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 compute nodes. 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.

.appion.cfg config file¶

The .appion.cfg config file is used to automatically create and submit job files to your job submission server. The sample config file provided in the Processing Server Installation instructions was created for the Torque Resource Manager. If a different resource manager is used, the .appion.cfg file will need to be modified appropriately.

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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.

Alternate instructions¶

It may be helpful to review the head node installation notes and client installation notes from a recent installation on CentOS 6.

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Head node installation¶

Install Torque-server¶

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

sudo yum -y install torque-server torque-scheduler torque-client

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

Make sure the directory containing the pbs_server executable is in your PATH. For CentOS this is usually /usr/sbin.

sudo pbs_server -t create

Activate Torque-server¶

Enable the torque pbs_mom daemon on reboot:

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

Add nodes to Torque-server nodes file: /var/lib/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

Configure node to receive jobs from headnode:¶

see http://docs.adaptivecomputing.com/torque/5-1-0/help.htm#topics/torque/1-installConfig/computeNodes.htm for more details

Edit the /var/torque/mom_priv/config (CentOS 5) OR /var/lib/torque/mom_priv/config (CentOS 6) file:

$pbsserver  headnode.INSTITUTE.EDU   # hostname running pbs_server

For the localhost add:

$pbsserver  localhost   # hostname running pbs_server

Activate Torque-mom¶

Enable the torque pbs_mom daemon on reboot:

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

Munge¶

http://docs.adaptivecomputing.com/torque/5-1-0/help.htm#topics/torque/1-installConfig/serverConfig.htm#usingMUNGEAuth

Munge is an authentication service that creates and validates user credentials and other features

sudo create-munge-key
sudo /sbin/chkconfig munge on
sudo service munge start
sudo qmgr -c 'set server authorized_users=user01@host01'
sudo qmgr -c 'set server authorized_users=user01@host02'
sudo qmgr -c 'set server authorized_users=user01@*'

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Test Torque Setup¶

On the head node, see if you can run a qstat:

qstat

You can type:

pbsnodes

to check the state of the compute clusters.

On the head node, create a job and submit it:

echo "sleep 60" > test.job
echo "echo hello" >> test.job
qsub test.job
qstat

get all settings

sudo qmgr -c 'list server'

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