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, January 13 2012

January 13, 2012 1:37 pm EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

Physical Chemistry Seminar Series

January 27, 2012 4:00 PM – 5:00 PM
MoSE 3201A
Prof. Yasuhiro Tachibana, RMIT University
Semiconductor Quantum Dots for Solar Light Energy Conversion

TIP OF THE WEEK

By Massimo

New Features of the Moab Scheduler

Here is a short list of new features of the latest version of the Moab scheduler (Version 6). These new features add some fine control to job execution, adding the capability of excluding certain nodes from a job, and better specifying how many processor per node a job should use. Note that for the moment these features are available only on egate and fgate, as ggate is still running Moab version 5. After ggate is reinstalled these new features should be available on ggate too.

  • Excluding nodes from a job:
    #PBS -l excludenodes=compute-1-1:compute-1-2
    The above line will tell the scheduler to do not run the job on nodes compute-1-1 and compute-1-2. The list of nodes to be excluded from the job is a colon separated list of host names.
  • Defining the number of tasks per node: Moab version 6 has a new resource, tpn (tasks per node) that allow to control how many tasks per node a job should have. The tpn number can be followed by an optional + sign, to indicate that the number of tasks per node is to be taken as the minimum required task per node. For instance, currently to run a job on 4 nodes with two processors per node (total of 8 processors) one would use:
    #PBS -l nodes=4:ppn=2
    Moab will interpret this as the user requesting at least 2 processors per node, and, depending on policies and node availability, might actually allocate more than 2 processors per node for the job. Using the tpn resource request, one can specify a job with a total of 8 processors and exactly two processors per node:
    #PBS -l nodes=8,tpn=2
    Note that there is a comma separating the tpn= request from the nodes= request (as opposed to the colon in the ppn case). Note also that the total number of processes is now given by the node number. In other words, when using the syntax
    #PBS -l nodes=X:ppn=Y
    the total number of processors allocated for the job is given by X*Y, but when using the tpn syntax:
    #PBS -l nodes=X,tpn=Y
    The total number of processors is given by X only. As mentioned before, tpn can be followed by an optional + sign:
    #PBS -l nodes=8,tpn=2+
    In this case the job will use a total of 8 processors, with at least 2 processor per node (this ia equivalent to specifying -l nodes=4:ppn=2).

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.