[gmx-users] Please give me advises for the computing system.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 26 13:43:51 CET 2009


Seungpyo Hong wrote:
> Dear Gromacs users,
> 
> I am planning to buy a computer system for MD.
> But don't know much about hardware.
> Help me please!
> 
> Currently we have three candidates with following list of CPUs:
> 
> 1. Core2 Quad (Q9550)
> 2. Xeon (E5440) x 2 (2-way SMP system)
> 3. Core i7 (i7-920)
> 
> We usually perform MD with 4 ~ 8 nodes. (preferentially 8 nodes, 1 node 
> = 1 core)
> 
> Then, which system will you recommend?
> 
> Additionally, I have two questions.
> 
> Question 1. <Whether 2-way SMP has great advantage?>
> Does Core 2 Quad or Core i7 connected by Gigabit Ethernet work well when 
> 8 nodes are used?

Probably neither work well with Gigabit ethernet. Search the archives. 
If you want to run efficient parallel simulations across your whole 
cluster, then you should probably look at something like Infiniband.

Mark

> Question 2. <Comparison between Core 2 Quad and Core i7>
> Does Core i7 work better than Core 2 Quad for Gromacs? (I heard that i7 
> work well in some simulation but not sure of Gromacs)
> 
> Thank you a lot!
> 
> Sincerely,
> Seungpyo Hong
> 
> -- 
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'At the same time, he allowed interaction among objects.'
> -Seungpyo Hong
> 
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
> Tel. (82)-18-372-2468
> sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>
> sp1020 at gmail.com <mailto:sp1020 at gmail.com>
> 
> 
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