Using MySQL on the GPC

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TechTalk by Ramses van Zon (SciNet)

Oct 16, 2013

MySQL is a relational database management system (RDBMS) that runs as a server providing multi-user access to a number of databases. It is often used by free-software/open-software projects requiring RDBMS. Running a single relational database version for all of SciNet is not a good fit, as the needs of our many users could easily conflict and uptime of the server could not always be guarranteed.

It is however possible to setup MySQL in user space, using a few homebrewed scripts to help resolve some of the common issues with running multiple database servers. In this TechTalk, we will show how you can use MySQL in user space on the General Purpose Cluster for short tests on the devel node, within a single node compute job, or even spanning multiple nodes.

Note: this is the content of the slides used in the TechTalk. This is also available in pdf format.

Data storage types

Data in all shapes and forms:

Standard binary data (hdf5, netcdf, grib2, jpg, pdb, …)
Standard/semi-structured text data (xml, json, csv, fasta)
Proprietary binary data format
Unstructured text data (logs, output and error files)
Databases

Databases

Database: an organized collection of data for storing, managing and retrieving information

Often back-end to a website or application.
Typically structured as tables.
Each row expresses a relation between columns.
SQL: Structured Query Language.
Implementations often have access control on databases and tables.

Exception to this structure: NoSQL. Not in this TechTalk.

Why use a relational database?

You like/are familiar with SQL.
Application relies on a RDBMS.
You want to be able express complex queries, such as:

List the directories of stored simulations in which the pressure was between 1 and 2 atm and the number of water molecules was between 4,000 and 50,000.
<source lang="bash">SELECT B.directory FROM simulations_attributes A INNER JOIN simulation_paths B WHERE A.simulation_id=B.simulation_id AND A.pressure>=1 AND A.pressure<=2 AND
A.molecules>=4000 AND A.molecules<=50000;</source>

Note that you rarely store your binary data in the DB,
but you could store paths and filenames with metadata.

Some Relational Database Management Systems

Commercial:
- Oracle Database
- IBM DB2
- Microsoft SQL Server
- SAP Sybase
Open Source:
- postgreSQL
- SQLite
- MySQL

What is MySQL?

Open-source RDBMS
Was owned by MySQL AB, now by Oracle
Often used by Free-software/open-software projects requiring RDBMS
Command-line interface (mysql)
Interfaces for C, python, php, perl, R, …
Third party graphical interfaces

Typical MySQL Deployment

Database server runs as root on some server
A ’root’ user can setup privileges on the databases and tables
Application/web service runs on client (sometimes server=client)
and contacts the server as a non-root user through a port or socket.

Why This Setup Doesn’t Work on SciNet:

Don’t want to maintain a database server accessible to 1000+ users:
- Scalability: Many nodes may try to access DB
- Conflicts: Users may run same application, access the same databases/tables.
- Security: What if privileges are not set correctly?
- Stability: If DB goes down, or becomes slow, all jobs go with it.
- File systems: RDBMS may not play nice with file system (iops-heavy).
Users cannot start root processes or setup privileges.

Luckily it is possible to install MySQL in user space.

User space MySQL Deployment

Database server runs as user on some machine.
Creates its own ’root’ user, sets up privileges on databases and tables
This is a database user called ’root’, which does not have, and should not, have anything at all to do with the linux root user.
Application runs on another or the same machine
Port numbers and sockets must be assigned properly to avoid conflicts with other users’ databases
Application contacts this server as a non-’root’ user through the properly assigned port or socket.

SciNet’s MySQL Module on the GPC

MySQL user deployment is a bit of a pain, and would mean a lot of duplication of effort.
So we’ve done that already, and wrote a few scripts to help you.
They are in the ’mysql’ module.

Let’s demonstrate how this works…

Basic Example

<source lang="bash">$ module load mysql $ mysqlsetup Creating directory (tree) $SCRATCH/.mysql-5.6.12/default for configuration files Creating directory $SCRATCH/mysqldata/default for databases Creating local configuration Initializing local mysql database Enter mysql root password: Confirm mysql root password: Starting mysql service 131011 15:05:31 mysqld_safe Logging to '$SCRATCH/mysqldata/default/gpc-f103n084.err'. 131011 15:05:31 mysqld_safe Starting mysqld daemon with databases from $SCRATCH/mysqldata/default Setting password Cleaning up Stopping mysql service 131011 15:05:36 mysqld_safe mysqld from pid file $SCRATCH/mysqldata/default/gpc-f103n084.pid ended $</source>

Next, starting the server: <source lang="bash">$ module load mysql $ mysqlsetup ... $ mysqlstart 131011 15:09:39 mysqld_safe Logging to '$SCRATCH/mysqldata/default/gpc-f103n084.err'. 131011 15:09:39 mysqld_safe Starting mysqld daemon with databases from $SCRATCH/mysqldata/default $ mysql -u root -p Enter password: Welcome to the MySQL monitor. Commands end with ; or \g. ... mysql> \q $ mysqlstop 131011 15:18:34 mysqld_safe mysqld from pid file $SCRATCH/mysqldata/default/gpc-f103n084.pid ended $ </source>

What happened?

Stuff was setup on scratch, so we can use this on compute nodes too.
Setup root password
Directories created:
- $SCRATCH/.mysql-5.6.12/default: contains configuration files
- $SCRATCH/mysqldata/default: contains database files
Configuration is such that non-default sockets and ports are used: multiple users can use this module simultaneously on devel nodes.
Tip: do not use the root user, create a new user.

Using Profiles

Note default in the above?

It’s possible to have other configurations, using different directories. This is required if you want to run a database server for each job.
Each setup is called a ’profile’.
Each profile has its own configuration and data directory.
Each profile has its own root password.
Data directory can even be on ramdisk!
(but you’ll have to copy it if you want to save your results).

Profile Example

<source lang="bash">$ module load mysql $ mysqlsetup -P compute $ mysqlstart -P compute $ export MYSQL_HOME=$MYSQL_HOMES/compute $ mysql -u root -p mysql> CREATE DATABASE computedb mysql> GRANT ALL PRIVILEGES ON computedb.* TO computeuser mysql> FLUSH PRIVILEGES mysql> \q $ mysqlstop -P compute</source>

Ramdisk Example

<source lang="bash">$ mkdir -p /dev/shm/rzon/mysqldata $ mysqlsetup -P ramdisk -D /dev/shm/rzon/mysqldata $ mysqlstart -P ramdisk $ mysqlstart -P default $ mysqlstatus PROFILE PID ramdisk 5243 default 5740 $ export MYSQL_HOME=$MYSQL_HOMES/ramdisk $ mysql -u root -p $ export MYSQL_HOME=$MYSQL_HOMES/default $ mysql -u root -p $ mysqlstop -P ramdisk $ cd /dev/shm/rzon/mysqldata $ tar cf $SCRATCH/ramdiskdb.tar .</source>

Next run can just do:

<source lang="bash">$ module load mysql $ cd /dev/shm/rzon/mysqldata $ tar xpf $SCRATCH/ramdiskdb.tar $ mysqlstart -P ramdisk $ export MYSQL_HOME=$MYSQL_HOMES/ramdisk $ ... $ mysqlstop -P ramdisk $ tar cf $SCRATCH/ramdiskdb.tar /dev/shm/rzon/mysqldata</source> Note that if there are several runs at the same time, you’ll have to have different tar files on the file system and may have to figure out how to merge databases.

Multi-node Example

A script that uses the mysql database but does not start it

<source lang="bash">#!/bin/bash

file: compute.sh

module load mysql export MYSQL_HOME=$MYSQL_HOMES/compute export mysqlhost=$1 export thiscase=$2 mysql -h $mysqlhost -u computeuser computedb ... $thiscase ... </source>