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
=======================================================
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
=======================================================
E-mail: tobias.kloef...@fau.de
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
