DSLab: Data Science Laboratory

Torque/PBS

Torque/PBS is a free open source job scheduler. In our day to day bioinformatics work, a system administrator want to run a job schduler that will run the user jobs automatically. if load on the server is high and all resources (CPUs) are in use, new job submitted by the user will be in queue. Portable Batch Submission will automatically look and run the queue job once the previous job is completed and resources are free. A naive user did not to be worry or login on each node to run fire their job. This will also work when you are going on a long holidays by just submut your job in through pbs and all will run one by one depending upon the source availabilty.

Instalation

  1. sudo apt-get install torque-server torque-client torque-mom torque-pam
  2. Now stop all Torque Servies
      • /etc/init.d/torque-mom stop
        /etc/init.d/torque-scheduler stop
        /etc/init.d/torque-server stop
        pbs_server -t create
  3. killall pbs_server
  4. Write your domain name in the following files as a root user
      • echo SERVER.DOMAIN > /etc/torque/server_name
        echo SERVER.DOMAIN > /var/spool/torque/server_priv/acl_svr/acl_hosts
        echo root@SERVER.DOMAIN > /var/spool/torque/server_priv/acl_svr/operators
        echo root@SERVER.DOMAIN > /var/spool/torque/server_priv/acl_svr/managers
  5. echo "SERVER.DOMAIN np=4" > /var/spool/torque/server_priv/nodes
  6. echo SERVER.DOMAIN > /var/spool/torque/mom_priv/config
  7. Restart all Torque Services
      • /etc/init.d/torque-server start
        /etc/init.d/torque-scheduler start
        /etc/init.d/torque-mom start
  8. Set the scheduling properties
      • qmgr -c 'set server scheduling = true'
        qmgr -c 'set server keep_completed = 300'
        qmgr -c 'set server mom_job_sync = true'
  9. Create default Queue
      • qmgr -c 'create queue batch'
        qmgr -c 'set queue batch queue_type = execution'
        qmgr -c 'set queue batch started = true'
        qmgr -c 'set queue batch enabled = true'
        qmgr -c 'set queue batch resources_default.walltime = 1:00:00'
        qmgr -c 'set queue batch resources_default.nodes = 1'
        qmgr -c 'set server default_queue = batch'
  10. Configure Submission Pool
      • qmgr -c 'set server submit_hosts = SERVER'
        qmgr -c 'set server allow_node_submit = true'
Finally, if all is work well without any problem run qsub -I command. For more information visit this link Click here

Environment Module

A software module that is used for setting the environment during the session. This could be easily install from Module. After, Installation type module at terminal and it will show the help option of the command.
A few important commands:
1. Type module avail: Showed all the availalbe module in the path.
2. Type module list : list the module.
3. Type module load name_of_module : Used to load a specific module in the linux environment.
4. Type module unload name_of_module: Used to unload a specific module from the linux environment.

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