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-rw-r--r--src/H5D.c14
-rw-r--r--src/H5Tconv.c59
-rw-r--r--src/H5Tpkg.h8
-rw-r--r--src/H5Tvlen.c32
4 files changed, 83 insertions, 30 deletions
diff --git a/src/H5D.c b/src/H5D.c
index 1bd7081..d125bd5 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -1545,7 +1545,13 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
if(IS_H5FD_MPIO(f) && dcpl_pline.nfilters > 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet");
#endif /*H5_HAVE_PARALLEL*/
-
+
+ if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time");
+
+ if(fill_time==H5D_FILL_TIME_NEVER && H5T_detect_class(type, H5T_VLEN))
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Dataset doesn't support VL datatype when fill value is not defined");
+
/* Initialize the dataset object */
if(NULL == (new_dset = H5D_new(dcpl_id)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed");
@@ -2876,6 +2882,10 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type");
need_bkg = MAX (tpath->cdata.need_bkg, need_bkg);
+ } else if(H5T_detect_class(dataset->type, H5T_VLEN)) {
+ /* Old data is retrieved into background buffer for VL datatype. The
+ * data is used later for freeing heap objects. */
+ need_bkg = H5T_BKG_YES;
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
} /* end else */
@@ -2887,7 +2897,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
/* Allocate background buffer */
H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
- if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL)
+ if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion");
} /* end if */
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index 1c23fc3..b155384 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -2141,8 +2141,9 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
* 2. Copy VL data from src buffer into dst buffer
* 3. Convert VL data into dst representation
* 4. Allocate buffer in dst heap
- * 5. Write dst VL data into dst heap
- * 6. Store (heap ID or pointer) and length in main dst buffer
+ * 5. Free heap objects storing old data
+ * 6. Write dst VL data into dst heap
+ * 7. Store (heap ID or pointer) and length in main dst buffer
*
* Return: Non-negative on success/Negative on failure
*
@@ -2157,12 +2158,17 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
* BUF_STRIDE bytes each time; otherwise assume both source and
* destination values are packed.
*
+ * Raymond Lu, 26 June, 2002
+ * Background buffer is used for freeing heap objects storing
+ * old data. At this moment, it only frees the first level of
+ * VL datatype. It doesn't handle nested VL datatypes.
+ *
*-------------------------------------------------------------------------
*/
herr_t
H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
size_t buf_stride, size_t bkg_stride, void *_buf,
- void UNUSED *_bkg, hid_t dset_xfer_plist)
+ void *_bkg, hid_t dset_xfer_plist)
{
H5T_path_t *tpath; /* Type conversion path */
hid_t tsrc_id = -1, tdst_id = -1;/*temporary type atoms */
@@ -2171,14 +2177,16 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
hsize_t olap; /*num overlapping elements */
uint8_t *s, *sp, *d, *dp; /*source and dest traversal ptrs */
uint8_t **dptr; /*pointer to correct destination pointer*/
- size_t src_delta, dst_delta; /*source & destination stride */
+ uint8_t *bg_ptr=NULL; /*background buf traversal pointer */
+ uint8_t *bg=NULL;
+ size_t src_delta, dst_delta, bkg_delta;/*source & destination stride*/
hssize_t seq_len; /*the number of elements in the current sequence*/
size_t src_base_size, dst_base_size;/*source & destination base size*/
size_t src_size, dst_size; /*source & destination total size in bytes*/
void *conv_buf=NULL; /*temporary conversion buffer */
size_t conv_buf_size=0; /*size of conversion buffer in bytes */
- void *bkg_buf=NULL; /*temporary background buffer */
- size_t bkg_buf_size=0; /*size of background buffer in bytes */
+ void *tmp_buf=NULL; /*temporary background buffer */
+ size_t tmp_buf_size=0; /*size of temporary bkg buffer */
uint8_t dbuf[64],*dbuf_ptr=dbuf;/*temp destination buffer */
int direction; /*direction of traversal */
hsize_t elmtno; /*element number counter */
@@ -2231,12 +2239,16 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
if (src->size==dst->size || buf_stride>0) {
olap = nelmts;
sp = dp = (uint8_t*)_buf;
+ if(_bkg!=NULL)
+ bg_ptr = (uint8_t*)_bkg;
direction = 1;
} else if (src->size>=dst->size) {
/* potentially this uses the destination buffer 1 extra
* time, but its faster that floating-point calcs */
olap = ((dst->size)/(src->size-dst->size))+1;
sp = dp = (uint8_t*)_buf;
+ if(_bkg!=NULL)
+ bg_ptr = (uint8_t*)_bkg;
direction = 1;
} else {
/* potentially this uses the destination buffer 1 extra
@@ -2246,6 +2258,9 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
(buf_stride ? buf_stride : src->size);
dp = (uint8_t*)_buf + (nelmts-1) *
(buf_stride ? buf_stride : dst->size);
+ if(_bkg!=NULL)
+ bg_ptr = (uint8_t*)_bkg + (nelmts-1) *
+ (bkg_stride ? bkg_stride : dst->size);
direction = -1;
}
@@ -2254,6 +2269,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
*/
src_delta = direction * (buf_stride ? buf_stride : src->size);
dst_delta = direction * (buf_stride ? buf_stride : dst->size);
+ bkg_delta = direction * (bkg_stride ? bkg_stride : dst->size);
/*
* If the source and destination buffers overlap then use a
@@ -2271,7 +2287,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
/* Get initial conversion buffer */
conv_buf_size=MAX(src_base_size,dst_base_size);
- if ((conv_buf=H5FL_BLK_ALLOC(vlen_seq,conv_buf_size,0))==NULL)
+ if ((conv_buf=H5FL_BLK_ALLOC(vlen_seq,conv_buf_size,1))==NULL)
HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
/* Set up conversion path for base elements */
@@ -2284,17 +2300,19 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
}
}
- /* Check if we need a background buffer for this conversion */
+ /* Check if we need a temporary buffer for this conversion */
if(tpath->cdata.need_bkg) {
/* Set up initial background buffer */
- bkg_buf_size=MAX(src_base_size,dst_base_size);
- if ((bkg_buf=H5FL_BLK_ALLOC(vlen_seq,bkg_buf_size,0))==NULL)
+ tmp_buf_size=MAX(src_base_size,dst_base_size);
+ if ((tmp_buf=H5FL_BLK_ALLOC(vlen_seq,tmp_buf_size,1))==NULL)
HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
} /* end if */
for (elmtno=0; elmtno<nelmts; elmtno++) {
s = sp;
d = *dptr;
+ if(bg_ptr!=NULL)
+ bg = bg_ptr;
/* Get length of sequences in bytes */
seq_len=(*(src->u.vlen.getlen))(src->u.vlen.f,s);
@@ -2317,25 +2335,24 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
HRETURN_ERROR(H5E_DATATYPE, H5E_READERROR, FAIL,
"can't read VL data");
- /* Check if background buffer is large enough, resize if necessary */
+ /* Check if temporary buffer is large enough, resize if necessary */
/* (Chain off the conversion buffer size) */
- if(tpath->cdata.need_bkg && bkg_buf_size<conv_buf_size) {
+ if(tpath->cdata.need_bkg && tmp_buf_size<conv_buf_size) {
/* Set up initial background buffer */
- bkg_buf_size=conv_buf_size;
- if((bkg_buf=H5FL_BLK_REALLOC(vlen_seq,bkg_buf,bkg_buf_size))==NULL)
+ tmp_buf_size=conv_buf_size;
+ if((tmp_buf=H5FL_BLK_REALLOC(vlen_seq,tmp_buf,tmp_buf_size))==NULL)
HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
+ HDmemset(tmp_buf,0,tmp_buf_size);
} /* end if */
/* Convert VL sequence */
H5_CHECK_OVERFLOW(seq_len,hssize_t,hsize_t);
- if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, bkg_stride,
- conv_buf, bkg_buf, dset_xfer_plist)<0)
+ if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, bkg_stride, conv_buf, tmp_buf, dset_xfer_plist)<0)
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
"datatype conversion failed");
/* Write sequence to destination location */
- if((*(dst->u.vlen.write))(dset_xfer_plist,dst->u.vlen.f,d,conv_buf,
- (hsize_t)seq_len,(hsize_t)dst_base_size)<0)
+ if((*(dst->u.vlen.write))(dset_xfer_plist,dst->u.vlen.f,d,conv_buf, bg, (hsize_t)seq_len,(hsize_t)dst_base_size)<0)
HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL,
"can't write VL data");
@@ -2347,6 +2364,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
if (d==dbuf) HDmemcpy (dp, d, dst->size);
sp += src_delta;
dp += dst_delta;
+ if(bg_ptr!=NULL)
+ bg_ptr += bkg_delta;
/* switch destination pointer around when the olap gets to 0 */
if(--olap==0) {
@@ -2361,8 +2380,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
H5FL_BLK_FREE(vlen_seq,conv_buf);
/* Release the background buffer, if we have one */
- if(bkg_buf!=NULL)
- H5FL_BLK_FREE(vlen_seq,bkg_buf);
+ if(tmp_buf!=NULL)
+ H5FL_BLK_FREE(vlen_seq,tmp_buf);
/* Release the temporary datatype IDs used */
if (tsrc_id >= 0)
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index 9be4778..f322641 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -92,7 +92,7 @@ typedef struct H5T_enum_t {
/* VL function pointers */
typedef hssize_t (*H5T_vlen_getlenfunc_t)(H5F_t *f, void *vl_addr);
typedef herr_t (*H5T_vlen_readfunc_t)(H5F_t *f, void *vl_addr, void *buf, size_t len);
-typedef herr_t (*H5T_vlen_writefunc_t)(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size);
+typedef herr_t (*H5T_vlen_writefunc_t)(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *buf, void *bg_addr, hsize_t seq_len, hsize_t base_size);
/* A VL datatype */
typedef struct H5T_vlen_t {
@@ -759,13 +759,13 @@ __DLL__ htri_t H5T_bit_inc(uint8_t *buf, size_t start, size_t size);
/* VL functions */
__DLL__ hssize_t H5T_vlen_seq_mem_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_seq_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
-__DLL__ herr_t H5T_vlen_seq_mem_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
+__DLL__ herr_t H5T_vlen_seq_mem_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, void *bg_addr, hsize_t seq_len, hsize_t base_size);
__DLL__ hssize_t H5T_vlen_str_mem_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_str_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
-__DLL__ herr_t H5T_vlen_str_mem_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
+__DLL__ herr_t H5T_vlen_str_mem_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, void *bg_addr, hsize_t seq_len, hsize_t base_size);
__DLL__ hssize_t H5T_vlen_disk_getlen(H5F_t *f, void *vl_addr);
__DLL__ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
-__DLL__ herr_t H5T_vlen_disk_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, hsize_t seq_len, hsize_t base_size);
+__DLL__ herr_t H5T_vlen_disk_write(hid_t dxpl_id, H5F_t *f, void *vl_addr, void *_buf, void *bg_addr, hsize_t seq_len, hsize_t base_size);
/* Array functions */
__DLL__ H5T_t * H5T_array_create(H5T_t *base, int ndims,
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index 24a9a1e..cc38b3c 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -204,7 +204,7 @@ herr_t H5T_vlen_seq_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
*
*-------------------------------------------------------------------------
*/
-herr_t H5T_vlen_seq_mem_write(hid_t plist_id, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
+herr_t H5T_vlen_seq_mem_write(hid_t plist_id, H5F_t UNUSED *f, void *vl_addr, void *buf, void UNUSED *bg_addr, hsize_t seq_len, hsize_t base_size)
{
H5MM_allocate_t alloc_func; /* Vlen allocation function */
void *alloc_info; /* Vlen allocation information */
@@ -332,7 +332,7 @@ herr_t H5T_vlen_str_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
*
*-------------------------------------------------------------------------
*/
-herr_t H5T_vlen_str_mem_write(hid_t plist_id, H5F_t UNUSED *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
+herr_t H5T_vlen_str_mem_write(hid_t plist_id, H5F_t UNUSED *f, void *vl_addr, void *buf, void UNUSED *bg_addr, hsize_t seq_len, hsize_t base_size)
{
H5MM_allocate_t alloc_func; /* Vlen allocation function */
void *alloc_info; /* Vlen allocation information */
@@ -464,13 +464,20 @@ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *buf, size_t UNUSED len)
*
* Modifications:
*
+ * Raymond Lu
+ * Thursday, June 26, 2002
+ * Free heap objects storing old data.
+ *
*-------------------------------------------------------------------------
*/
-herr_t H5T_vlen_disk_write(hid_t UNUSED plist_id, H5F_t *f, void *vl_addr, void *buf, hsize_t seq_len, hsize_t base_size)
+herr_t H5T_vlen_disk_write(hid_t UNUSED plist_id, H5F_t *f, void *vl_addr, void *buf, void *bg_addr, hsize_t seq_len, hsize_t base_size)
{
- uint8_t *vl=(uint8_t *)vl_addr; /* Pointer to the user's hvl_t information */
+ uint8_t *vl=(uint8_t *)vl_addr; /*Pointer to the user's hvl_t information*/
+ uint8_t *bg=(uint8_t *)bg_addr; /*Pointer to the old data hvl_t */
H5HG_t hobjid;
+ H5HG_t bg_hobjid;
size_t len;
+ hsize_t bg_seq_len=0;
FUNC_ENTER_NOAPI(H5T_vlen_disk_write, FAIL);
@@ -478,6 +485,23 @@ herr_t H5T_vlen_disk_write(hid_t UNUSED plist_id, H5F_t *f, void *vl_addr, void
assert(vl);
assert(buf);
assert(f);
+
+ /* Get the length of the sequence and heap object ID from background data.
+ * Free heap object for old data. */
+ if(bg!=NULL) {
+ UINT32DECODE(bg, bg_seq_len);
+
+ /* Free heap object for old data */
+ if(bg_seq_len!=0) {
+ /* Get heap information */
+ H5F_addr_decode(f, (const uint8_t **)&bg, &(bg_hobjid.addr));
+ INT32DECODE(bg, bg_hobjid.idx);
+ /* Free heap object */
+ if(H5HG_remove(f, &bg_hobjid)<0)
+ HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL,
+ "Unable to remove heap object");
+ } /* end if */
+ } /* end if */
/* Set the length of the sequence */
H5_CHECK_OVERFLOW(seq_len,hsize_t,size_t);
generated by cgit v0.12 at 2024-07-26 12:33:26 (GMT)