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<div class=Section1><pre><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Hello<o:p></o:p></span></font></pre><pre><font size=2
face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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!<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Thanks<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>John<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Hardware:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>User characteristics:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>User concerns:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Administration concerns:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Other concerns:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Cluster software requirements:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre
style='margin-left:42.0pt;text-indent:-24.0pt;mso-list:l2 level1 lfo1'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>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.<o:p></o:p></pre><pre
style='margin-left:42.0pt;text-indent:-24.0pt;mso-list:l2 level1 lfo1'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>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.<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Potential solutions:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sensible options for #1 seem to be:<o:p></o:p></span></font></pre><pre
style='margin-left:63.75pt;text-indent:-45.75pt;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>SystemImager (<a
href="http://www.systemimager.org/">www.systemimager.org</a>)<o:p></o:p></pre><pre
style='margin-left:63.75pt;text-indent:-45.75pt;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>FAI (<a
href="http://www.informatik.uni-koeln.de/fai/">http://www.informatik.uni-koeln.de/fai/</a>), maybe also involving the use of cfengine2 (<a
href="http://www.iu.hio.no/cfengine/">http://www.iu.hio.no/cfengine/</a>)<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sensible options for #2 seem to be:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre
style='margin-left:42.0pt;text-indent:-24.0pt;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>OpenMosix<o:p></o:p></pre><pre
style='margin-left:42.0pt;text-indent:-24.0pt;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>OpenPBS<o:p></o:p></pre><pre
style='margin-left:42.0pt;text-indent:-24.0pt;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face="Courier New"><span style='font-size:10.0pt'><span
style='mso-list:Ignore'>(3)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]>Sun GridEngine N1<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><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.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>What do you all should we try first?<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Thanks!<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>John<o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-style:italic'>John Speakman<o:p></o:p></span></font></i></p>
<p class=MsoNormal><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-style:italic'>Manager, Clinical Research Systems<o:p></o:p></span></font></i></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceName w:st="on"><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-style:
italic'>Memorial</span></font></i></st1:PlaceName><i><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;font-style:italic'> <st1:PlaceName
w:st="on">Sloan-Kettering</st1:PlaceName> <st1:PlaceName w:st="on">Cancer</st1:PlaceName>
<st1:PlaceType w:st="on">Center</st1:PlaceType></span></font></i></st1:place><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-style:
italic'><o:p></o:p></span></font></i></p>
<p class=MsoNormal><st1:address w:st="on"><st1:Street w:st="on"><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-style:
italic'>307 East 63rd Street</span></font></i></st1:Street><i><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial;font-style:italic'>,
<st1:City w:st="on">New York</st1:City> <st1:State w:st="on">NY</st1:State> <st1:PostalCode
w:st="on">10021</st1:PostalCode> <st1:country-region w:st="on">USA</st1:country-region></span></font></i></st1:address><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-style:
italic'><o:p></o:p></span></font></i></p>
<p class=MsoNormal><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-style:italic'>+1 646 735 8187 - SpeakmaJ@mskcc.org<o:p></o:p></span></font></i></p>
<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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