[Bioclusters] Newbie question: simple low-admin non-threaded
Debian-based cluster solution?
Glen Otero
gotero at linuxprophet.com
Thu Jan 20 19:15:15 EST 2005
On Jan 20, 2005, at 4:04 PM, Speakman, John
H./Epidemiology-Biostatistics wrote:
> Hi Glen
>
>
>
> Thanks – I agree – Rocks looks great – but I agreed with the users not
> to consider a non-Debian-based solution unless it simply will not work
> any other way… that’ll teach me to make pledges with users.
Bummer. Good luck. Everyone I talk to tells me that FAI is a pain in
the ass. You might look into running Warewulf
(http://warewulf-cluster.org/index.html) over Debian. You can pull the
tarball out of the available srpms or convert the rpm to a .deb
package.
Glen
>
>
>
> John
>
>
>
>
> From: bioclusters-bounces at bioinformatics.org
> [mailto:bioclusters-bounces at bioinformatics.org] On Behalf Of Glen
> Otero
> Sent: Thursday, January 20, 2005 6:56 PM
> To: Clustering, compute farming & distributed computing in life
> science informatics
> Subject: Re: [Bioclusters] Newbie question: simple low-admin
> non-threaded Debian-based cluster solution?
>
>
>
> 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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> _______________________________________________
>
> Bioclusters maillist - Bioclusters at bioinformatics.org
>
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>
>
> Glen Otero Ph.D.
>
> Linux Prophet
>
>
> _______________________________________________
> Bioclusters maillist - Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
Glen Otero Ph.D.
Linux Prophet
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