On 11 Sep 2014, at 05:03, Johnny Lu <johnny.lu...@gmail.com> wrote: > Does writing frequently (like position, velocity, energy, log every 10 > timesteps) significantly slow down the simulation? Probably yes, have a look at the md.log output file and how much percent is spent in write traj.
Carsten > > On Wed, Sep 10, 2014 at 10:31 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > >> tried that, and the result was: >> >> Reading file npt.tpr, VERSION 5.0.1 (double precision) >> Changing nstlist from 10 to 40, rlist from 1 to 1.028 >> >> The number of OpenMP threads was set by environment variable >> OMP_NUM_THREADS to 48 >> Using 1 MPI thread >> Using 48 OpenMP threads >> >> WARNING: Oversubscribing the available 24 logical CPU cores with 48 >> threads. >> This will cause considerable performance loss! >> >> ------------------------------------------------------- >> Program mdrun_d, VERSION 5.0.1 >> Source code file: >> /export/data1/kho/software/gromacs5.1/gromacs-5.0.1/src/gromacs/mdlib/nbnxn_search.c, >> line: 2577 >> >> Fatal error: >> 48 OpenMP threads were requested. Since the non-bonded force buffer >> reduction is prohibitively slow with more than 32 threads, we do not allow >> this. Use 32 or less OpenMP threads. >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> >> so. i guess that is not a good idea. >> >> On Wed, Sep 10, 2014 at 9:55 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: >> >>> that 8-20% performance increase was for gromacs 4.6.5 >>> >>> On Wed, Sep 10, 2014 at 9:52 PM, Johnny Lu <johnny.lu...@gmail.com> >>> wrote: >>> >>>> Is it a good idea to use 48 OpenMP thread, under 1 MPI thread on 24 Xeon >>>> Processors? >>>> >>>> The mail list say such practice give about 8-20% performance increase >>>> >>>> Should I try g_tune_pme when I searched for "imbalance" in the log file >>>> and found nothing (24 OMP thread under 1 MPI thread on 24 Xeon Processor)? >>>> Or is that done automatically? >>>> >>>> Does gromacs support double precision calculation on GPU if the hardware >>>> supports that? >>>> >>>> The optimize fft option is also obsolete. >>>> >>>> Thanks again. >>>> >>> >>> >> > -- > 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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.