On 1/3/13 9:39 PM, Xu Dong Huang wrote:
The average of all my variations contain about 802780 atoms.
The general rule of thumb is to aim for a few hundred or maybe a thousand atoms
per processor. Given that you have in excess of 130,000 atoms per processor, I
would say your observation of slow performance is entirely normal.
-Justin
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
[email protected]
On Jan 3, 2013, at 9:36 PM, Justin Lemkul <[email protected]> wrote:
On 1/3/13 9:33 PM, Xu Dong Huang wrote:
Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45
box system with water solvent + large multiple solutes.
Performance depends mostly on the number of atoms. You haven't provided that
information, so it's hard to judge what you might expect.
-Justin
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
[email protected]
On Jan 3, 2013, at 9:29 PM, Xu Dong Huang <[email protected]> wrote:
Dear gromac users,
I submitted my NPT run into a MPI cluster. The size of my run system is an
85x85x85 box filled with water solvent. and I set NPT steps to be 1000000
(1million) with dt 0.02. The log says It will finish sometime in mid or towards
end of february.
Is that normal for a NPT run of that size? Or am I just faced with slow
technology. Or am I doing something wrong (I requested 6 cores for my run)
Please let me know, thanks.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
[email protected]
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Virginia Tech
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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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