<div dir="ltr">Hi,<div><br></div><div>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.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 11 Feb 2019 at 23:27 titov_ai <<a href="mailto:titov_ai@pnpi.nrcki.ru">titov_ai@pnpi.nrcki.ru</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello.<br>
<br>
I've used a gromacs template to create a program for MD trajectory <br>
analysis.<br>
Omp threads were used in my code and it (omp) worked fine.<br>
I've been using gromacs 2016, then updated it for 2019 and omp stopped <br>
working, the template seems to be the same, but omp stopped working.<br>
After adding "SET( "CMAKE_CXX_FLAGS "-fopenmp")" it started to work once <br>
again. Although it should have been enabled through gromacs flags.<br>
Then another problem popped up. I was testing my code on my laptop with <br>
8 therads - worked fine, on stationary computer with 4 therads - fine, <br>
but when i try to run it on a machine with 40 therads it shows <br>
unexpected behavior such as: system gives 20 threads for my program, <br>
while only one running the actual code, then when the code askes for <br>
threads the system gives another 20, but they are all on one core inside <br>
the previous main thread.<br>
I suspect it has something to do with the number of avaliable threads <br>
and then it has nested therads.<br>
<br>
how should i solve this problem ?<br>
<br>
Best wishes,<br>
Anatoly Titov, phd student, PNPI.<br>
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