On 9/4/16 2:52 PM, Atila Petrosian wrote:
Dear Justin, Thanks for your good guidance (There is only one program now.). My previous problem was solved. Now, I have another question. I used two times following commands for my system (protein): gmx_mpi mdrun -v -deffnm npt >& npt_1.job & gmx_mpi mdrun -nb gpu -v -deffnm npt >& npt_2.job & In both cases, run will finish Mon Sep 5 06:33:19 2016 (same time). Run on gpu should faster than that on cpu. Why is not it for me? How to find mdrun run on gpu or cpu?
The default for the -nb option is "auto" so if there is a GPU, mdrun will find it and use it. So probably both of your runs are doing the same thing. Of course, reading the .log file will tell you exactly what mdrun is doing and why it is doing it.
Also relevant is http://www.gromacs.org/Documentation/Acceleration_and_parallelization
If you want specific help about why you're observing some given speed/performance, you need to provide actual details about the simulated system, hardware, etc. and upload full .log files to a file-sharing service (e.g. pastebin) and provide a URL.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
