Innodb – Safe values for InnoDB variables when using FULLTEXT searches

Conclusion and a workaround

After exhausting all options on Windows, I decided to switch to Linux, mostly because I was frustrated with inability to profile and debug in detail.

I have moved the whole setup to Ubuntu 14.04. I first tried XAMPP but gave up because of conflicts between XAMPP and MySQL and MySQL Workbench. Then I moved to vanilla MySQL (5.5, I think) and vanilla Apache 2.

However, I was still left with the same problem – no visible bottleneck and resources still underutilized. I suspected throttling in TCP sockets (used between Perl code and MySQL), but further profiling proved this not to be the case.

Then, I turned my attantion to Perl DBI module DBD::SQL, thinking that it may be doing some throttlinig. I did some tests where I replaced DBI calls in Perl with system calls (system("mysql -e'INSERT INTO blah blah …'). I have determined that the performance did not change, therefore absolving DBI as a culprit.

I need to add one important detail now: I was in fact always running a number of my Perl scripts in parallel. Given that the CPU has 8 cores, this is necessary to utilize all of them, of course. Further debugging showed that almost all my perl processes which were supposed to work furiously were sleeping most of the time. Ubunty System Monitor shawed them as waiting on Waiting Channels wait_answer_interruptible or unix_stream_recvmsg. CPU History graph in System Monitor showed all perl processes jumping to 100% CPU utilization and then dropping to ~0% in unison. I suspected that MySQL server is not configured for multi threading, but htop showed 17 mysqld threads activated, confirming that all should be ok.
I suspected that all MySQL threads were waiting on the same semaphore and were locked out for most of the time. I dreaded delving into the dark bowels of MySQL trying to figure out what goes on inside. Instead, I decided to replace MySQL with MariaDB, even though MariaDB seems to have had the same issue originally when I was running it on Windows.

Lo and behold – this finally worked. My perl scripts were screaming.

One last problem remained: I had a very rudimentary method of parallelising the perl scripts: I would just run 10 or 20 with their respective loads and hope that they would utilize all the resources.

This has obvious drawbacks: if too many processes are spawned, the OS may spend too much time swapping them (although not a serious issue with only 20 processes, it becomes an issue with e.g. 1000). If not enough processes are spawned (e.g. less than 8, for each core) the CPU will not be utilized fully for sure. If too many processes exhaust RAM, Linux will turn to disk and will start swapping. As soon as this starts happening, everything grinds to a halt.

I searched but could not find a perl library/script/code which would spawn new processes only when CPU, memory and disk are under utilized. Hence I created my own: raspawn.pl (resource aware spawn) which I placed on github. Raspawn.pl spawns a number of processes while trying to keep resources utilization just below the maximum. It constantly checks the CPU, memory and disk utilization and only if all are less than ~90% utilized, starts a new process.

Finally, this worked. I can now process my whole load in around 7 days, instead of many months...

First of all, with innodb_file_per_table=ON, all data and index pages are stored in the .ibd file of the table.

The growth of the system tablespace (ibdata1) can be a big headache.

I have mentioned this in earlier posts

• Apr 23, 2013 : How can Innodb ibdata1 file grows by 5X even with innodb_file_per_table set?
• Mar 31, 2014 : mysql directory grow to 246G after one query, which failed due to table is full
• Jun 16, 2014 : MySQL Index creation failing on table is full

In your case, there is transaction overhead. You have big transactions because of the mysqldump. Why ?

The default option called --opt has many options enabled, including --extended-insert. Extended inserts will cause mysqldump to INSERT INTO multiple rows in batches. Each batch of rows is a single transaction. Thus, you should expect ibdata1 to get bloated, especially if the table has TEXT or BLOB data (I suspect that since you have fulltext indexes).

The only way around this would be to run the mysqldump again with --skip-extended-insert. This will do three(3) very nasty things:

1. Runs INSERT for each row
2. Makes a much larger mysqldump file
3. Take a ton longer to reload

This makes each individual INSERT transaction hundreds or thousands of times faster because you are inserting one row instead of hundreds or thousands. Unfortunately, you are doing hundreds or thousands longer to execute because of the number of INSERTs. This is just one way to prevent ibdata1 from getting bloated.

Another thing you could try would be to drop the FULLTEXT index from the table, mysqldump it with skip-extended-insert, reload it, then add the FULLTEXT index back. This could help because the adding the FULLTEXT index is not a transaction.

Give it a Try !!!