Setup job submission server » History » Revision 36
Revision 35 (Neil Voss, 03/02/2012 01:36 PM) → Revision 36/43 (Neil Voss, 03/05/2012 01:20 PM)
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 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. ______ 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/ ______ h2. Head node installation h3. Install Torque-server Torque available with Fedora and CentOS 5.4 (through the EPEL). For YUM based systems type: <pre> sudo yum -y install torque-server torque-scheduler torque-client </pre> h3. 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. <pre> sudo pbs_server -t create </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 restart sudo /sbin/chkconfig pbs_sched on sudo /sbin/service pbs_sched start </pre> h3. Add nodes to Torque-server nodes file: /var/torque/server_priv/nodes The format is: <pre> node-name[:ts] [np=] [properties] </pre> To add the localhost with two processors as a node, you would add: <pre> localhost np=2 </pre> You should add every *compute node* to this file, e.g., <pre> node01.INSTITUTE.EDU np=2 node02.INSTITUTE.EDU np=4 node03.INSTITUTE.EDU np=2 </pre> ______ 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. Configure node to receive jobs from headnode: bq. see http://www.clusterresources.com/products/torque/docs/1.2basicconfig.shtml#initializenode for more details Edit the /var/torque/mom_priv/config (CentOS 5) OR /var/lib/torque/mom_priv/config (CentOS 6) file: <pre> $pbsserver headnode.INSTITUTE.EDU # hostname running pbs_server </pre> For the localhost add: <pre> $pbsserver localhost # hostname running pbs_server </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> h2. Munge http://www.clusterresources.com/torquedocs/1.3advconfig.shtml Munge is a tool to prevent users from certain nodes and other features <pre> 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@*' </pre> _________ h2. Test Torque Setup On the head node, see if you can run a @qstat@:<pre>qstat</pre> You can type: <pre> pbsnodes </pre> to check the state of the compute clusters. On the head node, create a job and submit it: <pre> echo "sleep 60" > test.job echo "echo hello" >> test.job qsub test.job qstat </pre> get all settings <pre> sudo qmgr -c 'list server' </pre> _________ [[Setup Remote Processing|^ Setup Remote Processing]] | [[Install SSH module for PHP|Install SSH module for PHP >]] ______