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-rw-r--r--src/H5Tconv.c56
-rw-r--r--src/H5Tvlen.c3
-rw-r--r--test/tvltypes.c196
3 files changed, 234 insertions, 21 deletions
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index 65b7c93..e61e2cb 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -2178,11 +2178,10 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
uint8_t *s, *sp, *d, *dp; /*source and dest traversal ptrs */
uint8_t **dptr; /*pointer to correct destination pointer*/
uint8_t *bg_ptr=NULL; /*background buf traversal pointer */
- uint8_t *bg=NULL;
- H5HG_t bg_hobjid;
+ H5HG_t bg_hobjid, parent_hobjid;
size_t src_delta, dst_delta, bkg_delta;/*source & destination stride*/
hssize_t seq_len; /*the number of elements in the current sequence*/
- hsize_t bg_seq_len=0;
+ hsize_t bg_seq_len=0, parent_seq_len=0;
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 */
@@ -2191,7 +2190,9 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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 */
+ int nested=0; /*flag of nested VL case */
hsize_t elmtno; /*element number counter */
+ hsize_t i;
FUNC_ENTER_NOAPI(H5T_conv_vlen, FAIL);
@@ -2241,16 +2242,14 @@ 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;
+ 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;
+ bg_ptr = (uint8_t*)_bkg;
direction = 1;
} else {
/* potentially this uses the destination buffer 1 extra
@@ -2309,14 +2308,16 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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 */
+
+ /* Set the flag for nested VL case */
+ if(dst->u.vlen.f!=NULL && H5T_detect_class(dst->parent,H5T_VLEN) && bg_ptr!=NULL)
+ nested=1;
for (elmtno=0; elmtno<nelmts; elmtno++) {
s = sp;
d = *dptr;
- if(bg_ptr!=NULL)
- bg = bg_ptr;
- /* Get length of sequences in bytes */
+ /* Get length of element sequences */
seq_len=(*(src->u.vlen.getlen))(src->u.vlen.f,s);
assert(seq_len>=0);
H5_CHECK_OVERFLOW(seq_len,hssize_t,size_t);
@@ -2345,15 +2346,23 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
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 */
/* If we are writing and there is a nested VL type, read
* the sequence into the background buffer */
- if(dst->u.vlen.f!=NULL && H5T_detect_class(dst->parent,H5T_VLEN) && bg!=NULL) {
- uint8_t *tmp=bg;
+ if(nested) {
+ uint8_t *tmp=bg_ptr;
UINT32DECODE(tmp, bg_seq_len);
if(bg_seq_len>0) {
+ if(tmp_buf_size<bg_seq_len*MAX(src_base_size,
+ dst_base_size)) {
+ tmp_buf_size=bg_seq_len*MAX(src_base_size,
+ dst_base_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");
+ }
H5F_addr_decode(dst->u.vlen.f, (const uint8_t **)&tmp,
&(bg_hobjid.addr));
INT32DECODE(tmp, bg_hobjid.idx);
@@ -2361,6 +2370,10 @@ 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 sequence into background buffer");
} /* end if */
+
+ /* If the sequence gets shorter, pad out the original sequence with zeros */
+ if(bg_seq_len<seq_len)
+ HDmemset((uint8_t *)tmp_buf+dst_base_size*bg_seq_len,0,(seq_len-bg_seq_len)*dst_base_size);
} /* end if */
/* Convert VL sequence */
@@ -2370,10 +2383,25 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, hsize_t nelmts,
"datatype conversion failed");
/* Write sequence to destination location */
- 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)
+ if((*(dst->u.vlen.write))(dset_xfer_plist,dst->u.vlen.f,d,conv_buf, bg_ptr, (hsize_t)seq_len,(hsize_t)dst_base_size)<0)
HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL,
"can't write VL data");
+ /* For nested VL case, free leftover heap objects from the deeper level if the length of new data elements is shorted than the old data elements.*/
+ if(nested && seq_len<bg_seq_len) {
+ uint8_t *tmp_p=tmp_buf;
+ tmp_p += seq_len*dst_base_size;
+ for(i=0; i<(bg_seq_len-seq_len); i++) {
+ UINT32DECODE(tmp_p, parent_seq_len);
+ if(parent_seq_len>0) {
+ H5F_addr_decode(dst->u.vlen.f, (const uint8_t **)&tmp_p, &(parent_hobjid.addr));
+ INT32DECODE(tmp_p, parent_hobjid.idx);
+ if(H5HG_remove(dst->u.vlen.f, &parent_hobjid)<0)
+ HRETURN_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to remove heap object");
+ }
+ }
+ }
+
/*
* If we had used a temporary buffer for the destination
* then we should copy the value to the true destination
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index cc38b3c..78e5b68 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -489,10 +489,11 @@ herr_t H5T_vlen_disk_write(hid_t UNUSED plist_id, H5F_t *f, void *vl_addr, void
/* Get the length of the sequence and heap object ID from background data.
* Free heap object for old data. */
if(bg!=NULL) {
+ HDmemset(&bg_hobjid,0,sizeof(H5HG_t));
UINT32DECODE(bg, bg_seq_len);
/* Free heap object for old data */
- if(bg_seq_len!=0) {
+ if(bg_seq_len>0) {
/* Get heap information */
H5F_addr_decode(f, (const uint8_t **)&bg, &(bg_hobjid.addr));
INT32DECODE(bg, bg_hobjid.idx);
diff --git a/test/tvltypes.c b/test/tvltypes.c
index 3aa7d65..1c51789 100644
--- a/test/tvltypes.c
+++ b/test/tvltypes.c
@@ -1305,12 +1305,12 @@ test_vltypes_vlen_vlen_atomic(void)
/****************************************************************
**
-** rewrite_vltypes_vlen_vlen_atomic(): Test basic VL datatype code.
+** rewrite_longer_vltypes_vlen_vlen_atomic(): Test basic VL datatype code.
** Tests VL datatype with VL datatypes of atomic datatypes.
**
****************************************************************/
static void
-rewrite_vltypes_vlen_vlen_atomic(void)
+rewrite_longer_vltypes_vlen_vlen_atomic(void)
{
hvl_t wdata[SPACE1_DIM1]; /* Information to write */
hvl_t rdata[SPACE1_DIM1]; /* Information read in */
@@ -1444,7 +1444,7 @@ rewrite_vltypes_vlen_vlen_atomic(void)
} /* end if */
for(k=0; k<t2->len; k++) {
if( ((unsigned int *)t1->p)[k] != ((unsigned int *)t2->p)[k] ) { num_errs++;
- printf("VL data values don't match!, t1->p[%d]=%d, t2->p[%d]=%d, i=%d, j=%d\n",(int)k, (int)((unsigned int *)t1->p)[k], (int)k, (int)((unsigned int *)t2->p)[k], i, j);
+ printf("VL data values don't match!, t1->p[%d]=%d, t2->p[%d]=%d\n",(int)k, (int)((unsigned int *)t1->p)[k], (int)k, (int)((unsigned int *)t2->p)[k]);
continue;
} /* end if */
} /* end for */
@@ -1482,7 +1482,190 @@ rewrite_vltypes_vlen_vlen_atomic(void)
ret = H5Fclose(fid1);
CHECK(ret, FAIL, "H5Fclose");
-} /* end rewrite_vltypes_vlen_vlen_atomic() */
+} /* end rewrite_longer_vltypes_vlen_vlen_atomic() */
+
+/****************************************************************
+**
+** rewrite_shorter_vltypes_vlen_vlen_atomic(): Test basic VL datatype code.
+** Tests VL datatype with VL datatypes of atomic datatypes.
+**
+****************************************************************/
+static void
+rewrite_shorter_vltypes_vlen_vlen_atomic(void)
+{
+ hvl_t wdata[SPACE1_DIM1]; /* Information to write */
+ hvl_t rdata[SPACE1_DIM1]; /* Information read in */
+ hvl_t *t1, *t2; /* Temporary pointer to VL information */
+ hid_t fid1; /* HDF5 File IDs */
+ hid_t dataset; /* Dataset ID */
+ hid_t sid1; /* Dataspace ID */
+ hid_t tid2; /* Datatype IDs */
+ hid_t xfer_pid; /* Dataset transfer property list ID */
+ hsize_t size; /* Number of bytes which will be used */
+ unsigned i,j,k; /* counting variables */
+ size_t mem_used=0; /* Memory used during allocation */
+ int increment=1;
+ herr_t ret; /* Generic return value */
+
+ /* Output message about test being performed */
+ MESSAGE(5, ("Check memory leak for VL Datatypes with VL Atomic Datatype Component Functionality\n"));
+
+ /* Allocate and initialize VL data to write */
+ for(i=0; i<SPACE1_DIM1; i++) {
+ wdata[i].p=malloc((i+increment)*sizeof(hvl_t));
+ if(wdata[i].p==NULL) {
+ printf("Cannot allocate memory for VL data! i=%u\n",i);
+ num_errs++;
+ return;
+ } /* end if */
+ wdata[i].len=i+increment;
+ for(t1=wdata[i].p,j=0; j<(i+increment); j++, t1++) {
+ t1->p=malloc((j+1)*sizeof(unsigned int));
+ if(t1->p==NULL) {
+ printf("Cannot allocate memory for VL data! i=%u, j=%u\n",i,j);
+ num_errs++;
+ return;
+ } /* end if */
+ t1->len=j+1;
+ for(k=0; k<(j+1); k++)
+ ((unsigned int *)t1->p)[k]=i*100000+j*1000+k*10;
+ } /* end for */
+ } /* end for */
+
+ /* Open file */
+ fid1 = H5Fopen(FILENAME, H5F_ACC_RDWR, H5P_DEFAULT);
+ CHECK(fid1, FAIL, "H5Fopen");
+
+ /* Open the dataset */
+ dataset=H5Dopen(fid1,"Dataset1");
+ CHECK(dataset, FAIL, "H5Dopen");
+
+ /* Get dataspace for datasets */
+ sid1 = H5Dget_space(dataset);
+ CHECK(sid1, FAIL, "H5Dget_space");
+
+ /* Open datatype of the dataset */
+ tid2 = H5Dget_type(dataset);
+ CHECK(tid2, FAIL, "H5Dget_type");
+
+ /* Write dataset to disk */
+ ret=H5Dwrite(dataset,tid2,H5S_ALL,H5S_ALL,H5P_DEFAULT,wdata);
+ CHECK(ret, FAIL, "H5Dwrite");
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+ CHECK(ret, FAIL, "H5Dclose");
+
+ /* Close datatype */
+ ret = H5Tclose(tid2);
+ CHECK(ret, FAIL, "H5Tclose");
+
+ /* Close disk dataspace */
+ ret = H5Sclose(sid1);
+ CHECK(ret, FAIL, "H5Sclose");
+
+ /* Close file */
+ ret = H5Fclose(fid1);
+ CHECK(ret, FAIL, "H5Fclose");
+
+
+ /* Open the file for data checking */
+ fid1 = H5Fopen(FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT);
+ CHECK(fid1, FAIL, "H5Fopen");
+
+ /* Open a dataset */
+ dataset=H5Dopen(fid1,"Dataset1");
+ CHECK(dataset, FAIL, "H5Dopen");
+
+ /* Get dataspace for datasets */
+ sid1 = H5Dget_space(dataset);
+ CHECK(sid1, FAIL, "H5Dget_space");
+
+ /* Get datatype for dataset */
+ tid2 = H5Dget_type(dataset);
+ CHECK(tid2, FAIL, "H5Dget_type");
+
+ /* Change to the custom memory allocation routines for reading VL data */
+ xfer_pid=H5Pcreate(H5P_DATASET_XFER);
+ CHECK(xfer_pid, FAIL, "H5Pcreate");
+
+ ret=H5Pset_vlen_mem_manager(xfer_pid,test_vltypes_alloc_custom,&mem_used,test_vltypes_free_custom,&mem_used);
+ CHECK(ret, FAIL, "H5Pset_vlen_mem_manager");
+
+ /* Make certain the correct amount of memory was used */
+ ret=H5Dvlen_get_buf_size(dataset,tid2,sid1,&size);
+ CHECK(ret, FAIL, "H5Dvlen_get_buf_size");
+
+ /* 10 hvl_t elements allocated = 1 + 2 + 3 + 4 elements for each array position */
+ /* 20 unsigned int elements allocated = 1 + 3 + 6 + 10 elements */
+ VERIFY(size,((SPACE1_DIM1*(SPACE1_DIM1+1))/2)*sizeof(hvl_t)+vlen_size_func(SPACE1_DIM1)*sizeof(unsigned int),"H5Dvlen_get_buf_size");
+
+ /* Read dataset from disk */
+ ret=H5Dread(dataset,tid2,H5S_ALL,H5S_ALL,xfer_pid,rdata);
+ CHECK(ret, FAIL, "H5Dread");
+
+ /* Make certain the correct amount of memory has been used */
+ /* 10 hvl_t elements allocated = 1 + 2 + 3 + 4 elements for each array position */
+ /* 20 unsigned int elements allocated = 1 + 3 + 6 + 10 elements */
+ VERIFY(mem_used,((SPACE1_DIM1*(SPACE1_DIM1+1))/2)*sizeof(hvl_t)+vlen_size_func(SPACE1_DIM1)*sizeof(unsigned int),"H5Dread");
+
+ /* Compare data read in */
+ for(i=0; i<SPACE1_DIM1; i++) {
+ if(wdata[i].len!=rdata[i].len) {
+ num_errs++;
+ printf("VL data length don't match!, wdata[%d].len=%d, rdata[%d].len=%d\n",(int)i,(int)wdata[i].len,(int)i,(int)rdata[i].len);
+ continue;
+ } /* end if */
+ for(t1=wdata[i].p, t2=rdata[i].p, j=0; j<rdata[i].len; j++, t1++, t2++)
+{
+ if(t1->len!=t2->len) {
+ num_errs++;
+ printf("VL data length don't match!, i=%d, j=%d, t1->len=%d, t2->len=%d\n",(int)i,(int)j,(int)t1->len,(int)t2->len);
+ continue;
+ } /* end if */
+ for(k=0; k<t2->len; k++) {
+ if( ((unsigned int *)t1->p)[k] != ((unsigned int *)t2->p)[k] ) {
+ num_errs++;
+/*printf("rdata[i].len=%d, t2->len=%d\n", rdata[i].len, t2->len);*/
+ printf("VL data values don't match!, t1->p[%d]=%d, t2->p[%d]=%d\n",(int)k, (int)((unsigned int *)t1->p)[k], (int)k, (int)((unsigned int *)t2->p)[k]);
+ continue;
+ } /* end if */
+ } /* end for */
+ } /* end for */
+ } /* end for */
+
+ /* Reclaim all the (nested) VL data */
+ ret=H5Dvlen_reclaim(tid2,sid1,xfer_pid,rdata);
+ CHECK(ret, FAIL, "H5Dvlen_reclaim");
+
+ /* Make certain the VL memory has been freed */
+ VERIFY(mem_used,0,"H5Dvlen_reclaim");
+
+ /* Reclaim the write VL data */
+ ret=H5Dvlen_reclaim(tid2,sid1,H5P_DEFAULT,wdata);
+ CHECK(ret, FAIL, "H5Dvlen_reclaim");
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+ CHECK(ret, FAIL, "H5Dclose");
+
+ /* Close datatype */
+ ret = H5Tclose(tid2);
+ CHECK(ret, FAIL, "H5Tclose");
+
+ /* Close disk dataspace */
+ ret = H5Sclose(sid1);
+ CHECK(ret, FAIL, "H5Sclose");
+
+ /* Close dataset transfer property list */
+ ret = H5Pclose(xfer_pid);
+ CHECK(ret, FAIL, "H5Pclose");
+
+ /* Close file */
+ ret = H5Fclose(fid1);
+ CHECK(ret, FAIL, "H5Fclose");
+
+} /* end rewrite_shorter_vltypes_vlen_vlen_atomic() */
/****************************************************************
**
@@ -1504,8 +1687,9 @@ test_vltypes(void)
rewrite_vltypes_vlen_compound(); /* Check VL memory leak */
test_vltypes_compound_vlen_atomic(); /* Test compound datatypes with VL atomic components */
rewrite_vltypes_compound_vlen_atomic();/* Check VL memory leak */
- test_vltypes_vlen_vlen_atomic(); /* Test VL datatype with VL atomic components */
- rewrite_vltypes_vlen_vlen_atomic(); /* Check VL memory leak */
+ test_vltypes_vlen_vlen_atomic(); /* Test VL datatype with VL atomic components */
+ rewrite_longer_vltypes_vlen_vlen_atomic(); /*overwrite with VL data of longer sequence*/
+ rewrite_shorter_vltypes_vlen_vlen_atomic(); /*overwrite with VL data of shorted sequence*/
} /* test_vltypes() */
generated by cgit v0.12 at 2024-11-01 13:09:26 (GMT)