Re: [gmx-users] Tabulated potentials and performance
>From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something like 50. The total table size for the critical point can depend on the hardware condition. Lanyuan On Mon, Jul 19, 2010 at 1:49 PM, ms wrote: > On 19/07/10 18:32, Da-Wei Li wrote: > >> I remember the manu states that it won't cost too much compared with >> standard potential function form. >> > > Well, I find in the manual exactly the opposite: > "Note that table lookup is significantly slower than computation of the most > simple Lennard-Jones and Coulomb interaction." (p.133) > > But I am already using tables for most nonbonded interactions and the > performance is OK. What I would like to know is, if I increase the *number > of tables* (keeping the number of particles/interactions the same, but, say, > using two tables where I used only one before), is it going to be > significantly worse or not? > > thanks! > > m. > > > dawei >> >> On Mon, Jul 19, 2010 at 1:22 PM, ms wrote: >> >>> On 19/07/10 17:32, Da-Wei Li wrote: >>> It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. >>> >>> Well, that's exactly what I tabulate. >>> >>> dawei On Mon, Jul 19, 2010 at 12:22 PM, mswrote: > > Hi, > > Do you know where can I find some information on how using tabulated > potential affects gmx performance, and how? I have to decide how to > project > a custom model but I don't want to calculate dozens of tables only to > find > that gmx grinds to a halt. > > thanks! > M. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replica exhange - no. of processors
No. For GMX4 each replica can be run on multiple processors. Lanyuan On Mon, Jul 19, 2010 at 10:36 AM, Sai Pooja wrote: > Hi, > > I would like to know if the Number_of_processors must be = > Number_of_replicas? > > Regards > Pooja > > -- > Quaerendo Invenietis-Seek and you shall discover. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Wrong pressure with "mdrun -rerun" option
Hi Mark, Thanks for your reply. Yes, I did save velocities in the same frequency as positions. And the length of two compared trajectories are exactly the same. I think I've figured it out and I did looked at the average values as the output of the g_energy. It seems the number 545.384 from the original MD edr file is incorrect. I opened the xvg file in xmgrace and found the average pressure should be 1153.22, which is close to the rerun result. I used the command "g_energy -f *.edr -o *.xvg" to dump the pressure from two edr files and found both of the two xvg files have time from 0 ps to 200 ps with 201 frames. I also found for each time step the pressure values are close for the two files. Therefore, I don't understand why I got the incorrect average pressure from the original edr output, while the rerun output was correct. Another test I did was to type "g_energy -f *.edr -o *.xvg -b 100" to get the last 100 ps results. And this time the average number from the original edr file is still incorrect. However, just as in the whole 200 ps case, I can get the right number if I manually calculate the average from the xvg file. Lanyuan - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Thursday, July 23, 2009 7:55 PM Subject: Re: [gmx-users] Wrong pressure with "mdrun -rerun" option LuLanyuan wrote: Hello all, From the notes for gmx 4.0.5, the pressure and virial from "-rerun" should be correct. However, I did a test for a box of tip3p water and found the pressure results from rerun were different compared to the original results. For the first MD simulation , I simulated it for 200 ps and use the neighbor list update frequency 1. I used "g_energy" to extract pressure results and the results were 545.384 and 1153.55 bars for the MD and rerun, respectively. The gromacs version is 4.0.5. Did you save velocities suitably? Did your primary mdrun include an equilibration period that the rerun did not? Are you quoting average pressures? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
