Working as a support engineer here at Percona is amazing, as you get a variety of requests, ranging from the most trivial questions to questions that require source code review and understanding of the internals of InnoDB, for example.
In our world where High Availability is a must, everything is about being pro-active, and when we need to be reactive we must act fast. To do so we need to ensure we have proper monitoring in place that covers all possible failure scenarios. Unfortunately, that is not always possible and we are always improving and learning as we face new types of issues.
A few days ago one of our customers faced an issue where MySQL identified an InnoDB secondary index corruption and marked that table as corrupted instead of crashing the server. Even though one would think that a single table marked as corrupted is not as bad as an entire server crash, this particular table was key for the whole application, which in the end caused an outage anyway. They wanted to artificially simulate this situation in order to improve their QA / Monitoring.
The Error
1 2 3 4 5 6 7 8 9 | 2019-08-26T15:47:10.526458Z 2 [ERROR] InnoDB: Database page corruption on disk or a failed file read of tablespace test/tb1 page [page id: space=48, page number=8]. You may have to recover from a backup. 2019-08-26T15:47:10.526465Z 2 [Note] InnoDB: Page dump in ascii and hex (16384 bytes): len 16384; hex dc67f35500000008ffffffff000000090000000000 ... InnoDB: End of page dump 2019-08-26T15:47:10.594440Z 2 [Note] InnoDB: Uncompressed page, stored checksum in field1 3697800021, calculated checksums for field1: crc32 3697800020/786197600, innodb 812191569, none 3735928559, stored checksum in field2 3697800020, calculated checksums for field2: crc32 3697800020/786197600, innodb 1337770384, none 3735928559, page LSN 0 3082690, low 4 bytes of LSN at page end 3082690, page number (if stored to page already) 8, space id (if created with >= MySQL-4.1.1 and stored already) 48 InnoDB: Page may be an index page where index id is 49 2019-08-26T15:47:10.594466Z 2 [Note] InnoDB: Index 49 is `b` in table `test`.`tb1` 2019-08-26T15:47:10.594474Z 2 [Note] InnoDB: It is also possible that your operating system has corrupted its own file cache and rebooting your computer removes the error. If the corrupt page is an index page. You can also try to fix the corruption by dumping, dropping, and reimporting the corrupt table. You can use CHECK TABLE to scan your table for corruption. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery. 2019-08-26T15:47:10.594571Z 2 [ERROR] Got error 126 when reading table './test/tb1' |
InnoDB will retry the read 100 times, and if it fails on all of the attempts, the server will assert – otherwise the behavior will vary depending on the version you are using. On 5.5 it will consider the table as corrupted while on 5.7 it will mark the table missing on the data dictionary. Either way, from this moment forward, all queries on that particular table will fail.
InnoDB Internals
InnoDB has a defined layout for it’s in disk structures (redo log, .ibd files, …).
If you are interested in learning or poking around, Jeremy Cole has a project to diagram most of the internal InnoDB structures at https://github.com/jeremycole/innodb_diagrams and also a powerful tool to extract data from innodb at https://github.com/jeremycole/innodb_ruby. The intention of this post is to show you how you can do it manually, so you can get more exposure to internals.
To simulate the corruption we will need to read only a small part of each page header. Here is the list and it’s location as per 5.7 source code:
- Each page is defined by a type – FIL_PAGE_TYPE
- An index page has a value of 45bf (or 17855 in decimal) – FIL_PAGE_INDEX
- Checksum is stored from byte/offset 0 to 4 of each page – FIL_PAGE_SPACE_OR_CHKSUM
- Index ID is stored at byte/offset 28 of each page data – PAGE_INDEX_ID
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | #define FIL_PAGE_TYPE 24 /*!< file page type: FIL_PAGE_INDEX,..., 2 bytes. */ #define FIL_PAGE_INDEX 17855 /*!< B-tree node */ #define FIL_PAGE_SPACE_OR_CHKSUM 0 /*!< in < MySQL-4.0.14 space id the page belongs to (== 0) but in later versions the 'new' checksum of the page */ /**************************************************************//** Gets the index id field of a page. @return index id */ UNIV_INLINE index_id_t btr_page_get_index_id( /*==================*/ const page_t* page) /*!< in: index page */ { return(mach_read_from_8(page + PAGE_HEADER + PAGE_INDEX_ID)); } #define PAGE_HEADER FSEG_PAGE_DATA /* index page header starts at this #define FSEG_PAGE_DATA FIL_PAGE_DATA #define FIL_PAGE_DATA 38U /*!< start of the data on the page */ #define PAGE_INDEX_ID 28 /* index id where the page belongs. This field should not be written to after page creation. */ |
Source code:
storage/innobase/include/fil0fil.h#L507
storage/innobase/include/fil0fil.h#L575
storage/innobase/include/fil0fil.h#L483
storage/innobase/include/btr0btr.ic#L109
storage/innobase/include/page0page.h#L56
storage/innobase/include/fsp0types.h#L68
storage/innobase/include/fil0fil.h#L560
storage/innobase/include/page0page.h#L82
To extract the above information from an .ibd file I will use a small bash script to read each page from the file and export the information we will need:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #!/bin/bash FILE=$1 echo "Reading ${FILE}" PAGE_SIZE=16384 SIZE=$(ls -l ${FILE} | awk '{print $5}') PAGES=$((SIZE / PAGE_SIZE)) echo "FILE HAS ${PAGES} pages" for ((page=1; page<=PAGES; page++)) do OFFSET=$((page * PAGE_SIZE)) PAGETYPE_OFFSET=$((OFFSET + 24)) PAGETYPE=$(xxd -p -l2 -s ${PAGETYPE_OFFSET} ${FILE}) PAGECHECKSUM_OFFSET=$((OFFSET)) PAGECHECKSUM=$(xxd -p -l4 -s ${PAGECHECKSUM_OFFSET} ${FILE}) INDEXID_OFFSET=$((OFFSET + 38 + 28)) INDEXID=$(xxd -p -l8 -s ${INDEXID_OFFSET} ${FILE}) echo "${page} at offset ${OFFSET} has type ${PAGETYPE} and checksum ${PAGECHECKSUM} - ID ${INDEXID}" done |
The last piece for the puzzle is to translate the Index ID to our secondary index. To do it we will make usage of the information_schema table:
1 | SELECT i.NAME, HEX(i.INDEX_ID) FROM information_schema.INNODB_SYS_INDEXES as i JOIN information_schema.INNODB_SYS_TABLES t USING (TABLE_ID) WHERE t.NAME = 'DB/TABLE'; |
Reproducible test case
To reproduce the corruption we will use a test table with one primary key, one secondary index, and 1000 rows:
1 2 3 4 5 | #create table mysql -u root -psekret -e "CREATE TABLE `tb1` ( `ID` int(11) NOT NULL, `b` varchar(100) DEFAULT NULL, PRIMARY KEY (`ID`), KEY `b` (`b`) ) ENGINE=InnoDB" test #populate table for i in $(seq 1 1000); do mysql -psekret -e "INSERT INTO test.tb1 VALUES (${i}, 'marcelo_$i')"; done |
At this point, InnoDB has all the table pages already loaded into InnoDB Buffer Pool. We will force it to read the pages from disk. The most efficient way will be by adding innodb_buffer_pool_load_at_startup=OFF to my.cnf and restart MySQL.
We would now like to check the list of Index ID’s of test/tb1 table:
1 2 3 4 5 6 7 8 | mysql -psekret -e "SELECT i.NAME, HEX(i.INDEX_ID) FROM information_schema.INNODB_SYS_INDEXES as i JOIN information_schema.INNODB_SYS_TABLES t USING (TABLE_ID) WHERE t.NAME = 'test/tb1';" mysql: [Warning] Using a password on the command line interface can be insecure. +---------+-----------------+ | NAME | HEX(i.INDEX_ID) | +---------+-----------------+ | PRIMARY | 30 | | b | 31 | +---------+-----------------+ |
We will be looking for pages which have a type 45bf (FIL_PAGE_INDEX) and Index ID 31. It’s time to execute our bash script to read the .ibd file:
1 2 3 4 5 6 7 8 9 10 11 12 13 | ./read.sh /var/lib/mysql/test/tb1.ibd Reading /var/lib/mysql/test/tb1.ibd FILE HAS 10 pages 1 at offset 16384 has type 0005 and checksum 50312eaf - ID 0000000000000000 2 at offset 32768 has type 0003 and checksum 563aeb4c - ID ffffffff0000ffff 3 at offset 49152 has type 45bf and checksum 30ad20b7 - ID 0000000000000030 4 at offset 65536 has type 45bf and checksum 96977741 - ID 0000000000000031 5 at offset 81920 has type 45bf and checksum 5aa506c9 - ID 0000000000000030 6 at offset 98304 has type 45bf and checksum 20f3fe3f - ID 0000000000000030 7 at offset 114688 has type 45bf and checksum 081fbb8f - ID 0000000000000030 8 at offset 131072 has type 45bf and checksum dc67f354 - ID 0000000000000031 9 at offset 147456 has type 45bf and checksum 370eb81c - ID 0000000000000031 10 at offset 163840 has type and checksum - ID |
Let’s get page eight as the page we will be manipulating. It starts at offset 131072 of tb1.ibd, has a page type 45bf, the index ID field is 31, and it has a checksum of dc67f354. To manipulate the page, we will be changing the checksum field to dc67f355.
1 2 3 4 | printf 'xdcx67xf3x55' | dd of=/var/lib/mysql/test/tb1.ibd bs=1 seek=131072 count=4 conv=notrunc 4+0 records in 4+0 records out 4 bytes (4 B) copied, 0.000121983 s, 32.8 kB/s |
Now, next time we try to read this particular page, MySQL will identify a corruption because the checksum doesn’t match. We don’t want the server to assert, so we will change the checksum back to its original value right after we attempt to read the table. This way MySQL will only mark this table as corrupted and as missing in the data dictionary:
1 | mysql -psekret -e "SELECT * FROM test.tb1" & sleep 0.1 && printf 'xdcx67xf3x54' | dd of=/var/lib/mysql/test/tb1.ibd bs=1 seek=131072 count=4 conv=notrunc |
That is it! We have provoked an InnoDB secondary index corruption and now all subsequent queries will fail. Now you can make sure your monitoring tool / QA process covers this type of situations.
If in your version of MySQL it has only marked the table as corrupted, a simple CHECK TABLE will bring it back to a usable state. If your version of MySQL is reporting the table as missing from the data dictionary, you can just restart MySQL to force it to re-read the table pages again, since we have changed the checksum back to its original value, it won’t report any error at this time.
Never try to change any MySQL file manually on a production environment. This can cause unrecoverable corruption and data loss.
for better understanding the corruption in practice
https://www.academia.edu/37741482/Corruption_as_a_net_of_influences_links_and_connections