Database servers

Database servers available for researchers

Compute Canada offers access to MySQL and Postgres database servers for researchers:

• Cedar MySQL server
  • Description: General purpose server for the researcher wanting to set up SQL tables in MySQL and issue SQL commands against them.
  • Server name: cedar-mysql-vm.int.cedar.computecanada.ca
  • Short server name: cedar-mysql-vm (can be used instead of long name on most compute nodes)
  • Version: MariaDB version 10.2 Community Edition
  • Documentation: http://www.mariadb.com
• Cedar Postgres server
  • Description: General purpose server for the researcher wanting to set up SQL tables in MySQL and issue SQL commands against them. Includes a PostGIS extension available for those needing to do geocoding.
  • Server name: cedar-pgsql-vm.int.cedar.computecanada.ca
  • Short server name: cedar-pgsql-vm (can be used instead of long name on most compute nodes)
  • Version: PostgreSQL version 10.1, PostGIS version 2.4 extension available
  • Documentation: https://www.postgresql.org and https://postgis.net/documentation

Cedar MySQL server

The Cedar MySQL server runs as a VM called "cedar-mysql-vm" (full name: cedar-mysql-vm.int.cedar.computecanada.ca) on a database machine. Users who have accounts on the MySQL server are able to connect only through the Cedar headnode (cedar.computecanada.ca), Cedar compute nodes and cedar portal (https://gateway.cedar.computecanada.ca).

For security, users cannot make an SSH connection to the database server directly.

MySQL account and connection

If you need the privileges to create your own database, you will need a MySQL account. To get a MySQL account on the Cedar MySQL server, please send a request to support@computecanada.ca with the following information:

• Your Compute Canada username
• Amount of database space needed for your project

We will then create an MySQL account with the same username as your computecanada username and a 16 digit random string password. The username, password, and database server name and other required information to make a MySQL connection will be stored in a file called .my.cnf located in your home directory on Cedar. The file is confidential and owned by root and only user can read that, e.g., user cannot modify it, however user can delete that. So, please do not delete this file.

Command

[name@server ~]$ mysql

from cedar head node can be used to connect to the MySQL server. Please do not use the -p or -h option as an argument in running mysql. The required password and server name is this case and any other information will be automatically taken from your .my.cnf file if you do not use such options.

It is acceptable to submit a long-running SQL command from the Cedar head node, as most of the CPU usage is taken from the database server side. However, if you are running a script which is issuing SQL commands and uses lots of CPU, then it needs to be submitted as a job to the scheduler. See Running jobs for details.

Rules to create a MySQL database

In order to be able to set up MySQL tables and query them, you need to create your own database. To create a database, the name of the database is arbitrary but it must start with "<username>_"

where <username> is your MySQL username. For example, if your username were "david" the name of the database must start with "david_" and the commands to create a database called "david_db1" would be:

[name@server ~]$ mysql
 mysql> CREATE DATABASE david_db1;
 mysql> quit

Users can create multiple MySQL databases if they all start with "<username>_".

Here is an example of how to work with your new database and create a table in it, populate it, and query it:

[name@server ~]$ mysql
 mysql> USE david_db1;
 mysql> CREATE TABLE fubar (age integer, id varchar(10));
 mysql> INSERT INTO fubar VALUES (34, '1122');
 mysql> INSERT INTO fubar VALUES (22, '2233');
 mysql> SELECT * FROM fubar WHERE age > 30;
 mysql> SELECT age FROM fubar WHERE id = '1122';
 mysql> quit

The created database will automatically be accessible from the cedar head node, cedar compute nodes, and cedar portal (gateway.cedar.computecanada.ca), so you should not need to do any other grant. However, if you want to share your database with other users you can issue this MySQL command:

[name@server ~]$ mysql
 mysql> GRANT SELECT ON [database name].* TO '[username 2]'@'172.%';
 mysql> quit

where [username 2] is the MySQL user who takes that grant.

MySQL connectivity for BioPerl

BioPerl is a collection of open source Perl tools for bioinformatics, genomics and life science. Documentation can be found at bioperl.org.

There are several BioPerl modules which can be used to upload data to a database. To connect to a MySQL server from one of these, the BioPerl command line should contain the -d option as follows:

-d [database name]:mysql_read_default_file=.my.cnf ....

MySQL connectivity for GBrowse

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.

Documentation: http://gmod.org/wiki/GBrowse

In order to connect to MySQL from gbrowse, the corresponding line to connect to MySQL should contain:

db_args       =     -adaptor DBI::mysql
                    -dsn [database name];mysql_read_default_file=/home/[username]/.my.cnf
                    -user [username]

where [username] is the corresponding user name and [database name] is the name of the database.

Cedar PostgreSQL server

The Cedar PostgreSQL server runs as a VM called "cedar-pgsql-vm" (full name: cedar-pgsql-vm.int.cedar.computecanada.ca) on a database machine. Users who have accounts on the PostgreSQL server are able to connect only through the Cedar headnode (cedar.computecanada.ca), Cedar compute nodes and Cedar portal machine.

For security, users cannot make an SSH connection to the database server directly.

To get an account and database on the Cedar PostgreSQL server, send a request to support@computecanada.ca with the following information:

• Your Compute Canada username
• Amount of database space needed for your project
• The name of the database you would like to have
• Do you need the PostGIS extension for the database?

PostgreSQL account and connection

Your created PostgreSQL account will have the same username as your computecanada. You will be given a database. The name of the database is arbitrary but it must start with "<username>_" where <username> is your computecanada username. Users are not able to create database. If you need more database please send us a request. PostgreSQL uses IDENT authentication for connection from cedar compute nodes which means no password is needed to be supplied to your PostgreSQL account. This also means that user A from cedar computenodes cannot make PostgreSQL connection to user B. Using passwordless connection from computenodes is adventurous because if you have a job script in which you need a PostgreSQL connection you do not need to hard code your computecanada password into your job script which would be potentially a big security concern.

When access is from the head node, however, PostgreSQL uses PAM authentication which means that you will be prompted for a password. Your password for PostgreSQL connection is the same as your Compute Canada password for this case. Example:

[name@server ~]$ psql -h cedar-pgsql-vm -d db_[username]

where db_[username] is the name of the database that was set up for you with your PostgreSQL account. (If you require more databases to be set up for your PostgreSQL account to use, please send a request to support@computecanada.ca).

The example above runs an older version of the psql Postgres interactive client that by default is installed on all the nodes:

[name@server ~]$ psql --version
psql (PostgreSQL) 9.6.2

You can load the most recent version of the psql Postgres client which will stay loaded until you log off from your session. Example:

[name@server ~]$ module load postgresql

[name@server ~]$ psql --version
psql (PostgreSQL) 10.2

PostgreSQL connectivity for BioPerl

To connect to Postgres from a Perl module, for example from one of BioPerl modules, the command line should contain "-a" and "-d" options as follows:

-a DBI::Pg  -d dbi:Pg:dbname=[database name] ....

where [database name] is the name of your database.

PostgreSQL connectivity for gbrowse

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.

Documentation: http://gmod.org/wiki/GBrowse

In order to connect to postres from gbrowse, the corresponding line in the configuration file should contain:

db_args       =    -dsn dbi:Pg:dbname=[database name ]
                   -user [username]