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perl

About

Perl is a scripting language with cross-platform standardization - scripts developed on one platform should run unchanged on another platform. It is heavily used in place of shell scripting, and is easily extensible, as evidenced by the large number of available modules on the Comprehensive Perl Archive Network.

Version and Availability

Softenv Keys for perl on philip
Machine Version Softenv Key
philip 5.10.1 +perl-5.10.1
philip 5.16.0 +perl-5.16.0
philip 5.16.2 +perl-5.16.2
▶ Display Softenv Keys for perl all clusters
Machine Version Softenv Key
philip 5.10.1 +perl-5.10.1
philip 5.16.0 +perl-5.16.0
philip 5.16.2 +perl-5.16.2
supermike2 5.16.3 +perl-5.16.3
▶ Softenv FAQ?

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

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

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 LSU HPC and LONI.

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

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.
Availability

softenv is available on all LSU HPC and LONI 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 on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with 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

Usage

The command to run the interpreter is perl, and it can be used in interactive and scripted modes. The details of the language can be found in the Resources documents.

▶ Executable Scripts FAQ?
Executable Scripts

All shells and most interpreters (i.e. Python, Tcl, gawk, R, etc.) can be used to create executable scripts. This is accomplished through the magic of the shell #! line, which is a special comment line. The line, which must be the first line of the script, specifies the path to the program that can interpret the main contents of the file, which are command lines the language understands. Once the script is written, set it executable with chmod. A few examples should serve to illustrate the general idea.

Executable Bash Script

A simple script to echo out Hello World and do a long ls listing.

#!/bin/bash
echo "Hello World!"
ls -l

If the above is in a file named hello.sh, it can be made executable for the user (i.e. see man chmod for other possibilities) and run with:

$ chmod u+x hello.sh
$ ./hello.sh
Other Scripts

Here are some line usable with other scripting languages. In most cases, options allowed by the command used can be provided on the #! line. Note: that the paths should be verified and not use blindly. In particular command shells tend to reside in different directories.

gawk:  #!/bin/gawk
tcsh:  #!/usr/bin/tcsh
tcl:   #!/usr/local/bin/tcl

Resources

Last modified: August 21 2014 13:48:49.