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Yep, the gap interface is pretty slow, due to the I/O approach (hence the time in select.select). Fortunately for lots of use cases this isn't the bottleneck, but in some cases it can be, more's the pity. Work on a faster Cythonic interface is progressing -- see http://trac.sagemath.org/sage_trac/ticket/6391 -- but it's not quite there yet.

Instead of calling a gap function explicitly to build a permutation group, it's more idiomatic Sage to write

G = PermutationGroup([(1,2,3)])

which can be a little faster (~2x, maybe). Underlying problem is still there, though.