Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

[Andreas Tille <andreas@an3as.eu>]

Hi Jeffrey,

thanks a lot for this analysis.  Any chance that somebody could
turn this into a patch I could try?

Kind regards

     Andreas.

On Thu, Apr 30, 2020 at 03:40:12PM -0400, Jeffrey Walton wrote:
> On Fri, Apr 17, 2020 at 7:21 AM Andreas Tille <andreas@an3as.eu> wrote:
> >  ...
> > So it seems the bus error occures somehow here:
> >
> >    https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346
> 
> NewProgress is at
> https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/progress.c#L53.
> It uses a progress_t at
> https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/progress.h#L25.
> 
> typedef struct {
>     /* where to write to */
>     FILE *prFile;
>     /* prefix printed before each step */
>     char *pcPrefix;
>     bool bPrintCR;
>     char pcLastLogMsg[1024];
>     Stopwatch_t *prStopwatch;
> } progress_t;
> 
> And stopwatch_t at
> https://salsa.debian.org/med-team/clustalo/-/blob/master/src/squid/stopwatch.h:
> 
> struct stopwatch_s {
>   time_t t0; /* Wall clock time, ANSI time()  */
> #ifdef SRE_STRICT_ANSI
>   clock_t cpu0; /* CPU time, ANSI clock()        */
> #else
>   struct tms cpu0; /* CPU/system time, POSIX times()*/
> #endif
> 
>   double elapsed; /* elapsed time, seconds */
>   double user; /* CPU time, seconds */
>   double sys; /* system time, seconds */
> };
> 
> There are your doubles that are likely the problem.
> 
> And what do we have here at
> https://salsa.debian.org/med-team/clustalo/-/blob/master/src/squid/stopwatch.c#L276
> ...
> 
> void
> StopwatchPVMPack(Stopwatch_t *w)
> {
>   pvm_pkdouble(&(w->elapsed), 1, 1);
>   pvm_pkdouble(&(w->user),    1, 1);
>   pvm_pkdouble(&(w->sys),     1, 1);
> }
> void
> StopwatchPVMUnpack(Stopwatch_t *w)
> {
>   pvm_upkdouble(&(w->elapsed), 1, 1);
>   pvm_upkdouble(&(w->user),    1, 1);
>   pvm_upkdouble(&(w->sys),     1, 1);
> }
> 
> I can't track the trail any further. The source code is missing for
> pvm_pkdouble and pvm_upkdouble. I would be very suspect of
> pvm_pkdouble and pvm_upkdouble.
> 
> Jeff
> 

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