[gmx-developers] MPI crash with ghost molecules

[Anton Feenstra]

Jason de Joannis wrote:
> I start with a 128 DPPC bilayer. I also have 128 D8PC which I turn off 
> at the beginning of the simulation. When I say 'turn off' I mean that 
> the atom types are set to 13 (same as HW) and the charges are zeroed. 
> Therefore these molecules will only experience their own intramolecular 
> forces and will not exert any influence on the system. They are probably 
> absent from the neighbor lists too right?
> 
> Now. During the simulation (in between move_x and ns) I pick a DPPC 
> molecule and turn it off while turning on a corresponding D8PC molecule. 
> The D8PC coordinates and velocities are mapped onto those of the 
> outgoing DPPC.
> 
> This is successful in single-thread runs but fails in MPI np=2 mode. For 
> example after such a conversion on step 50, the LINCS constraints diverge.
> 
> Any thoughts?

How are the coordinates of both molecules (in- and out-going) coupled?
If you copy over the coordinates (or something similar), but they end up 
on different CPU's in MPI, you may be reading the wrong data because not 
all CPU's have all coordinates all the time.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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