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.
Versions and Availability
Softenv Keys for perl on philip
▶ Softenv FAQ?
The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
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.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
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 ...
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:
To update the environment after modifying this file, one simply uses the resoft command:
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.
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?
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
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
Last modified: November 12 2014 09:49:09.