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slash.tgz file on the CD-ROM and replaces the hostname and IP address in the appropriate locations. A
4. Set up and configuration 6
Linux Cluster HOWTO
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.
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).
DHCP vs. hard-coded IP addresses 7
Linux Cluster HOWTO
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
" RAMP web page
" Ram Samudrala's research page (which describes the kind of research done with these clusters)
5.1 Rough benchmarks 8
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Dobre pomysły nie mają przeszłości, mają tylko przyszłość. Robert Mallet
De minimis - o najmniejszych rzeczach.
Dobroć jest ważniejsza niż mądrość, a uznanie tej prawdy to pierwszy krok do mądrości. Theodore Isaac Rubin
Dobro to tylko to, co szlachetne, zło to tylko to, co haniebne.
Dla człowieka nie tylko świat otaczający jest zagadką; jest on nią sam dla siebie. I z obu tajemnic bardziej dręczącą wydaje się ta druga. Antoni Kępiński (1918-1972)
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