[gmx-developers] MPI crash with ghost molecules

Jason de Joannis jdejoan at emory.edu
Fri Nov 3 15:23:55 CET 2006

Quoting Anton Feenstra <feenstra at few.vu.nl>:

> 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.
That is why I do it just after move_x is called. That way all cpu's 
have all coords. My stuff is repeated on every node. Then the neighbor 
lists are made. The run crashes whether nstlist is 10 or 1.

\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \

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