Python3 filter is evil

Personally I like Python for what it is - a quick prototype language for writing simple utilities/scripts. Unfortunately when you start writing important infrastructure code using Python it quickly falls apart due to its dynamic typing. And all the breaking changes in Python3 didn’t help either.

Go pattern for worker queue - a quick case study for go concurrency

A quick case study for go concurrency

Go pattern for worker queue - a quick case study for go concurrency

A classical computer science problem is a worker queue - imagine you have N WorkItems to be divided between M workers (of course this implies N » M). This pattern has many application such as generating lots of data and insert into database, processing CPU-intensive work, etc. This can be easily achieved with go routine and channels. I recently spend a bit of time working on a similar problem with go and I’d like to share the pattern that I came up with.

Hacking MySQL #1 - Overview, Building, and Testing

An overview of MySQL, as well as how to obtain source, build and run tests

Hacking MySQL #1 - Overview, Building, and Testing

Overview

MySQL is one of the most widely used OpenSource relational databases and is used by many companies such as Amazon, Facebook, Google, Alibaba, etc. In my current job we deploy MySQL widely within the company, we had our MySQL 5.6 own fork and moving towards MySQL 8.0 currently in a branch. We also have an “new” storage engine built on top of RocksDB, not surprisingly called MyRocks, which lives under storage/rocksdb folder in the MySQL 5.6 fork.

On a 10000-feet view, the architecture of MySQL server looks like this:

  1. Connection Management / Authentication
  2. Table/Schema Management/Caching
  3. SQL Parser
  4. SQL Optimizer and Query Executioner
  5. Execution Engine
  6. Replication and logging

If you dive deeper, an execution engine itself could include following pieces:

  1. Transaction / MVCC / Locking / Snapshot support
  2. Schema/Metadata
  3. In-memory core database data structure (B+ tree / LSM tree / etc) and operation (insert/delete/update) for records
  4. Indexing data structures, and searching/updating
  5. Logging, Checkpointing & Recovery
  6. Database storage persistence
  7. Caching (disk blocks/pages, etc)

One of the most amazing features in MySQL is to swap the underlying storage engine while keeping the same upper layers - this way you can have different in-memory and on-disk representation of databases for different workloads, while keeping the same SQL execution functionality so the client wouldn’t even know the underlying storage engine have changed. The default storage engine is InnoDB - a B+ tree based database storage engine, and the one that we have is MyRocks which is built on top of RocksDB, a LSM-tree based database storage engine. There is an API layer called handler that storage engine need to implement/override. You can go to Comparison of MySQL database engines to see a list of common storage engines in MySQL.

Of course, the statement that they wouldn’t know the storage engine has changed is not entirely accurate. There are specific configurations you might need to tune / config the storage engine to your needs, and different storage engine has different performance / behavior / features / capabilities, so it’s not completely transparent.

Building

You can obtain source code from MySQL website, but most folks probably would prefer a github mirror:

git clone https://github.com/mysql/mysql-server

This contains the latest MySQL 8.0.16.

In a typical Ubuntu system, you need to install following dependencies:

sudo apt install libssl-dev libzstd-dev libncurses5-dev libreadline-dev bison pkg-config

All my instructions below are tested on a Azure Linux Ubuntu 18.04 VM and on a MacBook Pro 2018. They may vary slightly due to your configuration/distribution if you are on a unix/linux system. Getting it to work on Windows wasn’t too bad either, if I remember correctly.

Now let’s create a debug directory to store all our build files, and start the debug build:

mkdir debug
cd debug
cmake .. -DWITH_DEBUG=1 -DDOWNLOAD_BOOST=1 -DWITH_BOOST=~/boost_1_69_0
make
  1. WITH_DEBUG=1 requests a debug build, which makes debugger easier
  2. DOWNLOAD_BOOST=1 WITH_BOOST=~/boost_1_69_0 downloads the boost at ~/boost_1_69_0 (that’s the version MySQL is asking for), and will skip the downloading if it is already there

One the build is done, you can find everything under debug/bin.

Don’t change the build directory after the fact once you done the build. The directory name is remembered and changing that naming requires a rebuild.

Running a test

To validate that we indeed have a working MySQL build, let’s try running a quick test called select_all.

To run any test, there is a script mysql-test-run.pl located under the mysql-test directory from the build directory, and it takes a test name in the form of <testname> or <testsuite>.<testname>:

cd debug/mysql-test
./mysql-test-run.pl select_all

This runs the test under mysql-test/t/select_all.test with baseline mysql-test/r/select_all.result. It runs a simple test language containing test directives/commands and SQL commands, and compare the output with the baseline. If the output diverges from the baseline the test would fail, otherwise it would pass. Simple enough, right?

Actually, not quite. The testing of MySQL can get quite complicated when it involves multiple connections / servers communicating with each other. And stablizing the results so that they are not affected by external environment / code changes can be also an headache.

Here is what you should see:

[~/local/github/mysql-server/debug/mysql-test, 8.0, 51s, SUDO]: ./mysql-test-run.pl select_all 
Logging: /home/yzha/local/github/mysql-server/mysql-test/mysql-test-run.pl  select_all       
MySQL Version 8.0.16                                                                         
Checking supported features                                                                  
 - Binaries are debug compiled                                                               
Using 'all' suites                                                                           
Collecting tests                                                                             
Checking leftover processes                                                                  
Removing old var directory                                                                   
Creating var directory '/home/yzha/local/github/mysql-server/debug/mysql-test/var'             
Installing system database                                                                   
Using parallel: 1                                                                            
                                                                                             
==============================================================================               
                  TEST NAME                       RESULT  TIME (ms) COMMENT                  
------------------------------------------------------------------------------               
[100%] main.select_all                           [ pass ]  36259                             
------------------------------------------------------------------------------               
The servers were restarted 0 times                                                           
The servers were reinitialized 0 times                                                       
Spent 36.259 of 70 seconds executing testcases                                               

Launching and connecting

Running a test seems straight-forward enough. If you want to launch mysql server and run some SQL commands against it, it takes a bit of work.

First we need to have mysqld initializes a blank data directory:

cd debug/bin
./mysqld --initialize

You should see:

2019-06-05T05:16:31.376510Z 0 [System] [MY-013169] [Server] /datadrive/github/mysql-server/debug/runtime_output_directory/mysqld (mysqld 8.0.16-debug) initializing of server in progress as process 70030
2019-06-05T05:16:44.066787Z 5 [Note] [MY-010454] [Server] A temporary password is generated for [email protected]: <.....>
2019-06-05T05:16:53.317610Z 0 [System] [MY-013170] [Server] /datadrive/github/mysql-server/debug/runtime_output_directory/mysqld (mysqld 8.0.16-debug) initializing of server has completed

Note the temporary password generated in the second line. You’ll need it later.

This means that mysqld has successfully initialized at debug/data directory:

'#innodb_temp'   auto.cnf   ca-key.pem   ca.pem   client-cert.pem   client-key.pem   ib_buffer_pool   ib_logfile0   ib_logfile1   ibdata1   mysql   mysql.ibd   performance_schema   private_key.pem   public_key.pem   server-cert.pem   server-key.pem   sys   undo_001   undo_002

Now we can finally start the server:

cd debug/bin
./mysqld --debug

--debug switch means we start the mysql server in debug mode.

Now launch another terminal / TMUX window / whatever, and connect to the mysql server:

cd debug/bin
./mysql -uroot --socket=/tmp/mysql.sock -p

You should see:

Enter password: 
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 28
Server version: 8.0.16-debug Source distribution

Copyright (c) 2000, 2019, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

However we are not quite done yet. Mysql will ask us to change the password - you can do it by using the following:

mysql> ALTER USER 'root'@'localhost' IDENTIFIED BY "<newpassword>";

Now any future login can be done using this new password you just gave.

Finally we can run some SQL command!

mysql> SELECT @@version;
+--------------+
| @@version    |
+--------------+
| 8.0.16-debug |
+--------------+
1 row in set (0.00 sec)

Before I leave, let me address a question that is absolutely going to be asked - how do I terminate the server gracefully? CTRL+C doesn’t work anymore.

The right way is to use mysqladmin:

cd debug/bin
./mysqladmin -uroot -p shutdown

You’ll see the server waving goodbye:

2019-06-05T05:54:09.028071Z 30 [System] [MY-013172] [Server] Received SHUTDOWN from user root. Shutting down mysqld (Version: 8.0.16-debug).
2019-06-05T05:54:10.670124Z 0 [System] [MY-010910] [Server] /datadrive/github/mysql-server/debug/runtime_output_directory/mysqld: Shutdown complete (mysqld 8.0.16-debug)  Source distribution

What’s next

I’m planning a series of articles that will go through many interesting aspects of MySQL:

  1. A quick tour of the source code and important concepts in MySQL source
  2. How is the parsing and AST tree generation done for complex statements
  3. How are statement being executed in MySQL
  4. How to add your own command
  5. How does MySQL optimizer / query execution work
  6. How does plugin / storage engine work
  7. How does system variables work
  8. How does replication work
  9. How does SHOW command work
  10. How does binlog work

I’m also planning to write about MyRocks, as well as RocksDB / LevelDB / InnoDB, but I’ll priorize MySQL articles first as they lay down a nice foundation for rest of the stuff and this also serves as documentation when people get lost in the vast amount of MySQL source code.

Let me know what do you think about the article and/or if you are running into issues. Feel free to suggest topics as well. But I probably can’t help much with your DBA questions…

Getting GDB to work on Mac OS X Mojave

How to get GDB to work on MacOSX Mojave

Starting from Mac OS X 10.5 (Leopard), Apple starts to lock down the system further and debuggers like GDB now have to be code signed. There is a great article describing steps to get it to work. However, there are a lot of conflicting information on the web and people are having trouble with some of those instructions, myself included. So I’d like to document what I did to get it to work, and highlight the issues I ran into:

On a high-level you need to perform these steps:

  1. You need to create a certificate in System Keychain that is self-sign and always trust for code signing
  2. Sign the GDB binary with the certificate. Include proper entitlements if you are on 10.14+.
  3. Reboot

The article has detailed steps on these steps so I’m not going to repeat them.

A few gotchas that I ran into myself:

  1. If you see this error complaining about code signing even though you had signed the GDB executable:
Starting program: /Users/yzha/github/mysql-server/debug/runtime_output_directory/mysqld
Unable to find Mach task port for process-id 55009: (os/kern) failure (0x5).
 (please check gdb is codesigned - see taskgated(8))

Double check if you had the proper entitlements in a XML file and pass to codesign when you are signing GDB. Many articles on the web in fact didn’t have the entitlement step as it likely is a new requirement 10.14+.

  1. If you are seeing this error even if you had signed with proper entitlements:
During startup program terminated with signal ?, Unknown signal.

or this:

/Users/yizhang/github/leveldb/debug/db_test": not in executable format: file format not recognized

Make sure you stay off GDB 8.2! Upgrade to 8.3 (available in Homebrew already) or downgrade to 8.0.

Sorting structured data using memcmp-friendly encoding part 2 - floats

Sorting structured data using memcmp-friendly encoding part 2 - sorting floats

In the last post we’ve discussed converting integers and strings into a memcmp / byte-comparable format for faster comparison (but at the trade off of doing decoding/encoding at reading/writing). In this post let’s take a look at how do we do the same for floating pointers.

Pagination