
const uint8 *buf)
{
int i, fd=-1;
- size_t to_write, cur, skip;
+ size_t to_write, cur, skip=0;
herr_t ret_value = FAIL;
FUNC_ENTER (H5O_efl_write, FAIL);
diff --git a/src/H5S.c b/src/H5S.c
index d3a1ff9..c371e4b 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -538,6 +538,7 @@ H5S_get_npoints_max(const H5S_t *ds)
FUNC_LEAVE(ret_value);
}
+
/*-------------------------------------------------------------------------
* Function: H5Sget_ndims
@@ -1310,6 +1311,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space)
_conv.mscat = H5S_simp_mscat;
_conv.mgath = H5S_simp_mgath;
_conv.fscat = H5S_simp_fscat;
+ _conv.read = H5S_simp_read;
+ _conv.write = H5S_simp_write;
conv = &_conv;
}
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index c8a3aae..fbce725 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -88,6 +88,18 @@ typedef struct H5S_tconv_t {
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, const void *tconv_buf);
+
+ /* Read from file to application w/o intermediate scratch buffer */
+ herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ void *buf/*out*/);
+
+ /* Write directly from app buffer to file */
+ herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const void *buf);
} H5S_conv_t;
H5S_t *H5S_copy (const H5S_t *src);
@@ -125,4 +137,12 @@ herr_t H5S_simp_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, const H5S_number_t *numbering,
size_t start, size_t nelmts, const void *tconv_buf);
+herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ void *buf/*out*/);
+herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const void *buf);
#endif
diff --git a/src/H5Ssimp.c b/src/H5Ssimp.c
index ee2d680..6f1f498 100644
--- a/src/H5Ssimp.c
+++ b/src/H5Ssimp.c
@@ -471,3 +471,218 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
FUNC_LEAVE (SUCCEED);
}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5S_simp_read
+ *
+ * Purpose: Reads a dataset from file F directly into application memory
+ * BUF performing data space conversion in a single step from
+ * FILE_SPACE to MEM_SPACE. The dataset is stored in the file
+ * according to the LAYOUT and EFL (external file list) and data
+ * point in the file is ELMT_SIZE bytes.
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Robb Matzke
+ * Thursday, March 12, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ void *buf/*out*/)
+{
+ size_t hslab_size[H5O_LAYOUT_NDIMS];
+ size_t file_offset[H5O_LAYOUT_NDIMS];
+ size_t mem_size[H5O_LAYOUT_NDIMS];
+ size_t mem_offset[H5O_LAYOUT_NDIMS];
+ int i;
+
+ FUNC_ENTER (H5S_simp_read, FAIL);
+
+#ifndef NDEBUG
+ assert (file_space->type==mem_space->type);
+ assert (file_space->u.simple.rank==mem_space->u.simple.rank);
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ if (file_space->hslab_def && mem_space->hslab_def) {
+ assert (1==file_space->h.stride[i]);
+ assert (1==mem_space->h.stride[i]);
+ assert (file_space->h.count[i]==mem_space->h.count[i]);
+ } else if (file_space->hslab_def) {
+ assert (1==file_space->h.stride[i]);
+ assert (file_space->h.count[i]==mem_space->u.simple.size[i]);
+ } else if (mem_space->hslab_def) {
+ assert (1==mem_space->h.stride[i]);
+ assert (file_space->u.simple.size[i]==mem_space->h.count[i]);
+ } else {
+ assert (file_space->u.simple.size[i]==
+ mem_space->u.simple.size[i]);
+ }
+ }
+#endif
+
+
+ /*
+ * Calculate size of hyperslab and offset of hyperslab into file and
+ * memory.
+ */
+ if (file_space->hslab_def) {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ hslab_size[i] = file_space->h.count[i];
+ }
+ } else {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ hslab_size[i] = file_space->u.simple.size[i];
+ }
+ }
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_size[i] = mem_space->u.simple.size[i];
+ }
+ if (file_space->hslab_def) {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ file_offset[i] = file_space->h.start[i];
+ }
+ } else {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ file_offset[i] = 0;
+ }
+ }
+ if (mem_space->hslab_def) {
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_offset[i] = mem_space->h.start[i];
+ }
+ } else {
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_offset[i] = 0;
+ }
+ }
+ hslab_size[file_space->u.simple.rank] = elmt_size;
+ mem_size[file_space->u.simple.rank] = elmt_size;
+ file_offset[file_space->u.simple.rank] = 0;
+ mem_offset[file_space->u.simple.rank] = 0;
+
+ /* Read the hyperslab */
+ if (H5F_arr_read (f, layout, efl, hslab_size,
+ mem_size, mem_offset, file_offset, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read dataset");
+ }
+
+ FUNC_LEAVE (SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5S_simp_write
+ *
+ * Purpose: Write a dataset from application memory BUF directly into
+ * file F performing data space conversion in a single step from
+ * MEM_SPACE to FILE_SPACE. The dataset is stored in the file
+ * according to the LAYOUT and EFL (external file list) and data
+ * point in the file is ELMT_SIZE bytes.
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Robb Matzke
+ * Thursday, March 12, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
+ const struct H5O_efl_t *efl, size_t elmt_size,
+ const H5S_t *file_space, const H5S_t *mem_space,
+ const void *buf)
+{
+ size_t hslab_size[H5O_LAYOUT_NDIMS];
+ size_t file_offset[H5O_LAYOUT_NDIMS];
+ size_t mem_size[H5O_LAYOUT_NDIMS];
+ size_t mem_offset[H5O_LAYOUT_NDIMS];
+ int i;
+
+ FUNC_ENTER (H5S_simp_write, FAIL);
+
+#ifndef NDEBUG
+ assert (file_space->type==mem_space->type);
+ assert (file_space->u.simple.rank==mem_space->u.simple.rank);
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ if (file_space->hslab_def && mem_space->hslab_def) {
+ assert (1==file_space->h.stride[i]);
+ assert (1==mem_space->h.stride[i]);
+ assert (file_space->h.count[i]==mem_space->h.count[i]);
+ } else if (file_space->hslab_def) {
+ assert (1==file_space->h.stride[i]);
+ assert (file_space->h.count[i]==mem_space->u.simple.size[i]);
+ } else if (mem_space->hslab_def) {
+ assert (1==mem_space->h.stride[i]);
+ assert (file_space->u.simple.size[i]==mem_space->h.count[i]);
+ } else {
+ assert (file_space->u.simple.size[i]==
+ mem_space->u.simple.size[i]);
+ }
+ }
+#endif
+
+
+ /*
+ * Calculate size of hyperslab and offset of hyperslab into file and
+ * memory.
+ */
+ if (file_space->hslab_def) {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ hslab_size[i] = file_space->h.count[i];
+ }
+ } else {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ hslab_size[i] = file_space->u.simple.size[i];
+ }
+ }
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_size[i] = mem_space->u.simple.size[i];
+ }
+ if (file_space->hslab_def) {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ file_offset[i] = file_space->h.start[i];
+ }
+ } else {
+ for (i=0; i<file_space->u.simple.rank; i++) {
+ file_offset[i] = 0;
+ }
+ }
+ if (mem_space->hslab_def) {
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_offset[i] = mem_space->h.start[i];
+ }
+ } else {
+ for (i=0; i<mem_space->u.simple.rank; i++) {
+ mem_offset[i] = 0;
+ }
+ }
+ hslab_size[file_space->u.simple.rank] = elmt_size;
+ mem_size[file_space->u.simple.rank] = elmt_size;
+ file_offset[file_space->u.simple.rank] = 0;
+ mem_offset[file_space->u.simple.rank] = 0;
+
+ /* Write the hyperslab */
+ if (H5F_arr_write (f, layout, efl, hslab_size,
+ mem_size, mem_offset, file_offset, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
+ "unable to write dataset");
+ }
+
+ FUNC_LEAVE (SUCCEED);
+}
+
+
+
+
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index a934b23..be52256 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -100,8 +100,6 @@ H5T_path_t *H5T_path_find (const H5T_t *src, const H5T_t *dst,
hbool_t create, H5T_conv_t func);
/* Conversion functions */
-herr_t H5T_conv_noop (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
- size_t nelmts, void *buf, void *bkg);
herr_t H5T_conv_order (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
size_t nelmts, void *_buf, void *bkg);
herr_t H5T_conv_struct (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
diff --git a/src/H5Tprivate.h b/src/H5Tprivate.h
index d67c38d..6af43b8 100644
--- a/src/H5Tprivate.h
+++ b/src/H5Tprivate.h
@@ -41,4 +41,11 @@ herr_t H5T_sort_by_offset (H5T_t *dt);
herr_t H5T_pack (H5T_t *dt);
herr_t H5T_debug (H5T_t *dt, FILE * stream);
H5T_conv_t H5T_find (const H5T_t *src, const H5T_t *dst, H5T_cdata_t **pcdata);
+
+/*
+ * This conversion function is here so we can determine whether a conversion
+ * is a no-op or not. The other conversion functions can go in H5Tpkg.h
+ */
+herr_t H5T_conv_noop (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
+ size_t nelmts, void *buf, void *bkg);
#endif
diff --git a/src/H5V.c b/src/H5V.c
index 85d8752..c9f3de2 100644
--- a/src/H5V.c
+++ b/src/H5V.c
@@ -502,23 +502,30 @@ H5V_stride_copy(intn n, size_t elmt_size, const size_t *size,
FUNC_ENTER(H5V_stride_copy, FAIL);
- H5V_vector_cpy(n, idx, size);
- nelmts = H5V_vector_reduce_product(n, size);
- for (i = 0; i < nelmts; i++) {
- /* Copy an element */
- HDmemcpy(dst, src, elmt_size);
+ if (n) {
+ H5V_vector_cpy(n, idx, size);
+ nelmts = H5V_vector_reduce_product(n, size);
+ for (i = 0; i < nelmts; i++) {
- /* Decrement indices and advance pointers */
- for (j = n - 1, carry = TRUE; j >= 0 && carry; --j) {
- src += src_stride[j];
- dst += dst_stride[j];
+ /* Copy an element */
+ HDmemcpy(dst, src, elmt_size);
- if (--idx[j]) carry = FALSE;
- else idx[j] = size[j];
+ /* Decrement indices and advance pointers */
+ for (j = n - 1, carry = TRUE; j >= 0 && carry; --j) {
+ src += src_stride[j];
+ dst += dst_stride[j];
+
+ if (--idx[j]) carry = FALSE;
+ else idx[j] = size[j];
+ }
}
+ } else {
+ HDmemcpy (dst, src, elmt_size);
+ HRETURN (SUCCEED);
}
+
FUNC_LEAVE(SUCCEED);
}