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