Appion

h1. 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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h2. PBS and the Torque Resource Manager

PBS stands for a "Portable Batch System":http://en.wikipedia.org/wiki/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":http://en.wikipedia.org/wiki/TORQUE_Resource_Manager. 

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.":http://www.clusterresources.com/products/torque/docs/

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h2. Head node installation

h3. Install Torque-server, because PATH setting you will need to become root

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

<pre>

sudo yum -y install torque-server torque-scheduler

</pre>

h3. Initialize Torque-server

<pre>

sudo su

/usr/share/doc/torque-2.3.10/torque.setup root

exit

</pre>

h3. Activate Torque-server

Enable the torque pbs_mom daemon on reboot:

<pre>

sudo /sbin/chkconfig pbs_server on

sudo /sbin/service pbs_server start

</pre>

h3. Configure Torque-server

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h2. Compute node installation

h3. Install Torque-mom

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

<pre>

sudo yum -y install torque-mom torque-client

</pre>

h3. Activate Torque-mom

Enable the torque pbs_mom daemon on reboot:

<pre>

sudo /sbin/chkconfig pbs_mom on

sudo /sbin/service pbs_mom start

</pre>

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

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