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wq

About

WQ (WorkQueuing) provides a dispatcher-worker service to allow tasks to be distributed across multiple nodes under PBS control. The tasks may be serial, or small parallel OpenMP and MPI tasks (MPI tasks may only use cores on a single node under WQ). The user customizes a PBS template file to fit their needs, and provides a task script or program to be control. The template, example task script, and user documentation are pointed to by environment variables (WQ_PBS_TEMPLATE, WQ_EXAMPLE_TASK, and WQ_DOC) defined by the module or softenv key for WQ.

Versions and Availability

Module Names for wq on smic
Machine Version Module Name
smic 264 wq/264
smic 272 wq/272
▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

Module is currently available only on SuperMIC.

Usage

  • Create a file with each line defining a file name, command line, or whatever the task script/program requires.
  • Create a task script, or command, that runs correctly when given a line from the above file. The variable WQ_EXAMPLE_TASK points to a sample script file.
  • Test the task script manually, just to be sure.
  • Make a copy of the file pointed to by WQ_PBS_TEMPLATE, and update the settings to suite your needs (user name, allocation code, other options.)
  • Submit the PBS script as usual.

Resources

Last modified: July 08 2016 12:42:29.