Getting Started with SeisComP

Once the Linux system is installed the SeisComP modules need to be configured including the initial configuration and the connection to the database. The central tool to configure and control the system is seiscomp which is explained more deeply in the next chapter. A user-friendly graphical frontend to seiscomp is scconfig.

Database Configuration

Once the database server is defined and optimized as described in the section Database Server Configuration you may configure SeisComP with the database. Initially execute the steps listed in this section. You will need to consider differences in databases:

MySQL

The initial configuration by the seiscomp script or the wizard of scconfig allows to create and configure the MySQL database for SeisComP. If you want to use MySQL continue with the general setup.

Warning

  • Using MySQL is currently not recommended. Preferably use MariaDB instead of MySQL as MariaDB is the default SQL flavor of most supported Linux systems!

  • As of MySQL 8.0 the password encryption and policy has changed resulting in errors when connecting to a MySQL server. In 04/2021 this does not seem to be fully supported in Ubuntu 20.04. Therefore, you need to use a native password on the MySQL server.

    $ sudo mysql -u root -p

  ALTER USER 'sysop'@'%%' IDENTIFIED WITH mysql_native_password BY 'my_super_secret_password_matching_the_mysql_password_validation_policy';

MariaDB

The initial configuration by the seiscomp script or the wizard of scconfig allows to create and configure the MySQL database for SeisComP.

For setting up the database manually with MariaDB follow the instructions below.

Note

With Ubuntu 16.04 MariaDB has become the standard flavor of MySQL in Ubuntu and either MariaDB or MySQL can be installed. The implementation of MariaDB in Ubuntu requires additional steps. They must be taken before the initial configuration in order to allow SeisComP to make use of MariaDB. Previously, the scconfig wizard and seiscomp setup could not be used to set up the MariaDB database. The option “Create database” had to be unchecked or answered with “no”. The issue is resolved in this release and both, scconfig wizard and seiscomp setup are now fully capable of the required actions.

The full procedure to create the seiscomp database:

user@host:~$ sudo mysql -u root -p
     CREATE DATABASE seiscomp CHARACTER SET utf8mb4;
     grant usage on seiscomp.* to sysop@localhost identified by 'sysop';
     grant all privileges on seiscomp.* to sysop@localhost;
     grant usage on seiscomp.* to sysop@'%' identified by 'sysop';
     grant all privileges on seiscomp.* to sysop@'%';
     flush privileges;
     quit

user@host:~$ mysql -u sysop -p seiscomp < ~/seiscomp/share/db/mysql.sql

Note

If character set ‘utf8mb4’ is not supported by your specific database server version then use the old ‘utf8’ format. For historical reasons, SeisComP would use then the ‘utf8_bin’ collation. The full statement looks as follows: CREATE DATABASE seiscomp CHARACTER SET utf8 COLLATE utf8_bin.

PostgreSQL

The initial configuration allows configuring the PostgreSQL database parameters for SeisComP. It also allows creating the database and the database tables.

For a manual setup of the PostgreSQL database first setup the database server, then create the user, the database and the tables.

  1. Create the user and the database

    CentOS:

    sudo@host:~$ sudo su
root@host:~$ sudo -i -u postgres
postgres@host:~$ psql

   postgres=# create database seiscomp;
   postgres=# create user sysop with encrypted password 'sysop';
   postgres=# grant all privileges on database seiscomp to sysop;
   postgres=# alter database seiscomp owner to sysop;
   postgres=# exit

root@host:~$ exit

  2. Create the database tables

    user@host:~$ psql -f ~/seiscomp/share/db/postgres.sql -t seiscomp -U sysop

Continue with the general setup considering the created database but do not create the database again.

General SeisComP Setup

Use seiscomp setup or the wizard from within scconfig (Ctrl+N) for the initial configuration including the database parameters. seiscomp setup is the successor of the former ./setup script.

In seiscomp setup default values are given in brackets []:

user@host:~$ seiscomp/bin/seiscomp setup

====================================================================
seiscomp setup
====================================================================

This initializes the configuration of your installation.
If you already made adjustments to the configuration files
be warned that this setup will overwrite existing parameters
with default values. This is not a configurator for all
options of your setup but helps to setup initial standard values.

--------------------------------------------------------------------
Hint: Entered values starting with a dot (.) are handled
      as commands. Available commands are:

      quit: Quit setup without modification to your configuration.
      back: Go back to the previous parameter.
      help: Show help about the current parameter (if available).

      If you need to enter a value with a leading dot, escape it
      with backslash, e.g. "\.value".
--------------------------------------------------------------------

This will ask for initial settings as database (if package trunk is installed) parameters and the logging backend.

Organization name []:

Sets the organisation name printed e.g. when you say hello to Seedlink or Arclink.

Enable database storage [yes]:

Enables or disables the database for the system. This option should be left enabled unless all modules should connect to remote processing machine which is already available. The database is required to store inventory information as well as processing results. The database is the central storage for all trunk modules and the default request handler of Arclink.

 0) mysql
      MySQL server.
 1) postgresql
      PostgreSQL server. There is currently no support in setup to create the
      database for you. You have to setup the database and user accounts on
      your own. The database schema is installed under share/db/postgresql.sql.
Database backend [0]:

If the database is enable the database backend can be selected. SeisComP supports two main backends: MySQL and PostgreSQL. Select the backend to be used here but be prepared that only for the MySQL backend the setup can help to create the database and tables for you. If you are using PostgreSQL you have to provide a working database with the correct schema. The schema files are part of the distribution and can be found in seiscomp/share/db/postgresql.sql.

Note

As of PostgreSQL version 9 the default output encoding has changed to hex. In order to fix issues with seiscomp log in to your database and run the following command.

ALTER DATABASE seiscomp SET bytea_output TO 'escape';

Create database [yes]:

Warning

If MySQL is selected it is possible to let seiscomp setup to create the database and all tables for you. Otherwise currently not and you need to set up the database manually following the given instructions. If the database has been created already, answer ‘no’ here.

MYSQL root password (input not echoed) []:

Give the MySQL root password for your database server to create the database tables. This is only required if the last question has been answered with ‘yes’.

Drop existing database [no]:

If a database with the same name (to be selected later) exists already and the database should be created for you, an error is raised. To delete an existing database with the same name, say ‘yes’ here.

Database name [seiscomp]:
Database hostname [localhost]:
Database read-write user [sysop]:
Database read-write password [sysop]:
Database public hostname [localhost]:
Database read-only user [sysop]:
Database read-only password [sysop]:

Setup the various database options valid for all database backends. Give help for more information.

If all question have been answered the final choice needs to be made to either create the initial configuration, go back to the last question or to quit without doing anything.

Finished setup
--------------

P) Proceed to apply configuration
B) Back to last parameter
Q) Quit without changes
Command? [P]:

Environment variables

Commands can be used along with the seiscomp script located in seiscomp/bin/seiscomp. Read the section seiscomp Commands for more details on seiscomp. E.g. SeisComP modules can be executed like

user@host:~$ seiscomp/bin/seiscomp exec scrttv

Calling seiscomp with its full path, e.g.

user@host:~$ seiscomp/bin/seiscomp [command]

will load the full SeisComP environment. Providing the full path allows starting other SeisComP modules in a specific SeisComP environment. Thus, multiple SeisComP installations can be maintained and referred to on the same machine.

seiscomp can also be used for printing the considered SeisComP environment

user@host:~$ seiscomp/bin/seiscomp print env

resulting in

export SEISCOMP_ROOT="/home/sysop/seiscomp"
export PATH="/home/sysop/seiscomp/bin:$PATH"
export LD_LIBRARY_PATH="/home/sysop/seiscomp/lib:$LD_LIBRARY_PATH"
export PYTHONPATH="/home/sysop/seiscomp/lib/python:$PYTHONPATH"
export MANPATH="/home/sysop/seiscomp/share/man:$MANPATH"
source "/home/sysop/seiscomp/share/shell-completion/seiscomp.bash"

For convenience, the default SeisComP installation can be referred to, when defining the required system variables, e.g. in ~/.bashrc. Then, the SeisComP environment is known to the logged in user and SeisComP modules can be executed without the seiscomp script.

For setting the environment

  1. Use the seiscomp script itself to generate the parameters and write the parameters to ~/.bashrc

    user@host:~$ seiscomp/bin/seiscomp print env >> ~/.bashrc

  2. Load the environment or log out and in again

    user@host:~$ source ~/.bashrc

Thereafter, modules can be executed by their names without involving seiscomp, e.g.

user@host:~$ scrttv

Activate/Enable Modules

After the installation all module are disabled for auto start. If seiscomp start is called, nothing will happen until modules are enabled. To enable a set of modules, seiscomp enable needs to be called with a list of modules. For example, for a processing system with SeedLink for data acquisition, you may use:

user@host:~$ seiscomp/bin/seiscomp enable seedlink slarchive scautopick scautoloc scamp scmag scevent
enabled seedlink
enabled slarchive
enabled scautopick
enabled scautoloc
enabled scamp
enabled scmag
enabled scevent

A successive call of seiscomp start will then start all enabled modules. This is also required to restart enabled modules with seiscomp check.

Alternatively, scconfig can be used to enable/disable and to start/stop/restart modules.

However, before starting seiscomp, station information (metadata) need to be provided and the configuration needs to be updated.

Supply Station Metadata

SeisComP requires the metadata from seismic network and stations including full responses for data acquisition and processing. The metadata can be obtained from network operators or various other sources in different formats. The metadata include, e.g.:

  • Network association

  • Operation times

  • Location

  • Sensor and data logger specifications with full response information

  • Data stream specifications

SeisComP comes with various importers to add metadata for networks and stations including full response information.

import_inv is the tool to import inventory data into SeisComP. Alternatively can be used.

user@host:~$ seiscomp/bin/seiscomp exec import_inv dlsv inventory.dataless

This will import a dataless SEED volume into etc/inventory/inventory.dataless.xml.

Repeat this step for all inventory data you want to import.

Configure Station Bindings

The configuration of modules and bindings is explained in Global parameters. To add bindings in a more convenient way, start scconfig.

user@host:~$ seiscomp/bin/seiscomp exec scconfig

Typical binding profiles or station bindings involve bindings configurations for data acquisition and processing modules:

  • seedlink: Configure the plugin for the real-time data acquisition.

  • slarchive: Configure the data archiving.

  • global: Configure detecStream and detecLocid to determine the default streams for phase detection and for showing stations and streams in GUIs like scmv, scrttv or scolv.

  • scautopick: Configure the automatic phase detection. You may overwrite global binding parameters.

Update Configuration, Start Everything

To update the configuration when new stations have been added or modified, seiscomp update-config needs to be run. This creates configuration files of modules that do not use the configuration directly, writes the trunk bindings to the database and synchronizes the inventory with the database.

user@host:~$ seiscomp/bin/seiscomp update-config
[output]

After the configuration has been updated and the inventory has been synchronized, call seiscomp start to start all enabled modules:

user@host:~$ seiscomp/bin/seiscomp start
starting seedlink
starting slarchive
starting scautopick
starting scautoloc
starting scamp
starting scmag
starting scevent

Now the system should run. To check everything again, seiscomp check can be run which should print is running for all started modules. If everything is working, the analysis tools can be started, e.g. MapView.

user@host:~$ seiscomp/bin/seiscomp exec scmv