77 lines
3.1 KiB
HTML
77 lines
3.1 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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<HTML>
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<HEAD>
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<META NAME="GENERATOR" CONTENT="LinuxDoc-Tools 0.9.21">
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<TITLE> Linux Cluster HOWTO : Performing tasks on the cluster</TITLE>
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<LINK HREF="Cluster-HOWTO-6.html" REL=next>
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<LINK HREF="Cluster-HOWTO-4.html" REL=previous>
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<LINK HREF="Cluster-HOWTO.html#toc5" REL=contents>
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</HEAD>
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<BODY>
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<A HREF="Cluster-HOWTO-6.html">Next</A>
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<A HREF="Cluster-HOWTO-4.html">Previous</A>
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<A HREF="Cluster-HOWTO.html#toc5">Contents</A>
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<HR>
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<H2><A NAME="s5">5.</A> <A HREF="Cluster-HOWTO.html#toc5">Performing tasks on the cluster</A></H2>
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<P> This section is still being developed as the usage on my cluster
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evolves, but so far we tend to write our own sets of message passing
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routines to communicate between processes on different machines. </P>
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<P> Many applications, particularly in the computational genomics
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areas, are massively and trivially parallelisable, meaning that
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perfect distribution can be achieved by spreading tasks equally across
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the machines (for example, when analysing a whole genome using a
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technique that operates on a single gene/protein, each processor can
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work on one gene/protein at a time independent of all the other
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processors). </P>
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<P> So far we have not found the need to use a professional queueing
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system, but obviously that is highly dependent on the type of
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applications you wish to run. </P>
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<H2><A NAME="ss5.1">5.1</A> <A HREF="Cluster-HOWTO.html#toc5.1">Rough benchmarks</A>
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</H2>
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<P> For the single most important program we run (our <I>ab
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initio</I> protein folding simulation program), using the Pentium 3 1
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GHz processor machine as a frame of reference, on average: </P>
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<P>
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<BLOCKQUOTE><CODE>
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<PRE>
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Xeon 1.7 GHz processor is about 22% slower
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Athlon 1.2 GHz processor is about 36% faster
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Athlon 1.5 GHz processor is about 50% faster
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Athlon 1.7 GHz processor is about 63% faster
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Xeon 2.4 GHz processor is about 45% faster
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Xeon 2.7 GHz processor is about 80% faster
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Opteron 1.4 GHz processor is about 70% faster
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Opteron 1.6 GHz processor is about 88% faster
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</PRE>
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</CODE></BLOCKQUOTE>
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</P>
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<P> Yes, the Athlon 1.5 GHz is faster than the Xeon 1.7 GHz since the
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Xeon executes only six instructions per clock (IPC) whereas the Athlon
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executes nine IPC (you do the math!). This is however an highly
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non-rigourous comparison since the executables were each compiled on
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the machines (so the quality of the math libraries for example will
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have an impact) and the supporting hardware is different. </P>
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<H2><A NAME="ss5.2">5.2</A> <A HREF="Cluster-HOWTO.html#toc5.2">Uptimes</A>
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</H2>
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<P> These machines are incredibly stable both in terms of hardware and
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software once they have been debugged (usually some in a new batch of
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machines have hardware problems), running constantly under very heavy
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loads. One common example is given below. Reboots have generally
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occurred when a circuit breaker is tripped.</P>
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<P>
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<BLOCKQUOTE><CODE>
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<PRE>
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2:29pm up 495 days, 1:04, 2 users, load average: 4.85, 7.15, 7.72
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</PRE>
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</CODE></BLOCKQUOTE>
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</P>
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<HR>
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<A HREF="Cluster-HOWTO-6.html">Next</A>
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<A HREF="Cluster-HOWTO-4.html">Previous</A>
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<A HREF="Cluster-HOWTO.html#toc5">Contents</A>
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</HTML>
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