[gmx-users] Various questions related to Gromacs performance tuning

[Tobias Klöffel]

Dear all,
I am very new to Gromacs so maybe some of my problems are very easy to fix:)
Currently I am trying to compile and benchmark gromacs on AMD rome cpus, 
the benchmarks are taken from:
https://www.mpibpc.mpg.de/grubmueller/bench

1) OpenMP parallelization: Is it done via OpenMP tasks? If the Intel 
toolchain is detected and  -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is 
used, even though -DGMX_OPENMP=on is set.

2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do 
not really understand what I have to specify for -mdrun. I tried -mdrun 
'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi 
-map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it 
just complains that mdrun is not working.
Normal  execution via $MPIRUN gmx_mpi mdrun -s ... works


3) As far as I understood, most time of PME is spent in a 3d FFT and 
hence probably most time is spent in a mpi alltoall communication. For 
that reason I would like to place all PME tasks on a separate node via 
-ddorder pp_pme. If I do so, the calculations just hangs. Specifying 
-ddorder interleave or cartesian works without problems. Is this a known 
issue?

Kind regards,
Tobias Klöffel

-- 
M.Sc. Tobias Klöffel
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HPC (High Performance Computing) group
Erlangen Regional Computing Center(RRZE)
Friedrich-Alexander-Universität Erlangen-Nürnberg
Martensstr. 1
91058 Erlangen

Room: 1.133
Phone: +49 (0) 9131 / 85 - 20101

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E-mail: tobias.kloeffel at fau.de