danymukesha / SGE-on-Ubuntu-servers

Tutorial for setting up SGE on Ubuntu servers, both as master and client nodes. It covers installation steps and configurations required for proper functioning of the Grid Engine system.

SGE-on-Ubuntu-servers

Tutorial for setting up SGE on Ubuntu servers, both as master and client nodes. It covers installation steps and configurations required for proper functioning of the Grid Engine system.

Setting up SGE (Sun Grid Engine) on Ubuntu

Master Server - Part 1

1. Update:

   apt-get update
   

2. Add a new user:

   adduser gsadmin --uid 500
   

3. Download Grid Engine package:

   wget http://downloads.sourceforge.net/project/gridscheduler/GE2011.11p1/GE2011.11p1.tar.gz
   tar -zxvf GE2011.11p1.tar.gz
   mv GE2011.11p1 /home/gsadmin/
   chown -R gsadmin:gsadmin /home/gsadmin/
   

4. Install NFS Server (Network File System):

   apt-get install nfs-kernel-server
   echo "/home/gsadmin *(rw,sync,no_subtree_check,no_root_squash)" >> /etc/exports
   exportfs -a
   service nfs-kernel-server restart
   

5. Install OpenJDK-8:

   apt-get install openjdk-8-jdk
   echo "export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/" >> ~/.bashrc
   export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/
   echo "export PATH=$PATH:/usr/lib/jvm/java-8-openjdk-amd64/bin" >> ~/.bashrc
   export PATH=$PATH:/usr/lib/jvm/java-8-openjdk-amd64/bin
   echo "export SGE_ROOT=/home/gsadmin/GE2011.11p1" >> ~/.bashrc
   export SGE_ROOT=/home/gsadmin/GE2011.11p1/
   source ~/.bashrc
   

Host (Client) Server - Part 1

1. Add a user:

   adduser gsadmin --uid 500
   

2. Install NFS client:

   apt-get install nfs-common
   

3. Mount shared directory:

   mount xxx.xxx.xxx.xxx:/home/gsadmin /home/gsadmin/
   # Note: Handle any errors if encountered
   

4. Set up auto-mount:

   echo "xxx.xxx.xxx.xxx:/home/gsadmin /home/gsadmin nfs" >> /etc/fstab
   

Master Server - Part 2

1. Install gridengine-master:

   apt-get install gridengine-master
   

2. Modify /etc/hosts:

   #127.0.0.1
   #127.0.1.1
   xxx.xxx.xxx.xxx master master
   yyy.yyy.yyy.yyy node01 node01
   zzz.zzz.zzz.zzz node02 node02
   

3. Restart after modifications:

   service gridengine-master restart
   

4. Confirm installation:

   qhost
   # Ensure qmaster entry in /etc/hosts and /var/lib/gridengine/default/common/act_qmaster match
   ln -s /var/lib/gridengine/default /home/gsadmin/GE2011.11.pl/default
   

Host (Client) Server - Part 2

1. Install gridengine-client:

   apt-get install gridengine-client
   

2. Install gridengine-exec:

   apt-get install gridengine-exec
   

3. Restart:

   /etc/init.d/gridengine-exec restart
   

Master Server - Part 3

1. Add nodes to admin list:

   qconf -ah node01
   qconf -ah node02
   

2. Add gsadmin group:

   qconf -au gsadmin gsadmin
   

3. Add nodes to commit hosts:

   qconf -as node01
   qconf -as node02
   

4. Add queues to cluster:

   qconf -aq main.q
   

5. Modify main.q:

   qconf -mq main.q
   # Configure hostlist and slots accordingly
   

6. Restart:

   service gridengine-master restart
   

Host (Client) Server - Part 3

1. Modify /etc/hosts to match master server:

   # Update /etc/hosts to match the master server
   

2. Restart:

   /etc/init.d/gridengine-exec restart
   

3. Check status:

   qhost
   

End

Additional commands such as qstat, qsub, qmod, etc., can be used for various tasks.

• qstat -f: To display full and detailed information about all jobs and queues.
• qstat -F: To display complete information about all jobs and queues.
• qmod -c main.q@hostname: To clear a job from a specific queue (main.q) at a given hostname.
• qmod -d main.q@hostname: To disable a job in a specific queue (main.q) at a given hostname.
• qmod -e main.q@hostname: To enable a job in a specific queue (main.q) at a given hostname.
• qdel listnum: To delete a job with the specified job number.
• qsub: To submit a job for execution.