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

[Tim Armstrong]

Can you attach to the mpiexec processes with gdb and get a stack trace?
This seems like an MPI-level problem since there's only the mpi launcher
process running.


On Thu, May 8, 2014 at 5:10 PM, Ketan Maheshwari <ketan at mcs.anl.gov> 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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