On Sat, Apr 11, 2009 at 10:52 PM, Joe Joe <[email protected]> wrote: > Hi Justin, > Thanks for helping me with this. > > On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <[email protected]> wrote: >> >> >> Joe Joe wrote: >>> >>> How do I determine what those values should be? How does it affect the >>> simulation? >>> >> >> The header of your log file should have printed what the initial guesses >> were. The -dd option sets how many PP nodes there are in the domain >> decomposition; using 4 cores, there are probably 3 PP: 1 PME, so you >> probably can't tweak this option, really. > > I do not get it. the input to -dd is a vector. What to the elements of the > vector represent?
WIth the dd option you give the number of nodes in the 3 dimensions. The product of the three number + the npme number has to be equal to the total number. Look at the parallelization chapter of the manual. >> >> The -rcon option is explained in mdrun -h or the manual. See what mdrun >> guessed, then increase this value. > > I tried -rcon 3.0 and got the same error. The error only occurs when I do > the exchange. If I increase the replex from 500 to 1000 then I do not see > the error for 1000 steps. How is the replex associated with the domain > decomposition? It shouldn't be. It is probably only a statistically difference you see. So if you let run longer with replex 1000 you will see it too. Roland >> >> -Justin >> >>> thanks, >>> >>> Ilya >>> >>> On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> >>> >>> Joe Joe wrote: >>> >>> Hi All, >>> >>> I get the following error when running replica exchange. I have >>> 32 replica's with each replica running on 4 processors (128 >>> total). How do I decrease the domain decomposition cell size, >>> -dss? What should I set it to? >>> >>> >>> <snip> >>> >>> You're getting some hints from mdrun, I'd start there: >>> >>> >>> ------------------------------------------------------- >>> Program mdrun_mpi, VERSION 4.0.4 >>> Source code file: domdec_con.c, line: 679 >>> >>> Fatal error: >>> DD cell 5 0 0 could only obtain 96 of the 108 atoms that are >>> connected via vsites from the neighboring cells. This probably >>> means your vsite lengths are too long compared to the domain >>> decomposition cell size. Decrease the number of domain >>> decomposition grid cells or use the -rcon option of mdrun. >>> ------------------------------------------------------- >>> >>> >>> ...So manually set -dd and/or -rcon. >>> >>> -Justin >>> >>> -- ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> http://www.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 [email protected] >>> <mailto:[email protected]>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
