[GE users] ncbi blast on SGE

foisysdiploide sylvain.foisy at diploide.net
Wed May 26 14:03:34 BST 2010


Hi reuti,

On 25/05/10 16:40, "[NAME]" <[ADDRESS]> wrote:

>> From experience, pseudo-parallel of multi-sequence blast requests and using
>> the -a flag for the single request (via a web page) is a very powerful
>> combo. Both can be easily done with SGE, using the -b y "blastall -a 4
>> blabla" :-)
> 
> thx for clarification. In this case a PE with allocation rule
> $pe_slots is necessary to avoid oversubscription of a node (often such
> a PE is called "smp"). If you put it in a job script, you can use:
> 
> blastall -a $NSLOTS
> 
> and you will automatically get inside the jobscript the number of
> granted slots for your PE request delivered to `blastall`.

I had forgotten about that... In the old days of SGE 5, I had to create a
loop in the script to check the actual number of cpu per machine to avoid
oversubscription. I'll put this in my book for future use ;-)

Best regards

Sylvain

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