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-rw-r--r--release_docs/RELEASE.txt2
-rw-r--r--src/H5Oalloc.c23
-rw-r--r--src/H5Odbg.c5
-rw-r--r--src/H5Omessage.c5
-rw-r--r--test/tattr.c135
5 files changed, 158 insertions, 12 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 7cfb763..8055516 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -365,6 +365,8 @@ Bug Fixes since HDF5-1.8.0 release
Library
-------
+ - Fixed rare corruption bugs that could occur when using the new object
+ header format. (NAF - 2012/3/15 - HDFFV-7879)
- Creating a dataset in a read-only file caused seg fault when the file
is closed. It's fixed. The error stack is returned correctly
now. (SLU - 2012/1/25. Issue 7756)
diff --git a/src/H5Oalloc.c b/src/H5Oalloc.c
index dfc844d..05322af 100644
--- a/src/H5Oalloc.c
+++ b/src/H5Oalloc.c
@@ -647,17 +647,18 @@ H5O_alloc_extend_chunk(H5F_t *f, hid_t dxpl_id, H5O_t *oh, unsigned chunkno,
/* Wipe new space for chunk */
HDmemset(oh->chunk[chunkno].image + old_size, 0, oh->chunk[chunkno].size - old_size);
+ /* Move chunk 0 data up if the size flags changed */
+ if(adjust_size_flags)
+ HDmemmove(oh->chunk[0].image + H5O_SIZEOF_HDR(oh) - H5O_SIZEOF_CHKSUM_OH(oh),
+ oh->chunk[0].image + H5O_SIZEOF_HDR(oh) - H5O_SIZEOF_CHKSUM_OH(oh) - extra_prfx_size,
+ old_size - (size_t)H5O_SIZEOF_HDR(oh) + extra_prfx_size);
+
/* Spin through existing messages, adjusting them */
for(u = 0; u < oh->nmesgs; u++) {
/* Adjust raw addresses for messages in this chunk to reflect new 'image' address */
- if(oh->mesg[u].chunkno == chunkno) {
+ if(oh->mesg[u].chunkno == chunkno)
oh->mesg[u].raw = oh->chunk[chunkno].image + extra_prfx_size + (oh->mesg[u].raw - old_image);
- /* Flag message as dirty directly */
- /* (we mark the entire chunk dirty when we update its size) */
- oh->mesg[u].dirty = TRUE;
- } /* endif */
-
/* Find continuation message which points to this chunk and adjust chunk's size */
/* (Chunk 0 doesn't have a continuation message that points to it and
* it's size is directly encoded in the object header) */
@@ -1331,8 +1332,9 @@ H5O_move_cont(H5F_t *f, hid_t dxpl_id, H5O_t *oh, unsigned cont_u)
move_end = cont_msg->raw + cont_msg->raw_size;
cont_chunkno = cont_msg->chunkno;
- /* Convert continuation message into a null message */
- if(H5O_release_mesg(f, dxpl_id, oh, cont_msg, TRUE) < 0)
+ /* Convert continuation message into a null message. Do not delete
+ * the target chunk yet, so we can still copy messages from it. */
+ if(H5O_release_mesg(f, dxpl_id, oh, cont_msg, FALSE) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTDELETE, FAIL, "unable to convert into null message")
/* Protect chunk */
@@ -1354,7 +1356,6 @@ H5O_move_cont(H5F_t *f, hid_t dxpl_id, H5O_t *oh, unsigned cont_u)
HDmemcpy(move_start, curr_msg->raw - H5O_SIZEOF_MSGHDR_OH(oh), move_size);
curr_msg->raw = move_start + H5O_SIZEOF_MSGHDR_OH(oh);
curr_msg->chunkno = cont_chunkno;
- curr_msg->dirty = TRUE;
chk_dirtied = TRUE;
/* Adjust location to move messages to */
@@ -1362,6 +1363,10 @@ H5O_move_cont(H5F_t *f, hid_t dxpl_id, H5O_t *oh, unsigned cont_u)
} /* end else */
} /* end if */
+ /* Delete the target chunk */
+ if(H5O_chunk_delete(f, dxpl_id, oh, deleted_chunkno) < 0)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTDELETE, FAIL, "unable to remove chunk from cache")
+
HDassert(move_start <= (move_end + gap_size));
/* Check if there is space remaining in the continuation message */
diff --git a/src/H5Odbg.c b/src/H5Odbg.c
index ce8b870..5c07b64 100644
--- a/src/H5Odbg.c
+++ b/src/H5Odbg.c
@@ -167,6 +167,8 @@ H5O_assert(const H5O_t *oh)
H5O_cont_t *cont = (H5O_cont_t *)curr_msg->native;
hbool_t found_chunk = FALSE; /* Found a chunk that matches */
+ HDassert(cont);
+
/* Increment # of continuation messages found */
cont_msgs_found++;
@@ -186,6 +188,9 @@ H5O_assert(const H5O_t *oh)
else {
meta_space += (size_t)H5O_SIZEOF_MSGHDR_OH(oh);
mesg_space += curr_msg->raw_size;
+
+ /* Make sure the message has a native form if it is marked dirty */
+ HDassert(curr_msg->native || !curr_msg->dirty);
} /* end else */
/* Make certain that the message is in a valid chunk */
diff --git a/src/H5Omessage.c b/src/H5Omessage.c
index a3d02d1..f12c835 100644
--- a/src/H5Omessage.c
+++ b/src/H5Omessage.c
@@ -2161,9 +2161,8 @@ H5O_msg_flush(H5F_t *f, H5O_t *oh, H5O_mesg_t *mesg)
/* Make certain that null messages aren't in chunks w/gaps */
if(H5O_NULL_ID == msg_id)
HDassert(oh->chunk[mesg->chunkno].gap == 0);
-
- /* Unknown messages should always have a native pointer */
- if(mesg->type == H5O_MSG_UNKNOWN)
+ else
+ /* Non-null messages should always have a native pointer */
HDassert(mesg->native);
#endif /* NDEBUG */
diff --git a/test/tattr.c b/test/tattr.c
index 82873b5..1285f0e 100644
--- a/test/tattr.c
+++ b/test/tattr.c
@@ -128,6 +128,8 @@ float attr_data5=(float)-5.123; /* Test data for 5th attribute */
#define ATTR7_NAME "attr 1 - 000000"
#define ATTR8_NAME "attr 2"
+#define LINK1_NAME "Link1"
+
#define NATTR_MANY_OLD 350
#define NATTR_MANY_NEW 35000
@@ -10421,6 +10423,137 @@ test_attr_bug7(hid_t fcpl, hid_t fapl)
/****************************************************************
**
+** test_attr_bug8(): Test basic H5A (attribute) code.
+** (Really tests object header code).
+** Tests adding a link and attribute to a group in such a
+** way as to cause the "chunk #0 size" field to expand
+** when some object header messages are not loaded into
+** cache. Before the bug was fixed, this would prevent
+** these messages from being shifted to the correct
+** position as the expansion algorithm marked them dirty,
+** invalidating the raw form, when there was no native
+** form to encode.
+**
+****************************************************************/
+static void
+test_attr_bug8(hid_t fcpl, hid_t fapl)
+{
+ hid_t fid; /* File ID */
+ hid_t aid; /* Attribute ID */
+ hid_t sid; /* Dataspace ID */
+ hid_t gid; /* Group ID */
+ hid_t oid; /* Object ID */
+ hsize_t dims = 256; /* Attribute dimensions */
+ H5O_info_t oinfo; /* Object info */
+ H5A_info_t ainfo; /* Attribute info */
+ haddr_t root_addr; /* Root group address */
+ herr_t ret; /* Generic return status */
+
+ /* Output message about test being performed */
+ MESSAGE(5, ("Testing attribute expanding object header with undecoded messages\n"));
+
+
+ /* Create committed datatype to operate on. Use a committed datatype so that
+ * there is nothing after the object header and the first chunk can expand and
+ * contract as necessary. */
+ fid = H5Fcreate(FILENAME, H5F_ACC_TRUNC, fcpl, fapl);
+ CHECK(fid, FAIL, "H5Fcreate");
+ gid = H5Gcreate2(fid, GROUP1_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ CHECK(gid, FAIL, "H5Gcreate2");
+
+ /* Get root group address */
+ ret = H5Oget_info(fid, &oinfo);
+ CHECK(ret, FAIL, "H5Oget_info");
+ root_addr = oinfo.addr;
+
+ /*
+ * Create link to root group
+ */
+ ret = H5Lcreate_hard(fid, "/", gid, LINK1_NAME, H5P_DEFAULT, H5P_DEFAULT);
+ CHECK(ret, FAIL, "H5Lcreate_hard");
+
+ /* Close file */
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+ ret = H5Gclose(gid);
+ CHECK(ret, FAIL, "H5Gclose");
+
+ /* Open file */
+ fid = H5Fopen(FILENAME, H5F_ACC_RDONLY, fapl);
+ CHECK(fid, FAIL, "H5Fopen");
+
+ /* Check link */
+ gid = H5Gopen2(fid, GROUP1_NAME, H5P_DEFAULT);
+ CHECK(gid, FAIL, "H5Gopen2");
+ oid = H5Oopen(gid, LINK1_NAME, H5P_DEFAULT);
+ CHECK(oid, FAIL, "H5Oopen");
+ ret = H5Oget_info(oid, &oinfo);
+ CHECK(ret, FAIL, "H5Oget_info");
+ if(oinfo.addr != root_addr)
+ TestErrPrintf("incorrect link target address: addr: %llu, expected: %llu\n", (long long unsigned)oinfo.addr, (long long unsigned)root_addr);
+
+ /* Close file */
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+ ret = H5Gclose(gid);
+ CHECK(ret, FAIL, "H5Gclose");
+ ret = H5Oclose(oid);
+ CHECK(ret, FAIL, "H5Oclose");
+
+ /* Open file */
+ fid = H5Fopen(FILENAME, H5F_ACC_RDWR, fapl);
+ CHECK(fid, FAIL, "H5Fopen");
+
+ /*
+ * Create attribute. Should cause chunk size field to expand by 1 byte
+ * (1->2).
+ */
+ gid = H5Gopen2(fid, GROUP1_NAME, H5P_DEFAULT);
+ CHECK(gid, FAIL, "H5Gopen2");
+ sid = H5Screate_simple(1, &dims, NULL);
+ CHECK(sid, FAIL, "H5Screate_simple");
+ aid = H5Acreate2(gid, ATTR1_NAME, H5T_STD_I8LE, sid, H5P_DEFAULT, H5P_DEFAULT);
+ CHECK(aid, FAIL, "H5Acreate2");
+
+ /* Close file */
+ ret = H5Aclose(aid);
+ CHECK(ret, FAIL, "H5Aclose");
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+ ret = H5Gclose(gid);
+ CHECK(ret, FAIL, "H5Gclose");
+
+ /* Open file */
+ fid = H5Fopen(FILENAME, H5F_ACC_RDONLY, fapl);
+ CHECK(fid, FAIL, "H5Fopen");
+
+ /* Check link and attribute */
+ gid = H5Gopen2(fid, GROUP1_NAME, H5P_DEFAULT);
+ CHECK(gid, FAIL, "H5Gopen2");
+ oid = H5Oopen(gid, LINK1_NAME, H5P_DEFAULT);
+ CHECK(oid, FAIL, "H5Oopen");
+ ret = H5Oget_info(oid, &oinfo);
+ CHECK(ret, FAIL, "H5Oget_info");
+ if(oinfo.addr != root_addr)
+ TestErrPrintf("incorrect link target address: addr: %llu, expected: %llu\n", (long long unsigned)oinfo.addr, (long long unsigned)root_addr);
+ ret = H5Aget_info_by_name(gid, ".", ATTR1_NAME, &ainfo, H5P_DEFAULT);
+ CHECK(ret, FAIL, "H5Aget_info_by_name");
+ if(ainfo.data_size != dims)
+ TestErrPrintf("attribute data size different: data_size=%llu, should be %llu\n", (long long unsigned)ainfo.data_size, (long long unsigned)dims);
+
+ /* Close IDs */
+ ret = H5Oclose(oid);
+ CHECK(ret, FAIL, "H5Oclose");
+ ret = H5Gclose(gid);
+ CHECK(ret, FAIL, "H5Gclose");
+ ret = H5Sclose(sid);
+ CHECK(ret, FAIL, "H5Sclose");
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+} /* test_attr_bug8() */
+
+/****************************************************************
+**
** test_attr(): Main H5A (attribute) testing routine.
**
****************************************************************/
@@ -10566,6 +10699,7 @@ test_attr(void)
test_attr_bug5(my_fcpl, my_fapl); /* Test opening/closing attributes through different file handles */
test_attr_bug6(my_fcpl, my_fapl); /* Test reading empty attribute */
test_attr_bug7(my_fcpl, my_fapl); /* Test creating and deleting large attributes in ohdr chunk 0 */
+ test_attr_bug8(my_fcpl, my_fapl); /* Test attribute expanding object header with undecoded messages */
} /* end for */
} /* end if */
else {
@@ -10593,6 +10727,7 @@ test_attr(void)
/* Skip test_attr_bug7 because it is specific to the new object
* header format and in fact fails if used with the old format, due
* to the attributes being larger than 64K */
+ test_attr_bug8(fcpl, my_fapl); /* Test attribute expanding object header with undecoded messages */
} /* end else */
} /* end for */
generated by cgit v0.12 at 2024-07-08 05:36:27 (GMT)