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[svn-r29969] Description:

Browse Source 
Bring r29934 from revise_chunks branch to trunk:

(1) Fix for HDFFV-9434: throw an error instead of assertion when v1 btree level hits the 1 byte limit.
(2) Modifications to better handle error recovery when conversion by h5format_convert fails.

Tested on:
    MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
    (h5committest forthcoming)
This commit is contained in:
Quincey Koziol 2016-05-29 05:57:47 -05:00
parent 29a5f10619
commit bf566b775b
14 changed files with 324 additions and 26 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
MANIFEST
View File

@ -1247,6 +1247,7 @@
./tools/h5format_convert/h5format_convert.c
./tools/h5format_convert/testfiles/h5fc_v_n_all.ddl
./tools/h5format_convert/testfiles/h5fc_v_bt1.ddl
./tools/h5format_convert/testfiles/h5fc_v_err.ddl
./tools/h5format_convert/testfiles/h5fc_v_non_chunked.ddl
./tools/h5format_convert/testfiles/h5fc_d_file.ddl
./tools/h5format_convert/testfiles/h5fc_v_ndata_bt1.ddl
@ -1259,6 +1260,7 @@
./tools/h5format_convert/testfiles/h5fc_nonexistfile.ddl
./tools/h5format_convert/testfiles/h5fc_non_v3.h5
./tools/h5format_convert/testfiles/h5fc_edge_v3.h5
./tools/h5format_convert/testfiles/h5fc_err_level.h5
./tools/h5format_convert/testfiles/h5fc_ext1_f.h5
./tools/h5format_convert/testfiles/h5fc_ext1_i.h5
./tools/h5format_convert/testfiles/h5fc_ext1_s.h5

35
src/H5AC.c
View File

@ -2464,6 +2464,41 @@ done:
} /* H5AC_flush_tagged_metadata */
/*------------------------------------------------------------------------------
* Function: H5AC_expunge_tag_type_metadata()
*
* Purpose: Wrapper for cache level function which expunge entries with
* a specific tag and type id.
*
* Return: SUCCEED on success, FAIL otherwise.
*
* Programmer: Vailin Choi; May 2016
*
*------------------------------------------------------------------------------
*/
herr_t
H5AC_expunge_tag_type_metadata(H5F_t *f, hid_t dxpl_id, haddr_t tag, int type_id, unsigned flags)
{
/* Variable Declarations */
herr_t ret_value = SUCCEED;
/* Function Enter Macro */
FUNC_ENTER_NOAPI(FAIL)
/* Assertions */
HDassert(f);
HDassert(f->shared);
/* Call cache level function to expunge entries with specified tag and type id */
if(H5C_expunge_tag_type_metadata(f, dxpl_id, tag, type_id, flags)<0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Cannot expunge tagged type entries")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5AC_expunge_tag_type_metadata*/
#if H5AC_DO_TAGGING_SANITY_CHECKS
/*-------------------------------------------------------------------------

1
src/H5ACprivate.h
View File

@ -365,6 +365,7 @@ H5_DLL herr_t H5AC_get_entry_ring(const H5F_t *f, haddr_t addr, H5AC_ring_t *rin
H5_DLL herr_t H5AC_set_ring(hid_t dxpl_id, H5AC_ring_t ring, H5P_genplist_t **dxpl,
H5AC_ring_t *orig_ring);
H5_DLL herr_t H5AC_reset_ring(H5P_genplist_t *dxpl, H5AC_ring_t orig_ring);
H5_DLL herr_t H5AC_expunge_tag_type_metadata(H5F_t *f, hid_t dxpl_id, haddr_t tag, int type_id, unsigned flags);
#ifdef H5_HAVE_PARALLEL
H5_DLL herr_t H5AC_add_candidate(H5AC_t * cache_ptr, haddr_t addr);

5
src/H5Bcache.c
View File

@ -312,6 +312,11 @@ H5B__serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED len,
/* node type and level */
*image++ = (uint8_t)shared->type->id;
/* 2^8 limit: only 1 byte is used to store node level */
if(bt->level >= HDpow(2, LEVEL_BITS))
HGOTO_ERROR(H5E_BTREE, H5E_CANTENCODE, FAIL, "unable to encode node level")
H5_CHECK_OVERFLOW(bt->level, unsigned, uint8_t);
*image++ = (uint8_t)bt->level;

1
src/H5Bpkg.h
View File

@ -42,6 +42,7 @@
/* Get the native key at a given index */
#define H5B_NKEY(b, shared, idx) ((b)->native + (shared)->nkey[(idx)])
#define LEVEL_BITS 8 /* # of bits for node level: 1 byte */
/****************************/

53
src/H5C.c
View File

@ -9900,6 +9900,59 @@ H5C_retag_entries(H5C_t * cache_ptr, haddr_t src_tag, haddr_t dest_tag)
FUNC_LEAVE_NOAPI_VOID
} /* H5C_retag_entries */
/*-------------------------------------------------------------------------
*
* Function: H5C_expunge_tag_type_metadata
*
* Purpose: Search and expunge from the cache entries associated
* with 'tag' and type id.
*
* Return: FAIL if error is detected, SUCCEED otherwise.
*
* Programmer: Vailin Choi; May 2016
*
*-------------------------------------------------------------------------
*/
herr_t
H5C_expunge_tag_type_metadata(H5F_t *f, hid_t dxpl_id, haddr_t tag, int type_id, unsigned flags)
{
unsigned u; /* Local index variable */
H5C_t *cache_ptr = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* Sanity check */
HDassert(f);
HDassert(f->shared);
HDassert(f->shared->cache);
HDassert(f->shared->cache->magic == H5C__H5C_T_MAGIC);
/* Get cache pointer */
cache_ptr = f->shared->cache;
/* Iterate through hash table entries, expunge those with specified tag and type id */
for(u = 0; u < H5C__HASH_TABLE_LEN; u++) {
H5C_cache_entry_t *entry_ptr; /* Entry pointer */
entry_ptr = cache_ptr->index[u];
while(entry_ptr != NULL) {
/* Found one with the same tag and type id */
if(entry_ptr->tag == tag && entry_ptr->type->id == type_id) {
if(H5C_expunge_entry(f, dxpl_id, entry_ptr->type, entry_ptr->addr, flags) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "H5C_expunge_entry() failed.")
} /* end if */
entry_ptr = entry_ptr->ht_next;
} /* end while */
} /* end for */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5C_expunge_tag_type_metadata */
/*-------------------------------------------------------------------------
* Function: H5C_get_entry_ring

1
src/H5Cprivate.h
View File

@ -1970,6 +1970,7 @@ H5_DLL herr_t H5C_expunge_entry(H5F_t *f, hid_t dxpl_id,
const H5C_class_t *type, haddr_t addr, unsigned flags);
H5_DLL herr_t H5C_flush_cache(H5F_t *f, hid_t dxpl_id, unsigned flags);
H5_DLL herr_t H5C_flush_tagged_entries(H5F_t * f, hid_t dxpl_id, haddr_t tag);
H5_DLL herr_t H5C_expunge_tag_type_metadata(H5F_t *f, hid_t dxpl_id, haddr_t tag, int type_id, unsigned flags);
#if H5C_DO_TAGGING_SANITY_CHECKS
herr_t H5C_verify_tag(int id, haddr_t tag, H5C_tag_globality_t globality);
#endif

2
src/H5Dchunk.c
View File

@ -6471,7 +6471,7 @@ H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx
udata.dset_dims = dset->shared->curr_dims;
/* terate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
if((dset->shared->layout.storage.u.chunk.ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0)
if((idx_info->storage->ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
done:

79
src/H5Dint.c
View File

@ -2848,10 +2848,12 @@ done:
herr_t
H5D__format_convert(H5D_t *dataset, hid_t dxpl_id)
{
H5O_t *oh = NULL; /* Pointer to dataset's object header */
H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */
H5D_chk_idx_info_t idx_info; /* Index info for the current layout */
H5O_layout_t newlayout; /* The new layout */
hbool_t init_new_index = FALSE; /* Indicate that the new chunk index is initialized */
hbool_t delete_old_layout = FALSE; /* Indicate that the old layout message is deleted */
hbool_t add_new_layout = FALSE; /* Indicate that the new layout message is added */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL)
@ -2888,37 +2890,42 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id)
new_idx_info.storage = &newlayout.storage.u.chunk;
/* Initialize version 1 B-tree */
if(newlayout.storage.u.chunk.ops->init && (newlayout.storage.u.chunk.ops->init)(&new_idx_info, dataset->shared->space, dataset->oloc.addr) < 0)
if(new_idx_info.storage->ops->init &&
(new_idx_info.storage->ops->init)(&new_idx_info, dataset->shared->space, dataset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information")
init_new_index = TRUE;
/* If the current chunk index exists */
if(H5F_addr_defined(dataset->shared->layout.storage.u.chunk.idx_addr)) {
if(H5F_addr_defined(idx_info.storage->idx_addr)) {
/* Create v1 B-tree chunk index */
if((newlayout.storage.u.chunk.ops->create)(&new_idx_info) < 0)
if((new_idx_info.storage->ops->create)(&new_idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index")
/* Iterate over the chunks in the current index and insert the chunk addresses
* into the version 1 B-tree chunk index */
if(H5D__chunk_format_convert(dataset, &idx_info, &new_idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate/convert chunk index")
} /* end if */
/* Release the old (i.e. current) chunk index */
if(dataset->shared->layout.storage.u.chunk.ops->dest && (dataset->shared->layout.storage.u.chunk.ops->dest)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
/* Delete the "layout" message */
if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, TRUE, dxpl_id) < 0)
/* Delete the old "current" layout message */
if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE, dxpl_id) < 0)
HGOTO_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message")
HDmemcpy(&dataset->shared->layout, &newlayout, sizeof(H5O_layout_t));
if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
delete_old_layout = TRUE;
/* Append the new layout message to the object header */
if(H5O_msg_append_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &newlayout) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message")
if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &newlayout, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout header message")
add_new_layout = TRUE;
/* Release the old (current) chunk index */
if(idx_info.storage->ops->dest && (idx_info.storage->ops->dest)(&idx_info) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
/* Copy the new layout to the dataset's layout */
HDmemcpy(&dataset->shared->layout, &newlayout, sizeof(H5O_layout_t));
break;
@ -2935,17 +2942,41 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id)
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type")
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type")
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type")
} /* end switch */
done:
/* Release pointer to object header */
if(oh != NULL)
if(H5O_unpin(oh) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header")
if(ret_value < 0 && dataset->shared->layout.type == H5D_CHUNKED) {
/* Remove new layout message */
if(add_new_layout)
if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE, dxpl_id) < 0)
HDONE_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message")
/* Add back old layout message */
if(delete_old_layout)
if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &dataset->shared->layout, dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to add layout header message")
/* Clean up v1 b-tree chunk index */
if(init_new_index) {
if(H5F_addr_defined(new_idx_info.storage->idx_addr)) {
/* Check for valid address i.e. tag */
if(!H5F_addr_defined(dataset->oloc.addr))
HDONE_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "address undefined")
/* Expunge from cache all v1 B-tree type entries associated with tag */
if(H5AC_expunge_tag_type_metadata(dataset->oloc.file, dxpl_id, dataset->oloc.addr, H5AC_BT_ID, H5AC__NO_FLAGS_SET))
HDONE_ERROR(H5E_DATASET, H5E_CANTEXPUNGE, FAIL, "unable to expunge index metadata")
} /* end if */
/* Delete v1 B-tree chunk index */
if(new_idx_info.storage->ops->dest && (new_idx_info.storage->ops->dest)(&new_idx_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL)
} /* end H5D__format_convert() */

149
tools/h5format_convert/h5fc_gentest.c
View File

@ -28,6 +28,7 @@
#define NON_V3_FILE "h5fc_non_v3.h5"
#define EDGE_V3_FILE "h5fc_edge_v3.h5"
#define ERR_LEVEL_FILE "h5fc_err_level.h5"
const char *FILENAME[] = {
"h5fc_ext1_i.h5", /* 0 */
@ -56,8 +57,13 @@ const char *FILENAME[] = {
#define DSET_NDATA_NONE "DSET_NDATA_NONE"
#define DSET_EDGE "DSET_EDGE"
#define DSET_ERR "DSET_ERR"
#define ISTORE_IK 64
#define ISTORE_ERR 1
#define NUM 500
/*
* Function: gen_non()
@ -377,6 +383,146 @@ error:
} /* gen_edge() */
/*
* Function: gen_err_level()
*
* Generate a file to test the situtation described in HDFFV-9434:
* Exceed the limit of v1-btree level
*
* Create a file with H5Pset_istore_k(fcpl, 1).
* Create a chunked dataset with extensible array chunk index and
* appends many chunks to the dataset.
*
* When h5format_convert tries to convert the dataset with
* extensive array index in the file to v1-btree chunk index,
* it will insert the dataset chunks to the v1-btree chunk index.
* The tree will split quickly due to the 'K' value of 1 and the
* tree level will eventually hit the maximum: 2^8(256).
*/
static void
gen_err_level(const char *fname)
{
hid_t fid = -1; /* file ID */
hid_t fapl = -1; /* file access property list */
hid_t fcpl = -1; /* file creation property list */
hid_t sid = -1; /* dataspace id */
hid_t dcpl = -1; /* dataset creation property list */
hid_t did = -1; /* dataset ID */
hid_t fsid = -1; /* file dataspace ID */
hid_t msid = -1; /* memory dataspace ID */
unsigned char *buf = NULL; /* buffer for data */
hsize_t dims[2] = {0, 1}; /* dataset dimension sizes */
hsize_t max_dims[2] = {1, H5S_UNLIMITED}; /* dataset maximum dimension sizes */
hsize_t chunk_dims[2] = {1, 1}; /* chunk dimension sizes */
int n = 0; /* local index variable */
/* Create a new format file */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
goto error;
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
goto error;
/* Set 'K' value to 1 in file creation property list */
if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
goto error;
if(H5Pset_istore_k(fcpl, ISTORE_ERR) < 0)
goto error;
/* Initialize data buffer */
buf = (unsigned char *)HDmalloc(NUM * sizeof(unsigned char *));
HDmemset(buf, 42, NUM * sizeof(unsigned char));
/* Create the test file */
if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
goto error;
/* Create a chunked dataset with extensible array chunk index */
if((sid = H5Screate_simple(2, dims, max_dims)) < 0)
goto error;
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
goto error;
if(H5Pset_chunk(dcpl, 2, chunk_dims) < 0)
goto error;
if((did = H5Dcreate2(fid, DSET_ERR, H5T_NATIVE_UCHAR, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
/* Closing */
if(H5Pclose(dcpl) < 0)
goto error;
if(H5Sclose(sid) < 0)
goto error;
if(H5Dclose(did) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
/* Re-open the file */
if((fid = H5Fopen(fname, H5F_ACC_RDWR, fapl)) < 0)
goto error;
/* Open the dataset */
if((did = H5Dopen2(fid, DSET_ERR, H5P_DEFAULT)) < 0)
goto error;
/* Loop through appending 1 element at a time */
for(n = 0; n < NUM; n++) {
hsize_t start[2] = {0, 0};
hsize_t count[2] = {1, 1};
hsize_t extent[2] = {0, 0};
start[0] = 0;
start[1] = n;
extent[0] = 1;
extent[1] = n+1;
/* Set current dimension sizes for the dataset */
if(H5Dset_extent(did, extent) < 0)
goto error;
/* Set up memory dataspace */
if((msid = H5Screate_simple(2, count, NULL)) < 0)
goto error;
/* Get file dataspace */
if((fsid = H5Dget_space(did)) < 0)
goto error;
if((H5Sselect_hyperslab(fsid, H5S_SELECT_SET, start, NULL, count, NULL)) < 0)
goto error;
/* Write to the dataset */
if(H5Dwrite(did, H5T_NATIVE_UCHAR, msid, fsid, H5P_DEFAULT, buf) < 0)
goto error;
if(H5Sclose(fsid) < 0)
goto error;
if(H5Sclose(msid) < 0)
goto error;
}
/* Closing */
if(H5Dclose(did) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
if(H5Pclose(fapl) < 0)
goto error;
if(buf) free(buf);
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(sid);
H5Dclose(did);
H5Sclose(msid);
H5Sclose(fsid);
H5Fclose(fid);
H5Pclose(fapl);
H5Pclose(fcpl);
} H5E_END_TRY;
} /* gen_err_level() */
/*
* Function: gen_ext()
*
@ -642,6 +788,9 @@ int main(void)
/* Generate a new format file with a no-filter-edge-chunk dataset */
gen_edge(EDGE_V3_FILE);
/* Generate a new format file with 'K' value of 1 in H5Pset_istore_k() */
gen_err_level(ERR_LEVEL_FILE);
/* Generate old/new format file with/without messages in the superblock extension */
for(latest = FALSE; latest <= TRUE; latest++) {
for(i = 0; i < 8; i++) {

2
tools/h5format_convert/h5format_convert.c
View File

@ -310,7 +310,7 @@ convert(hid_t fid, const char *dname)
/* Downgrade the dataset */
if(H5Dformat_convert(did) < 0) {
error_msg("unable to downgrade dataset for \"%s\"\n", dname);
error_msg("unable to downgrade dataset \"%s\"\n", dname);
h5tools_setstatus(EXIT_FAILURE);
goto error;
} else if(verbose_g)

BIN
tools/h5format_convert/testfiles/h5fc_err_level.h5 Normal file
View File

Binary file not shown.

13
tools/h5format_convert/testfiles/h5fc_v_err.ddl Normal file
View File

@ -0,0 +1,13 @@
Process command line options
Open the file tmp.h5
Processing all datasets in the file...
Going to process dataset:/DSET_ERR...
Open the dataset
Retrieve the dataset's layout
Dataset is a chunked dataset
Retrieve the dataset's chunk indexing type
Dataset's chunk indexing type is not version 1 B-tree
Converting the dataset...
Error encountered
Close the file
h5format_convert error: unable to downgrade dataset "/DSET_ERR"

7
tools/h5format_convert/testh5fc.sh.in
View File

@ -99,6 +99,7 @@ $SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_if.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_is.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_sf.h5
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext3_isf.h5
$SRC_H5FORMCONV_TESTFILES/h5fc_err_level.h5
"
LIST_OTHER_TEST_FILES="
@ -128,6 +129,7 @@ $SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_if.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_is.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext2_sf.ddl
$SRC_H5FORMCONV_TESTFILES/old_h5fc_ext3_isf.ddl
$SRC_H5FORMCONV_TESTFILES/h5fc_v_err.ddl
"
#
@ -369,6 +371,11 @@ TOOLTEST_OUT h5fc_v_n_all.ddl h5fc_non_v3.h5 -v -n
#
#
#
# h5format_convert -v h5fc_err_level.h5 (error encountered in converting the dataset)
TOOLTEST_OUT h5fc_v_err.ddl h5fc_err_level.h5 -v
#
#
#
# No output from tests
# 1) Use the tool to convert the dataset
# 2) Verify the chunk indexing type is correct