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

[Tim Armstrong]

Nice!


On Fri, May 9, 2014 at 9:30 AM, Ketan Maheshwari <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>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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