Using the Expect scripting environment

What to Expect

Article from ADMIN 05/2011

By AEleen Frisch

Automate interactive processes with Expect.

As I've shown in previous columns, Bash has a number of mechanisms for automating interactive processes. For example, the input redirection feature called a "here document" can place standard input for a command within a script, as shown in Listing 1.

Listing 1

Input Redirection

01 for jobname in $jobs; do
02 for molecule in $mlist; do
03
04 g09 <<END >$molecule.log
05 @$jobname
06
07 $charge $spin
08 @$molecule.xyz
09
10 END
11
12 done
13 done

The Gaussian 09 (g09) computational chemistry simulation package uses a small input that tells it what type of predictions are desired and which molecule or reaction should be studied. A specific input file can obviously be created for a specific job, but placing commands like these into a script allows you to run a series of jobs on each molecule in a set in an automated way. This approach is clearly easier and more efficient than setting up tens or hundreds of input files manually. And, it makes running a new simulation on an existing molecule set trivial.

However, as a general solution, the here document technique has several disadvantages. First, not every interactive prompt will accept input from scripts in this way. For example, many password prompts and the key exchange prompt on an initial SSH connection are configured to accept input only from the terminal.

Second, when using this technique, it is not easy for the script to process the output from the command and make decisions based on it. More importantly, whereas the responses to multiple commands can be included before the end of the here document, the script cannot examine the responses to individual prompts to respond appropriately to them on the fly.

The Expect facility is a

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