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[svn-r6632] Purpose:

Browse Source 
Bug fix

Description:
    This fixes a bug in the low-level metadata caching code in the library
which could possibly lose metadata during file I/O when a lot of objects are
inserted into a group.

    This also fixes a couple of (similar) fencepost bugs in the B-tree
deletion code.

Solution:
    For the metadata bug - call the low-level driver's 'write' routine instead
of H5FD_write.

    For the B-tree bug - include the correct number of keys.

Platforms tested:
    FreeBSD 4.8 (sleipnir) w/C++
    Linux 2.4 (burrwhite) w/FORTRAN
    Solaris 2.7 (arabica) w/FORTRAN
    IRIX64 6.5 (modi4) w/FORTRAN & parallel

    (h5committest is still not working for me on burrwhite)

Misc. update:
This commit is contained in:
Quincey Koziol 2003-04-11 11:37:18 -05:00
parent 705194a4ea
commit e804b4c75b
5 changed files with 118 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
release_docs/RELEASE.txt
View File

@ -35,6 +35,12 @@ Bug Fixes since HDF5-1.4.0
Library
-------
* Fixed error in B-tree deletion routine which could cause groups to be
corrupted when objects are removed from them.
QAK - 2003/04/11
* Fixed error in file space freeing code which could cause metadata to
fail to be written to the file.
QAK - 2003/04/11
* -O caused errors in AIX 5.x platforms. Removed it from
--enable-production mode. AKC - 2003/03/31
* Corrected metadata caching bug in parallel I/O which could cause hangs

4
src/H5B.c
View File

@ -1738,7 +1738,7 @@ H5B_remove_helper(H5F_t *f, hid_t dxpl_id, haddr_t addr, const H5B_class_t *type
HDmemmove(bt->child,
bt->child+1,
bt->nchildren * sizeof(haddr_t));
for (i=0; i<bt->nchildren; i++) {
for (i=0; i<=bt->nchildren; i++) {
bt->key[i].dirty = bt->key[i+1].dirty;
if (bt->key[i+1].nkey) {
bt->key[i].nkey = bt->native + i*type->sizeof_nkey;
@ -1787,7 +1787,7 @@ H5B_remove_helper(H5F_t *f, hid_t dxpl_id, haddr_t addr, const H5B_class_t *type
HDmemmove(bt->child+idx,
bt->child+idx+1,
(bt->nchildren-idx) * sizeof(haddr_t));
for (i=idx; i<bt->nchildren; i++) {
for (i=idx; i<=bt->nchildren; i++) {
bt->key[i].dirty = bt->key[i+1].dirty;
if (bt->key[i+1].nkey) {
bt->key[i].nkey = bt->native + i*type->sizeof_nkey;

3
src/H5FD.c
View File

@ -2154,7 +2154,8 @@ H5FD_free(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t si
H5_ASSIGN_OVERFLOW(tail_size,(file->accum_loc+file->accum_size)-tail_addr,haddr_t,size_t);
/* Write out the part of the accumulator after the block to free */
if (H5FD_write(file, H5FD_MEM_DEFAULT, dxpl_id, tail_addr, tail_size, file->meta_accum+(tail_addr-file->accum_loc))<0)
/* (Use the driver's write call directly - to avoid looping back and writing to metadata accumulator) */
if ((file->cls->write)(file, H5FD_MEM_DEFAULT, dxpl_id, tail_addr, tail_size, file->meta_accum+(tail_addr-file->accum_loc))<0)
HGOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "file write request failed");
} /* end if */

2
test/h5test.h
View File

@ -50,7 +50,7 @@ extern MPI_Info h5_io_info_g; /* MPI INFO object for IO */
* spaces. If the h5_errors() is used for automatic error handling then
* the H5_FAILED() macro is invoked automatically when an API function fails.
*/
#define TESTING(WHAT) {printf("%-70s", "Testing " WHAT); fflush(stdout);}
#define TESTING(WHAT) {printf("Testing %-62s",WHAT); fflush(stdout);}
#define PASSED() {puts(" PASSED");fflush(stdout);}
#define H5_FAILED() {puts("*FAILED*");fflush(stdout);}
#define SKIPPED() {puts(" -SKIP-");fflush(stdout);}

109
test/unlink.c
View File

@ -24,11 +24,16 @@ const char *FILENAME[] = {
"unlink",
"new_move_a",
"new_move_b",
"lunlink",
NULL
};
#define THE_OBJECT "/foo"
/* Macros for test_create_unlink() */
#define GROUPNAME "Group"
#define NGROUPS 1000
/*-------------------------------------------------------------------------
* Function: test_one
@ -451,6 +456,83 @@ check_new_move(void)
return -1;
}
/*-------------------------------------------------------------------------
* Function: test_create_unlink
*
* Purpose: Creates and then unlinks a large number of objects
*
* Return: Success: 0
* Failure: number of errors
*
* Programmer: Quincey Koziol
* Friday, April 11, 2003
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int test_create_unlink(const char *msg, hid_t fapl)
{
hid_t file, group;
unsigned u;
char groupname[1024];
char filename[1024];
TESTING(msg);
/* Create file */
h5_fixname(FILENAME[3], fapl, filename, sizeof filename);
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0)
{
H5_FAILED();
puts(" Creating file failed");
goto error;
}
/* Create a many groups to remove */
for(u=0; u<NGROUPS; u++) {
sprintf(groupname,"%s %u",GROUPNAME,u);
if((group = H5Gcreate (file, groupname, 0))<0)
{
H5_FAILED();
printf("group %s creation failed\n",groupname);
goto error;
}
if(H5Gclose (group)<0)
{
H5_FAILED();
printf("closing group %s failed\n",groupname);
goto error;
}
} /* end for */
/* Remove the all the groups */
for(u=0; u<NGROUPS; u++) {
sprintf(groupname,"%s %u",GROUPNAME,u);
if(H5Gunlink (file, groupname)<0)
{
H5_FAILED();
printf("Unlinking group %s failed\n",groupname);
goto error;
}
} /* end for */
/* Close file */
if(H5Fclose(file)<0)
{
H5_FAILED();
printf("Closing file failed\n");
goto error;
}
PASSED();
return 0;
error:
return -1;
} /* end test_create_unlink() */
/*-------------------------------------------------------------------------
* Function: main
@ -471,10 +553,16 @@ check_new_move(void)
int
main(void)
{
hid_t fapl, file;
hid_t fapl, fapl2, file;
int nerrors = 0;
char filename[1024];
/* Metadata cache parameters */
int mdc_nelmts;
size_t rdcc_nelmts;
size_t rdcc_nbytes;
double rdcc_w0;
/* Open */
h5_reset();
fapl = h5_fileaccess();
@ -482,6 +570,19 @@ main(void)
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0)
goto error;
/* Make copy of regular fapl, to turn down the elements in the metadata cache */
if((fapl2=H5Pcopy(fapl))<0)
goto error;
/* Get FAPL cache settings */
if(H5Pget_cache(fapl2,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0)<0)
printf("H5Pget_cache failed\n");
/* Change FAPL cache settings */
mdc_nelmts=1;
if(H5Pset_cache(fapl2,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0)<0)
printf("H5Pset_cache failed\n");
/* Tests */
nerrors += test_one(file);
nerrors += test_many(file);
@ -489,6 +590,11 @@ main(void)
nerrors += test_rename(file);
nerrors += test_new_move();
nerrors += check_new_move();
/* Test creating & unlinking lots of objects with default FAPL */
nerrors += test_create_unlink("create and unlink large number of objects",fapl);
/* Test creating & unlinking lots of objects with a 1-element metadata cache FAPL */
nerrors += test_create_unlink("create and unlink large number of objects with small cache",fapl2);
/* Close */
if (H5Fclose(file)<0) goto error;
@ -503,4 +609,3 @@ main(void)
return 1;
}