Hi All,
As I tried MPI code of the latest AMBER for both the CPU and GPU versions,
energies output from the MPI code start to deviate from those of serial
code after hundreds of MD steps. The energies are so different that they
lead to different temperatures (and probably trajectories) of system:
diff md-1-cpu.out md-1-cpu-mpi.out | grep "NSTEP " | more
< NSTEP = 583 TIME(PS) = 41.166 TEMP(K) = 306.91 PRESS
= 0.0
> NSTEP = 583 TIME(PS) = 41.166 TEMP(K) = 306.90 PRESS
= 0.0
...
< NSTEP = 900 TIME(PS) = 41.800 TEMP(K) = 302.37 PRESS
= 0.0
> NSTEP = 900 TIME(PS) = 41.800 TEMP(K) = 300.97 PRESS
= 0.0
The system I tested was the very small alanine dipeptide (input files are
attached). I would expect the deviation may happen sooner for bigger
systems like proteins. Yes, there could be accumulated rounding errors, but
how do we evaluate whether our MPI simulations are still accurate, with no
errors in the code?
A naive question, but I will appreciate any suggestions ...
Yinglong
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Received on Fri Dec 01 2017 - 09:30:02 PST
