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saga

About

SAGA is an API that provides the basic functionality required to build distributed applications, tools and frameworks so as to be independent of the details of the underlying infrastructure. SAGA can be used to provide simple access layers for distributed systems and abstractions for applications and thereby address the fundamental application design objectives of Interoperability across different infrastructure, Distributed Scale-Out, Extensibility, Adaptivity whilst preserving simplicity.

Versions and Availability

Softenv Keys for saga on oliver
Machine Version Softenv Key
▶ 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

Usage requires creating a job definition file. It would be best to start with the tutorial material, then move on to other documentation pointed to in the Resources section..

Resources

Last modified: November 12 2014 10:07:50.