[GE users] Program don't run correctly when submiting

jeromeverleyen jerome at ibt.unam.mx
Tue Jan 26 23:22:17 GMT 2010

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Hi Reuti

reuti a écrit :
> Hi,
> Am 26.01.2010 um 23:19 schrieb jeromeverleyen:
>> Dear all
>> I'm facing a really strange problem with a bioinformatic program. At
>> first, i thought that was a problem from the program itself. When i
>> submit a job like the following script, the program run into
>> Segmentation fault:
>> ----------------------
>> #!/bin/bash
>> #$ -N SOAP
>> #$ -l h_vmem=4G
> for some programs you have to set h_stack in addition to h_vmem to  
> allow memory allocation (if all is infinity/unlimited it's also  
> fine). Usually a value between 32M and 128M will do. But when this is  
> the reason and the program just segfaults it looks like the  
> programmers don't check the returned pointer from memory allocation  
> call (to output a nice error), but when the nil pointer is used then  
> it segfaults.

That all rght now! I don't figure out about this option h_stack. I've 
request about 128Mb (-l h_stack=128M) and the programm run well.
I learn something every day :-)

Thank's a lot!


-- Jérôme
- Et son mari n'a rien dit ?
- Non... tu sais, quand les types de 130K disent certaines choses,
   ceux de 60K les écoutent.
	(Michel Audiard)


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