normal How much can I increase the -rdd option in GROMACS?

  • sajjad.ir
  • sajjad.ir's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
1 month 1 week ago #7800 by sajjad.ir
sajjad.ir created the topic: How much can I increase the -rdd option in GROMACS?
Hi,

In the DNA tutorial it is mentioned that this value must kept large (-rdd 2).
I ran a simulation (just a DNA along with another molecule inside a 10 10 10 box) and the system reached the equilibrium state.
But for a larger system (25 25 25), when I use gpu, I constantly getting the error:

"Fatal error:
1 of the 13939 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance..." etc.

I am not sure (please correct me if I am wrong), but it seems that by increasing the number of cores, the cell size decreases and the simulation tends to abort.

So would you please help me in this matter that how much can I increase the rdd?
Is increasing this value significantly affects the final results?

Please Log in or Create an account to join the conversation.

More
1 month 1 week ago #7802 by peterkroon
peterkroon replied the topic: How much can I increase the -rdd option in GROMACS?
Hey,

If I recall correctly -rdd influences (is) the minimum cell size for domain decomposition. So larger -rdd means less possibility of decomposing the system across mpi instances (note that it doesn't affect openmp mulitprocessing).
The final results should not be affected.

Please Log in or Create an account to join the conversation.

Time to create page: 0.087 seconds