Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error)

From: Ross Walker <>
Date: Mon, 04 Aug 2014 09:23:06 -0700

Hi Ying-chieh,

It's not clear what you are asking here - or what you actually want to do.
Are you trying to rerun the exact same simulation? - if yes this is NOT
possible with the CPU MPI code due to the load balancer. You can either 1)
Hack the code to turn off the loadbalancer, you may still get divergence
due to order of summation issues in other parts of the code, vector
libraries etc. 2) use the serial CPU code, 3) use the GPU code - this is
deterministic for both single and multi-GPU.

The FFT is completely controllable through the ewald namelist - you can
set the FFT dimensions. NFFT1, NFFT2, NFFT3. You can also specify that it
should always use a slab fft instead of switching to columns at a set MPI
task count - see the PMEMD section of the manual.

With more details about what you actually want to do we can try to help

All the best

On 8/4/14, 8:39 AM, "sun" <> wrote:

>I know this is not new, was discussed years back, and is NOT considered a
>problem. But further comments will help us more.
>I think in our case, possible causes are:
>1). order of addition of forces are different due to network
>indeterminacy, and the rounding error causes the difference.
>2). some verion of FFT which has feature of automatic algorithm selection
>depending on network condition is used in PME calculation.
>For 1), we are running with 24 cores on the CPUs of 12 cores each.
>Further comments are appreaciated.
>For 2), can someone describe more or point out where ther FFT source code
>Thank you very much.
>AMBER mailing list

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Received on Mon Aug 04 2014 - 09:30:02 PDT
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