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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Glen<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>John<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
bioclusters-bounces@bioinformatics.org
[mailto:bioclusters-bounces@bioinformatics.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Glen Otero<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, January 20, 2005
6:56 PM<br>
<b><span style='font-weight:bold'>To:</span></b> Clustering, compute farming
& distributed computing in life science informatics<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Bioclusters] Newbie
question: simple low-admin non-threaded Debian-based cluster solution?</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Check out Rocks (http://www.rocksclusters.org). IMHO it is much better
than FAI and SIS. It also includes SGE. <o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Jan 20, 2005, at 3:47 PM, Speakman, John
H./Epidemiology-Biostatistics wrote: <o:p></o:p></span></font></p>
</div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Hello</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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!</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>John</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Hardware:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>User characteristics:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>User concerns:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Administration concerns:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Other concerns:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Cluster software requirements:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(1)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(2)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Potential solutions:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Sensible options for #1 seem to be:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(1)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>SystemImager (<font color=blue><span style='color:blue'>www.systemimager.org</span></font>)</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(2)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>FAI (<font color=blue><span style='color:blue'>http://www.informatik.uni-koeln.de/fai/</span></font>),
maybe also involving the use of cfengine2 (<font color=blue><span
style='color:blue'>http://www.iu.hio.no/cfengine/</span></font>)</span></font></tt>
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Sensible options for #2 seem to be:</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(1)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>OpenMosix</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(2)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>OpenPBS</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(3)</span></font></tt><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'> </span></font><o:p></o:p></p>
</div>
</blockquote>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Sun GridEngine N1</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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.</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>What do you all should we try first?</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks!</span></font></tt> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><tt><font size=2 face="Courier New"><span style='font-size:
10.0pt'>John</span></font></tt> <o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font> <o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><i><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial;font-style:italic'>John Speakman</span></font></i> <o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><i><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial;font-style:italic'>Manager, Clinical Research Systems</span></font></i>
<o:p></o:p></p>
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12.0pt'><o:p> </o:p></span></font></p>
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style='font-family:Arial;font-style:italic'> <st1:PlaceName w:st="on">Sloan-Kettering</st1:PlaceName>
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<p class=MsoNormal><i><font size=3 face=Arial><span style='font-size:12.0pt;
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>_______________________________________________ <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Bioclusters maillist - Bioclusters@bioinformatics.org <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>https://bioinformatics.org/mailman/listinfo/bioclusters <o:p></o:p></span></font></p>
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</blockquote>
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<p class=MsoNormal><font size=3 color="#1b1d26" face="Times New Roman"><span
style='font-size:12.0pt;color:#1B1D26'>Glen Otero Ph.D. <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 color="#1b1d26" face="Times New Roman"><span
style='font-size:12.0pt;color:#1B1D26'>Linux Prophet <o:p></o:p></span></font></p>
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