Contents


Deprecated: please see new documentation site.



Shells on LONI

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.

Changing One's Shell on the P5 575s

LONI users can change their shell by issuing the following command on an interactive node (eg - ducky.loni.org):

# loni_chsh

When run with no arguments, this command will display a list of available shells as well as the user's current shell and prompts for a replacement shell. Optional arguments to the command are -l, which lists the available shells only, and -s, which, when followed by a shell name, will change the shell to the given value without prompting the user


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

Softenv

LONI IBM P5 575s

Bluedawg, Ducky, Zeke, Neptune, LaCumba

Available for TCSH and Bash

Originally, SoftEnv was limited to users of Bash, but with a newer version came the ability for TCSH users to take advantage of this system.

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

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ 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
....

Listing of Available Packages

See Packages Available via SoftEnv on LONI 575s.

For an more accurate, up to date list, use the softenv command.

Administrative Information

If you are a LONI systems administrator, please see the administrative Wiki article Administrating SoftEnv on p575s.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.

64 bit x86 Linux Clusters

QueenBee, Eric, Oliver, Louie, Poseidon

Availability

softenv is available on all LONI Linux clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler.

Packages Availability

This information can be viewed using the softenv command:

% softenv

Managing the 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

Users may direct questions to sys-help@loni.org.

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