Scripting

Once you start using a supercomputing system, you will probably at some stage need to use a scripting language to help you automate things you are trying to do...like renaming a large list of files in a directory or moving a selected set of files to a new location for example. A scripting (or script) language is a programming language that supports the writing of scripts. Scripts are programs written for a software environment that automate the execution of tasks which could alternatively be executed one-by-one by a human operator.

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Captured

Bash is the command processor that you are (most likely) using when you log in to a supercomputer. It allows the user to type commands (like 'ls') which cause actions. A shell program, called a script, is an easy-to-use tool for building applications by "gluing together" system calls, tools, utilities, and compiled binaries.

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Bash scripting

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Credit: The Linux Documentation Project

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Added to our repository: 2014-03-26 by Stelios

Python

Python is everywhere, if you want advanced scripting features spend your time learning this! Python is a general-purpose, interpreted high-level programming language whose design philosophy emphasizes code readability. Like other dynamic languages, Python is often used as a scripting language. Python supports multiple programming paradigms, including object-oriented (like C++), imperative and functional programming styles. Using third-party tools, Python code can be packaged into standalone executable programs. Python interpreters are available for many operating systems.

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Python

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Credit: Python

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Added to our repository: 2014-03-26 by Stelios

Automated Builds

Most languages require you to compile programs before running them.Typing "gcc -c -Wall -ansi -I/pkg/chempak/include dat2csv.c" once is bad enough, typing it dozens of times as you edit and debug is tedious and error-prone. Most large programs contain dependencies: Module A uses modules B and C, B uses D and E, C uses E and F, etc. If E changes, ought to recompile B and C, then A. Anything worth repeating is worth automating. We need a standard way and place to save project-related commands…that keeps track of what depends on what.

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Automated Builds

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Credit: Software Carpentry

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Added to our repository: 2015-03-27 by Super User

Balancing Scripts and Compiled Code

Scripting can be much easier to use than the typical high performance computing languages, C++ and Fortran, but scientific programmers choose compiled languages for their speed. You may already be combining scripting and compiled code when you write Bash or Csh scripts to run applications. This module suggests ways to incorporate scripting languages more deeply within scientific applications in order to write less code and more capable applications quickly.

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Balancing Scripts and Compiled Code

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Credit: Cornell Virtual Workshop

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Added to our repository: 2014-03-26 by Stelios

Captured

Automated Builds

To view the material please click on the link in the box below:

Automated Builds

If or you wish to view the site in a new tab or window click here.

Credit: Software Carpentry

(to open their website click here)
Added to our repository: 2015-03-27 by Super User

Scripting

Recommended

Bash scripting

Python

Automated Builds

Balancing Scripts and Compiled Code