[gmx-users] Biomolecule shuffling in parallel runs crash MD
nitramus at hypnos.chem.pg.gda.pl
Thu Dec 19 15:11:34 CET 2002
Problem is as follows:
I have a system with one protein neutralized with ions and solvated in
water box. I runned it for a total 1ns of MD on 16 cpu cluster. Recently i
tried to start it on 32 cpus ('cos i have scali mpi and scaling on 32 is
acceptable, approx. 60%). Unfortunatelly i always had an error regarding
LINCS warnings and terminating the simulation. The facts I observed:
1. Division over CPUs is like 1 protein on 1 cpu and some waters, plus
rest of the water on other cpus (shuffle and sort used): no problem,
simulation goes fine.
2. Division over CPUSs is like 1 protein and 0 waters (when you use more
cpus), plus rest of the water on other cpus (shuffle and sort used): MD
crash after first step (LINCS warnangle warnings).
3. Turning off shuffle and sort does't work. MD also crash.
So to choose maximum allowable number of CPUs i have to make trial&error
runs of grompp and select MD where at least some waters "accompany"
protein on the same CPU.
Have anybody encountered somethig similar?
I runned "homogenous systems" like dppc benchmark up to 64 CPUs and it was
My protein system was after 1 ns so i assume it's equilibriated enough.
Best regards, Martin.
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