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@ -523,7 +523,7 @@ partition images to and from a TFTP server. </Para>
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Cluster-HOWTO</ULink>,
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<CiteTitle>Linux Cluster HOWTO</CiteTitle>
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</Para><Para>
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<CiteTitle>Updated: November 2002</CiteTitle>.
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<CiteTitle>Updated: March 2003</CiteTitle>.
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How to set up high-performance Linux computing clusters. </Para>
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</ListItem>
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@ -100,7 +100,7 @@ various issues related to this. </Para>
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Cluster-HOWTO</ULink>,
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<CiteTitle>Linux Cluster HOWTO</CiteTitle>
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</Para><Para>
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<CiteTitle>Updated: November 2002</CiteTitle>.
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<CiteTitle>Updated: March 2003</CiteTitle>.
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How to set up high-performance Linux computing clusters. </Para>
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</ListItem>
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@ -5,7 +5,7 @@
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<title> Linux Cluster HOWTO </title>
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<author>Ram Samudrala <tt>(me@ram.org)</tt> </author>
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<date> v0.98, November 11, 2002 </date>
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<date> v1.0, March 17, 2003 </date>
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<abstract>
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How to set up high-performance Linux computing clusters.
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@ -33,11 +33,13 @@ and includes not only details the compute aspects, but also the
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desktop, laptop, and public server aspects. This is done mainly for
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local use, but I put it up on the web since I received several e-mail
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messages based on my newsgroup query requesting the same information.
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Even today, as I plan another 64-node cluster, I find there is a
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Even today, as I plan another 64-node cluster, I find that there is a
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dearth of information about exactly how to assemble components to form
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a node that works reliably under Linux. The main use of this HOWTO as
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it stands is that it's a report on what kind of hardware works well
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with Linux and what kind of hardware doesn't. </p>
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a node that works reliably under Linux that includes information not
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only about the compute nodes, but about hardware that needs to work
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well with the nodes for productive research to happen. The main use
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of this HOWTO as it stands is that it's a report on what kind of
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hardware works well with Linux and what kind of hardware doesn't. </p>
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</sect>
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@ -246,7 +248,7 @@ following setup:
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<item> 2 Pentium III 1 GHz Intel CPUs </item>
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<item> Supermicro 370 DE6 Dual PIII-FCPGA motherboard </item>
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<item> 4 256 MB 168-pin PC133 Registered ECC Micron RAM </item>
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<item> 3 40 GB Maxtor UDMA/100 7200 RPM HD </item>
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<item> 3 40 GB Maxtor UDMA/100 7200 RPM hard disk </item>
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<item> Ricoh 32x12x10 CDRW/DVD Combo EIDE </item>
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<item> 1.4 MB floppy drive </item>
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<item> Asus V7700 64mb GeForce2-GTS AGP video card </item>
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@ -261,6 +263,27 @@ following setup:
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<!-- ************************************************************* -->
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<sect1> Firewall/gateway hardware
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<p> 1 firewall with the following setup:
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<itemize>
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<item> AMD Palamino XP 1700+ 1.47GHz CPU </item>
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<item> MSI KT3 Ultra2 KT333 MS-6380E motherboard </item>
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<item> 512 MB PC2100 DDR-266MHz DIMM RAM </item>
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<item> 40GB Seagate 7200rpm ATA/100 hard disk </item>
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<item> Asus 52X CD-A520 INT IDE cdrom </item>
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<item> 1.44 MB floppy drive </item>
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<item> ATI Expert 2000 Rage 128 32mb video card </item>
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<item> 4 Intel Pro/1000T Gigabit Server ethernet cards </item>
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<item> 4U Black Rackmount Steel case </item>
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</itemize>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Miscellaneous/accessory hardware
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<p> Backup:
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@ -282,6 +305,13 @@ following setup:
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</itemize>
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</p>
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<p> Printers:
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<itemize>
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<item> HP colour laserject 4600dn </item>
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</itemize>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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@ -294,7 +324,7 @@ at all the machines:
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<itemize>
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<item> 15" .28dp XLN CTL Monitor </item>
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<item> 3 Belkin Omniview 16-Port Pro Switches </item>
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<item> 40 KVM cables </item>
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<item> Belkin Omniview 2-Port Switch </item>
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</itemize>
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</p>
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@ -306,6 +336,8 @@ more monitor switches/KVM cables. </p>
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<p> Networking is important:
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<itemize>
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<item> 1 Netgear FSM750S 48 port/2 git network switch </item>
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<item> 1 Netgear FS517TS 16 port/1 git network switch </item>
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<item> 1 Netgear FS750NA 48 port network switch </item>
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<item> 1 Netgear FS524 24 port network switch </item>
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<item> 1 Cisco Catalyst 3448 XL Enterprise Edition 48 port network switch </item>
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@ -340,12 +372,27 @@ below $2000.00 (which is what our desktop machines cost). </p>
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<sect1> Operating system: Linux, of course!
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<p> We use Linux systems with a 2.4.9-7 kernel based on the KRUD 7.2
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distribution, and 2.2.17-14 kernel based on the KRUD 7.0
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distribution. These distributions work very well for us since updates
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are sent to us on CD and there's no reliance on an external network
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connection for updates. They also seem "cleaner" than the regular Red
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Hat distributions. </p>
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<p> The following kernels and distributions are what are being used:
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<itemize>
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<item> Kernel 2.2.16-22, distribution KRUD 7.0
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<item> Kernel 2.4.9-7, distribution KRUD 7.2
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<item> Kernel 2.4.18-10, distribution KRUD 7.3
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</itemize>
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These distributions work very well for us since updates are sent to us
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on CD and there's no reliance on an external network connection for
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updates. They also seem "cleaner" than the regular Red Hat
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distributions, and the setup is extremely stable. </p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Networking software
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<p> We use Shorewall 1.3.14a ((<htmlurl url="http://www.shorewall.net"
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name="http://www.shorewall.net">) for the firewall. </p>
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</sect1>
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@ -433,7 +480,32 @@ to configure desktops as they wish. </p>
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<!-- ************************************************************* -->
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<sect2> Cloning
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<sect2> Cloning and maintenance packages
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<sect3> FAI
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<p> FAI (<htmlurl url="http://www.informatik.uni-koeln.de/fai/"
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name="http://www.informatik.uni-koeln.de/fai/">) is an automated
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system to install a Debian GNU/Linux operating system on a PC
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cluster. You can take one or more virgin PCs, turn on the power and
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after a few minutes Linux is installed, configured and running on the
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whole cluster, without any interaction necessary.
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</sect3>
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<sect3> SystemImager
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<p> SystemImager (<htmlurl url="http://systemimager.org"
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name="http://systemimager.org">) is software that automates Linux
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installs, software distribution, and production deployment. </p>
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</sect3>
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</sect2>
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<!-- ************************************************************* -->
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<sect2> Personal cloning strategy
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<p> I believe in having a completely distributed system. This means
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each machine contains a copy of the operating system. Installing the
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@ -500,16 +572,6 @@ name="http://www.ram.org/computing/linux/cluster/fantini_contribution.tgz">.
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<!-- ************************************************************* -->
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<sect2> Cloning and maintenance packages
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<p> SystemImager (<htmlurl url="http://systemimager.org"
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name="http://systemimager.org">) is software that automates Linux
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installs, software distribution, and production deployment. </p>
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</sect2>
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<!-- ************************************************************* -->
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<sect2> DHCP vs. hard-coded IP addresses
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<p> If you have DHCP set up, then you don't need to reset the IP
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@ -576,8 +638,8 @@ routines to communicate between processes on different machines. </p>
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areas, are massively and trivially parallelisable, meaning that
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perfect distribution can be achieved by spreading tasks equally across
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the machines (for example, when analysing a whole genome using a
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technique that operates on a single gene/proteom, each processor can
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work on one gene at a time independent of all the other
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technique that operates on a single gene/protein, each processor can
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work on one gene/protein at a time independent of all the other
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processors). </p>
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<p> So far we have not found the need to use a professional queueing
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@ -612,7 +674,7 @@ loads. One example is given below. Reboots have generally occurred
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when a circuit breaker is tripped.
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<tscreen><verb>
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12:39pm up 439 days, 14:45, 1 user, load average: 1.19, 1.08, 1.02
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2:29pm up 495 days, 1:04, 2 users, load average: 4.85, 7.15, 7.72
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</verb></tscreen>
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</p>
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