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https://github.com/HDFGroup/hdf5.git
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[svn-r5764]
Purpose:
Bug Fix.
Description:
VL type memory leak when data is overwritten.
Solution:
Free heap objects holding old data.
Platforms tested:
Linux 2.2(eirene), IRIX 6.5(paz).
This commit is contained in:
Raymond Lu
parent
e858a1310d
commit
d934f081d2
14
src/H5D.c
14
src/H5D.c
@ -1545,7 +1545,13 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
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if(IS_H5FD_MPIO(f) && dcpl_pline.nfilters > 0)
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HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet");
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#endif /*H5_HAVE_PARALLEL*/
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if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
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HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time");
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if(fill_time==H5D_FILL_TIME_NEVER && H5T_detect_class(type, H5T_VLEN))
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HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Dataset doesn't support VL datatype when fill value is not defined");
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/* Initialize the dataset object */
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if(NULL == (new_dset = H5D_new(dcpl_id)))
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HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed");
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@ -2876,6 +2882,10 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
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if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0)
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HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type");
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need_bkg = MAX (tpath->cdata.need_bkg, need_bkg);
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} else if(H5T_detect_class(dataset->type, H5T_VLEN)) {
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/* Old data is retrieved into background buffer for VL datatype. The
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* data is used later for freeing heap objects. */
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need_bkg = H5T_BKG_YES;
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} else {
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need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
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} /* end else */
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@ -2887,7 +2897,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
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if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) {
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/* Allocate background buffer */
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H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t);
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if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL)
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if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL)
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HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion");
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} /* end if */
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@ -2141,8 +2141,9 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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* 2. Copy VL data from src buffer into dst buffer
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* 3. Convert VL data into dst representation
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* 4. Allocate buffer in dst heap
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* 5. Write dst VL data into dst heap
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* 6. Store (heap ID or pointer) and length in main dst buffer
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* 5. Free heap objects storing old data
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* 6. Write dst VL data into dst heap
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* 7. Store (heap ID or pointer) and length in main dst buffer
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*
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* Return: Non-negative on success/Negative on failure
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*
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@ -2157,12 +2158,17 @@ H5T_conv_enum(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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* BUF_STRIDE bytes each time; otherwise assume both source and
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* destination values are packed.
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*
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* Raymond Lu, 26 June, 2002
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* Background buffer is used for freeing heap objects storing
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* old data. At this moment, it only frees the first level of
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* VL datatype. It doesn't handle nested VL datatypes.
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*
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*-------------------------------------------------------------------------
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*/
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herr_t
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H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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size_t buf_stride, size_t bkg_stride, void *_buf,
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void UNUSED *_bkg, hid_t dset_xfer_plist)
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void *_bkg, hid_t dset_xfer_plist)
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{
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H5T_path_t *tpath; /* Type conversion path */
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hid_t tsrc_id = -1, tdst_id = -1;/*temporary type atoms */
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@ -2171,14 +2177,16 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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hsize_t olap; /*num overlapping elements */
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uint8_t *s, *sp, *d, *dp; /*source and dest traversal ptrs */
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uint8_t **dptr; /*pointer to correct destination pointer*/
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size_t src_delta, dst_delta; /*source & destination stride */
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uint8_t *bg_ptr=NULL; /*background buf traversal pointer */
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uint8_t *bg=NULL;
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size_t src_delta, dst_delta, bkg_delta;/*source & destination stride*/
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hssize_t seq_len; /*the number of elements in the current sequence*/
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size_t src_base_size, dst_base_size;/*source & destination base size*/
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size_t src_size, dst_size; /*source & destination total size in bytes*/
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void *conv_buf=NULL; /*temporary conversion buffer */
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size_t conv_buf_size=0; /*size of conversion buffer in bytes */
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void *bkg_buf=NULL; /*temporary background buffer */
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size_t bkg_buf_size=0; /*size of background buffer in bytes */
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void *tmp_buf=NULL; /*temporary background buffer */
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size_t tmp_buf_size=0; /*size of temporary bkg buffer */
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uint8_t dbuf[64],*dbuf_ptr=dbuf;/*temp destination buffer */
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int direction; /*direction of traversal */
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hsize_t elmtno; /*element number counter */
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@ -2231,12 +2239,16 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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if (src->size==dst->size || buf_stride>0) {
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olap = nelmts;
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sp = dp = (uint8_t*)_buf;
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if(_bkg!=NULL)
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bg_ptr = (uint8_t*)_bkg;
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direction = 1;
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} else if (src->size>=dst->size) {
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/* potentially this uses the destination buffer 1 extra
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* time, but its faster that floating-point calcs */
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olap = ((dst->size)/(src->size-dst->size))+1;
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sp = dp = (uint8_t*)_buf;
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if(_bkg!=NULL)
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bg_ptr = (uint8_t*)_bkg;
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direction = 1;
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} else {
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/* potentially this uses the destination buffer 1 extra
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@ -2246,6 +2258,9 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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(buf_stride ? buf_stride : src->size);
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dp = (uint8_t*)_buf + (nelmts-1) *
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(buf_stride ? buf_stride : dst->size);
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if(_bkg!=NULL)
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bg_ptr = (uint8_t*)_bkg + (nelmts-1) *
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(bkg_stride ? bkg_stride : dst->size);
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direction = -1;
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}
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@ -2254,6 +2269,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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*/
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src_delta = direction * (buf_stride ? buf_stride : src->size);
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dst_delta = direction * (buf_stride ? buf_stride : dst->size);
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bkg_delta = direction * (bkg_stride ? bkg_stride : dst->size);
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/*
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* If the source and destination buffers overlap then use a
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@ -2271,7 +2287,7 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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/* Get initial conversion buffer */
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conv_buf_size=MAX(src_base_size,dst_base_size);
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if ((conv_buf=H5FL_BLK_ALLOC(vlen_seq,conv_buf_size,0))==NULL)
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if ((conv_buf=H5FL_BLK_ALLOC(vlen_seq,conv_buf_size,1))==NULL)
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HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
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/* Set up conversion path for base elements */
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@ -2284,17 +2300,19 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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}
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}
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/* Check if we need a background buffer for this conversion */
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/* Check if we need a temporary buffer for this conversion */
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if(tpath->cdata.need_bkg) {
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/* Set up initial background buffer */
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bkg_buf_size=MAX(src_base_size,dst_base_size);
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if ((bkg_buf=H5FL_BLK_ALLOC(vlen_seq,bkg_buf_size,0))==NULL)
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tmp_buf_size=MAX(src_base_size,dst_base_size);
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if ((tmp_buf=H5FL_BLK_ALLOC(vlen_seq,tmp_buf_size,1))==NULL)
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HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
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} /* end if */
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for (elmtno=0; elmtno<nelmts; elmtno++) {
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s = sp;
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d = *dptr;
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if(bg_ptr!=NULL)
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bg = bg_ptr;
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/* Get length of sequences in bytes */
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seq_len=(*(src->u.vlen.getlen))(src->u.vlen.f,s);
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@ -2317,25 +2335,24 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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HRETURN_ERROR(H5E_DATATYPE, H5E_READERROR, FAIL,
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"can't read VL data");
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/* Check if background buffer is large enough, resize if necessary */
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/* Check if temporary buffer is large enough, resize if necessary */
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/* (Chain off the conversion buffer size) */
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if(tpath->cdata.need_bkg && bkg_buf_size<conv_buf_size) {
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if(tpath->cdata.need_bkg && tmp_buf_size<conv_buf_size) {
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/* Set up initial background buffer */
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bkg_buf_size=conv_buf_size;
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if((bkg_buf=H5FL_BLK_REALLOC(vlen_seq,bkg_buf,bkg_buf_size))==NULL)
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tmp_buf_size=conv_buf_size;
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if((tmp_buf=H5FL_BLK_REALLOC(vlen_seq,tmp_buf,tmp_buf_size))==NULL)
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HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion");
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HDmemset(tmp_buf,0,tmp_buf_size);
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} /* end if */
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/* Convert VL sequence */
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H5_CHECK_OVERFLOW(seq_len,hssize_t,hsize_t);
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if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, bkg_stride,
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conv_buf, bkg_buf, dset_xfer_plist)<0)
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if (H5T_convert(tpath, tsrc_id, tdst_id, (hsize_t)seq_len, 0, bkg_stride, conv_buf, tmp_buf, dset_xfer_plist)<0)
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HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
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"datatype conversion failed");
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/* Write sequence to destination location */
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if((*(dst->u.vlen.write))(dset_xfer_plist,dst->u.vlen.f,d,conv_buf,
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(hsize_t)seq_len,(hsize_t)dst_base_size)<0)
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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)
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HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL,
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"can't write VL data");
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@ -2347,6 +2364,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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if (d==dbuf) HDmemcpy (dp, d, dst->size);
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sp += src_delta;
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dp += dst_delta;
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if(bg_ptr!=NULL)
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bg_ptr += bkg_delta;
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/* switch destination pointer around when the olap gets to 0 */
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if(--olap==0) {
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@ -2361,8 +2380,8 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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H5FL_BLK_FREE(vlen_seq,conv_buf);
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/* Release the background buffer, if we have one */
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if(bkg_buf!=NULL)
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H5FL_BLK_FREE(vlen_seq,bkg_buf);
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if(tmp_buf!=NULL)
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H5FL_BLK_FREE(vlen_seq,tmp_buf);
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/* Release the temporary datatype IDs used */
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if (tsrc_id >= 0)
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@ -92,7 +92,7 @@ typedef struct H5T_enum_t {
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/* VL function pointers */
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typedef hssize_t (*H5T_vlen_getlenfunc_t)(H5F_t *f, void *vl_addr);
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typedef herr_t (*H5T_vlen_readfunc_t)(H5F_t *f, void *vl_addr, void *buf, size_t len);
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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);
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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);
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/* A VL datatype */
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typedef struct H5T_vlen_t {
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@ -759,13 +759,13 @@ __DLL__ htri_t H5T_bit_inc(uint8_t *buf, size_t start, size_t size);
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/* VL functions */
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__DLL__ hssize_t H5T_vlen_seq_mem_getlen(H5F_t *f, void *vl_addr);
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__DLL__ herr_t H5T_vlen_seq_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
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__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);
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__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);
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__DLL__ hssize_t H5T_vlen_str_mem_getlen(H5F_t *f, void *vl_addr);
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__DLL__ herr_t H5T_vlen_str_mem_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
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__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);
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__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);
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__DLL__ hssize_t H5T_vlen_disk_getlen(H5F_t *f, void *vl_addr);
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__DLL__ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *_buf, size_t len);
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__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);
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__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);
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/* Array functions */
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__DLL__ H5T_t * H5T_array_create(H5T_t *base, int ndims,
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@ -204,7 +204,7 @@ herr_t H5T_vlen_seq_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
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*
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*-------------------------------------------------------------------------
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*/
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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)
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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)
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{
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H5MM_allocate_t alloc_func; /* Vlen allocation function */
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void *alloc_info; /* Vlen allocation information */
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@ -332,7 +332,7 @@ herr_t H5T_vlen_str_mem_read(H5F_t UNUSED *f, void *vl_addr, void *buf, size_t l
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*
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*-------------------------------------------------------------------------
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*/
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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)
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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)
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{
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H5MM_allocate_t alloc_func; /* Vlen allocation function */
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void *alloc_info; /* Vlen allocation information */
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@ -464,13 +464,20 @@ herr_t H5T_vlen_disk_read(H5F_t *f, void *vl_addr, void *buf, size_t UNUSED len)
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*
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* Modifications:
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*
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* Raymond Lu
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* Thursday, June 26, 2002
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* Free heap objects storing old data.
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*
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*-------------------------------------------------------------------------
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*/
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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)
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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)
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{
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uint8_t *vl=(uint8_t *)vl_addr; /* Pointer to the user's hvl_t information */
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uint8_t *vl=(uint8_t *)vl_addr; /*Pointer to the user's hvl_t information*/
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uint8_t *bg=(uint8_t *)bg_addr; /*Pointer to the old data hvl_t */
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H5HG_t hobjid;
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H5HG_t bg_hobjid;
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size_t len;
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hsize_t bg_seq_len=0;
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FUNC_ENTER_NOAPI(H5T_vlen_disk_write, FAIL);
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@ -478,6 +485,23 @@ herr_t H5T_vlen_disk_write(hid_t UNUSED plist_id, H5F_t *f, void *vl_addr, void
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assert(vl);
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assert(buf);
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assert(f);
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/* Get the length of the sequence and heap object ID from background data.
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* Free heap object for old data. */
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if(bg!=NULL) {
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UINT32DECODE(bg, bg_seq_len);
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/* Free heap object for old data */
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if(bg_seq_len!=0) {
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/* Get heap information */
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H5F_addr_decode(f, (const uint8_t **)&bg, &(bg_hobjid.addr));
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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);
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user