Jon Dehdari




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Installation & Configuration of SGE / GridEngine

The instructions below are general overviews for Debian/Ubuntu-based systems.

Master Server

The master server controls how, when, and where jobs are executed. It doesn't (necessarily) run jobs itself.

Installation

sudo apt-get install gridengine-master gridengine-qmon xfonts-100dpi xfonts-75dpi
Questions it will ask during installation:
  1. Configure SGE automatically? Yes
  2. SGE master hostname: Type the full domain name of the this computer. You can find that out by typing host $(hostname -i). The last part of the output is the full domain name (minus the trailing dot).
Further reading:

Configuration

You can then configure it using the qconf command (or graphically with Qmon). The command-line arguments for qconf follow general patterns. For example you can add something with -a, delete something with -d, modify something with -m, show something with -s. Uppercase variants of the above read-in from a text file, rather than invoking a text editor (where applicable).

The most important things to add/configure are queues, execution server list, execution servers (esp. if you're using GPUs), parallel environments, complex configurations (like GPUs), and users. Read the full man page for more details.

Man Pages

Enabling GPUs

The basic setup for using GPUs within SGE/GridEngine is described here.

Other possible setups are described below:

Email Notifications

Users might want email notifications in qsub by adding the -M user@example.com argument. You can install a simple SMTP server to allow this:
sudo apt-get install ssmtp
sudo chgrp mail /etc/ssmtp/ssmtp.conf
sudo chmod 640  /etc/ssmtp/ssmtp.conf
sudo usermod -a -G mail sgeadmin

# Now modify line: "mailhub=mail" to something like "mailhub=mail.yourdomain.com"
# If your company doesn't have an email server, follow the GMail instructions at https://wiki.debian.org/sSMTP
sudo vi /etc/ssmtp/ssmtp.conf

# Now test it out, sending the test email to myemail@gmail.com
echo 'This is a test' | sudo -u sgeadmin mail -s 'Testing' myemail@gmail.com


Execution Server

Execution servers run the actual computing, outputing the results to whatever path was specified using qsub -o ... (or #$ -o ... in a script).

Installation

sudo apt-get install gridengine-exec
Questions it will ask during installation:
  1. Configure SGE automatically? Yes
  2. SGE master hostname: Type the full domain name of the master server
Add info about the execution server on the master server by typing sudo qconf -ae host . You can later modify it replacing -ae with -me .

Client

The clients submit jobs, typically using the qsub command, just as you could use bash or sh before a shell script. More info about using qsub is described in the instructions for users.

Installation

sudo apt-get install gridengine-client
Questions it will ask during installation:
  1. Configure SGE automatically? Yes
  2. SGE master hostname: Type the full domain name of the master server

User Commands

SGE commands for normal users is described here.