Big Cluster Project 11 April 2006

(Note: this page is under construction and hasn't been announced yet, so is in massive flux.)

Come help us make a big parallel cluster on 11 April 2006 from 3:15 in the 7th floor lounge!

If you are in CS 521, you'll get five points credit for participating (details below).
It's after instruction ends but before exams start, so you have no excuse.
It'll be right before Tuesday Tea.
Brett has a budget from Google for pizza that he's eager to spend on this event.
It'll be fun!

We want to get a lot of computers, where "a lot" is on the order of 40.

We want to run a cool parallel program on the cluster. If you have a suggestion, add it to the list below. The suggestions we have so far

Finding large prime numbers
LINPACK

Something graphical -- something interesting to watch -- would be more fun than something purely textual like prime numbers.

CS 521 credit

To get CS 521 credit, you need to do the following:

Burn a bootable BCCD CD (see below).
Boot your laptop from that CD at home to make sure that the burn was correct, that your system will boot, etc.
- Note what kind of network card you have so that you can boot faster on the spot.
Bring your computer(s) and the CD to the 7th floor lounge by 3:15. Laptops are preferable, since we might be limited in the number of power outlets we will have.
- If you don't have a laptop, you can bring in your desktop; we will have at least one monitor that we can swap around.
- If you don't have a laptop, you can borrow one for four hours (not renewable) from Koerner Library or Woodward Library, Circulation Desk, entrance level.
Be fully prepared to boot your own computer, and to help out anyone who showed up who is not in 521 (i.e. who has even less experience than you have).

Making a bootable CD

There are a number of different distributions of MPI/LAM, but we will use BCCD

. It is specifically designed for educational use, and has a PPC version so that Mac users can play too.

Windows/x86 users, use http://bccd.cs.uni.edu/BCCD-Images/bccd-2.2.1c.iso. PPC users, use http://bccd.cs.uni.edu/BCCD-Images/BCCD-2.2-BETA-IMAGES/bccd-ppc-2006-02-21T04-0500.iso.

It is important to burn the CD in "raw" format. (A raw image contains special error detection and correction codes that the CDR software will generate as it is writing the ISO image to the CD. You cannot simply add the image file to the CD layout as you would when recording normal files off your hard drive.) You can't just use the standard method of burning a file onto disk like you would an MP3.

Linux

Making bootable CD's can be a little confusing in linux, specially for those who have not done it before. It's probably not something that you do all the time, so you might have challenges with media, drivers, kernels, applications, or all of the above. Anirban suggests that you use an updated 2.6 kernel machine (I know of Fedora builds 3, 4 & 5 has this updated 2.6 kernels) with atleast 256 MB ram for burning your CD's. K3b is a nifty utility that has a very good user interface (just type k3b in console). From tools menu you can find burn CD Image or burn DVD iso image which works fine for me. Before you burn images, it might be a good idea to cross verify the MD5 hash value for your image just in case your file got corrupt while downloading. Type md5sum image_name in colsole and it will give you the MD5 hash value for that image. You can then cross check with its official value from the website.

On Linux, there are some unspecified issues with cdrecord for kernels newer than 2.5; there is some documentation on the Web that says they have been fixed in 2.6.11, but DuckySherwood had problems even with 2.6.11.

If you have trouble burning from Linux, you can is burn a CD from Windows and then boot that from Linux. Note that if everything is working, you should not need to burn anything except an iso file (Windows) or an iso.img file (Linux) to your CD.

Note that if everything is working, you should be able to stick the CD in your drive and restart; you should not need to hold down magic key combinations.
If you do have trouble, you might need to change the boot device order in your BIOS.
If you have trouble, see also the note in the Mac section below about "raw" mode.
Ducky successfully burned BCCD from Windows and booted on Linux (Kannotix distro, 2.6.11 kernel) using just what Windows offered (::RecordNow, which appears to be distributed with IBM Thinkpads).
Ducky found that she had trouble booting from the CD when she had previously booted into Linux from her hard drive -- she had to boot into Windows, then reboot with the CD in the tray.

Windows

Windows should be easy. Just burn http://bccd.cs.uni.edu/BCCD-Images/bccd-2.2.1c.iso

(in raw format) and reboot. You might need to change the boot device order in your BIOS.

Mac

Burn http://bccd.cs.uni.edu/BCCD-Images/BCCD-2.2-BETA-IMAGES/bccd-ppc-2006-02-21T04-0500.iso

to disk in raw format.

Here are instructions from mkLinux on how to burn a raw image:

Download a BCCD image
Open Disk Copy, which can be found in /Applications/Utilities
Choose "Burn Image..." from the "Image" menu.
Locate the image you wish to burn (i.e. maindisk.img).
Insert a blank CD-R or CD-RW.
Click the "Burn" button!

This is slightly different from the UI Ducky found with version 10.2 (Panther) of OS X:

Download a BCCD image
Open Disk Utility from /Applications/Utilities
Choose "Burn..." from the "Images" menu
Select the .iso BCCD image from the file picker
When it prompts you for a blank CD, insert one
Click the "Burn" button!

Note that when you boot from the CD on your Mac, you must hold down the "c" button to make it boot from the CD.

Ducky had trouble rebooting into OS X immediately after booting into BCCD. She found that Control-Command-Power after an non-starting boot worked.

On the Day Of

On the day of the event, several things need to happen.

Equipment

We need some extra equipment:

Switches -- Alan Wagner will bring those
Spare CAT5 cables (from where? @@@)
A drive somewhere with the code to run (source, since we'll have Macs on the network as well)

Boot

DHCP Server: One machine needs to boot as a DHCP server. That must be an x86 machine, not a Mac. Ducky will do this, following the BigClusterDHCPInstructions.

Everyone else needs to follow the BigClusterNodeInstructions.

Setup needs

There are a few one-of things to do ahead of time:

~~Instructions on what everyone needs to bring -- Ducky~~
Instructions for what to do on the day of -- Ducky
~~Locate switches -- Alan~~
~~Locate CAT5 cables -- Ducky~~
~~Reserve a room with an adequate amount of tables and space~~
- Estimate head/node count, adjust room if needed
~~Post information to class -- Ducky w/input from Alan~~
~~Post information more widely -- Ducky w/input from Alan~~
Figure out what code to run -- class, Brett
- Adaptive Poisson Boltzmann Solver -- some nice viz, but perhaps not realtime
- GROMACS and demos (needs fftw too), some command line options -- not realtime; lots of dependencies
  - build fftw with MPI
- StarCrash needs fftw, set up for mpich
- ParaView toolkit, has some demo code (requires CMake)
- Chromium (no obvious demos, but listing anyway) -- toolkit
- PyMOL (requires Python, numeric, Tcl, Tk, pmw, libpng, zlib, freeglut, and freetype)
- fun.c MPE demo
- mpich demos
- mpich examples from book
- mpe/contrib: ~ducky/src/mpe2-1.0.3p1/src/graphics/contrib/ -- mastermind, life, mandel, test -- needs f77, which IIRC is on BCCD but not on ducky's machine. time for bed
- PetSCGraphics
- mpi Povray
  - povray original
  - mpi-povray help
  - POV manual (ducky local)
  - to watch it run qsub -v np=#,DISPLAY=$DISPLAY -l nodes=# /home/username/runpovray
  - Demo files
    - http://biobos.nih.gov/apps/povray/povray_examples.html
    - some povray demo files

Make sure code compiles on Macs and Linux both with near-forehead install (meaning two directories) -- Ducky, Brett
- Update instructions for copying/compiling code to reflect whatever code we decide to run
Make spare boot CDs for stragglers, people who forget, etc
load the demo code onto a thumb drive

On the day of:

Tags for computers and cables to indicate ownership
print copies of instructions with index cards with hostnumber
Power strips

Projector -- Alan?
Switches -- Alan
Router -- Alan
2 Linux boxes -- Alan
Extra CAT5 cables (?)
Pizza -- Google via Brett
Printouts of instructions

DHCP server boot
Put code in ~bccd/cs521

People who are known to be coming:

Ducky (1 x86, 1 PPC)
Alan Wagner (1 x86?, two headless Linux machines)
Brett (PPC)
Andrew C (x86)
Nels (x86)
Allan R (way old x86) not in class
Karen Parker (PPC)
Ivan (x86)
Ying (x86)
Peng Li(x86 Laptop 2.0Hz Centrino, 1GB)
Tristram (PPC)
Andrei (x86)
LeCuong (x86)
Gitika (x86)
Argun (x86)
Andrew (PPC)
Mike (x86)
Chris (x86)
James (x86)
Gang (x86)
Sharath (x86)
JeremyHilliker (x86, PII-233, 48MB -- don't hate!)
Arjun (x86)
Stanley (PPT)
Jelena (x86)
Michael Patrick Bonner (x86)
Joel (x86)

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Topic revision: r35 - 2006-04-11 - TWikiGuest