One more thing. If I remove this patch from sowing - the valgrind log is clean.
http://petsc.cs.iit.edu/petsc/externalpackages/sowing-1.1.11/rev/e591c037e500 Perhaps you can find the bug in this change. If not - I'll send a bug report to Bill. Satish On Fri, 25 Dec 2009, Satish Balay wrote: > Can you send me the valgrind.log - with the patch applied to the > unmodified sowing-1.1.11-a.tar.gz? > > Also the command you are using to generate this log? > > > I've used the following: > valgrind --tool=memcheck -q --log-file=valgrind.log bfort -dir `pwd`/ftn-auto > -ansi -nomsgs -noprofile -anyname -mapptr -mpi -mpi2 -ferr -ptrprefix Petsc > -ptr64 PETSC_USE_POINTER_CONVERSION -fcaps PETSC_HAVE_FORTRAN_CAPS -fuscore > PETSC_HAVE_FORTRAN_UNDERSCORE matrix.c > > Satish > > On Fri, 25 Dec 2009, Matthew Knepley wrote: > > > Valgrind is not clean for me with the change. > > > > Matt > > > > On Fri, Dec 25, 2009 at 10:28 AM, Satish Balay <balay at mcs.anl.gov> wrote: > > > > > Well - normally the first step with detecting the bugs is to report > > > them to the author - and ask for a fix.. > > > > > > Satish > > > > > > On Fri, 25 Dec 2009, Matthew Knepley wrote: > > > > > > > I can try, but I still think replacement is the only real alternative. > > > This > > > > is not > > > > able to be debugged, or you would not recommend sticking in random > > > numbers > > > > in malloc() and I would be able to see where an SEGV occurs with gdb. > > > > > > > > Matt > > > > > > > > On Fri, Dec 25, 2009 at 10:16 AM, Satish Balay <balay at mcs.anl.gov> > > > wrote: > > > > > > > > > BTW: What linux are you using? ubuntu version? i686 or x86_64? etc... > > > > > > > > > > also try: > > > > > > > > > > arg->name = (char *)MALLOC( strlen(p) + 100 ); > > > > > > > > > > satish > > > > > > > > > > > > > > > On Fri, 25 Dec 2009, Satish Balay wrote: > > > > > > > > > > > Did my suggested change not work for you? > > > > > > > > > > > > Satish > > > > > > > > > > > > On Thu, 24 Dec 2009, Matthew Knepley wrote: > > > > > > > > > > > > > I spent a bunch of time on this today. This shit is hopelessly > > > broken. > > > > > It > > > > > > > sucks completely. > > > > > > > I cannot get it to run, nor see why it is causing stack overruns > > > and > > > > > SEGVs. > > > > > > > If anyone does > > > > > > > not think it is hopeless, speak up now. This is a complete fucking > > > > > > > embarrassment. > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > On Mon, Dec 21, 2009 at 4:42 PM, Matthew Knepley < > > > knepley at gmail.com> > > > > > wrote: > > > > > > > > > > > > > > > This does not make any sense to me because it would be a heap > > > > > violation, > > > > > > > > not a stack smash. > > > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > > > > > > > > On Mon, Dec 21, 2009 at 4:30 PM, Satish Balay <balay at > > > > > > > > mcs.anl.gov > > > > > > > > > wrote: > > > > > > > > > > > > > > > >> [I don't know the correct fix for this - but ] The following > > > change > > > > > is > > > > > > > >> getting rid of valgrind messages for me. Maybe you can use > > > > > > > >> this, > > > > > build > > > > > > > >> sowing separately - and continue.. > > > > > > > >> > > > > > > > >> Satish > > > > > > > >> > > > > > > > >> ---------- > > > > > > > >> > > > > > > > >> diff -r dbe25084c0e4 src/bfort/bfort.c > > > > > > > >> --- a/src/bfort/bfort.c Mon Dec 15 22:20:58 2008 -0600 > > > > > > > >> +++ b/src/bfort/bfort.c Mon Dec 21 16:29:09 2009 -0600 > > > > > > > >> @@ -2157,7 +2157,7 @@ > > > > > > > >> > > > > > > > >> /* Current token is name */ > > > > > > > >> arg->has_star = (nstar > 0); > > > > > > > >> - arg->name = (char *)MALLOC( strlen(p) + 1 ); > > > > > > > >> + arg->name = (char *)MALLOC( strlen(p) + 10 ); > > > > > > > >> strcpy( arg->name, p ); > > > > > > > >> > > > > > > > >> /* We can't output the name just yet, because if it is > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> On Mon, 21 Dec 2009, Matthew Knepley wrote: > > > > > > > >> > > > > > > > >> > The problem appears to be in OutputRoutine() in bfort.c, but > > > that > > > > > code > > > > > > > >> is > > > > > > > >> > impossible > > > > > > > >> > to debug. I can't see where something is getting overwritten, > > > and > > > > > it > > > > > > > >> looks > > > > > > > >> > like the check > > > > > > > >> > only happens when the routine returns. bfort is such crap. > > > > > > > >> > > > > > > > > >> > Matt > > > > > > > >> > > > > > > > > >> > On Mon, Dec 21, 2009 at 3:25 PM, Matthew Knepley < > > > > > knepley at gmail.com> > > > > > > > >> wrote: > > > > > > > >> > > > > > > > > >> > > On Mon, Dec 21, 2009 at 3:21 PM, Satish Balay < > > > > > balay at mcs.anl.gov> > > > > > > > >> wrote: > > > > > > > >> > > > > > > > > > >> > >> On Mon, 21 Dec 2009, Lisandro Dalc?n wrote: > > > > > > > >> > >> > > > > > > > >> > >> > On Mon, Dec 21, 2009 at 5:37 PM, Matthew Knepley < > > > > > > > >> knepley at gmail.com> > > > > > > > >> > >> wrote: > > > > > > > >> > >> > > > > > > > > > >> > >> > > It says there is a stack smash and no other info. This > > > is > > > > > > > >> completely > > > > > > > >> > >> fucking > > > > > > > >> > >> > > my development right now. > > > > > > > >> > >> > > > > > > > > > >> > >> > > > > > > > > >> > >> > Any chance bfort was built with -fstack-protector flag? > > > This > > > > > > > >> failure > > > > > > > >> > >> > could could be signaling an actual old bug in bfort... I > > > > > would > > > > > > > >> > >> > re-build bfort with debug and re-run under valgrind... > > > > > > > >> > >> > > > > > > > >> > >> That must be it. > > > > > > > >> > >> > > > > > > > >> > >> I just ran my build [which is without -fstack-protector] - > > > and > > > > > > > >> > >> valgrind does flag a bunch of things with bfort. > > > > > > > >> > >> > > > > > > > >> > > > > > > > > > >> > > 1) That flag is nowhere in my build. > > > > > > > >> > > > > > > > > > >> > > 2) Something changed > > > > > > > >> > > > > > > > > > >> > > Matt > > > > > > > >> > > > > > > > > > >> > > > > > > > > > >> > >> I normally install sowing separately and have it in my > > > > > > > >> > >> PATH > > > - > > > > > so that > > > > > > > >> > >> it doesn't have to be rebuilt each time I build petsc. > > > > > > > >> > >> > > > > > > > >> > >> I guess we should sync up [our patches] with latest sowing > > > and > > > > > make > > > > > > > >> > >> sure its valgrind clean aswell. > > > > > > > >> > >> > > > > > > > >> > >> Satish > > > > > > > >> > > > > > > > > > >> > > > > > > > > > >> > > > > > > > > > >> > > > > > > > > > >> > > -- > > > > > > > >> > > What most experimenters take for granted before they begin > > > their > > > > > > > >> > > experiments is infinitely more interesting than any results > > > to > > > > > which > > > > > > > >> their > > > > > > > >> > > experiments lead. > > > > > > > >> > > -- Norbert Wiener > > > > > > > >> > > > > > > > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > What most experimenters take for granted before they begin their > > > > > > > > experiments is infinitely more interesting than any results to > > > which > > > > > their > > > > > > > > experiments lead. > > > > > > > > -- Norbert Wiener > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
