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<!doctype Linuxdoc system>
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<article>
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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> v0.2, June 10, 2001</date>
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<abstract>
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How to set up high-performance Linux computing clusters.
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</abstract>
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<!-- ************************************************************* -->
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<toc>
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<sect> Introduction
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<p> This document describes how I set up my Linux computing clusters
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for high-performance computing which I need for <htmlurl
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url="http://compbio.washington.edu" name="my research">. </p>
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<p> Use the information below at your own risk. I disclaim all
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responsibility for anything you may do after reading this HOWTO. The
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latest version of this HOWTO will always be available at <htmlurl
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url="http://www.ram.org/computing/linux/linux_cluster.html"
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name="http://www.ram.org/computing/linux/linux_cluster.html">. </p>
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<p> Unlike other documentation that talks about setting up clusters in
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a general way, this is a specific description of how our lab is setup
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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 figure I might as well put it up on the web and
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perhaps someone else will find it useful. The main use as it stands
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is that it's a report on what kind of hardware works well with Linux
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and what kind of hardware doesn't. </p>
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</sect>
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<!-- ************************************************************* -->
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<!-- ************************************************************* -->
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<sect> Hardware
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<p> This section covers the hardware choices I've made. Unless noted,
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assume that everything works <it>really</it> well. </p>
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<!-- ************************************************************* -->
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<sect1> Node hardware
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<p> 32 machines have the following setup each:
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<itemize>
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<item> 2 Pentium III 1 GHz Intel CPUs
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<item> Supermicro 370 DLE Dual PIII-FCPGA motherboard
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<item> 2 256 MB 168-pin PC133 Registered ECC Micron RAM
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<item> 1 20 GB Maxtor ATA/66 5400 RPM HD
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<item> 1 40 GB Maxtor UDMA/100 7200 RPM HD
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<item> Asus CD-S500 50x CDROM
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<item> 1.4 MB floppy drive
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<item> ATI Expert 98 8 MB PCI video card
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<item> Mid-tower case
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</itemize>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Server hardware
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<p> 1 external server with the following setup:
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<itemize>
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<item> 2 Pentium III 1 GHz Intel CPUs
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<item> Supermicro 370 DLE Dual PIII-FCPGA motherboard
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<item> 2 256 MB 168-pin PC133 Registered ECC Micron RAM
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<item> 1 20 GB Maxtor ATA/66 5400 RPM HD
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<item> 2 40 GB Maxtor UDMA/100 7200 RPM HD
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<item> Asus CD-S500 50x CDROM
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<item> 1.4 MB floppy drive
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<item> ATI Expert 98 8 MB PCI video card
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<item> Full-tower case
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</itemize>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Desktop hardware
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<p> 4 desktops with the following setup:
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<itemize>
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<item> 2 Pentium III 1 GHz Intel CPUs
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<item> Supermicro 370 DE6 Dual PIII-FCPGA motherboard
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<item> 4 256 MB 168-pin PC133 Registered ECC Micron RAM
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<item> 3 40 GB Maxtor UDMA/100 7200 RPM HD
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<item> Ricoh 32x12x10 CDRW/DVD Combo EIDE
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<item> 1.4 MB floppy drive
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<item> Asus V7700 64mb GeForce2-GTS AGP video card
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<item> Creative SB Live Platinum 5.1 sound card
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<item> Microsoft Natural Keyboard
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<item> Microsoft Intellimouse Explorer
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<item> Full-tower case
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</itemize>
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</p>
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<p> 2 desktops with the following setup:
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<itemize>
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<item> 2 Pentium III 1 GHz Intel CPUs
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<item> Supermicro 370 DLE Dual PIII-FCPGA motherboard
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<item> 4 256 MB 168-pin PC133 Registered ECC Micron RAM
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<item> 3 40 GB Maxtor UDMA/100 7200 RPM HD
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<item> Mitsumi 8x/4x/32x CDRW
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<item> 1.4 MB floppy drive
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<item> Jaton Nvidia TNT2 32mb PCI
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<item> Creative SB LIVE Value PCI
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<item> Microsoft Natural Keyboard
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<item> Microsoft Intellimouse Explorer
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<item> Full-tower case
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</itemize>
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</p>
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<p> 2 desktops with the following setup:
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<itemize>
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<item> 2 Pentium III 1 GHz Intel CPUs
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<item> Supermicro 370 DLE Dual PIII-FCPGA motherboard
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<item> 4 256 MB 168-pin PC133 Registered ECC Micron RAM
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<item> 3 40 GB Maxtor UDMA/100 7200 RPM HD
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<item> Asus CD-S500 50x CDROM
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<item> 1.4 MB floppy drive
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<item> Jaton Nvidia TNT2 32mb PCI
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<item> Creative SB LIVE Value PCI
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<item> Microsoft Natural Keyboard
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<item> Microsoft Intellimouse Explorer
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<item> Full-tower case
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</itemize>
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</p>
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<p> Backup:
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<itemize>
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<item> 2 Sony 20/40 GB DSS4 SE LVD DAT
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</itemize>
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</p>
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<p> Monitors:
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<itemize>
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<item> 4 21" Sony CPD-G500 .24mm monitor
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<item> 2 18" Viewsonic VP-181 TFT-LCD monitor
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</itemize>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Putting-it-all-together hardware
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<p> We use KVM switches with a cheap monitor to connect up and "look"
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at all the machines:
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<itemize>
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<item> 15" .28dp XLN CTL Monitor
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<item> 3 Belkin Omniview 16-Port Pro Switches
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<item> 40 KVM cables
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</itemize>
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</p>
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<p> Networking is important.
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<itemize>
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<item> 1 Cisco Catalyst 3448 XL Enterprise Edition network switch.
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</itemize>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Costs
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<p> Our vendor is Hard Drives Northwest (<htmlurl
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url="http://www.hdnw.com" name="http://www.hdnw.com">). For each
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compute node in our cluster (containing two processors), we paid about
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$1500, including taxes. Generally, our goal is to keep each node to
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below $2000.00 (which is what our desktop machines cost). </p>
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</sect1>
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<!-- ************************************************************* -->
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</sect>
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<!-- ************************************************************* -->
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<sect> Software
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<!-- ************************************************************* -->
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<sect1> Linux, of course!
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<p> Specfically we use 2.2.17-14 kernel based on the KRUD 7.0
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distribution. We use our own software for parallising applications but
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have experimented with PVM and MPI. In my view, the overhead for these
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pre-packaged programs is too high. </p>
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<!-- ************************************************************* -->
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<sect1> Costs
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<p> Linux is freely copiable. </p>
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</sect1>
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<!-- ************************************************************* -->
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</sect>
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<!-- ************************************************************* -->
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<sect> Configuration
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<!-- ************************************************************* -->
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<sect1> Disk configuration
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<p> This section describes disk partitioning strategies. </p>
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<p>
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<tscreen><verb>
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desktops (without windows):
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hda1 - swap (2 * RAM)
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hda2 - / (4 GB)
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hda3 - /home (remaining disk space)
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hdb1 - /maxa (total disk)
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hdd1 - /maxb (total disk)
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desktops (with windows):
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hda1 - /win (total disk)
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hdb1 - swap (2 * RAM)
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hdb2 - / (4 GB)
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hdb3 - /home (remaining disk space)
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hdd1 - /maxa (total disk)
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laptops (single disk):
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hda1 - /win (half the total disk size)
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hda2 - swap (2 * RAM)
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hda3 - / (4 GB)
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hda4 - /home (remaining disk space)
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farm machines:
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hda1 - swap (2 * RAM)
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hda2 - / (remaining disk space)
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hdb1 - /maxa (total disk)
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</verb></tscreen>
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</p>
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</sect1>
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<!-- ************************************************************* -->
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<sect1> Package configuration
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<p> Install a minimal set of packages for the farm. Users are allowed
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to configure desktops as they wish. </p>
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</sect1>
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</sect>
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<!-- ************************************************************* -->
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<sect> Acknowledgements
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<p> The following people have been helpful in getting this HOWTO
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done:
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<itemize>
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<item> Michael Levitt (<htmlurl url="mailto:michael.levitt@stanford.edu" name="Michael Levitt">)
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</itemize>
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</p>
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</sect>
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<!-- ************************************************************* -->
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<sect> Bibliography <label id="references">
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<p> The following documents may prove useful to you---they are links
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to sources that make use of high-performance computing clusters:
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<itemize>
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<item> <url url="http://www.ram.org/computing/rambin/rambin.html"
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name="RAMBIN web page">
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<item> <url url="http://www.ram.org/computing/ramp/ramp.html"
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name="RAMP web page">
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<item> <url url="http://www.ram.org/research/research.html" name="Ram
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Samudrala's research page (which describes the kind of research done with these clusters)">
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</itemize>
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</p>
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</sect>
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<!-- ************************************************************* -->
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</article>
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