[Beowulf] Slection from processor choices; Requesting Giudence

Douglas Eadline deadline at clustermonkey.net
Mon Jun 19 15:36:49 EDT 2006


For my tests I used version GROMACS 3.3

The Gromacs page does not mention what version was used for the
benchmarks reported in their table.

 --
 Doug



> On Sat, 2006-06-17 at 11:34, Mark Hahn wrote:
>> > >> desktop (32 bit PCI) cards. I managed to get 14.6 HPL GFLOPS
>> > >> and 4.35 GROMACS GFLOPS out of 8 nodes consisting of hardware
>> > > ...
>> > >> As a point of reference, a quad opteron 270 (2GHz) reported
>> > >> 4.31 GROMACS GFLOPS.
>> > >
>> > > that's perplexing to me, since the first cluster has semp/2500's,
>> > > right?  that's a 1.75 GHz K8 core with 128K L2 and 64b memory
>> > > interface.  versus the same number of 2.0 GHz, 1M cores each with
>> > > 4x 128b memory.  I really wouldn't expect them to be that close -
>> > > any speculation on why GROMACS runs so poorly on the much better
>> > > SMP machine?
>> >
>> > <googling for motherboard specs>
>> > Aha, Socket 462. The Semprons he used are K7 based.
>>
>> OK, even more so - how does an even older cpu with lower clock,
>> slower memory and only gigabit interconnect beat a quad-opt.
>> it seems like some other factors were determining performance.
>
>   Could anyone comment on what version of GROMACS was being used?  This
> code tends to use computational kernels coded in assembly, and until 3.3
> released, there were no x86_64 assembly kernels.  The configure script
> wasn't smart enough to figure out that an Opteron could run the x86
> assembly, so it would use auto-generated fortran or C code instead.
>
>   Hacking the configure script to use x86 assembly and compiling 32-bit
> resulted in about a 2x speedup on Opteron.  I believe the new x86_64
> kernel and 64-bit compilation in GROMACS 3.3 is even faster, but I don't
> have numbers on hand.
>
> -Kevin
>
>
>>
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-- 
Doug
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