> Dear gmx-users, > > Would you mind giving me some instruction on this. > > I am learning Gromacs tutorial #1 of mdtutotials.com. However to the 5th > step: EM, http://www.mdtutorials.com/gmx/lysozyme/05_EM.html > I got the error: > "Domain decomposition does not support simple neighbor searching, use grid > searching or run with one MPI rank"
Did you use the .mdp file in the tutorial (http://www.mdtutorials.com/gmx/lysozyme/Files/minim.mdp)? You can see that the "ns-type" (neighbor search type) parameter is set to "grid" in that file. Whatever you had in your .mdp file set the ns-type to "simple", which does not support domain decomposition and thus cannot be run on more than one thread. Best, John > > Running on 1 thread of PC by changing from > gmx mdrun -v -deffnm em > to > gmx mdrun -nt 1 -s -v -deffnm em > gives no problem but it's too slow, (50k steps, 2seconds/1step) > > Thank you very much for your kind helps, > Best regards, > > The full log is as follows > ------------------------------------------------------------------------------------- > GROMACS: gmx mdrun, VERSION 5.1.1 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Command line: > gmx mdrun -s -deffnm em > > Back Off! I just backed up em.log to ./#em.log.33# > > Running on 1 node with total 12 cores, 24 logical cores > Hardware detected: > CPU info: > Vendor: GenuineIntel > Brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz > SIMD instructions most likely to fit this hardware: SSE4.1 > SIMD instructions selected at GROMACS compile time: SSE4.1 > > Reading file em.tpr, VERSION 5.1.1 (single precision) > ------------------------------------------------------- > Program gmx mdrun, VERSION 5.1.1 > Source code file: > /home/nguyenduyvy/Downloads/gromacs-5.1.1/src/gromacs/domdec/domdec.cpp, > line: 6542 > > Fatal error: > Domain decomposition does not support simple neighbor searching, use grid > searching or run with one MPI rank > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------------------------------------- > > Yours sincerely, > Nguyen Duy Vy > -- > 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. > -- 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.