On Tue, Sep 26, 2017 at 07:30:40PM +0200, Andreas Tille wrote: > Hi Marc, > > thanks for the quick response. > > On Tue, Sep 26, 2017 at 06:45:42PM +0200, Marc Rehmsmeier wrote: > > Hi Andreas, > > > > I am not entirely sure what I was doing there and then. That seems to be > > version 2.1.2, correct? > > Yes, that's correct. We always try to package the latest upstream > > > > In version 2.1.1, the array is allocated with ALPHASIZE+1. The <= in the > > k-loop is originally not a mistake; the function's sibling, > > init_dl_dangle_dg_ar, has the <= in the first loop (the i-loop). These are > > the allocations in version 2.1.1: > > > > double dr_dangle_dg_ar[ALPHASIZE][ALPHASIZE][ALPHASIZE+1]; > > double dl_dangle_dg_ar[ALPHASIZE+1][ALPHASIZE][ALPHASIZE]; > > > > You see that there's a +1 on the corresponding sides. > > Yes, I see. Would you like to express that the better fix for that > issue would be to restore this allocation inside energy.h instead of > fixing the loop index?
So someone broke the allocation size in 2.1.2? Seems like a valid fix too, especially if there is some actual use for the extra slot. > > At some point I introduced an additional letter to the alphabet, the X (a > > masking letter; see input.h). I am not sure about the program logic > > anymore, whether X can actually be used for lookups in the energy tables > > (as the N could). In hybrid_core.c, where the energy functions are used, I > > check for X in a few places, so the idea was perhaps to not use X for > > lookups (in fact, I do not want to consider any masked sequence at all). > > Should that be true, ALPHASIZE being 6 would be wasteful, but it shouldn't > > harm otherwise. Of course, you could change the two for-loops (the k-loop > > in init_dr_dangle_dg_ar and the i-loop in its sibling) so that they use < > > instead of <=, but, while that might fix the array bound bug, it might not > > solve an underlying logic problem. In effect you might have a program that > > works technically, but produces the wrong result. Unfortunately I can't > > help with that. You could try fixing the loops and then do a few runs and > > compare the outputs, as a minimal test. > > So it seems to me that it is safer to leave the loop untouched ... Makes sense if the energy.h is fixed instead. -- Len Sorensen
