[GE users] Jobs sticking in grid

olesen Mark.Olesen at emconTechnologies.com
Wed Jan 27 15:10:57 GMT 2010


On Wed, 2010-01-27 at 06:54 -0800, gclark wrote:
> For example, we have a job called validate_all. A user would submit
> this one job to the grid and it would spawn several hundred smaller
> jobs/scripts. These secondary jobs aren't all submitted at once.
> 
> The export is the standard linux export command.
> 
> Some of the scripts won't run unless some environment variables are
> set, so the job gets submitted to the grid, once the job has been
> assigned to a node the export command is run, and then the secondary
> scripts and jobs start to trigger.
> 
> Its just the export that seems to stay running on the grid. I've
> ssh'ed into 2 of the affected nodes and there is no export command
> listed in the ps list so theres nothing to run a trace on. Aside from
> the export command everything runs to completion successfully. We know
> the export command is running successfully because the secondary jobs
> are all being completed successfully.


Note 'export' isn't a command per se, but a shell builtin.
Eg,
$ type export
export is a shell builtin

so you'll only see the bash, ksh or sh process in the ps table, but
never any of the builtins (like cd, if, export, ...).

Perhaps your exported variables aren't actually making their way through
to the secondary scripts (which I assume are GridEngine job scripts).
Have you experimented with the '-v' option for qsub?

       -v variable[=value],...


/mark

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