[GE users] threaded jobs (no PE) and consumable memory

txema_heredia txema.heredia at upf.edu
Thu Jan 14 16:05:23 GMT 2010


> Am 14.01.2010 um 15:25 schrieb txema_heredia:
> 
> > Thanks for your answers
> >
> >> Hi,
> >>
> >> you might try to set an additional "-l h_stack=20M" (or whatever size
> >> you need), as some threaded applications allocate the whole stack  
> >> space
> >> (which is in older versions of the SGE set equally to the h_vmem  
> >> size -
> >> in newer versions it is left as "unlimited", therefore avoiding this
> >> problem).
> >>
> >> Hope it helps,
> >> Sabine
> >
> > I have tried it alone (-l h_stack=4G), and the program runs OK. The  
> > problem is that this attribute is not restrictive at all, so I have  
> > used -l h_stack=50M, but the job is still able to use 4G without  
> > receiving any termination signal (unlike if I use -l h_vmem=50M,  
> > which aborts the job when exceeded).
> >
> > If combined -l h_stack and -l h_vmem, h_vmem takes preference and  
> > the job is killed as usual (the malloc error and segment violation  
> > thing).
> 
> You also tried it with different settings: -l  
> h_stack=50M,h_vmem=4G ... ?
> 
> -- Reuti
> 

Thank you very much Sabine and Reuti, that worked! At first I didn't understood Sabine's answer, but combining both h_stack and h_vmem, it works. In fact, the crashing malloc is now asking for the h_stack memory amount.

I've tried h_stack=50M and it worked fine. On the other hand, h_stack=1G worked but really slow, and in the previous set of tests, without any memory-related option, I saw malloc is allocating ~20M.

So this arises a new question: Is there any way or best practice to determine how big my stack should be?

Txema

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