[gmx-developers] Regression test GmxapiMpiTests fails for GROMACS 2020.1

[Christoph Pospiech]

Hi,

the regression test GmxapiMpiTests fails for GROMACS 2020.1 when run on a node 
with more than 12 (virtual) cores. Apparently, the test is run with two MPI 
ranks and chooses the number of threads to fill up the available resources.

The error message is the following.

On host cmp2645.hpc.eu.lenovo.com 2 GPUs selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
  PP:0,PP:1
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 2 MPI processes

Non-default thread affinity set, disabling internal thread affinity

Using 32 OpenMP threads per MPI process


-------------------------------------------------------
Program:     gmxapi-mpi-test, version 2020.1-dev-20200407-9b056e2-unknown
Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 626)
MPI rank:    0 (out of 2)

-------------------------------------------------------
Program:     gmxapi-mpi-test, version 2020.1-dev-20200407-9b056e2-unknown
Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 626)
MPI rank:    1 (out of 2)

Fatal error:
Your choice of number of MPI ranks and amount of resources results in using 32
OpenMP threads per rank, which is most likely inefficient. The optimum is
usually between 2 and 6 threads per rank. If you want to run with this setup,
specify the -ntomp option. But we suggest to change the number of MPI ranks.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
[repeated for the other rank]

Trying to set OMP_NUM_THREADS to a fixed value < 6 fails other tests, such as
MdrunMpiCoordinationTestsOneRank
MdrunMpiCoordinationTestsTwoRanks

Please advise! Thanks!
-- 
Dr. Christoph Pospiech
Senior HPC & AI Performance Engineer

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E cpospiech at lenovo.com

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