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Emptying MySQL Tables Without Impact

In a discussion with some Jr. DBAs I found the knowledge of how to prune tables in MySQL varies widely from person to person, as such I thought I would write a post on my two preferred methods. I know, some people work with datasets small enough they can just run DELETE FROM atable WHERE pk < 123456; but this is not the case for most of us.

Truncate = Bad

Truncate table, in modern versions of MySQL, takes out a global metadata lock, drops the old table, purges references from the LRU list, creates the new table then releases the lock. This can cause some significant locking. In addition it provides no rollback if, suddenly, your application team finds out in horror that they do actually need some or all of the data they asked to be removed.
In larger production environments there is still a need to remove data from tables, so how can one achieve this without causing impact?
The two methods I will discuss are the rename method or the pt-archiver method, both of which are kinder gentler method of doing the same thing, however there are also significantly different from each other.

pt-archiver vs table rename method

Concern Archiver Rename
Time to truncate a table Linear increase with size of table Consistently fast
Reclaimed ibd space No Yes **Assuming file per table
Persistent trimming Yes No
Complex initiation No Yes
Needs to be monitored Yes no
System resource utilization Proportional with time to completion Consistently small cpu and io impact. Io impact can be scheduled for a time different then the time of table rename.
Works with PK targets Very well Not so well
Rollback and Data Recovery Difficulty proportional to amount of data. Fairly easy
Locking concern Small range lock potential for deleted records for the duration of a run segment.  Single sub-second lock during atomic rename

Summary:

pt-archiver is best when you have tables that need to be maintained at a small size or when cretin records need to be purged or the tables are small enough that personal preference matters.

Table rename works best when you have large tables that need to be truncated. However, both methods provide overlapping areas of use.

Scenario: Truncate table

Method: pt-archiver

# Using the `--dry-run` argument to verify query before executing
$ pt-archiver --source h=db1020.region.company.com,D=mapping_shard99,t=user --purge --primary-key-only --bulk-delete --bulk-delete-limit --limit 1000 --where 'user_id > 0' --dry-run
SELECT /*!40001 SQL_NO_CACHE */ `user_id` FROM `mapping_shard99`.`user_move_queue` FORCE INDEX(`PRIMARY`) WHERE (user_id > 0) AND (`user_id` < '12358132134') ORDER BY `user_id` LIMIT 1000
SELECT /*!40001 SQL_NO_CACHE */ `user_id` FROM `mapping_shard99`.`user_move_queue` FORCE INDEX(`PRIMARY`) WHERE (user_id > 0) AND (`user_id` < '12358132134') AND ((`user_id` >= ?)) ORDER BY `user_id` LIMIT 1000
DELETE FROM `mapping_shard99`.`user_move_queue` WHERE (((`user_id` >= ?))) AND (((`user_id` <= ?))) AND (user_id > 0) LIMIT 1000
  • Time to set up is typically 5 min or less
  • Time to complete is based on table size, row_size (io), limit_number, etc. 

Method: Table Rename

Impact is kept small and broken into several controllable areas

  • Rename (truncate)
  • Drop
  • File deletion

Rename

Table rename

master_mysql> CREATE TABLE sometable_tmp LIKE sometable; RENAME TABLE sometable TO sometable_old, sometable_temp TO sometable; 

At this point the effects of the truncation are completed from the applications point of view. However, you still have effective rollbacks as all the data is still available.

Rollback:

  • You can either rename the tables again and backfill the new information
  • Or fill specific records from the old table to the new one.

Whatever makes the most sense for your data. You can do selective MySQL dump from the old table on a slave to preserve the data in perpetuity or wait for a period of time or simply delete it. However, if it is a large table you may want to provide a hard link before dropping it. 

Here are some sample times to create and rename a table

Create table

+----------------------+----------+    +----------------------+----------+ 
| Status               | Duration |    | Status               | Duration |
+----------------------+----------+    +----------------------+----------+
| starting             | 0.000067 |    | starting             | 0.000064 |
| checking permissions | 0.000006 |    | checking permissions | 0.000006 |
| checking permissions | 0.000005 |    | checking permissions | 0.000005 |
| Opening tables       | 0.000381 |    | Opening tables       | 0.000100 |
| creating table       | 0.002232 |    | creating table       | 0.002707 |
| After create         | 0.000012 |    | After create         | 0.000011 |
| query end            | 0.000031 |    | query end            | 0.000027 |
| closing tables       | 0.000009 |    | closing tables       | 0.000008 |
| freeing items        | 0.000017 |    | freeing items        | 0.000018 |
| cleaning up          | 0.000018 |    | cleaning up          | 0.000017 |
+----------------------+----------+    +----------------------+----------+

Rename profile  Expand source

+----------------------+----------+   +----------------------+----------+   +----------------------+----------+    +----------------------+----------+
| Status               | Duration |   | Status               | Duration |   | Status               | Duration |    | Status               | Duration |
+----------------------+----------+   +----------------------+----------+   +----------------------+----------+    +----------------------+----------+
| starting             | 0.000017 |   | starting             | 0.000019 |   | starting             | 0.000057 |    | starting             | 0.000040 |
| checking permissions | 0.000002 |   | checking permissions | 0.000001 |   | checking permissions | 0.000004 |    | checking permissions | 0.000003 |
| checking permissions | 0.000002 |   | checking permissions | 0.000003 |   | checking permissions | 0.000004 |    | checking permissions | 0.000003 |
| checking permissions | 0.000001 |   | checking permissions | 0.000001 |   | checking permissions | 0.000001 |    | checking permissions | 0.000001 |
| checking permissions | 0.004110 |   | checking permissions | 0.002985 |   | checking permissions | 0.004485 |    | checking permissions | 0.005110 |
| query end            | 0.000019 |   | query end            | 0.000020 |   | query end            | 0.000038 |    | query end            | 0.000042 |
| closing tables       | 0.000005 |   | closing tables       | 0.000005 |   | closing tables       | 0.000010 |    | closing tables       | 0.000007 |
| freeing items        | 0.000013 |   | freeing items        | 0.000008 |   | freeing items        | 0.000033 |    | freeing items        | 0.000132 |
| cleaning up          | 0.000008 |   | cleaning up          | 0.000017 |   | cleaning up          | 0.000023 |    | cleaning up          | 0.000016 |
+----------------------+----------+   +----------------------+----------+   +----------------------+----------+    +----------------------+----------+

Drop the table:

Hard links

It can take several seconds to remove the underlying inodes from a large file. During which time innobd has a global mutex, and here is where the impact of the original truncate comes in to play. To help prevent this we can create hard links on large .ibd file so that the file system believes the inodes are in use and will not remove them. This means when MySQL reaches out to the underlying OS to remove the files the OS simply removes the file handle and returns instantly.
At this point you can delete your hard link, which will cause some IO issues,but will otherwise not effect MySQL’s operations. 

On all servers:
Create hard link:

bash> ln dir/database/sometable_old.ibd  hardlinks/sometable_old.ibd 

Drop Table:

To purge the ibdata from MySQL you simply drop the table like always, and again, this can be done anytime, such as during non-peak hours. Unfortunately, this can still cause micro stalls in opining tables due to InnoDB’s need to go through LRU list and discard the pages which belong to this table. But since you can do this at any time you can reduce the impact. Furthermore since the tables are not in use you can do this one node at time by SET GLOBAL BINLOG = 0

Drop Table

master_mysql> DROP TABLE sometable_old

Again, the above can also be done no-binlog on any one server giving you further control

Here are some times for dropping some medium files:

drop table bigtest1                   drop table sbtest21 
(105GB 200Million Rows)               (48GB 200Million rows)
+----------------------+----------+   +----------------------+----------+
| Status               | Duration |   | Status               | Duration |
+----------------------+----------+   +----------------------+----------+
| starting             | 0.000053 |   | starting             | 0.000043 |
| checking permissions | 1.761864 |   | checking permissions | 4.183406 |
| query end            | 0.000037 |   | query end            | 0.000035 |
| closing tables       | 0.000010 |   | closing tables       | 0.000008 |
| freeing items        | 0.000024 |   | freeing items        | 0.000023 |
| logging slow query   | 0.000001 |   | logging slow query   | 0.000003 |
| logging slow query   | 0.000002 |   | logging slow query   | 0.000002 |
| cleaning up          | 0.000016 |   | cleaning up          | 0.000017 |
+----------------------+----------+   +----------------------+----------+

File deletion:
At some point, we will want to remove the underlying inodes, which can cause some IO issues just like deleting any large amount of data but also frees up space and since this is no longer visible toMySQL causes no internal locking.

rmfile

rm hardlinks/sometable_old.ibd

Caution:
Just like truncate this can cause issues for tables that have triggers or foreign key relationships. Ensure they are removed before proceeding.
Also consider not using them in the future with MySQL 😉

Prologue

Other examples of overlap include things like keeping ~30 days of records in a table.

pt-archiver can constantly delete anything over 30 days. Otherwise you can partition on time, and drop old tables. Method chosen depends mostly on the amount of data flowing and complexity vs performance desired.   

Similarly, if you want to keep all records newer then a few days, and you need them prepopulated before swap the tables, you would simply need to populate the new table with those records in a loop until the difference is small. Then take out a global read lock (this will cause impact if your application does not auto retry) while the final transfer and rename occur. This would spew errors and is not practical in many environments making pt-archiver the obvious choice. If you use an external sequence for primary keys and an application smart enough to hold and retry for half second of impact, then using rename may be a viable choice.

Should We Teach Cursive In School?

This has been a controversial topic for a while. And I thought we had put this matter to rest. But across my social media feed I still see arguments and it is time I simply wrote something out. This way I won’t have to repeat my self on each retort and can simply post this link.

Arguments:

Cementing knowledge by writing:

This is one I hear a lot of, that forming the letters with your hands some how causes you to remember the information better.
If this was the case, then would it not be even better to mold them out of clay then to write the? And how does writing in cursive some how make you remember better then printing or writing in short hand – what magic in this English cursive writing that some how has rocketed those, globally, few people into memory stardom – and how jealous must the Chinese, or Japanese, be given that their kids are not thought cursive writing?
The whole idea that cursive is magic in this regard is ridicules – the fact is this memory boost comes from re-encoding – the form does not matter. It is funny because if you ask a computer programmer the syntax for some boiler plate piece of code goes they will not write it! But they will start miming the movements of their hands on a keyboard and mouse as they recall it. Cursive is nothing special in this regard

It helps with spelling

Again, there is no proof in that cursive has anything to do with the effect..
All the studies say it is purely a matter of re-encoding the information and route practice. Be it printing, cursive, or typing.

Our hands should be multilingual:

This was a direct quote from an article published by the Federalist on the topic and using some work by Dr. Virginia Berniger to justify it. The argument goes writing in different characters activates different sections of the brain and aids in cognitive development. Why not use that time to teach the kids to be truly multilingual? learn Mandarin or Cantonese or Korean – And learn how to write them. They would certainly be more usefully he learning cursive or Latin – since both are dead and Chinese is not.

It is a faster:

Actually, no. Typing is the faster.
Most people can type 30 words per minute with very little effort. With a margin of practice, you can double that. And if you work on it for as much as kids work on had writing you can perhaps achieve 120WPM – although I have to admit getting much above that is very difficult.
However, in contrast writing is painfully slow. Most people write cursive around 40 characters a minute. The absolute fastest of us do 120 characters a minuet, again characters, not words. And this can not be done for hours on end without significant pain. Of coerce, if they were to give up cursive, and move to something performance driven, like shorthand, those same dedicated people could bump that to 300 words per minuet.

It helps with Dyslexia:

This one offends me, not only is it based on bad science but dyslexia are a very real and debilitating problem. I can tell you, as some one who suffers from it, I have almost no issue reading printed word, preferably in a fixed width serif font.
But cursive? It is certainly not easier to read. Perhaps it may have been easier to write as a child – I have no recollection if it being easier. However, it is in no way easier then typing. Don’t believe me? Look at the research put out by the association for people with dyslexia.

But what about historic documents!

I have never heard anyone say this that has actually had to do primary research on historical documents. Why? Because they are not easy to read, even if you know cursive. Hand writing is almost universally atrocious, the documents are not in the best condition, the language has shifted, etc. The point I am trying to make is you need to put effort into it Here is an example of something PRINTED http://www.bl.uk/learning/timeline/external/coffee-tl.jpg
Now here is something hand written with impeccable penmanship https://s-media-cache-ak0.pinimg.com/originals/c2/4e/5e/c24e5e5212bf1e24fd5676920a752f47.jpg
This one is also extremely legible http://www.bl.uk/learning/timeline/large126714.html
And you know what – give this to a kid who has never seen cursive with a primmer and after a few weeks they can read it to you just as easily as any one else.
All of this is in English – a rear treat when doing research
But how many kids in our classrooms today are going to grow up to be historians and read original works that have not been scanned, translated into digital text, and put up on the web. Ask most 30 year olds to day if they have ever gone to a library and pulled up a copy of a document from the 1600’s and had to read it for some reason?
And if this is the case – why are we not teaching shorthand so kids can read those documents? Or teaching English from before the great vowel shift so kids can understand those documents? Because very very few people need that specialized knowledge. Are you shocked I know I’m not.
(short hand example http://www.thehistoryblog.com/wp-content/uploads/2014/01/WWI-diary.jpg)

It keeps our brains active in old age

I kid you not – one of the major arguments of wasting time teaching a 2nd grader to write in cursive is so they will have active minds in their old age. using chopsticks and painting does the same thing – no need to learn cursive. Something they won’t likely use in 80 years anyway.

You need it for your job:

These days typing and the ability to use computers is the new literacy, without these skills it is very difficult to remain employed. Cursive? Not so much

There are simply NO jobs that require cursive writing – well almost no jobs… If you teach cursive, such as a grade school teacher, or are a professional calligrapher, or an administrative assistance for some really old guy who still writes in cursive all day, then yes. Your job will require you to read cursive, maybe even write it. I bet you could find perhaps a half dozen jobs in the US paying over $100K per year that require cursive.
Rounding, 0.00% of all US Jobs paying 100K/year or more require cursive handwriting. While nearly 20% of all US jobs making over 100K / year require programming experience. The cost is the same to teach our children a useful skill, or a useless one. Which will it be?

 

Conclusion:

It is simply a waste of time, like teaching kids how to use a slid ruler in order to perform log functions. Did you need to learn how to use a slid rule in high school? No? Then shut up you are too young to be giving the “Back in my day” speech to anyone!
Kids speed over 200 hours learning cursive writing. In 200 hours we could be teaching more math, more science, more logic, engendering and technology skills, how to program, serious home economics and other life skills – like how to manage money and invest! I think if we took 200 hours and thought kid’s serious macro and micro economics our country would be far better off then teaching them cursive hand writing.
Let us face it – very few six figure salaries are held by people who write by hand all day. Most are held by people who type all day.
If you are under 50 and you want to make a decent living and write by hand you need to be a doctor, particularly one with a nurse who translates your hand written into typed notes latter. 10 years ago I said Doctor or lawyer, but now days you are not going to make partner in a decent law firm if cursive is your primary form of written communication.

There is no reason our kids should have to learn writing, a difficult and painful process, twice. And if you are going to pick on, pick print. It is in every book, news paper (remember those?), and web page.

So why the outrage?

So what is the real reason people are upset over the cut of cursive from the curriculum? Something is different then when they were kids and that both scares and angers them. Much like if Pluto is a planet or not.

But this is one old American’s opinion. If you, you want to see what our counterparts across the pond think please read this article by Philip Ball 😉

Curse of cursive handwriting

Managing the OOM Killer among us

Like me you have probably had your share off issues when something runs amok and OOM (The default out of memory killer) slaughters something that was behaving well and is, as it turns out, critical to your operation.
In my case MySQL is the primary target for OOM because it consumes the most memory on any given server. But occasionally someones PHP code will start to get out of hand on those same servers. And I want OOM to kill said out of hand code and thus protect my primary application! But oom does not… Instead it kills my one big app to protect the small but hungry programs. And this is not a gentle death either, it is a full blown Kill -9 to the face! So how do I make my app less of a target?

The method changes over the course of OS’s and versions but the two ways showcased here are mostly compatible and work on a wide variety of systems.
The Adjustment, and the Score.

Continue “Managing the OOM Killer among us”

Worlds Largest CRIT Database

Mongo Achievement

Our CRIT database manages over a million signatures and as of December 2014 is the worlds larges and keeps growing. We have plenty of room for it to grow with less then 3% of the clusters theoretical capacity purchased we can keep adding nodes for the foreseeable future. I implemented Mongo for a few projects before this but this was the first large auto shareded system where I had to pre-allocate shards to keep the system from collapsing when the application started. I built these servers from scratch and configured the systems and given the hardware I had to work with I am quite pleased with how it turned out.

Worlds Largest PKI Implementation

PKI Achievements

We are clearly one of the largest CA’s in the world, however the largest depends highly on one how you measure. In any case we represent, again depending on how you measure, between 1/4th and 1/3rd of the worlds total SSL certs. And I am told by a number of people who have worked on our system and others, as well as by our auditors, that we are one of the finest CA’s in the world.

While I have little to do with the application development, and the current architecture was mostly inherited, I do manage the databases for this. At one time we also boasted the worlds most efficient OSCP responded written by my former boss Chris G.  I can not say enough good things about him, and the entire team I work with. They are all amazing people! The environment went stagnant for a bit but I am proud of where we are going with PKI; as these handful of instances our now my secure baby  🙂

Worlds Largest Spacewalk installation

PostgreSQL Achievement

We have the worlds largest Spacewalk installation with many tens of thousands of nodes. This is all managed by a single PostgreSQL database (with a wall replica for disaster recovery). This lovely piece of kit was set up by an amazing former coworker Bo J. I inherited it and really wish I could spend more time optimizing. The servers resource utilization is sub optimal as is performance and I wish I had more postgreSQL skill, but my expertise lies in MySQL and Mongo. Give me six months and I will make postgreSQL sing 😉

Worlds Largest Authoritative DNS

DNS Achievements:

I am responsible for the MySQL back-end for the worlds largest authoritative DNS with over 37 million zones.
When I inherited this system (Over 10 million zones ago) it was fraught with problems. However with diligence and an eye for detail, and lots of help from the application team, I was able to remove the land minds, document the complicated infrastructure, and implement a streamlined design that lends it’s self to automation. I started with 4, significantly expensive, anycast pods and a hodgepodge of master. Since then we have increased our zones by over a third and while added we added a new pod I also worked hard to stabilized the masters and pods with little additional hardware.
We are on the verge of completing a new phase where the masters will be bi-coastal and dozens of new pods will drop our premium DNS to response time. Continue “Worlds Largest Authoritative DNS”