[GE users] SSH and host keys

craffi dag at sonsorol.org
Tue Feb 24 20:26:18 GMT 2009


The basic issue here is that the Solexa pipeline uses qmake under the  
hood to to distribute a massive amount of qsub calls. Under the "old"  
rsh based SGE methods this would cause the system to run out of  
available ports.

Prior to SGE 6.2 the workaround was to switch qrsh integration to use  
SSH; I suspect the problem does not occur or has a much higher limit  
with the new "builtin" methods in SGE 6.2

-Chris


On Feb 24, 2009, at 2:07 PM, crhea wrote:

> On Tue, Feb 24, 2009 at 04:12:04PM +0100, murple wrote:
>>> No, we have dedicated cluster nodes on a private network... the  
>>> switch
>>> from rsh to ssh is being driven by a known issue with Solexa  
>>> Pipeline
>>> code (that runs out of ports/ptys if you use rsh).
>>
>> Since we are also running Solexa Pipeline I like to know more about  
>> this
>> error. You're talking about the GAPipeline, right? What triggers this
>> bug?
>>
>> Andreas
>
> This is the error one sees:
>
> 	rcmd: socket: All ports in use
>
>
> ------------------------------------
> qsub -q 1-day -cwd -v PATH -pe make 1-8 ~/GAPipelineParallel.sh
>
> The GApipelineParallel.sh file contains the following:
>
> #!/bin/sh
> qmake -q 1g-mem -cwd -v PATH -inherit -- recursive
>
> -----------------------------------
>
> See this reference-- 1/4 way down the page under Distributed make /  
> Sun Grid Engine...
>
> http://analysis.yellowcouch.org/dsf/ga0.3/Pipeline%20parallelisation.html
>
> -----------------------------------------
>
> -- 
> Cristopher J. Rhea
> Mayo Clinic - Research Computing Facility
> 200 First St SW, Rochester, MN 55905
> crhea at Mayo.EDU
> (507) 284-0587
>

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