[gmx-developers] odd resource-division behaviour gromacs git master

Berk Hess hess at kth.se
Mon Aug 28 16:29:16 CEST 2017


This is due to the recent commit 795ad1f8
We'll fix it. Thanks for reporting this.



On 2017-08-28 15:42, Johannes Wagner wrote:
> Hey all,
> I have an odd behaviour of how threads are divided between OMP and MPI 
> for gromacs 2017 git master (25.08.).
> Following setup: CentOS 7, 2x8core Xeon *v4*, HT enabled, *1x1080* GPU 
> and compiling with gcc 4.8.5, -DGMX_GPU=ON, hwloc installed
> If I run something CPU only with -nb cpu , it picks 1 MPI x 32 OMP 
> threads and I get the following fatal error:
> Fatal error:
> Your choice of 1 MPI rank and the use of 32 total threads leads to the 
> use of
> 32 OpenMP threads, whereas we expect the optimum to be with more MPI ranks
> with 1 to 6 OpenMP threads. If you want to run with this many OpenMP 
> threads,
> specify the -ntomp option. But we suggest to increase the number of 
> MPI ranks
> (option -ntmpi).
> If I run the same system with CPU+GPU, it picks 1 MPI x 32 OMP threads 
> and works.
> If I do the exact same on a 2x8 core Xeon *v3*, HT enabled, *2xTitanX* 
> GPU, also compiling with -DGMX_GPU=ON. Running this with or without 
> -nb cpu gives 8 MPI x 4 OMP and works. No errors.
> Compiling gromacs with -DGMX_GPU=OFF gives for both machines 32 MPI x 
> 1 OMP threads and is working.
> Does anyone have a clue what causes the different behaviour on the 2 
> machines? Is it single vs. dual gpu? And moreover why do I get that 
> fatal error? And why is there a different MPI/OMP configuration 
> depending on compiling with or without gpu support, but in both cases 
> running on cpu only?
> I did not file a bug report on redmine, but could also do. Any hints 
> appreciated!
> cheers, Johannes

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