[ExM Users] turbine call does not return when invoking from Galaxy

[Ketan Maheshwari]

Hi Mike,

Thanks! Redirecting stdin from /dev/null with turbine call worked right
away!

So, now  we have a first working version of Swift/T-foreach-Galaxy.

Thanks,
Ketan


On Thu, May 8, 2014 at 8:33 PM, Wilde, Michael J. <wilde at mcs.anl.gov> wrote:

>  Perhaps try redirecting stdin on the $turbine call with "< /dev/null"
>
> Some older versions of mpiexec had a bug when stdin was not a tty or ptty.
>
> Not sure if thats the case here, but easy to try.
>
> - Mike
>
>
> On 5/8/14, 5:10 PM, Ketan Maheshwari wrote:
>
> Hi,
>
> Trying invoke turbine from Galaxy as follows:
>
> $turbine -V -n $n $wdir/script.tcl "${swiftargs}"
>
> Each of the variables being set in previous lines.
>
> The process tree shows mpiexec as defunct processes:
>  PID TTY          TIME CMD
>   389 ?        00:00:00 sshd
>   390 pts/39   00:00:00   bash
>   804 pts/39   00:00:00     sh
>   990 pts/39   00:00:38       python
>  1189 pts/39   00:00:00         sh
>  1190 pts/39   00:00:00           bash
>  1330 pts/39   00:00:00             turbine
>  1332 pts/39   00:00:00               mpiexec <defunct>
>  1547 pts/39   00:00:00         sh
>  1548 pts/39   00:00:00           bash
>  1683 pts/39   00:00:00             turbine
>  1686 pts/39   00:00:00               mpiexec <defunct>
>  2046 pts/39   00:00:00         sh
>  2047 pts/39   00:00:00           bash
>  2299 pts/39   00:00:00             turbine
>  2302 pts/39   00:00:00               mpiexec <defunct>
>
>
> Not sure how to debug this. The same call works outside of Galaxy.
>
> Any suggestions?
>
> Thanks,
> Ketan
>
>
>
>
> _______________________________________________
> ExM-user mailing listExM-user at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/exm-user
>
>
> --
> Michael Wilde
> Mathematics and Computer Science          Computation Institute
> Argonne National Laboratory               The University of Chicago
>
>
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