Installing and configuring EMEN2

Generally, you will want to create a user account for running emen2, e.g. 'emen2.' This has the benefit of working well with the default config file. Running as any other user also works fine, you will just have to change one or two paths in config.yml.

Install Dependencies

You will first need to install the various EMEN2 dependencies. They are all straight-forward to install, and can generally be installed using Python's easy_install system.

Download EMEN2

Download the latest EMEN2 source code release and untar

http://ncmi.bcm.edu/ncmi/software/software_details?selected_software=EMEN2

cd /home/emen2
tar -xvzf emen2.03.28.2010.tar.gz
cd emen2

If there is an existing source tree installed, you may want to rename it in case you need to revert to the previous version, e.g. mv emen2 emen2.old.03.20.2010.

If you have an existing EMEN2 environment, I strongly recommend taking an additional tar backup of that directory before proceeding, in addition to normal backup procedures (log archive, db hot backup) in case you need to revert without the difficulty of performing a full recovery from archives.

Create EMEN2 Environment

The instructions below assume you are setting EMEN2 up in a separate user account called 'emen2', with a default home directory '/home/emen2'.

You will need to create a directory for your EMEN2 environment. A reasonable default is /home/emen2/db.

It is strongly recommended to set the DB_HOME environment variable to this path for convenience. You will also need to add the parent of the EMEN2 source directory to your PYTHONPATH environment variable. Adjust the paths below, and place in your .bash_profile:

export DB_HOME=/home/emen2/db
export PYTHONPATH=$PYTHONPATH:/home/emen2/emen2

Create the DB_HOME directory and copy the default configuration file.

mkdir $DB_HOME
cp config/config.sample.yml $DB_HOME/config.yml

Edit Configuration

Edit the various settings in $DB_HOME/config.yml. See EMEN2/config.yml. Primarily, you will want to check the path and network settings. A simple configuration will have most EMEN2 directories (db, applog, archive, db_hotbackup, emen2files, etc.) placed under the path specified by the "&root" element, which is /home/emen2/ by default.

  root: &root
    /home/emen2/

Initialize EMEN2 Environment

After config.yml is to your liking, run

python ./setup.py

The rest of the EMEN2 environment will be created, skeleton parameter/protocol definitions will be installed, and a root user created. You will be prompted on the shell for a root password.

Test Web Server

python ./TwistSupport.py

You should be able to connect to this web server instance once it is "listening..." The default port is 8080. You may login with the root password you specified previously.

Optional: Import

You may want to import the parameter and protocol definitions from the EMEN2 installation at the NCMI. In the future, these will be published in an open format, and made available by default.

python ./clients/clone.py -- --defs --host http://ncmidb.bcm.edu

Note: the first "--" is intentional and required at the moment. Command arguments for the local database go before "--", arguments to the cloning script go after ("--defs")

You will be prompted for two sets of credentials. First, an NCMI DB account, and second, the root password for the local database. If you do not have an NCMI DB account, you may specify "anonymous" as the username, and your email address as the password.

Optional: Accelerator Module

EMEN2 includes a C module that increases index read speed by using some features of the Berkeley DB interface that are not exposed by the bsddb3 module. See EMEN2/bulk.so for information on how to build this module. This module is not required, and can be enabled/disabled at any time.

Run as daemon

After you are satisfied with your setup, you can run EMEN2 in the background

python ./emen2control.py --start