Re: Bug#861281: rnahybrid: FTBFS on armel
Hi Lennart,
thanks for your suggestions. I hereby will forward it upstream hoping
for comments.
Kind regards
Andreas.
On Tue, Sep 26, 2017 at 11:10:04AM -0400, Lennart Sorensen wrote:
> On Tue, Sep 26, 2017 at 09:57:09AM +0100, Edmund Grimley Evans wrote:
> > The infinite loop is still there with gcc-7. I've created bug #876825.
> >
> > Before you exclude armel, you could perhaps try doing something about
> > this warning, which is given not just on armel and may or may not be
> > related to the compiler going into an infinite loop:
> >
> > energy.c:539:104: warning: iteration 6 invokes undefined behavior
> > [-Waggressive-loop-optimizations]
>
> Is it because of this:
> energy.c:539:53: note: within this loop
> for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
>
> Perhaps that that k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.
>
> ALPHASIZE is 6, so the k loop would try go one too far. Every array allocated with ALPHASIZE certainly don't add one anywhere, so any look going from 0 to ALPHASIZE must use < not <= so there are two places in the file that are wrong.
>
> I think this might help:
>
> --- rnahybrid-2.1.2.orig/src/energy.c 2013-08-25 11:51:20.000000000 -0400
> +++ rnahybrid-2.1.2/src/energy.c 2017-09-26 11:04:34.747986466 -0400
> @@ -536,7 +536,7 @@
> void init_dr_dangle_dg_ar()
> {
> int i,j,k;
> - for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
> + for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
>
> dr_dangle_dg_ar[A][U][A] = -0.700;
> dr_dangle_dg_ar[A][U][C] = -0.100;
> @@ -568,7 +568,7 @@
> void init_dl_dangle_dg_ar()
> {
> int i,j,k;
> - for(i=0;i<=ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
> + for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
>
> dl_dangle_dg_ar[A][A][U] = -0.300;
> dl_dangle_dg_ar[C][A][U] = -0.300;
>
> > There are other warnings, too, but undefined behaviour is particularly scary.
>
> The pointers being converted to integers concern me a bit. That might
> cause big problems on 64 bit systems.
>
> It sure looks like some seriously sloppy coding.
>
> --
> Len Sorensen
>
--
http://fam-tille.de
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