[Bioclusters] OS X and NFS

David Kramer dave at princetonsolutionsgroup.com
Thu Jul 14 18:24:45 EDT 2005

Respectfully, and at the risk of sounding, ridiculously naive -- why not 
consider upgrading the I/O switching technology to Myrinet or Infiniband for 
higher-bandwidth and ultra-low latency, before buying more servers?


Quoting Juan Carlos Perin <bic at genome.chop.edu>:

> I had a question to see if anyone had any knowledge of a problem we've 
> been encountering.  It seems our Apple cluster is crashing due to NFS.  
> When we run large batch jobs that frequently access an NFS mount, the 
> system ends up accumulating  'stuck' processes.  If the job is able to 
> finish it eventually cleans the 'stuck' processes, and all is well.  
> But, if the job continues to allow accumulation of these stuck 
> processes, if a given job runs long enough, the system slowly 
> deteriorates and becomes less and less responsive, eventually freezing 
> up and not allowing anything to function at all.
> We started the maximum number of NFS servers (20) and this improved 
> things, but didn't fix them.  We also limited the jobs to 10 nodes (20 
> processors) to theoretically allow one node to access one NFS pipeline 
> at any given time.  I'm not sure if anyone has run into this before, or 
> if anyone has ideas on how to approach fixing this problem.  The only 
> errors we're seeing otherwise are in the system log, complaining about 
> PasswordService not matching the clients response.
> We're still running OSX 10.3.8 and our jobs are running through SGE 
> 5.3.  And we've got a 16 node (32 processor G5 system) with at least 2gb 
> RAM per node.   The programs running are a mixture of text mining 
> algorithms in both Perl and Java.  Both requiring frequent reads on 
> large .txt files residing on NFS shared directories.
> Thanks in advance, for any ideas or suggestions.
> Juan Perin
> Children's Hospital of Philadelphia
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David Kramer
Managing Director
Princeton Solutions Group, LLC


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