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

reuti reuti at staff.uni-marburg.de
Tue Jan 26 23:10:26 GMT 2010


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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.

-- Reuti


> #$ -j y
> #$ -S /bin/sh
>
>
> echo $HOSTNAME
>
> /home/jerome/soap_1.11/soap.huge -d /home/jerome/SOAP/chr1.fasta .....
> ----------------------
>
> But when i connect to the node with ssh, and run the same ultimate  
> line
> of command, it complete! It seems to be the initial steps of SGE that
> generate this problem, but i can't figure out why.
>
> The SGE version is GE 6.2u2_1, Rocks 5.2 version.
>
> Can someone help me in this issue?
>
> Regards
>
> -- 
> -- Jérôme
> ?a doit ?tre chouette de tout savoir comme ?a!
> C'est dommage que ?a ne lui sert plus ? rien, ? papa,
> puisqu'il ne va plus ? l'école.
>   	(Histoires inédites du Petit Nicolas, Goscinny & Sempé)
>
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