[Bioclusters] Sequest Cluster problems

Chris Dagdigian dag at sonsorol.org
Fri Nov 25 15:47:35 EST 2005


This may be the wrong forum for this question -- many of the people  
here run non-Windows clusters almost exclusively.

Also, Sequest is commercial software -- is there any reason why  
Thermo Electron can't fix this for you?

I've done work some work on Sequest clusters a while back but they  
were pure-Windows clusters and were just using perl under the hood to  
fire off jobs on the "slave" nodes. I don't recall seeing any sort of  
PVM involved so this may be new or simply part of the Thermo BioWorks  

My first recommendation is to get support direct from the makers of  
BioWorks on this. If this does not work, drop me a line personally  
(dag at sonsorol.org) and I'll see if I can make some introductions on  
your behalf - I know some people working daily with Thermo on various  

Side note: 40K for a sequest cluster? Consider yourself lucky :)  I  
once saw an official "recommended configuration"  list for a Sequest  
cluster and there was more than $100,000 US worth of unnecessary  
items stuffed into the bill of materials.


On Nov 25, 2005, at 3:33 PM, Ken Sin Lo wrote:

> Hi,
> We have some problems while running Sequest Cluster.  Our cluster  
> is configured as follows:
> Master Node:
>   Dell Precision 670, with 2 Xeon 3GHz CPUs and 2 gb of RAM
>   Microsoft Windows XP Professionnal, with Service Pack 2
> Slave Node 1:
>   Dell Precision 670, with 2 Xeon 3GHz CPUs and 2 gb of RAM
>   Linux Fedora Core 4
> Slave Node 2:
>   Dell Precision 670, with 2 Xeon 3GHz CPUs and 2 gb of RAM
>   Linux Fedora Core 4
> We are using BioWorks version 3.1 SR1.
> The first problem we have is when we start the PVM (by clicking  
> "Start PVM" in the Cluster Manager), we always get the following  
> error for Node 2, even if "Cleanup Nodes" has been clicked prior to  
> starting PVM:
> "Error connecting to the stderr server port!error in receive on  
> socket: Socket shutdown by remote."
> Therefore, in the PVM console, we have to type "add sequestnode2"  
> to have Node 2 connected.  Is there any reason for this error to  
> happen only for Node 2, knowing that Node 1 and Node 2 should be  
> configured exactly the same way (except for the IP) ? ... Imagine  
> if we have to manually type "add node#" 16 times, or 32 times or  
> more!?!!
> The second problem, which is unacceptable, is that when  
> TurboSEQUEST Cluster is running, some of its slave process  
> (sequest27_slave.exe) fails after only a few hours of computing  
> (Windows will pop-up a "Send Report" window).  And some failures  
> just bring down the whole search process, by freezing  
> sequest27_master.exe.
> Does anyone have encountered the same problems and have any  
> solution for that?  Considering the fact that we invested close to  
> 40 000$ into this cluster (hardware and software costs), we really  
> wish to make it works without having to restart our computers every  
> few hours!!
> And does anyone know if it's more stable to run the nodes under  
> Windows rather than Linux?
> Thank you.
> Ken Sin Lo
> Centre de recherche du CHUL
> Quebec, Canada
> G1V 4G2
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
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