> Am 26.03.2020 um 17:00 schrieb Tobias Klöffel <tobias.kloef...@fau.de>: > > Hi Carsten, > > > On 3/24/20 9:02 PM, Kutzner, Carsten wrote: >> Hi, >> >>> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel <tobias.kloef...@fau.de>: >>> >>> 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? >> Yes, all over the code loops are parallelized via OpenMP via #pragma omp >> parallel for >> and similar directives. > Ok but that's not OpenMP tasking:) >> >>> If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is >>> set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. >> GROMACS uses only the serial transposes - allowing mkl to open up its own >> OpenMP threads >> would lead to oversubscription of cores and performance degradation. > Ah I see. But then it should be noted somewhere in the docu that all FFTW/MKL > calls are inside a parallel region. Is there a specific reason for this? > Normally you can achieve much better performance if you call a threaded > library outside of a parallel region and let the library use its own threads. >>> 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 >> Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call >> gmx tune_pme. Most queueing systems don't like it if one parallel program >> calls >> another parallel program. >> >>> 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. >> There should be an output somewhere with the exact command line that >> tune_pme invoked to test whether mdrun works. That should shed some light >> on the issue. >> >> Side note: Tuning is normally only useful on CPU-nodes. If your nodes also >> have GPUs, you will probably not want to do this kind of PME tuning. > Yes it's CPU only... I will tune pp:ppme procs manually. However, most of the > times it is failing with 'too large prime number' what is considered to be > 'too large'? I think 2, 3, 5, 7, 11, and 13 and multiples of these are ok, but not larger prime numbers. So for a fixed number of procs only some of the combinations PP:PME will actually work. The ones that don't work would not be wise to choose from a performance point of view.
Best, Carsten -- 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.
