With InnoDB’s Transportable Tablespaces, Recovering Data from Stranded .ibd Files is a Thing of the Past

Being a data recovery specialist and having recovered countless GBs of corrupted, and/or stranded, InnoDB data in my days, I am very happy to hear about the new InnoDB Transportable Tablespaces coming in MySQL 5.6!

Back in the day, if you had a stranded .ibd file (the individual InnoDB data file with –innodb-file-per-table option), you basically had nothing (even though that file contained all of the data). This was because unless you had the original instance that that particular .ibd file (table) originated from, there was no way to load it, import, or dump from it. So it was not of much use, though all the data was *right* there.

Thus I created the method of Recovering an InnoDB table from only an .ibd file (I should note that this was before the InnoDB Recovery Tool had been released, which can also be used to recover data from a stranded .ibd file too).

However, if you’ve used either my method or the InnoDB Recovery Tool for such a job, it can be a bit of work to get the data dumped. For those experienced, it goes much faster. But still, you cannot get any faster than just being able to (roughly) import the individual tablespace right into any running MySQL 5.6 instance. 🙂

Nice work! 🙂

Note: Again, I must mention this is only in MySQL 5.6, so if you have a stranded .ibd file you need to recover data from pre-5.6, you’ll either need to use my method or the InnoDB Recovery Tool.


Dealing with Assertion failure in file fut0lst.ic : addr.page == FIL_NULL || addr.boffset >= FIL_PAGE_DATA

I recently wrote an article on dealing with an assertion failure in log/log0recv.c, specifically !page || (ibool)!!page_is_comp(page) == dict_table_is_comp(index->table).

I mention it because this occurred after a system outage, and I just encountered another system outage (either HDD power outage or some other serious HDD event), with a completely different assertion failure and error message. Similar to the one above, it’s also kind of obscure, so I wanted to post this so people searching for it will find this.

For reference, the first outage assertion failure was this:

InnoDB: Assertion failure in thread 139838283589376 in file 
log/log0recv.c line 1094
InnoDB: Failing assertion: !page || (ibool)!!page_is_comp(page) == 

Here is the new assertion failure:

111201 16:45:00 InnoDB: Assertion failure in thread 4500 in 
file fut0lst.ic line 83
InnoDB: Failing assertion: addr.page == FIL_NULL || addr.boffset >= 

As you can see, they are completely different, yet both due to similar, catastrophic events:

In fact, there are a number of relevant/useful snippets from this error log (in case you see one or more of these):

InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Warning: a page in the doublewrite buffer is not within space
InnoDB: bounds; space id 0 page number 2248, page 22 in doublewrite buf.
InnoDB: Warning: a page in the doublewrite buffer is not within space
InnoDB: bounds; space id 0 page number 1775, page 31 in doublewrite buf.
111201 16:45:00 InnoDB: ERROR: We were only able to scan the log up to
InnoDB: 670800896, but a checkpoint was at 670801309.
InnoDB: It is possible that the database is now corrupt!
111201 16:45:00 InnoDB: Error: page 7 log sequence number 924466223
InnoDB: is in the future! Current system log sequence number 670801309.
111201 16:45:00 InnoDB: Assertion failure in thread 4500 in file 
fut0lst.ic line 83
InnoDB: Failing assertion: addr.page == FIL_NULL || addr.boffset
111201 16:45:00 - mysqld got exception 0xc0000005 ;
000000013F6A4C6F mysqld.exe!my_osmaperr()
000000013F69B9A0 mysqld.exe!my_osmaperr()
000000013F4727D6 mysqld.exe!?ha_initialize_handlerton@@
000000013F46C172 mysqld.exe!?plugin_lock_by_name@@
000000013F4713E9 mysqld.exe!?plugin_init@@YAHPEAHPEAPEADH@Z()
000000013F45BDA7 mysqld.exe!handle_shutdown()
000000013F45C91A mysqld.exe!?win_main@@YAHHPEAPEAD@Z()
000000013F45CD90 mysqld.exe!?mysql_service@@YAHPEAX@Z()
000000013F45D0A3 mysqld.exe!?mysqld_main@@YAHHPEAPEAD@Z()
000000013F7FBB27 mysqld.exe!my_mb_ctype_mb()
00000000777F652D kernel32.dll!BaseThreadInitThunk()
0000000077A2C521 ntdll.dll!RtlUserThreadStart()

As you can see, the corruption was severe … so severe that InnoDB wouldn’t even start with innodb_force_recovery set to 6!

As discussed in the previous post, setting innodb_doublewrite=1, innodb_flush_log_at_trx_commit=1, sync_binlog=1, and having a battery backed cache can be the best bets against such issues.

However, I will say that in this case, innodb_flush_log_at_trx_commit=1 and innodb_doublewrite=1 were both set, and binary logging had been disabled, leaving only the battery backed cache to be desired.

Luckily, this was a test environment (and recovery from a backup was possible). Otherwise, using the InnoDB Recovery Tool would be necessary, which can be an undertaking.

Morals of the story: take regular backups (as always) and invest in a battery backed cache. 🙂


Added a Table of Contents

Not a big deal, but I just added a “Table of Contents” page to my blog to make finding older articles much easier.

I noticed most of my posts are quite lengthy, and it can take a bit of searching/clicking to find an older entry. So unless you happen to recall the ‘month/year’ it was published, which I don’t even remember that, then hopefully this will help.

Really simple, and looks just like this:

My hopes are that this will aid in making some posts easier to find (such as ones about InnoDB Recovery, Recovery with an Individual .ibd, Proxy-related articles, Error-related articles, How-to posts, and so forth).

You can see the full “table of contents” here:


Happy reading 🙂


How to Recover Data using the InnoDB Recovery Tool

As you may or may not know, there is a tool called the InnoDB Recovery Tool which can allow you to recover data from InnoDB tables that you cannot otherwise get the data from.

“This set of tools could be used to check InnoDB tablespaces and to recover data from damaged tablespaces or from dropped/truncated InnoDB tables.”


This is a very handy tool, however, the documentation on how to use it is a bit limited when it comes to actually recovering the data, so I thought I’d post a step-by-step tutorial on how to use this tool.

1. Download the InnoDB Recovery Tool (latest version is 0.3)

2. Unpack the download to the location of your choice

3. Create your table_defs.h file using the create_defs.pl script. Note the below creates a table_defs.h file based on only one table, t1, from the database named test:

cd innodb-recovery-tool-0.3/
./create_defs.pl --user=root --password=mysql --db=test --table=t1 > table_defs.h

4. Copy the newly created table_defs.h fle to the innodb-recovery-tool-0.3/include/ directory.

5. Now is time to build/compile the InnoDB Recovery Tool

cd innodb-recovery-tool-0.3/mysql-source/
cd ..

At this point, you’re almost ready to begin to recover the data. However, let me point out a couple items at this stage. The InnoDB Recovery Tool documentation says you can use the page_parser program to split up the tablespace. Since this page_parser program is now created (after compilation and make), you can use this to break apart the tablespace. However, in my case, I did this, but the page_parser didn’t work as well as I expected. This could be due to the corruption in the tablespace files (ibdata1 and ibdata2). So, I simply tried to recover based off the entire ibdata files. I found that I recovered much more data by just running the recovery against the ibdata files, rather than against the split-up pages. If you opt for this method, then you can skip steps 6, 7, and 8.

6. Should you want to use the page_parser, here is how you run it:

cd innodb-recovery-tool-0.3/
./page_parser -f /home/chris/Desktop/test/ibdata1 /home/chris/Desktop/test/ibdata2 -5

Note that the -f indicates the file(s) to use, and the -5 indicates the ibdata files are from MySQL version 5.0.

7. Should you use the page_parser, you must also load the ibdata file(s) and capture the InnoDB tablespace monitor output. This part is described on the InnoDB Tools how-to.

8. After running the above, you’ll want to capture all of the primary key index positions for each table you want to recover. For instance, you might see something like “0 135” for the index position of a primary key. This will correspond to the folder named “0-135” that is created by page_parser.

9. Now you are ready to recover the data for the first table.

(Note that you could create a table_defs.h file based on all of the tables you want to recover. And then you can recover all of the data at once, however, the problem with this is the data is all mis-matched into one big file. So you might have a row for one table followed by a row from another table. If you’re good with sed/awk, this might not be a problem for you, as you can then split it apart. However, it might be easier to create a single table_defs.h file for each table, and then recover the data table-by-table.)

If you want to recover the data based on the page_parser output, then you would use the following command:

./constraints_parser -f /home/chris/Desktop/innodb-recovery-0.3/pages-1239037839/0-135/50-00000050.page -5 -V

Note that the -V is for verbose mode. It is best to use this initially to make sure the data being recovered looks to be correct. Once you’ve verified it looks correct, then simply run the above command without the -V and pipe the output to a text file.

Should you not want to use the page_parser, and just run constraints_parser directly against the ibdata file(s), then issue the following command instead:

./constraints_parser -f /home/chris/Desktop/test/ibdata1 /home/chris/Desktop/test/ibdata2 -5 > output.txt

As for the recovered data itself, note that this data is displayed in a tab-delimited text format that the InnoDB Recovery tool dumps it in (default, not configurable yet).

For instance, here is a sample of data recovered for the t1 table:

t1 128992703 84118144 301989888 224000 33558272 268435456 ""
t1 0 0 34796032 0 530 838926338 ""
t1 1886545261 268455808 256 497 880803840 2949392 ""
t1 1398034253 1953654117 1952672116 2037609569 1952801647 1970173042 ""
t1 402667648 755047491 1431524431 1296388657 825372977 825308725 "5"
t1 536884352 755050563 1431524431 1296388658 842150450 842162531 "t"
t1 671103872 755053635 1431524431 1296388663 926365495 926365495 "77"
t1 524288 0 755056707 1431524431 1296388705 1668573558 ""
t1 524288 0 755059779 1431524431 1296388705 1668573558 ""
t1 524288 0 755062851 1431524431 1296388705 1668573558 ""
t1 525312 0 755065923 1431524431 1296388705 1668573558 ""
t1 524288 0 755068995 1431524431 1296388705 1668573558 ""
t1 524288 0 755072067 1431524431 1296388705 1668573558 ""
t1 524288 0 755075139 1431524431 1296388705 1668573558 ""
t1 525312 0 755078211 1431524431 1296388705 1668573558 ""
t1 524288 0 755081283 1431524431 1296388705 1668573558 ""
t1 524288 0 755084355 1431524431 1296388705 1668573558 ""
t1 524288 0 755047491 1431524431 1296388705 1668573558 ""
t1 524288 0 755047491 1431524431 1296388705 1668573558 ""
t1 0 0 0 0 0 0 ""
t1 0 0 0 0 0 0 ""
t1 0 0 0 0 0 0 ""
t1 0 0 0 0 0 0 ""
t1 0 0 0 0 0 0 ""

You can see each line is pre-pended with the table name (followed by a tab).

You can also see at the end (of the above output) there are a number of empty rows. These are just garbage rows, and can be deleted before you import or afterwards. You’ll see similar such rows in most of the recovered tables’ data as well. However, don’t just delete from the end of the file, as actual data rows are scattered all throughout the files.

I’d also suggest creating some temporary tables using the same CREATE TABLE commands but without any keys or indexes. This will allow you to import the data easier, and then you can clean it up with simple SQL commands. And after that, then you could simply add back your primary keys, indexes, and referential keys.

Should you follow my approach and do this per-table, then you just need to create your new table_defs.h file, re-compile and make, then re-run the constraints_parser just as you did above. Since it is built with the new table_defs.h file, it will now extract the data for this table, so no other changes need to be made.

10. Format the dump file(s) so that it can be imported into the appropriate table(s).

11. Import the data, and clean up the garbage rows.

12. Re-create any needed indexes and/or referential keys.

Recovering an InnoDB table from only an .ibd file.

Sometime you may need to recover a table when all you have is the .ibd file. In this case, if you try to load it into a new instance, your likely to encounter some errors about the table id not matching. And there is not really a way around this.

However, I’ve found two work-arounds for this:

Note: You will need the .ibd file and the CREATE TABLE statement for each table you want to recover using these methods.

  1. Simulate the internal InnoDB table counter. That is, create work tables (with innodb_file_per_table enabled) until you have the internal pointer of table id equal to (1 – id_of_ibd_table_you_need_to_restore). (See Method #1)
  2. Manually hex edit the .ibd file, changing the table id. (See Method #2)

*Note: There are some internal structures with this meta information, so you’ll need to dump/import that data after you get it loaded, so you avoid unpleasantries that will inevitably show their face.

Method #1 – Create work tables

1. Start up clean/fresh instance of MySQL with innodb_file_per_table enabled.

2. Now, we need to find the table id that MySQL is currently set at, as well as the table id for the table we need to recover.

Step 2 (2a – 2f) is simply to find the table id that is stored inside of the .ibd file. I’ve written a PHP script to determine this, so using the script can save a bunch of time. See the bottom of this page (under “Associated Files”) for the exact script.

2a. Create a test database:

mysql> CREATE DATABASE test1;
mysql> USE test1;

2b. Issue the create table command for the table:

mysql> CREATE TABLE `product` (
  `PRODUCT_ID` bigint(20) unsigned NOT NULL auto_increment,
  `BRAND_ID` int(10) unsigned default NULL,
  `PRODUCT_TYPE_ID` int(10) unsigned default NULL,
  `GROUP_ID` int(10) unsigned default NULL,
  `PRODUCT_NAME` varchar(500) NOT NULL,
  `DEFAULT_EMAIL_ID` varchar(48) default NULL,
  `CLIENT_ID` bigint(20) unsigned default NULL,
  `LAST_MODIFIED_BY` varchar(45) NOT NULL,
  ) ENGINE=InnoDB;

2c. Discard the tablespace, which will delete the newly created .ibd file:


2d. Copy the pre-existing .ibd file to the datadir/test1 folder

2e. Import this tablespace:


This should produce the following error (at least this is most likely). The only way it would not is if MySQL’s current table id matched that of the preexisting ibd table id. In which case, you can now dump your table.

ERROR 1030 (HY000): Got error -1 from storage engine

2f. So, now to check the error log (manually). Look for the following entry:

081010 11:47:40  InnoDB: Error: tablespace id in file 
'.test1product.ibd' is 1193, but in the InnoDB
InnoDB: data dictionary it is 1.

So, now we know the internal table id is at 1, and that of the ibd table is 1193.

3. Clean up working database:

3a. Manually move the ibd file from the $datadir to a safe location (as you will need this file again).

3b. Drop this table.

mysql> DROP TABLE product;

Note this does not re-set the internal table counter.

4. You’ll need to create the number of tables you need to increase the internal table id value.

In this case, you’d create 1191 test InnoDB tables (already at 1, and need to leave 1 for the actual table, so 1193-2=1191). Run below in a loop.

for ($1=1; $i<=1191; $1++) {
  CREATE TABLE t# (id int) ENGINE=InnoDB;

I accomplished this via a simple php script. See the bottom of this page (under "Associated Files") for the exact script.

5. After these are created, go ahead and drop this database and all tables (as they are not needed).

DROP DB test1;

6. Now, re-perform steps 2a through 2e.

mysql> CREATE DATABASE test1;
mysql> USE test1;
mysql> CREATE TABLE `product` ( ... ) ENGINE=InnoDB;

<--  Here is where you copy back the original ibd file to /$datadir/test1/ -->



mysql> show tables;
| Tables_in_test1 |
| product         |
1 row in set (0.00 sec)

7. Now, dump the table using mysqldump, and then you can import this to any MySQL instance. Note, you must dump this and re-import it, or you'll run into problems.

However, it's possible to encounter crashes and/or reports of corruption in the logs.

If this happens, try to force innodb recovery (which is most likely), and then dump the table.

Start by setting innodb_force_recovery=1 (and try 2,3,4,5,6) until the dump works.

For this example table, I had to set innodb_force_recovery=5 before the dump would succeed.

The # in the output file name is the value I had innodb_force_recovery set to when trying to perform the dump:

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump1.txt
mysqldump: Couldn't execute 'show table status like 'product'': 
Lost connection to MySQL server during query (2013)

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump2.txt
mysqldump: Couldn't execute 'show table status like 'product'': 
Lost connection to MySQL server during query (2013)

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump3.txt
mysqldump: Couldn't execute 'show table status like 'product'': 
Lost connection to MySQL server during query (2013)

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump4.txt
mysqldump: Couldn't execute 'SELECT /*!40001 SQL_NO_CACHE */ 
* FROM `product`': Lost connection to MySQL server during 
query (2013)

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump5.txt

C:Program FilesMySQLmysql-5.0.68bin>
mysqladmin -u root -P 3385 shutdown

C:Program FilesMySQLmysql-5.0.68bin>
mysqldump -uroot -P3385 test1 product > product_dump6.txt

In fact, in this case, I could have simply started with 5. This is because the error log stated this:

InnoDB: Error: trying to access update undo rec field 19 
in index PRIMARY of table test1/product
InnoDB: but index has only 12 fields

So, I knew there was a problem trying to look at the undo logs, and from the manual, a setting of 5 says this:

"Do not look at undo logs when starting the database: InnoDB treats even incomplete transactions as committed"

However, it's best to start at 1 and work your way forward so as to prevent as much data loss as possible.

Method #2 - Hex Edit .ibd file

First of all, you'll need to backup everything (ibdata files, ib_logfile(s), data). I'd also perform a mysqldump of everything you currently have, just so you have a mysqldump of it in the event that you need it.

Also, very important, be sure to make a copy of the .ibd file for the specific table in question.

Lastly, get a copy of the CREATE TABLE statement that will recreate this table.

Then, you'll follow the steps #1-5 (but do not perform step #6 yet) outlined on the following page:


Let me post them here for completeness, however:

  1. Use mysqldump to dump all your InnoDB tables.
  2. Stop the server.
  3. Remove all the existing tablespace files, including the ibdata and ib_log files. If you want to keep a backup copy of the information, then copy all the ib* files to another location before the removing the files in your MySQL installation.
  4. Remove any .frm files for InnoDB tables.
  5. Configure a new tablespace.
  6. Restart the server.
  7. Import the dump files.

At this point, MySQL should be running fine with an empty slate (and should have just re-created your new ibdata and log files).

Now, you'll want to recreate the table (just using the CREATE TABLE output from above), and its database to hold it.

Then, you'll basically be following the steps #1-3 outlined on the following page:


1. Issue this ALTER TABLE statement:


Caution: This statement deletes the current .ibd file.

2. Put the backup .ibd file back in the proper database directory (the one that you copied above).

3. Issue this ALTER TABLE statement:


Everything should go smoothly until step #3 (above). More than likely, this will produce an error like the following on your console:

"Got error -1 from storage engine"

Now, if you look in the error log, you'll see something like:

"InnoDB: Error: tablespace id in file '.testt2.ibd' is 2, 
but in the InnoDB data dictionary it is 1."

It would not produce the above error and would work fine if the existing table already had a tablespace id of 1. However, this is unlikely.

So, assuming you see the above errors, then you can modify the tablespace id actual ibd file using a hex editor. I would do this on a different copy of the ibd file (other than the original, just in case).

Note that I used "Freeware Hex Editor XVI32" for Windows for this step. Start the program, and then open the .ibd file. You'll see each byte in it's own cell. You can then click on a cell, click edit, and then edit that byte. (http://www.chmaas.handshake.de/delphi/freeware/xvi32/xvi32.htm)

Now, in this file, there are 2 places where this tablespace id is located.

For me, and I assume it should be the same for you, but just look at the values to be sure, I see the tablespace id values listed at position 37 and 41 (positions 25 and 29 in hex). In the actual hex column, if you're previous tablespace id was 2, then in positions 37 and 41, you'd see 02 and 02.

(Note these positions can change. For instance, I tested on a table with an internal id of 1193. This in hex is 04A9. However, when searching the file, for the first instance of the table id, I found the '04' in position 39 and 'A9' in position 40. Then, for the second instance of the table id, the '04' was at position 43 and the 'A9' was at position 44. So, you'll have to convert the table id to hex, and then search for that value, near the beginning of the file.)

Note that this value (02) may vary depending on what your actual tablespace id is.

Then, simply modify both of those fields to 01, and save the file.

Then, re-do the following 3 steps:

2. Put the newly saved .ibd file back in the proper database directory

This time, step #3 works fine.

It is at this point you should dump/import the data. At least, get a good mysqldump of this table now. You may find that this causes corruption in InnoDB, and you may need to start MySQL using --force-innodb-recovery.

http://dev.mysql.com/doc/refman/5.0/en/forcing-recovery.html Forcing InnoDB Recovery

Associated Files :: PHP Scripts

Simple PHP script - Used to create a number of InnoDB tables (to increase internal table id counter):

$dbhost = "localhost:3385";
$dbname = "test1";
$dbuser = "root";
$dbpwd  = "";

mysql_connect($dbhost,$dbuser,$dbpwd) or die(mysql_error());

for ($i = 1033; $i <= 1190; $i++) {
   $dbquery = "CREATE TABLE test1.t" . $i . " (id int) ENGINE=InnoDB";
   echo "" . $dbquery . "";
      $result = mysql_db_query($dbname,$dbquery) or die(mysql_error());
      $j = 0;
      while($row = mysql_fetch_array($result)) {
         echo $row[0];


PHP Internal Table ID Finder - Used to determine the internal Table ID from the binary .ibd file:

Tested with tables from 4.1.23, 5.0.68, 5.1.28, and 6.0.7.

// Set the filename
$filename = "C:\Users\Chris\Desktop\mysql\working\ibds\z1.ibd";

// Read 2 bytes in at a time
$offset = 2;

// Echo filename and path
echo "filename = $filename

"; // Open the filename - need 'rb' for binary file on Windows $handle = fopen($filename, "rb"); // Define redundant, local variables for possible later functionality and/or checks $ibd_id_bin = 0; $ibd_id_hex = 0; $ibd_id_dec = 0; $ibd_id_bin2 = 0; $ibd_id_hex2 = 0; $ibd_id_dec2 = 0; // Find the filesize (note: below command messes up script) //$filesize = filesize($filename)); // Only loop through first 21 bytes - as table is is in $array[18] and $array[20] for ($z = 0; $z <= 20; $z++) { // Set variable $contents equal to 2 ($offset) bytes of binary data $contents = fread($handle, $offset); // Convert $contents from binary data to hex data $contents2 = bin2hex($contents); // Convert $contents2 from hex data to decimal data $contents3 = hexdec($contents2); // Debug Output //echo "contents[$z] = " . $contents . "
"; //echo "contents2[$z] = " . $contents2 . "

"; //echo "contents3[$z] = " . $contents3 . "

"; // If position 19, array position [18], then store the values if ($z == 18) { $ibd_id_bin = $contents; $ibd_id_hex = $contents2; $ibd_id_dec = $contents3; } // If position 21, array position [20], then store the values if ($z == 20) { $ibd_id_bin2 = $contents; $ibd_id_hex2 = $contents2; $ibd_id_dec2 = $contents3; } } fclose($handle); // More Debug output //echo "

The table id is $ibd_id_dec

"; //echo "

The table id is $ibd_id_dec2

"; // Check to see if both values are equal. If so, then it's // most certain this is the correct value. // If not, then there's a chance the positions are off for // this table (due to versions, etc.). if ($ibd_id_dec == $ibd_id_dec2) { echo "

The table id is $ibd_id_dec

"; } else { echo "The values from positions [18] and [20] did not match,"; echo "so please enable debug output, and check for proper positions."; }