[Bioclusters] Newbie question: simple low-admin non-threaded Debian-based cluster solution?

Glen Otero gotero at linuxprophet.com
Thu Jan 20 18:55:35 EST 2005

Check out Rocks (http://www.rocksclusters.org). IMHO it is much better 
than FAI and SIS. It also includes SGE.

On Jan 20, 2005, at 3:47 PM, Speakman, John 
H./Epidemiology-Biostatistics wrote:

> Hello
> If anyone can review the below and suggest a way to go, or even better 
> something I have gotten completely wrong, it would be much 
> appreciated!
> Thanks
> John
> Hardware:
> Ten HP Proliant nodes, one DL380 and nine DL140.  Each node has two 
> 3.2Ghz Xeon processors.  They do not have a dedicated switch; the 
> infrastructure folks say they want to implement this using a VLAN.  We 
> have some performance concerns here but have agreed to give it a try.
> User characteristics:
> The users are biostatisticians who typically program in R; they often 
> use plug-in R modules like bioconductor.  They always want the newest 
> version of R right away.  Also they may also write programs in C or 
> Fortran.  Data files are usually small.  Nothing fancy like BLAST, 
> etc.
> User concerns:
> Users require a Linux clustering environment which enables them to 
> interact with the cluster as though it were a single system (via ssh 
> or X) but which will distribute compute-intensive jobs across nodes.  
> As the code is by and large not multithreaded, it is expected that 
> each job will be farmed out to an idle compute node and probably stay 
> there until it is done.   That’s fine.  In other words, to use all 
> twenty CPUs we will need twenty concurrent jobs.
> Administration concerns:
> The cluster must require the absolute minimum of configuration and 
> maintenance, because I’ve got to do it and I’m hardly ever around 
> these days.
> Other concerns:
> Users and administrators alike have a preference for Debian Linux over 
> other distributions.  Users also have an aversion to non-free 
> software.  Either or both of these considerations could be overridden 
> if the reasons were pressing.
> Cluster software requirements:
> (1)    The cluster must have a mean of deploying Linux to the nodes 
> and keeping their configurations (including updates to the operating 
> system and applications, lists of users, printers, etc.) in 
> synchronization.
> (2)    The cluster must have a means of transparently distributing 
> jobs to idle CPUs.  It’s not necessarily to actively rebalance this 
> when a job has started – it’s okay if, once tied to a node, it stays 
> there.
> Potential solutions:
> We like the look of NPACI Rocks but its non-Debian-ness makes it a 
> last resort only.  What we would really like to try is a Debian 
> version of NPACI Rocks; in its absence we will probably have to use 
> two separate packages to fulfil the requirements of #1 and #2 above.
> Sensible options for #1 seem to be:
> (1)       SystemImager (www.systemimager.org)
> (2)       FAI (http://www.informatik.uni-koeln.de/fai/), maybe also 
> involving the use of cfengine2 (http://www.iu.hio.no/cfengine/)
> SystemImager is the better-established product and looks to be simpler 
> to set up than FAI and/or cfengine2, in both of which the learning 
> curve looks steep.  However, FAI seems more elegant and more like the 
> idea of “NPACI Rocks Debian” that we’re looking for, implying that 
> once set up FAI/cfengine2 will require less ongoing maintenance.
> Sensible options for #2 seem to be:
> (1)    OpenMosix
> (2)    OpenPBS
> (3)    Sun GridEngine N1
> Note: all of the above have commercial versions; we’d be reluctant to 
> consider them unless it means big savings in administration time and 
> effort.  We get the impression OpenMosix (and, to a lesser extent, 
> OpenPBS) have question marks over how much time and resources the 
> people maintaining these products have, suggesting bugs, instability 
> and not keeping up with kernel/library updates, etc.  Sun GridEngine 
> seems more robust but does not seem to have a big Debian user base.
> What do you all should we try first?
> Thanks!
> John
> John Speakman
> Manager, Clinical Research Systems
> Memorial Sloan-Kettering Cancer Center
> 307 East 63rd Street, New York NY 10021 USA
> +1 646 735 8187 - SpeakmaJ at mskcc.org
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Glen Otero Ph.D.
Linux Prophet

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