> Here is the post: http://biohaskell.org/GSoC_blog/Weeks_1and2
Great! Is this (i.e. the profiling numbers) from running the benchmark I sent you? So you got it running, and it's generating acceptable output? As you noticed, we spend way too much time garbage collecting. The solution is not *necessarily* to use less space, but I suspect this is due to the sparse representation using lists generating (and GC'ing) many, many cons cells. By using a non-sparse representation (that is, a matrix), space use might be larger, but more predictable/constant (but make sure to use a mutable matrix). What you could do, is run with memory profiling (-h or -hd, IIRC) to see exactly what data is generated. And - it is possible to alleviate this somewhat by tuning GC (RTS options like -A, -M, and -H, IIRC) -k PS: the options are from memory, but can be looked up easily enough. -- If I haven't seen further, it is by standing in the footprints of giants
