There are two reasons for this: the input data has to be passed on to the stand-alone program and the stand-alone program has to be started from within GAP.
There are two principal ways of doing this.
The first possibility is to write all the data for the stand-alone to one or several files, then start the stand-alone which then writes the output data to file and finally read in the standalone's output file.
The second way is interfacing via streams (see chapter Streams in the reference manual). The support for this however is not yet fully implemented.
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GAP 4 manual