GROMACS version: 5.1.4
i used this command for my ＭＤ simulation box set up
gmx_mpi editconf -f filename.pdb -o filename.pdb -d 1.2
after checking my log files, i noticed this error
DD load balancing is limited by minimum cell size in dimension Y
Does this means my MD performance is affected or should i ignore this error. how to fix these kinds of issues in the future.
This error means my MD result is not reliable anymore?
The domain decomposition dynamic load balancer tries to equalize the time computation takes on each MPI rank during the run and it does so by scaling the size of the domains by shrinking domains with more work (e.g. higher particle density, more bonded interactions). The amount of scaling possible has certain algorithmic limitations (which you’ll find in the log file file section following the “Initializing Domain Decomposition on N ranks” message.
In runs that display this warning there is sufficient load imbalance that for the given decomposition the load balancer runs into domain size limitations and can not scale a/some domains further.
This will only affect performance. By how much that’s estimated in the log, at the end of the run in the DLB report. Whether you can recover that depends on many factors including your simulation system, hardware, and run setup. A few simple things you can try:
- first: make sure that your run scales to the number of CPUs you are trying to use i.e. that your run is not slower than with half the number of resources;
- reduce the total number of ranks (decomposition into fewer domains allows these to be larger → more room for scaling); you can do so e.g. by using more threads per rank
- change the decomposition to use fewer domain in the dimension that DLB is limited in; e.g. if your automatic decomposition chooses 8x8x2, you can try 16x4x2 (see the
mdrun -dd N M K option)