GROMACS version: 5.1.4
GROMACS modification: No
I am trying to run the command
$ gmx mdrun -v -deffnm em
The error I am getting is Fatal error:
The number of ranks you selected (14) contains a large prime factor 7. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually.
Can someone explain where i am going wrong?
Thank you in advance.
You are trying to launch 14=2*7 ranks. As some of the decomposition algorithms do work very efficiently with “large” prime factors, the error message warns you about this are suggests that you either use a different rank count, e.g. by under-utilizing your hardware you can use 12 of the 14 cores if this is faster than the alternative of specifying a manual decomposition using (here that can be
-dd 14 1 1 or
-dd 7 2 1). A third alternative is to simply avoid domain-decomposition at all and use OpenMP parallelization especially if are only trying to use 14 cores (that is
-ntmpi 1 -ntomp 14).
Thank you Szilárd for your suggestion, this solved the problem I was having. Thank you very much for your suggestion :).