[Beowulf] Newbie Question

Vincent Diepeveen diep at xs4all.nl
Sun Feb 6 07:10:39 PST 2005

At 02:23 5-2-2005 +0700, Monang Setyawan wrote:
>Hi. I'm a newbie in this parallel computing thing. 
>(sorry for my bad english, I'm Indonesian)
>My current project is a software that analyze DNA/Protein sequence
>data that needs high performance aspect on it. I plan to deploy this
>software on network of workstations (mm, may be just about 10 PCs on
>the network). Am I in wrong place now?

>I am going to use message passing paradigm (MPI) to write the
>software. I've read that there are several choice of MPI
>implementation. The problem is, I'm bad in both C or Fortran (I
>usually use Java as my favorite language). Some source said that Java
>(or it's MPI wrapper or pure MPI implementation) isn't good enough to
>implement a parallel computing solution. Is that right?

You definitely want to write it in C. 

Basically protein research, which might touch a field which is forbidden to
research in EU countries, but not forbidden to research in USA, Israel and
i must admit i'm amazed that's legal in Indonesia usually is heavily
floating point oriented. Just calculating what i would classify as matrix
invariants to determine origins and consequences of modifications.

In C there is superb libraries you want to consider. Certain calculations
can get speeded up bigtime by FFT, but not always, as sometimes you just
want accurate results and not approximations. C is ideal because it's
easier to use SSE2 for it which is what you need of course. Please note
both P4 and A64/Opteron have that functionality and Opteron is 2 times
faster than P4 there, but perhaps you can get the P4 hardware factor 2
cheaper, which would make it very attractive for such a cluster.

In all cases such software is embarassingly parallel. gigabit ethernet is
more than sufficient. Yet taking care the pc's have relative fast floating
point possibilities is very relevant. Cheapest gflop per dollar might be
probably surprising hardware. 

A beowulf definitely is ideal for this type of software.

>My third question is, is there any pdf/ps/one file version of
>"Engineering a Beowulf-style Compute Cluster''?
>Thanks in advance.
>For the sake of time..
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