diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 2 | ||||
| -rw-r--r-- | src/H5Oalloc.c | 23 | ||||
| -rw-r--r-- | src/H5Odbg.c | 5 | ||||
| -rw-r--r-- | src/H5Omessage.c | 5 | ||||
| -rw-r--r-- | test/tattr.c | 135 |
5 files changed, 158 insertions, 12 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 6d4708a..142a9cc 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -112,6 +112,8 @@ Bug Fixes since HDF5-1.8.8 Library ------- + - Fixed rare corruption bugs that could occur when using the new object + header format. (NAF - 2012/3/15 - HDFFV-7879) - Fixed error when creating a contiguous dataset with a zero-sized dataspace and space allocation time set to 'early'. (QAK - 2012/3/12) - Creating a dataset in a read-only file caused seg fault when the file 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 13ad73d..8d1c318 100644 --- a/src/H5Omessage.c +++ b/src/H5Omessage.c @@ -2171,9 +2171,8 @@ 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 ed2a861..b23080c 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 */ |