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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

Softenv Keys for wq on supermike2
Machine Version Softenv Key
supermike2 264 +wq-264
supermike2 272 +wq-272
▶ Softenv 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.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of available packages. The listing will look something like:

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
... some stuff deleted ...
Managing SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

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

  • WQ_DOCS environment variable that points to the full user manual in PDF form.

Last modified: August 23 2017 10:59:58.