[gmx-developers] omp usage

[Mark Abraham]

Hi,

Such issues are normally related to the value of things like the
OMP_NUM_THREADS environment variable, which different clusters manage
differently. Either adapt your job submission scripts so that they set them
appropriately, or manage such variables directly.

Mark

On Mon, 11 Feb 2019 at 23:27 titov_ai <titov_ai at pnpi.nrcki.ru> wrote:

> Hello.
>
> I've used a gromacs template to create a program for MD trajectory
> analysis.
> Omp threads were used in my code and it (omp) worked fine.
> I've been using gromacs 2016, then updated it for 2019 and omp stopped
> working, the template seems to be the same, but omp stopped working.
> After adding "SET( "CMAKE_CXX_FLAGS "-fopenmp")" it started to work once
> again. Although it should have been enabled through gromacs flags.
> Then another problem popped up. I was testing my code on my laptop with
> 8 therads - worked fine, on stationary computer with 4 therads - fine,
> but when i try to run it on a machine with 40 therads it shows
> unexpected behavior such as: system gives 20 threads for my program,
> while only one running the actual code, then when the code askes for
> threads the system gives another 20, but they are all on one core inside
> the previous main thread.
> I suspect it has something to do with the number of avaliable threads
> and then it has nested therads.
>
> how should i solve this problem ?
>
> Best wishes,
> Anatoly Titov, phd student, PNPI.
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