[gmx-users] Exceeding of Maximum allowed number of DD cells

Chao Zhang c.zhang at grs-sim.de
Sun Jan 10 16:24:19 CET 2010

Dear GMX-Users,

I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out the right number for "-npme", as mdrun can not estimate itself successfully.

I met the problem that how to match the maxinum allowed number for DD cells with large number of CPU cores.

My simulation box size  is about 8x8x9nm^3, with normal LINCS parameter and dds=0.8. The log file said that the maximum allowed number of DD cells is 8x8x9.

As far as I understand, DD assigns one core to one cell, so the maximum core I can use in this case for PP part is 8x8x9=576 cores.

I then ran with 512 cores with -npme=128. My system runs without problem.

What if I want to use more cores?

Then I try to increase the "-dds" from 0.8 to 0.9, this leads to an increasing of "the maximum allowed number of DD cells" to  8x10x10. 

This time is 1024 cores in total and I set -npme=224, then PP part will have 800 cores which are within 10x10x10.

The system ran initially but corrupted very soon with warning that "DD cell 2 1 4 could on obtain 56 of the 57 atoms that are connected via constraints from the neighboring cells ...."

Therefore the dilemma is if I increase the "-dds", I can meet the requirement for the maximum allowed number of DD cells, but fail the maximum length of constraints in LINCS.

Does it mean that for a relative small system, it is not possible to using up to thousand of cores by domain decomposition?

I know that if it makes more sense to use thousand of cores for huge system, but if my purpose is simply to speed up the simulation, what should I do?

Thank you.


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