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

Speakman, John H./Epidemiology-Biostatistics speakmaj at MSKCC.ORG
Thu Jan 20 19:12:25 EST 2005

Hi Chris

Indeed I do know Joanne and co - I'm in the same building and met you
when you came over.  She is an SGE fan.  But our requirements are, and
thus our solution, I hope, could be, a bit simpler.  Plus of course
she's a SuSE fan and I get the impression there's not much SGE-on-Debian

"Users having to think a tiny bit" is indeed a bit of a stretch.  Sounds
like you're saying that OpenPBS likewise would require them to do so
(evidence I haven't really done my homework here), in which case I
agree, there's no reason to select it over SGE.

So Mosix it is, then SGE as a backup.


-----Original Message-----
From: bioclusters-bounces at bioinformatics.org
[mailto:bioclusters-bounces at bioinformatics.org] On Behalf Of Chris
Sent: Thursday, January 20, 2005 7:00 PM
To: Clustering, compute farming & distributed computing in life science
Subject: Re: [Bioclusters] Newbie question: simple low-admin
non-threaded Debian-based cluster solution?


There is already a 50 node dual-Xeon cluster at MSKCC using Sun Grid 
Engine 6.0u1 and SystemImager with Suse 9.1 linux. I'm sure you know 
those folks already so see what they think about SGE :)

Your notes are complete and it sounds as though you have a plan.

Some comments --

"most" people doing similar work use a dedicated switch for performance 
and reduction of administrative burden. The VLAN should work as long as 
the performance is reasonable.

Systemimager works great and I think it was originally developed on 
debian although they've since changed the codebase such that you don't 
need to be running debian to work as a developer on it. For your desire 
to install Linux and sync updates easily and with little effort I'd 
recommend SystemImager as one path-of-least-resistance option.

If your users really want transparency without having to think much 
about the cluster then maybe you should try the MOSIX approach first to 
see if the transparent distribution will suit your needs.

You may find that you want, need or require the features that a batch 
scheduler or distributed resource management layer will give you. In 
this case the clear winner is Grid Engine over OpenPBS (no contest 
really in my opinion).

The "problem" with Grid Engine or any other similar product (when 
compared to your stated requirements) is that your users will have to 
think at least a *tiny* bit about the cluster and how to run jobs. At 
the bare minimum they'll need to use the qsub program to submit their 
jobs for execution. After that Grid Engine handles the load balancing, 
remote execution and policy based resource allocation.

This is why I recommend experimenting with MOSIX first -- it may be more

"transparent" for your users at first brush.

If MOSIX does not work out well for you then you'll need to spend a bit 
of time educating your users how to use Grid Engine to get their work 
done. Not terribly difficult and there are some SGE savvy users at MSKCC

by now anyway.

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
> 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,
> 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
> X) but which will distribute compute-intensive jobs across nodes.  As
> the code is by and large not multithreaded, it is expected that each
> will be farmed out to an idle compute node and probably stay there
> 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
> days.
> Other concerns:
> Users and administrators alike have a preference for Debian Linux over
> other distributions.  Users also have an aversion to non-free
> 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
> keeping their configurations (including updates to the operating
> and applications, lists of users, printers, etc.) in synchronization.
> (2)    The cluster must have a means of transparently distributing
> 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
> 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
> <http://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
> looks steep.  However, FAI seems more elegant and more like the idea
> "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
> maintaining these products have, suggesting bugs, instability and not
> keeping up with kernel/library updates, etc.  Sun GridEngine seems
> robust but does not seem to have a big Debian user base.
> What do you all should we try first?
> Thanks!
> John

Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
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Bioclusters maillist  -  Bioclusters at bioinformatics.org

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