Re: [gmx-users] not guaranteed to be binary identical ?

[Justin A. Lemkul]

Yun Shi wrote:
Hi all,

I am doing my MD simulations piece by piece, with -maxh and -noappend 
options, so that I can link pieces of trajectories together afterward.

But as I did part0001 with 48 cores, and part0002 with 72 cores, the log 
file told me that:

  #nodes mismatch,
    current program: 72
    checkpoint file: 48

  #PME-nodes mismatch,
    current program: -1
    checkpoint file: 16

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

I do not quite understand what it really means by "binary identical"?

Would this affect my results? In other words, would using different # 
cores for each part give me different conformational assembles from 
using the same # cores each part?


Several resources:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

Thanks for any help!
Yun


--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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