Running EMEN2 at system boot

Similar to Apache's "apachectl" script, EMEN2 includes an "emen2ctl" script. This can be used to start and stop the server and perform some basic administration tasks.

Create a system account for EMEN2

For systems that will run EMEN2 continuously, I highly recommend creating a dedicated "emen2" account. This will run EMEN2 using regular user-level permissions instead of as root. Please see your operating system documentation for creating a new account.

Start EMEN2 using init.d

emen2ctl can be run as a traditional "init.d" script, but this is not recommended because it will run with root privileges. You will also have to find a way to pass the "-h" database environment flag. Instead, I recommend starting EMEN2 using crontab as described below.

Start EMEN2 using crontab

Cron is a tool for running commands (jobs) at specified times and intervals and is generally available on unix-like systems. Modern cron implementations also include an "@reboot" setting that will run a job the system is started. Additionally, each user account can usually schedule their own cron jobs using the "crontab" command. This will allow us to have EMEN2 run as under a regular user account (e.g. "emen2") at boot.

bash$ crontab -e

This will open a text editor (usually vi or pico) to edit your cron file. On a typical Linux installation, insert the following line:

@reboot . $HOME/EMAN2/eman2.bashrc; $HOME/EMAN2/Python/bin/emen2ctl start -h $HOME/db.test -e default,em,eman2,site

The first argument is "@reboot" that will schedule this job to run whenever the system is booted. The remainder of the line is a command to start EMEN2 using emen2ctl. First, the EMAN2 shell init file is loaded because cron jobs start with a very minimal environment. The second part runs "emen2ctl start" to start the server, passing two arguments:

• -h $HOME/db.test

This should point to your EMEN2 database environment. Alternatively, you can set the $EMEN2DBHOME environment variable.

• -e default,em,eman2,site

This specifies the extensions that will be loaded. You could put this in the config.json file.

Note: Currently, on Linux you will need to patch one file. Edit $HOME/EMAN2/Python/bin/twistd and change the first line to the EMAN2 Python interpreter:

 #!/home/emen2/EMAN2/Python/bin/python

I will correct this in future releases.