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octave

About

Octave is a high-level open-source language for technical computation. It is mostly compatible with Matlab, as it uses m-language for programming. With a little care, programs are portable between Matlab and Octave.

Versions and Availability

Softenv Keys for octave on painter
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

Octave is an interactive program. Use of the graphical interface requires having an X-windows server running on the local machine, and enabling X11 pass-through in the SSH connection.

▶ X11 FAQ?

From *nix

Since ssh and X11 are already on most client machines running some sort of unix (Linux, FreeBSD, etc), one would simply use the following command:

% ssh -X -Y username@remote.host.tdl

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, email us.

From Mac OS X

An X11 service is not installed by default, but one is available for installation on the OS distribution disks as an add-on. An alternative would be to install the XQuartz version. Make sure the X11 application is running and connect to the cluster using:

% ssh -X -Y username@remote.host.tdl

From Windows

Microsoft Windows does not provide an X11 server, but there are both open source and commercial versions available. You also need to install an SSH client. Recommended applications are:

  • Xming - a Windows X11 server
  • PuTTY - a Windows ssh client

When a PuTTY session is created, make sure the "X11 Forwarding Enabled" option is set, and that the X11 server is running before starting the session.

Testing

Once Xming and puTTY have been set up and in stalled, the following will provide a simple test for success:

  1. start Xming
  2. start puTTY
  3. connect to the remote host (make sure puTTY knows about Xming for this host)

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, refer to "Trouble with Xming?" or email us.

Note About Cygwin

Cygwin is still a useful environment, but is to complicated and contains too many unnecessary parts when all one wants is to interface with remote X11 sessions. For these reasons, we recommend Xming and PuTTY as listed above.

Advanced Usage

The most important connection that is made is from the user's client machine to the first remote host. One may "nest" X11 forwarding by using the ssh -XY command to jump to other remote hosts.

For example:

1. on client PC (*nix or Windows), ssh to remotehost1

2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2

3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3

...

8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9

9. on remotehost9, running an X11 application like xterm should propagate the remote window back to the initial client PC through all of the additional remote connects.

Resources

Last modified: November 12 2014 09:49:09.