I thik I finally found a good way (easy & accurate) to compare the run times between bazaar and cairo. I was wrong about there not being any timing in the .log files, but what I have seen so far I don't quite understand or trust (the log files claim that bazaar is sometimes faster than cairo, which does not match my experience).
I read all three articles. And the first half of the FFTW doc.
The literature search is going poorly, I have never been good at finding stuff, but I will continue trying.
I don't think I understand how to diagram the gromacs code. Is this a graphic representation of gprof's call graph? Or is it something else?
If it is a visually structured call graph, it would be good to know where the -pg flag goes. Dawitt and I were wrestling with it yesterday.