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[svn-r9322] Purpose:

Browse Source 
Bug fix

Description:
    Fix situation where deleting a chunked datasets with B-tree nodes that
weren't in the metadata cache would die with a core dump.

Platforms tested:
    FreeBSD 4.10 (sleipnir)
    Linux 2.4 (heping)
    Solaris 2.7 (arabica)
This commit is contained in:
Quincey Koziol 2004-09-27 13:06:11 -05:00
parent 643811be02
commit 3f2fb8bed1
3 changed files with 203 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

170
src/H5Distore.c
View File

@ -144,6 +144,7 @@ typedef struct H5D_istore_ud1_t {
/* Private prototypes */
static void *H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline);
static void *H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline);
static herr_t H5D_istore_shared_create (H5F_t *f, H5O_layout_t *layout);
static herr_t H5D_istore_shared_free (void *page);
/* B-tree iterator callbacks */
@ -927,9 +928,6 @@ H5D_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, hadd
herr_t
H5D_istore_init (H5F_t *f, H5D_t *dset)
{
H5D_istore_ud1_t udata;
H5B_shared_t *shared; /* Shared B-tree node info */
size_t u; /* Local index variable */
H5D_rdcc_t *rdcc = &(dset->cache.chunk);
herr_t ret_value=SUCCEED; /* Return value */
@ -943,36 +941,9 @@ H5D_istore_init (H5F_t *f, H5D_t *dset)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed");
} /* end if */
/* Initialize "user" data for B-tree callbacks, etc. */
udata.mesg = &dset->layout;
/* Allocate space for the shared structure */
if(NULL==(shared=H5FL_MALLOC(H5B_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "global" information for this file's groups */
shared->type= H5B_ISTORE;
shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE);
shared->sizeof_rkey = H5D_istore_sizeof_rkey(f, &udata);
assert(shared->sizeof_rkey);
shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys);
assert(shared->sizeof_rnode);
if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
#ifdef H5_USING_PURIFY
HDmemset(shared->page,0,shared->sizeof_rnode);
#endif /* H5_USING_PURIFY */
if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
/* Initialize the offsets into the native key buffer */
for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++)
shared->nkey[u]=u*H5B_ISTORE->sizeof_nkey;
/* Make shared B-tree info reference counted */
if(NULL==(dset->layout.u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
/* Allocate the shared structure */
if(H5D_istore_shared_create(f, &dset->layout)<0)
HGOTO_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_init() */
@ -1275,6 +1246,65 @@ done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_dest() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_shared_create
*
* Purpose: Create & initialize B-tree shared info
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Monday, September 27, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_istore_shared_create (H5F_t *f, H5O_layout_t *layout)
{
H5D_istore_ud1_t udata;
H5B_shared_t *shared; /* Shared B-tree node info */
size_t u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_shared_create)
/* Initialize "user" data for B-tree callbacks, etc. */
udata.mesg = layout;
/* Allocate space for the shared structure */
if(NULL==(shared=H5FL_MALLOC(H5B_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "global" information for this file's groups */
shared->type= H5B_ISTORE;
shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE);
shared->sizeof_rkey = H5D_istore_sizeof_rkey(f, &udata);
assert(shared->sizeof_rkey);
shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys);
assert(shared->sizeof_rnode);
if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
#ifdef H5_USING_PURIFY
HDmemset(shared->page,0,shared->sizeof_rnode);
#endif /* H5_USING_PURIFY */
if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
/* Initialize the offsets into the native key buffer */
for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++)
shared->nkey[u]=u*H5B_ISTORE->sizeof_nkey;
/* Make shared B-tree info reference counted */
if(NULL==(layout->u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
done:
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_istore_shared_create() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_shared_free
@ -1601,7 +1631,7 @@ H5D_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
} /* end if */
#ifdef H5_USING_PURIFY
else
HDmemset(ret_value,0,size);
HDmemset(chunk,0,chunk_size);
#endif /* H5_USING_PURIFY */
rdcc->ninits++;
} /* end else */
@ -2014,9 +2044,7 @@ H5D_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
{
H5D_istore_ud1_t udata; /*B-tree pass-through */
haddr_t chunk_addr; /* Chunk address on disk */
#ifndef NDEBUG
size_t u; /* Local index variables */
#endif
ssize_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_writevv, FAIL);
@ -2078,16 +2106,38 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
uint8_t *chunk; /* Pointer to cached chunk in memory */
unsigned idx_hint=0; /* Cache index hint */
ssize_t naccessed; /* Number of bytes accessed in chunk */
size_t total_bytes; /* Total # of bytes accessed on disk & memory */
hbool_t relax; /* Whether whole chunk is selected */
/*
* Lock the chunk, copy from application to chunk, then unlock the
* chunk.
*/
#ifdef OLD_WAY
/* Note that this is technically OK, since eventually all the data in the chunk
* will be overwritten. However, it seems risky and a better approach would
* be to lock the chunk in the dataset I/O routine (setting the relax flag
* appropriately) and then unlock it after all the I/O the chunk was finished. -QAK
*/
if(chunk_max_nseq==1 && chunk_len_arr[0] == dset->layout.u.chunk.size)
relax = TRUE;
else
relax = FALSE;
#else /* OLD_WAY */
relax=TRUE;
total_bytes=0;
for(u=*chunk_curr_seq; u<chunk_max_nseq; u++)
total_bytes+=chunk_len_arr[u];
if(total_bytes!=dset->layout.u.chunk.size)
relax=FALSE;
if(relax) {
total_bytes=0;
for(u=*mem_curr_seq; u<mem_max_nseq; u++)
total_bytes+=mem_len_arr[u];
if(total_bytes!=dset->layout.u.chunk.size)
relax=FALSE;
} /* end if */
#endif /* OLD_WAY */
if (NULL==(chunk=H5D_istore_lock(f, dxpl_cache, dxpl_id, dset, store,
&udata, relax, &idx_hint)))
@ -3117,22 +3167,32 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout)
H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout)
{
H5D_istore_ud1_t udata; /* User data for B-tree iterator call */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_delete, FAIL);
/* Check if the B-tree has been created in the file */
if(H5F_addr_defined(layout->u.chunk.addr)) {
H5O_layout_t tmp_layout=*layout;/* Local copy of layout info */
H5D_istore_ud1_t udata; /* User data for B-tree iterator call */
/* Set up user data for B-tree deletion */
HDmemset(&udata, 0, sizeof udata);
udata.mesg = layout;
udata.mesg = &tmp_layout;
/* Allocate the shared structure */
if(H5D_istore_shared_create(f, &tmp_layout)<0)
HGOTO_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
/* Delete entire B-tree */
if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, &udata)<0)
if(H5B_delete(f, dxpl_id, H5B_ISTORE, tmp_layout.u.chunk.addr, &udata)<0)
HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree");
/* Free the raw B-tree node buffer */
if(H5RC_DEC(tmp_layout.u.chunk.btree_shared)<0)
HGOTO_ERROR (H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page");
} /* end if */
done:
@ -3366,39 +3426,17 @@ H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int inden
{
H5O_layout_t layout;
H5D_istore_ud1_t udata;
H5B_shared_t *shared; /* Shared B-tree node info */
size_t u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_debug,FAIL);
HDmemset (&udata, 0, sizeof udata);
layout.u.chunk.ndims = ndims;
HDmemset (&udata, 0, sizeof udata);
udata.mesg = &layout;
/* Allocate space for the shared structure */
if(NULL==(shared=H5FL_MALLOC(H5B_shared_t)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info")
/* Set up the "global" information for this file's groups */
shared->type= H5B_ISTORE;
shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE);
shared->sizeof_rkey = H5D_istore_sizeof_rkey(f, &udata);
assert(shared->sizeof_rkey);
shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys);
assert(shared->sizeof_rnode);
if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page")
/* Initialize the offsets into the native key buffer */
for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++)
shared->nkey[u]=u*H5B_ISTORE->sizeof_nkey;
/* Make shared B-tree info reference counted */
if(NULL==(layout.u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free)))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info")
/* Allocate the shared structure */
if(H5D_istore_shared_create(f, &layout)<0)
HGOTO_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info")
H5B_debug (f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata);

3
test/Makefile.in
View File

@ -69,7 +69,8 @@ MOSTLYCLEAN=cmpd_dset.h5 compact_dataset.h5 dataset.h5 extend.h5 istore.h5 \
getname.h5 getname[1-3].h5 sec2_file.h5 \
family_file000[0-3][0-9].h5 multi_file-[rs].h5 core_file \
new_move_[ab].h5 ntypes.h5 dangle.h5 error_test.h5 err_compat.h5 \
dtransform.h5 test_filters.h5 get_file_name.h5 tstint[1-2].h5
dtransform.h5 test_filters.h5 get_file_name.h5 tstint[1-2].h5 \
unlink_chunked.h5
CLEAN=$(TIMINGS)

97
test/unlink.c
View File

@ -30,6 +30,7 @@ const char *FILENAME[] = {
"filespace",
"slashes",
"resurrect",
"unlink_chunked",
NULL
};
@ -1852,6 +1853,7 @@ test_resurrect_dataset(void)
/* Close things */
if(H5Dclose(d)<0) TEST_ERROR;
if(H5Fclose(f)<0) TEST_ERROR;
if(H5Pclose(fapl)<0) TEST_ERROR;
PASSED();
return 0;
@ -1861,10 +1863,102 @@ error:
H5Sclose(s);
H5Dclose(d);
H5Fclose(f);
H5Pclose(fapl);
} H5E_END_TRY;
return 1;
} /* end test_resurrect_dataset() */
/*-------------------------------------------------------------------------
* Function: test_unlink_chunked_dataset
*
* Purpose: Tests deleting a chunked dataset
*
* Return: Success: 0
* Failure: number of errors
*
* Programmer: Quincey Koziol
* Monday, September 27, 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
test_unlink_chunked_dataset(void)
{
hid_t fapl_id=-1;
hid_t file_id=-1;
hid_t dset_id=-1;
hid_t space_id=-1;
hid_t dcpl_id=-1;
hsize_t dims[FILESPACE_NDIMS]={FILESPACE_DIM0,FILESPACE_DIM1,FILESPACE_DIM2};
hsize_t max_dims[FILESPACE_NDIMS]={H5S_UNLIMITED,H5S_UNLIMITED,H5S_UNLIMITED};
hsize_t chunk_dims[FILESPACE_NDIMS]={FILESPACE_CHUNK0,FILESPACE_CHUNK1,FILESPACE_CHUNK2};
char filename[1024];
TESTING("Unlinking chunked dataset");
/* Create file */
fapl_id = h5_fileaccess();
h5_fixname(FILENAME[7], fapl_id, filename, sizeof filename);
/* Create the file */
if((file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id))<0) TEST_ERROR;
/* Create the dataspace */
if((space_id=H5Screate_simple(FILESPACE_NDIMS,dims,max_dims))<0) TEST_ERROR;
/* Create the dataset creation filter */
if((dcpl_id=H5Pcreate(H5P_DATASET_CREATE))<0) TEST_ERROR;
/* Set to chunked storage */
if(H5Pset_chunk(dcpl_id,FILESPACE_NDIMS,chunk_dims)<0) TEST_ERROR;
/* Set to early space allocation */
if(H5Pset_alloc_time(dcpl_id,H5D_ALLOC_TIME_EARLY)<0) TEST_ERROR;
/* Create the dataset */
if((dset_id = H5Dcreate(file_id,DATASETNAME,H5T_NATIVE_INT,space_id,dcpl_id))<0) TEST_ERROR;
/* Close the dataspace */
if(H5Sclose(space_id)<0) TEST_ERROR;
/* Close the dataset creation property list */
if(H5Pclose(dcpl_id)<0) TEST_ERROR;
/* Close the dataset */
if(H5Dclose(dset_id)<0) TEST_ERROR;
/* Close the file */
if(H5Fclose(file_id)<0) TEST_ERROR;
/* Re-open the file */
if((file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT))<0) TEST_ERROR;
/* Delete the dataset */
if(H5Gunlink(file_id, DATASETNAME)<0) TEST_ERROR;
/* Close the file */
if(H5Fclose(file_id)<0) TEST_ERROR;
/* Close the file access property list */
if(H5Pclose(fapl_id)<0) TEST_ERROR;
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl_id);
H5Sclose(space_id);
H5Dclose(dset_id);
H5Fclose(file_id);
H5Pclose(fapl_id);
} H5E_END_TRY;
return 1;
} /* end test_unlink_chunked_dataset() */
/*-------------------------------------------------------------------------
* Function: main
@ -1942,6 +2036,9 @@ main(void)
/* Test "resurrecting" objects */
nerrors += test_resurrect_dataset();
/* Test unlinking chunked datasets */
nerrors += test_unlink_chunked_dataset();
/* Close */
if (H5Fclose(file)<0) TEST_ERROR;
if (nerrors) {