Center for Computational Molecular Science and Technology Georgia Institute of Technology Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry

CCMST Weekly News, March 2 2012

March 2, 2012 3:54 pm EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

School Colloquim

March 8, 2012 4:00 PM – 5:00 PM
MoSE G011
Prof. Pablo Debenedetti, Princeton University
Theoretical and Computational Studies of Nano-Scale Hydration Phenomena

TIP OF THE WEEK

By Massimo

Using Hostlists With the MOAB Scheduler

The new version of the Moab scheduler (Version 6) has some new features that allow a fine control of the hosts where a job is going to run. In a recent TOTW I covered how to specify an exclude list and how to control how many task per node are allocated to the job. Here we will discuss how to specify an hostlist for the job. Note that these new feature at the moment are available only on egate and fgate. This will be available on ggate only after the upcoming reinstall and upgrade of the cluster.

A first way is to specify directly the nodes (and processors per node) where the job must run. This is done directly in the node request line:

#PBS -l nodes=n1:ppn=2+n2:ppn=4

The above line will specify that the job must run using 2 processors on none n1 and 4 processors on node n2. Of course the above way is not very convenient, as the job will not run until the nodes and processors explicitly requested are available, and thus the waiting time in queue might be very long.

A more convenient way is to specify a superset of nodes from which the scheduler can chose to run the job from. In this way one maintains a control of the location where the job is going to run, while leaving some  flexibility to the scheduler, and tuis increasing the chances of an early start of the job. This is achieved using the hostlist resource:

#PBS -l hostlist=n1+n2+n3_n4+n5+n6+n7^
#PBS -l nodes=4,tpn=1+

The above syntax will tell MOAB to run the job using a total of four processors, using one or more processors per node, and choosing the nodes between the specified hostlist. The hostlist is a list of host names separated by the + character. A caret (^) at the end of the list will tell the scheduler that the hostlist is a superset of the hosts where the job is required to run.

To learn more about hostlists, please check the on line Moab documentation.

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo (massimo.malagoli@chemistry.gatech.edu) for inclusion in the Tip of the Week section.