• • StarCrash needs fftw, set up for mpich

• • • 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

• Joel (x86)

• • GROMACS and demos (needs fftw too), some command line options -- not realtime; lots of dependencies

• • 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

• • mpi Povray
    • povray original
    • mpi-povray help
    • POV manual (ducky local)

• • PetSCGraphics

• Michael Patrick Bonner (x86)

• Michael Patrick Bonner, Born July 29, 1977, Walnut Creek California USA.... or.. maybe the one in the class (x86)

• • ParaView toolkit, has some demo code (requires CMake)

• • PyMOL (requires Python, numeric, Tcl, Tk, pmw, libpng, zlib, freeglut, and freetype)

• • • build fftw with MPI

• Mike B (x86)

• • ParaView toolkit, has some demo code

• • fun.c MPE demo
  • mpich demos

• Router -- Alan
• 2 Linux boxes -- Alan

• Printouts of instructions

• Alan Wagner (1 x86?, two headless Linux machines)

• • StarCrash needs fftw
  • http://www.paraview.org/HTML/Download.html[ParaView]] toolkit, has some demo code
  • Chromium (no obvious demos, but listing anyway) -- toolkit
  • PyMOL
  • MPE demo
  • [[http://parallel.ru/docs/Parallel/mpich/userguide/node19.html][mpich demos]
  • mpich examples from book
  • mpe/contrib: ~ducky/src/mpe2-1.0.3p1/src/graphics/contrib/ -- mastermind, life, mandel, test

• • Adaptive Poisson Boltzmann Solver -- some nice viz, but perhaps not realtime
  • GROMACS and demos (needs fftw too), some command line options

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

• Projector -- Alan?

• Arjun (x86)
• Stanley (PPT)

• Jelena (x86)

• Instructions on what everyone needs to bring -- Ducky

• Locate switches -- Alan

• 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

• print copies of instructions with hostnumber written on them

• Arjun/Stanley (x86)

• JeremyHilliker (x86, PII-233, 48MB -- don't hate!)

• Sharath (x86)

• Mike (x86)
• Chris (x86)
• James (x86)
• Gang (x86)

• Andrew (PPC)

• Argun (x86)

• Gitika (x86)

• LeCuong (x86)

• Allan R (way old x86) not in class
• Karen Parker (PPC)

• Tristram (PPC)
• Andrei (x86)

• Peng Li(x86 Laptop 2.0Hz Centrino, 1GB)

http://bccd.cs.uni.edu/BCCD-Images/bccd-2.2.1c.iso

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.

• If you do have trouble, you might need to change the boot device order in your BIOS.

Windows

http://bccd.cs.uni.edu/BCCD-Images/bccd-2.2.1c.iso

• Locate CAT5 cables -- Ducky
• Reserve a room with an adequate amount of tables and space

• 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

• Duct tape (?) to tape cables down onto the floor avoid if at all possible

• Ducky (1 x86, 1 PPC)
• Alan Wagner (1 x86?)
• Brett (PPC)
• Andrew C (x86)
• Nels (x86)
• Allan R (way old x86)
• KP (PPC)
• Ivan (x86)
• Ying (x86)

• Type framebuffer_mode_number nodemode (framebuffer_mode_number just refers to what screen resolution to use; 4 is 1024x768.)

DHCP server, follow this sequence:

• • Say NO when it asks if it should autoconfigure with DHCP and YES/OK for everything else.
  • When it asks for IP addresses, configure as in the examples. You can just type in the addresses they use in the dialogs, which are
    • IP address 192.168.1.1
    • netmastk 255.255.255.0
    • router address 192.168.1.254
    • DNS server 192.168.1.1

• When you get to the option of logging in:
  • Login as root, using the password listed at the login prompt
  • Change the password. If you are helping the owner, let the owner set the password.

• 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.

• Tags for computers and cables to indicate ownership
• Duct tape (?) to tape cables down onto the floor
• Power strips

• Enter the password we decide on the day of the event.
• Follow directions for trivial-net-setup. Hit Enter to select the highlighted answer and the arrow keys to change the selection.
  • Say NO when it asks if it should autoconfigure with DHCP and YES/OK for everything else
  • When it asks for IP addresses, just type in the ones they use in the examples, which are
    • 192.168.1.1
    • @@@? 192.168.1.255? @@@
    • 192.168.1.1

• Enter the password we give you on the day of the event.
• Follow directions for trivial-net-setup; say YES/OK to everything.
• When you get the option of logging in, you might want to sign in as root and unmount all of your own partitions:
  • login as root, using the password listed at the login prompt

• • exit

• edit ~/.bashrc (vi, emacs, and pico should all be available -- check@@@)
  • edit the PATH line so that the line reads export PATH=/lam-mpi/bin:$PATH
  • write file and quit
• source ~/.bashrc (or log out and log back in)

• • su - root (using the root password given)

• lamboot -v ~/machines @@@ not sure if we want people to do this here or make it part of the makefile

• The DHCP server machine needs to run bccd-syncdir source_dir_name ~/machines, where source_dir_name is the directory with the code. Note that there might need to be two versions.
• Everyone: the code will show up in a directory named something like /tmp/6g2w98s.
• cp -r dirname/cs521.arch ~bccd/cs521 (where dirname is the tmp dir name and arch is either x86 or ppc, e.g. cp -r /tmp/6g2w98s/cs521.x86 ~bccd/cs521)

Mac users, if you have trouble rebooting into OS X immediately after booting into BCCD, try holding Control-Command-Power after an non-starting boot.

• It'll be fun!

• 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 have trouble, see also the note in the Mac section below about "raw" mode.

• 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.

• Boot up to the BCCD splash screen
• Hit F3, then type framebuffer_mode_number startdhcp (framebuffer_mode_number just refers to what screen resolution to use; 4 is 1024x768.)
• Follow directions.
  • Say NO when it asks if it should autoconfigure with DHCP and YES to everything else
  • When it asks for IP addresses, just type in the ones they use in the examples.

• Boot up to the BCCD splash screen.

• Type framebuffer_mode_number automode (framebuffer_mode_number just refers to what screen resolution to use; 4 is 1024x768.)
• Follow directions; say YES to everything.
• We will give you a password for bccd at the event.

• You might want to sign in as root and unmount all of your own partitions:

• • umount partition for all of your partitions, (e.g. umount /mnt/rw/discs/disc0/part3/home/fred)

• Sign in as bccd, with the password given earlier.
• Answer yes when it asks if you want to run a heartbeat.

• • exit (back to bccd)
• bccd-allowall (Answer yes.)
• bccd-snarfhosts

• startx

• The DHCP server machine needs to run bccd-syncdir dirname ~/machines; it will show up for all machines in a directory named something like /tmp/6g2w98s.
• cp -r dirname/cs521.arch ~bccd/cs521 (e.g. cp -r /tmp/6g2w98s/cs521.x86 ~bccd/cs521)
• cd ~bccd/cs521

• wait for instructions, eat pizza, etc.

As more machines come online, you might need to refresh your system state:

• bccd-allowall
• bccd-snarfhosts
• recon -v ~/machines

• Make sure code compiles on Macs and Linux both with near-forehead install (meaning two directories) -- Ducky

• • Note what kind of network card you have so that you can boot faster on the spot.

• 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).

On the Day Of

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

The DHCP server op might need to know the "static IP address, netmask, gateway, IP for DNS, and broadcast address for localhost and network" @@@ not sure if all that really needed.

It looks like this is the sequence (not tested yet):

• Boot up to the splash screen
  • Hit F3, then type framebuffer mode # startdhcp or start in default mode or @@@
  • Let it boot by default @@@

All the other machines need to be clients:

• Boot up to the splash screen
• Hit F3
• Type framebuffer mode # automode

Everyone then:

• Follow directions
• Sign in as root and unmount all of your own partitions.
  • df to get a list of the mounted partitions
  • umount partition for all of yours, e.g. @@@
• Log out.
• Sign in as bccd, with a password that we will determine on the day of the event.

Synchronize services

• pkbcast @@@ is this LAM or BCCD?
• bccd-allowall
• bccd-snarfhosts

Switch to LAM

• vi ~/.bashrc
  • edit PATH so that the line reads export PATH=/lam-mpi/bin:$PATH
• source ~/.bashrc in all appropriate shells (or log out and log back in)
• For each node, rebuild the library cache:
  • su - root
  • ldconfig -v | less
• recon -v ~/machines
• lamboot -v ~/machines

Compile the target code

• mkdir ~bccd/cs521
• The DHCP server machine needs to put the code into ~bccd/cs521
• All the other nodes need to run bccd-synchdir ~bccd/cs521 ~/machines
• make

Setup needs

• Instructions on what everyone needs to bring -- Ducky
• Instructions for what to do on the day of -- Ducky
• Locate switches -- Alan
• Locate CAT5 cables
• 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
• Make sure code compiles on Macs and Linux both with near-forehead install -- Ducky

On the day of:

• Switches -- Alan
• Extra CAT5 cables (?)
• Pizza -- Google via Brett
• Printouts of instructions -- Ducky (maybe a projector with instructions as well?)
• DHCP server boot
• Put code in ~bccd/cs521

Mac

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

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

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

1. Download a BCCD image
2. Open Disk Utility from /Applications/Utilities
3. Choose "Burn..." from the "Images" menu
4. Select the .iso BCCD image from the file picker
5. When it prompts you for a blank CD, insert one
6. 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.

Other distributions of bootable Linux with clustering tools:

• Brett has a budget from Google for pizza that he's eager to spend on this event.

• 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.

Linux

On Linux, there are some unspecified issues with cdburner for kernels newer than @@@; 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

• 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).

Other distributions of bootable Linux with clustering tools:

• http://www.geocities.com/potato.geo/bootlinuxcd.html (no reports yet from students who have successfully booted from this)
• RockLinux http://www.rocklinux.org/149.html (no reports yet from students who have successfully booted from this)

Making a bootable CD

• http://www.geocities.com/potato.geo/bootlinuxcd.html

These are links that Ducky is in the process of looking at in trying to figure stuff out...

• Mandrake bootable CD instructions:

http://marc.theaimsgroup.com/?l=mandrake-cooker-ppc&m=99441208917647&w=

• IBM http://penguinppc.org/ppc64/power-bootable-iso/

http://www.netbsd.org/Documentation/bootcd.html#creating-the-image

Eroaster

Macs:

• There is some shareware called BootCD that makes a boot CD ?from currently running OS?
• LiveLinux distros of Ubuntu
• RockLinux http://www.rocklinux.org/149.html

• • BCCD, with booting instructions -- advertised as working on Macs with different downloads

Big Cluster Project 11 April 2006

Come help us make a big parallel cluster on 11 April 2006!

• 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 says he'll get Google to buy pizza for us.
• 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

CS 521 credit

• Burn a (tbd) CD.
  • http://bccd.cs.uni.edu/
• Boot your laptop from that CD to make sure that the burn was correct, that your system will boot, etc.
• Bring your computer(s) and the CD to (tbd location). 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 as a slave, and to help out anyone who showed up who is not in 521 (i.e. who has even less experience than you have).