SciClone Local Manual

pbsmobius


Purpose

Run Möbius 2.2 under TORQUE or PBS.

Synopsis

pbsmobius [-hv] [-D projdir]

Description

The TORQUE job scheduling system (a derivative of OpenPBS) allocates resources for parallel programs, but does not provide the system-specific procedures for actually initiating and executing parallel programs on those resources. pbsmobius provides such an interface between TORQUE and Möbius, including the following services:
 

Arguments

-D
Specifies an alternate project directory for Möbius to use. The default is $HOME/MobiusProject.
 
-h
Print a help message, listing the available options with a brief description of each.
 
-v
Verbose mode. Generate additional output about the progress of pbsmobius, as well as a listing of allocated nodes and processors.

Usage Notes

pbsmobius is intended to be run from within an interactive TORQUE or PBS job initiated via a qlogin or "qsub -I" command. qlogin will forward X11 connections through the login server back to the user's desktop. For improved interactive response, users may choose to use "qsub -I" in conjunction with xauth to establish a direct (but less secure) X11 connection between a compute node and the user's desktop system, using the procedure described in the SciClone User's Guide.

Because every instance of Möbius accesses network configuration information through the same file ($HOME/.mobius/network.cp), simultaneous execution of more than one copy of Möbius by a single user through PBS or TORQUE is problematic. pbsmobius partially circumvents this problem by creating a .network.cp file in the user's local scratch directory (/local/scr/$USER) and then installing a symbolic link in ~/.mobius/network.cp to reference this local file. This will permit multiple Möbius jobs belonging to a single user to execute properly on different nodes, but care should be taken to ensure that the nodespecs used with qlogin or "qsub -I" cannot be mapped to the same node at runtime. One simple way to ensure this is to request all of the available processors on a node. For example, on SciClone's dual processor "c8" nodes, the nodespecs used in the following commands would allocate both processors, thereby preventing TORQUE from scheduling any other jobs on the same node:

qlogin -t 120 1:c8:ppn=2
qsub -I -l walltime=02:00:00 -l nodes=1:c8:ppn=2
Note that this technique is inefficient if the Möbius job is essentially serial, i.e,. unable to effectively exploit multiple processors in the back end simulator or solver. In this case the extra allocated processor(s) will be held idle and unavailable for other work.

Environment Variables

pbsmobius queries the MOBIUS_HOME environment variable to determine which version of Möbius to use. This variable is automatically set when the user loads the mobius environment module. For more info, see the Möbius documentation page. pbsmobius also depends on several environment variables which are automatically set when running within a TORQUE or PBS environment.

Exit Status

If pbsmobius detects an error condition, it returns a non-zero value. Otherwise, it returns the exit status from the mobius command.

Bugs and Limitations

See Usage Notes, above.

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