Install SGE (Sun Grid Engine) on Linux

Install SGE on Ubuntu 16.04

0. Install some package:

deimos@deimos:~$ sudo apt-get install xfs*

deimos@deimos:~$ sudo apt-get install libguestfs-xfs

deimos@deimos:~$ sudo apt-get install xfonts-75dpi xfonts-100dpi

deimos@deimos:~$ sudo apt-get install t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-non

deimos@deimos:~$ xset +fp /usr/share/fonts/X11/75dpi

deimos@deimos:~$ xset fp rehash

1. Install SGE on master node:

deimos@deimos:~$ sudo apt-get install gridengine-client gridengine-common gridengine-master gridengine-qmon gridengine-exec

• Remove gridengine-exec from the list if master node is not supposed to run jobs
• During the installation, we need to set the cluster CELL name (such as 'default')

2. Install SGE on other nodes:

deimos@deimos:~$ sudo apt-get install gridengine-client gridengine-exec

• The CELL name is set the same as that of the master node

However, you can install all in the same machine (master and client), but you must set:
deimos@deimos:~$ sudo apt-get install gridengine*

3. Set SGE_ROOT and SGE_CELL environment variables:

We need edit three files /etc/profile, /etc/bash.bashrc and ~/.bashrc, and add the following two lines:

• export SGE_CELL=default

Set this line if it is necessary:

• export SGE_ROOT='path of SGE'

4. Set domain:

Edit /etc/hosts with your domain

5. Configure SGE

We need launch qmon as superuser:
deimos@deimos:~$ sudo qmon

5.1 Configure host

• Host Configuration => Administration Host => add master node and other administrative nodes
• Host Configuration => Submit Host => add master node and other submitted nodes
• Host Configuration => Execution Host => add slave nodes
• Click Done

5.2 Configure user

In this configuration, you can add or delete users that are allowed to access SGE.

• User Configuration => Userset => Highlight userset 'arusers' and click on 'Modify' => input user name in 'User/Group' field
• Click Done

5.3 Configure queue

Queue Control define ways to connect hosts and users.

• Queue Control => Hosts => Confirm the execution hosts show up there.
• Queue Control" => Cluster Queues => Click on "Add" => Name the queue, add execution nodes to Hostlist
• Use access => allow access to user group arusers;
• General Configuration => Field 'Slots' => Raise the number to total CPU cores on slave nodes (ok to use a bigger number than actual CPU cores).
• Queue Control" => Queue Instances => This is the place to manually assign hosts to queues, and control the state (active, suspend ...) of hosts.

5.4 Configure parallel environnent

• Queue Control => Cluster Queues => select a queue that it will run parallel jobs => click on 'Modify' => 'Parallel Environment' => click on 'PE' below the right and left arrows => click on 'add' => name the PE, slot = 999, start_proc_args = $SGE_ROOT/mpi/startmpi.sh $pe_hostfile, stop_proc_args = $SGE_ROOT/mpi/stopmpi.sh, allocation_rule= $fill_up, check 'Control slaves' to make this variable checked

6. Check SGE hosts

• The system info from all nodes

deimos@deimos:~$ qhost

• The hostnames of nodes

deimos@deimos:~$ qconf -sel

• List the queues

deimos@deimos:~$ qconfi -sql

• Check master daemon

deimos@deimos:~$ ps aux | grep sge_master

• Check execute daemon

deimos@deimos:~$ ps aux | grep sge_execd

• If sge_master or sge_execd is not running, you can start the service

deimos@deimos:~$ sudo service gridengine-master start

deimos@deimos:~$ sudo service gridengine-exec start

Reference
N1 Grid Engine 6 Administration Guide

https://web.njit.edu/topics/HPC/basement/sge/817-5677.pdf