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

[Michael Wilde]

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
>
>
>
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-- 
Michael Wilde
Mathematics and Computer Science          Computation Institute
Argonne National Laboratory               The University of Chicago

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