[gmx-users] number of cores with a large prime factor

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Jan 14 03:26:30 CET 2011

Dear users:

I received this error message that gromacs 4.5.3 does not allow me to  
run on 34 cores. I suggest that this gets put in as a warning (so that  
I can avoid it if I choose and actually run on 34 cores).

A run on 32 cores -npme -1 choose to use 24 particle-particle nodes  
and 8 PME nodes. I therefore selected 34 cores and -nmpe 10. I don't  
see how the large prime factor is relevant when -nmpme is not equal to  

The error message was:

Fatal error:
The number of nodes you selected (34) contains a large prime factor  
17. In most cases this will lead to bad performance. Choose a number  
with smaller prime factors or set the decomposition (option -dd)  
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


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