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

[Justin M Wozniak]

Can you tell us which MPI you are using?  We will have to address this...

On 05/09/2014 10:08 AM, Tim Armstrong wrote:
> Nice!
>
>
> On Fri, May 9, 2014 at 9:30 AM, Ketan Maheshwari <ketan at mcs.anl.gov 
> <mailto:ketan at mcs.anl.gov>> wrote:
>
>     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 <mailto: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
>>
>>
>>
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>
>         -- 
>         Michael Wilde
>         Mathematics and Computer Science          Computation Institute
>         Argonne National Laboratory               The University of Chicago
>
>
>
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-- 
Justin M Wozniak

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