[gmx-users] NTMPI / NTOMP combination: 10 threads not "reasonable" for GROMACS?

Stéphane Téletchéa stephane.teletchea at univ-nantes.fr
Wed Mar 20 22:52:03 CET 2019

Dear all,

I am wondering why i am getting this error message while launching 
GROMACS (2016.6 for instance):

"NOTE: Your choice of number of MPI ranks and amount of resources 
results in using 10 OpenMP
threads per rank, which is most likely inefficient. The optimum is 
usually between 2 and 6 threads per rank."

The node I am trying to compute on is:


Running on 1 node with total 20 cores, 40 logical cores, 2 compatible GPUs
Hardware detected:
   CPU info:
     Vendor: Intel
     Brand:  Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
     SIMD instructions most likely to fit this hardware: AVX2_256
     SIMD instructions selected at GROMACS compile time: AVX2_256

   Hardware topology: Basic
   GPU info:
     Number of GPUs detected: 2
     #0: NVIDIA Tesla P100-PCIE-12GB, compute cap.: 6.0, ECC: yes, stat: 
     #1: NVIDIA Tesla P100-PCIE-12GB, compute cap.: 6.0, ECC: yes, stat: 


Those CPUs are 10 cores +HT (so not 4 or 6). Is it only a warning.

I have tried to launch mdrun using -ntmpi 4 (1 per CPU, 1 per GPU) 
-ntomp 10 but I'm not really
"sure" of what should be used in this situation.

Any clarification / precision appreciated (and I am aware of Best Bang 
for your bucks if that matters :-).



Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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