  Linux Cluster HOWTO
  Ram Samudrala (me@ram.org)
  v0.92,  April 8, 2002

  How to set up high-performance Linux computing clusters.
  ______________________________________________________________________

  Table of Contents


  1. Introduction

  2. Hardware

     2.1 Node hardware
     2.2 Server hardware
     2.3 Desktop hardware
     2.4 Miscellaneous/accessory hardware
     2.5 Putting-it-all-together hardware
     2.6 Costs

  3. Software

     3.1 Linux, of course!
     3.2 Costs

  4. Set up and configuration

     4.1 Disk configuration
     4.2 Package configuration
     4.3 Operating system installation
        4.3.1 Cloning
        4.3.2 DHCP vs. hard-coded IP addresses
     4.4 Known hardware issues

  5. Performing tasks on the cluster

     5.1 Rough benchmarks
     5.2 Uptimes

  6. Acknowledgements

  7. Bibliography



  ______________________________________________________________________

  1.  Introduction

  This document describes how I set up my Linux computing clusters for
  high-performance computing which I need for my research.

  Use the information below at your own risk.  I disclaim all
  responsibility for anything you may do after reading this HOWTO. The
  latest version of this HOWTO will always be available at
  http://www.ram.org/computing/linux/linux_cluster.html.

  Unlike other documentation that talks about setting up clusters in a
  general way, this is a specific description of how our lab is setup
  and includes not only details the compute aspects, but also the
  desktop, laptop, and public server aspects.  This is done mainly for
  local use, but I put it up on the web since I received several e-mail
  messages based on my newsgroup query requesting the same information.
  Even today, as I plan another 64-node cluster, I find there is a
  dearth of information about exactly how to assemble components to form
  a node that works reliably under Linux.  The main use of this HOWTO as
  it stands is that it's a report on what kind of hardware works well
  with Linux and what kind of hardware doesn't.

  2.  Hardware

  This section covers the hardware choices I've made. Unless noted in
  the ``known hardware issues'' section, assume that everything works
  really well.

  Hardware installation is also fairly straight-forward unless otherwise
  noted, with most of the details covered by the manuals. For each
  section, the hardware is listed in the order of purchase (most recent
  is listed first).

  2.1.  Node hardware

  32 machines have the following setup each:


    2 AMD Palamino MP XP 1800+ 1.53 GHz CPUs

    Tyan S2460 Dual Socket-A/MP motherboard

    Kingston 512mb PC2100 DDR-266MHz REG ECC RAM

    1 20 GB Maxtor UDMA/100 7200rpm HD

    1 120 GB Maxtor 5400rpm ATA100 HD

    Asus CD-A520 52x CDROM

    1.44mb floppy drive

    ATI Expert 98 8mb AGP video card

    IN-WIN P4 300ATX Mid Tower case

    Intel PCI PRO-100 10/100Mbps network card

  32 machines have the following setup each:


    2 Pentium III 1 GHz Intel CPUs

    Supermicro 370 DLE Dual PIII-FCPGA motherboard

    2 256 MB 168-pin PC133 Registered ECC Micron RAM

    1 20 GB Maxtor ATA/66 5400 RPM HD

    1 40 GB Maxtor UDMA/100 7200 RPM HD

    Asus CD-S500 50x CDROM

    1.4 MB floppy drive

    ATI Expert 98 8 MB PCI video card

    IN-WIN P4 300ATX Mid Tower case

  2.2.  Server hardware

  1 server for external use (dissemination of information) with the
  following setup:

    2 Pentium III 1 GHz Intel CPUs

    Supermicro 370 DLE Dual PIII-FCPGA motherboard

    2 256 MB 168-pin PC133 Registered ECC Micron RAM

    1 20 GB Maxtor ATA/66 5400 RPM HD

    2 40 GB Maxtor UDMA/100 7200 RPM HD

    Asus CD-S500 50x CDROM

    1.4 MB floppy drive

    ATI Expert 98 8 MB PCI video card

    Full-tower case with 300W PS

  2.3.  Desktop hardware

  1 desktop with the following setup:


    2 Intel Xeon 1.7 GHz 256K 400FS

    Supermicro P4DCE Dual Xeon motherboard

    4 256mb RAMBUS 184-Pin 800 MHz memory

    2 120 GB Maxtor ATA/100 5400 RPM HD

    1 60 GB Maxtor ATA/100 7200 RPM HD

    52X Asus CD-A520 INT IDE CDROM

    1.4 MB floppy drive

    Leadtex 64 MB GF2 MX400 AGP

    Creative SB LIVE Value PCI 5.1

    Microsoft Natural Keyboard

    Microsoft Intellimouse Explorer

    Supermicro SC760 full-tower case with 400W PS



  2 desktops with the following setup:


    2 AMD K7 1.2g/266 MP Socket A CPU

    Tyan S2462NG Dual Socket A motherboard

    4 256mb PC2100 REG ECC DDR-266Mhz

    3 40 GB Maxtor UDMA/100 7200 RPM HD

    50X Asus CD-A520 INT IDE CDROM

    1.4 MB floppy drive

    Chaintech Geforce2 MX200 32mg AGP

    Creative SB LIVE Value PCI

    Microsoft Natural Keyboard

    Microsoft Intellimouse Explorer

    Full-tower case with 300W PS


  2 desktops with the following setup:


    2 Pentium III 1 GHz Intel CPUs

    Supermicro 370 DLE Dual PIII-FCPGA motherboard

    4 256 MB 168-pin PC133 Registered ECC Micron RAM

    3 40 GB Maxtor UDMA/100 7200 RPM HD

    Asus CD-S500 50x CDROM

    1.4 MB floppy drive

    Jaton Nvidia TNT2 32mb PCI

    Creative SB LIVE Value PCI

    Microsoft Natural Keyboard

    Microsoft Intellimouse Explorer

    Full-tower case with 300W PS


  2 desktops with the following setup:


    2 Pentium III 1 GHz Intel CPUs

    Supermicro 370 DLE Dual PIII-FCPGA motherboard

    4 256 MB 168-pin PC133 Registered ECC Micron RAM

    3 40 GB Maxtor UDMA/100 7200 RPM HD

    Mitsumi 8x/4x/32x CDRW

    1.4 MB floppy drive

    Jaton Nvidia TNT2 32mb PCI

    Creative SB LIVE Value PCI

    Microsoft Natural Keyboard

    Microsoft Intellimouse Explorer

    Full-tower case with 300W PS


  4 desktops with the following setup:


    2 Pentium III 1 GHz Intel CPUs

    Supermicro 370 DE6 Dual PIII-FCPGA motherboard

    4 256 MB 168-pin PC133 Registered ECC Micron RAM

    3 40 GB Maxtor UDMA/100 7200 RPM HD

    Ricoh 32x12x10 CDRW/DVD Combo EIDE

    1.4 MB floppy drive

    Asus V7700 64mb GeForce2-GTS AGP video card

    Creative SB Live Platinum 5.1 sound card

    Microsoft Natural Keyboard

    Microsoft Intellimouse Explorer

    Full-tower case with 300W PS


  2.4.  Miscellaneous/accessory hardware

  Backup:


    2 Sony 20/40 GB DSS4 SE LVD DAT

  Monitors:


    1 22" Viewsonic P220F 0.25-0.27m monitor

    4 21" Sony CPD-G500 .24mm monitor

    2 18" Viewsonic VP181 LCD monitor

    1 17" Viewsonic VE170 LCD monitor

  2.5.  Putting-it-all-together hardware

  We use KVM switches with a cheap monitor to connect up and "look" at
  all the machines:


    15" .28dp XLN CTL Monitor

    3 Belkin Omniview 16-Port Pro Switches

    40 KVM cables

  While this is a nice solution, I think it's kind of needless. What we
  need is a small hand held monitor that can plug into the back of the
  PC (operated with a stylus, like the Palm). I don't plan to use more
  monitor switches/KVM cables.

  Networking is important:


    1 Cisco Catalyst 3448 XL Enterprise Edition 48 port network switch.

    1 Netgear FS524 24 port network switch



  2.6.  Costs

  Our vendor is Hard Drives Northwest (http://www.hdnw.com). For each
  compute node in our cluster (containing two processors), we paid about
  $1500-$2000, including taxes. Generally, our goal is to keep each node
  to below $2000.00 (which is what our desktop machines cost).

  3.  Software

  3.1.  Linux, of course!

  We use Linux systems with a 2.4.9-7 kernel based on the KRUD 7.2
  distribution, and 2.2.17-14 kernel based on the KRUD 7.0 distribution.
  These distributions work very well for us since updates are sent to us
  on CD and there's no reliance on an external network connection for
  updates. They also seem "cleaner" than the regular Red Hat
  distributions.

  We use our own software for parallelising applications but have
  experimented with PVM and MPI. In my view, the overhead for these pre-
  packaged programs is too high.  I recommend writing application-
  specific code for the tasks you perform (that's one person's view).

  3.2.  Costs

  Linux is freely copiable.

  4.  Set up and configuration

  4.1.  Disk configuration

  This section describes disk partitioning strategies.



       farm/cluster machines:

       hda1 - swap  (2 * RAM)
       hda2 - /     (remaining disk space)
       hdb1 - /maxa (total disk)

       desktops (without windows):

       hda1 - swap  (2 * RAM)
       hda2 - /     (4 GB)
       hda3 - /home (remaining disk space)
       hdb1 - /maxa (total disk)
       hdd1 - /maxb (total disk)

       desktops (with windows):

       hda1 - /win  (total disk)
       hdb1 - swap  (2 * RAM)
       hdb2 - /     (4 GB)
       hdb3 - /home (remaining disk space)
       hdd1 - /maxa (total disk)

       laptops (single disk):

       hda1 - /win  (half the total disk size)
       hda2 - swap  (2 * RAM)
       hda3 - /     (4 GB)
       hda4 - /home (remaining disk space)



  4.2.  Package configuration

  Install a minimal set of packages for the farm. Users are allowed to
  configure desktops as they wish.

  4.3.  Operating system installation

  4.3.1.  Cloning

  I believe in having a completely distributed system. This means each
  machine contains a copy of the operating system.  Installing the OS on
  each machine manually is cumbersome. To optimise this process, what I
  do is first set up and install one machine exactly the way I want to.
  I then create a tar and gzipped file of the entire system and place it
  on a CD-ROM which I then clone on each machine in my cluster.

  The commands I use to create the tar file are as follows:



       tar -czvlps --same-owner --atime-preserve -f /maxa/slash.tgz /



  I use have a script called go that takes a hostname and IP address as
  its arguments and untars the slash.tgz file on the CD-ROM and replaces
  the hostname and IP address in the appropriate locations. A version of
  the go script and the input files for it can be accessed at:
  http://www.ram.org/computing/linux/linux/cluster/. This script will
  have to be edited based on your cluster design.

  To make this work, I also use Tom's Root Boot package
  http://www.toms.net/rb/ to boot the machine and clone the system.  The
  go script can be placed on a CD-ROM or on the floppy containing Tom's
  Root Boot package (you need to delete a few programs from this package
  since the floppy disk is stretched to capacity).

  More conveniently, you could burn a bootable CD-ROM containing Tom's
  Root Boot package, including the go script, and the tgz file
  containing the system you wish to clone.  You can also edit Tom's Root
  Boot's init scripts so that it directly executes the go script (you
  will still have to set IP addresses if you don't use DHCP).

  Thus you can develop a system where all you have to do is insert a
  CDROM, turn on the machine, have a cup of coffee (or a can of coke)
  and come back to see a full clone. You then repeat this process for as
  many machines as you have. This procedure has worked extremely well
  for me and if you have someone else actually doing the work (of
  inserting and removing CD-ROMs) then it's ideal.

  Rob Fantini has contributed modifications of the scripts above that he
  used for cloning a Mandrake 8.2 system accessible at
  http://www.ram.org/computing/linux/cluster/fantini_contribution.tgz.

  4.3.2.  DHCP vs. hard-coded IP addresses

  If you have DHCP set up, then you don't need to reset the IP address
  and that part of it can be removed from the go script.

  DHCP has the advantage that you don't muck around with IP addresses at
  all provided the DHCP server is configured appropriately. It has the
  disadvantage that it relies on a centralised server (and like I said,
  I tend to distribute things as much as possible). Also, linking
  hardware ethernet addresses to IP addresses can make it inconvenient
  if you wish to replace machines or change hostnames routinely.
  4.4.  Known hardware issues

  The hardware in general has worked really well for us. Specific issues
  are listed below:

  The AMD dual 1.2 GHz machines run really hot. Two of them in a room
  increase the temperature significantly. Thus while they might be okay
  as desktops, the cooling and power consumption when using them as part
  of a large cluster is a consideration. The AMD Palmino configuration
  described previously seems to work really well.

  5.  Performing tasks on the cluster

  This section is still being developed as the usage on my cluster
  evolves, but so far we tend to write our own sets of message passing
  routines to communicate between processes on different machines.

  Many applications, particularly in the computational genomics areas,
  are massively and trivially parallelisable, meaning that perfect
  distribution can be achieved by spreading tasks equally across the
  machines (for example, when analysing a whole genome using a single
  gene technique, each processor can work on one gene at a time
  independent of all the other processors).

  So far we have not found the need to use a professional queueing
  system, but obviously that is highly dependent on the type of
  applications you wish to run.

  5.1.  Rough benchmarks

  For the single most important program we run (our ab initio protein
  folding simulation program), using the Pentium 3 1 GHz processor
  machine as a reference frame, the Athlon 1.2 GHz processor machine is
  about 16% faster on average, the Pentium 4 1.7 GHz machine is about
  25-32% faster on average, and the Athlon 1.5 GHz processor is about
  80% faster on average (yes, the Athlon 1.5 GHz is faster than the Xeon
  1.7 GHz since the Xeon executes only six instructions per clock (IPC)
  whereas the Athlon executes nine IPC (you do the math!)).

  5.2.  Uptimes

  These machines are incredibly stable both in terms of hardware and
  software once they have been debugged (usually some in a new batch of
  machines have hardware problems).  Reboots have generally occurred
  when a circuit breaker is tripped.  The first machine I installed has
  been up since its birth!



       ~ ram@fp1 % uptime
         4:49am  up 374 days,  2:47,  1 user,  load average: 2.08, 2.02, 2.01



  6.  Acknowledgements

  The following people have been helpful in getting this HOWTO done:


    Michael Levitt (Michael Levitt)



  7.  Bibliography

  The following documents may prove useful to you---they are links to
  sources that make use of high-performance computing clusters:


    RAMBIN web page <http://www.ram.org/computing/rambin/rambin.html>

    RAMP web page <http://www.ram.org/computing/ramp/ramp.html>

    Ram Samudrala's research page (which describes the kind of research
     done with these clusters)
     <http://www.ram.org/research/research.html>



