Setup job submission server¶

In this case, we are setting up a job submission server that will have all of the data directories mounted and external packages installed (EMAN, Xmipp, etc.) on the system. Most institutions have a job submission server already, but the data is not accessible. Appion is not set up for this scenario except for large reconstruction jobs.

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PBS and the Torque Resource Manager¶

PBS stands for a Portable Batch System. It is a job submission system meaning that users submit many jobs and the server prioritizes and executes each job as resources permit. Below we show how to install the popular open source PBS system called TORQUE.

A TORQUE cluster consists of one head node and many compute nodes. The head node runs the pbs_server daemon and the compute nodes run the pbs_mom daemon. Client commands for submitting and managing jobs can be installed on any host (including hosts not running pbs_server or pbs_mom). More documentation about Torque is available here.

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Head node installation¶

Install Torque-server¶

Torque available in with Fedora and CentOS 5.4 (through the EPEL). For YUM based systems type:

sudo yum -y install torque-server torque-scheduler

Initialize Torque-server, because PATH setting you will need to become root¶

sudo su
/usr/share/doc/torque-2.3.10/torque.setup root
exit

Activate Torque-server¶

Enable the torque pbs_mom daemon on reboot:

sudo /sbin/chkconfig pbs_server on
sudo /sbin/service pbs_server restart

Add nodes to Torque-server nodes file: /var/torque/server_priv/nodes¶

The format is:

node-name[:ts] [np=] [properties]

To add the localhost with two processors as a node, you would add:

localhost np=2

You should add every compute node to this file, e.g.,

node01.INSTITUTE.EDU np=2
node02.INSTITUTE.EDU np=4
node03.INSTITUTE.EDU np=2

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Compute node installation¶

Install Torque-mom¶

Torque available in with Fedora and CentOS 5.4 (through the EPEL). For YUM based systems type:

sudo yum -y install torque-mom torque-client

Activate Torque-mom¶

Enable the torque pbs_mom daemon on reboot:

sudo /sbin/chkconfig pbs_mom on
sudo /sbin/service pbs_mom start

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^ Setup Remote Processing | Configure web server to submit jobs >

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