[gmx-developers] some benchs on cray xt4 and xt5

andrea spitaleri spitaleri.andrea at hsr.it
Wed Dec 10 15:09:52 CET 2008

Dear all,
I am using gromacs-4.0.2 on two systems: cray xt4 and xt5 (csc louhi). Here you are in short a table
with some tests:

MD simulation 9ns on a system protein+water (ca. 200,000 atoms):

128 cpu 64 pme 15h 30min on hector (xt4)
128 cpu 64 pme 15h 20min on louhi (xt4)
128 cpu 64 pme 20h on louhi (xt5)

256 cpu 128 pme 12h on hector (xt4)
256 cpu 128 pme 21h on louhi (xt5)

One explanation should be (from one of the administrators):

"One possibility for this is, that Gromacs is message intensive, and is
thefore slower on xt5 because of the xt5 architecture. (Basically 2
nodes (8 cores) share the same Hypertransport, whereas on xt4 each node
(4 cores) has that of its own, see eg.
http://www.csc.fi/english/pages/louhi_guide/hardware/computenodes/index_html )"

what do you think about it?

thanks in advance



Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153

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