Hi, You should start from here:
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Terry On Fri, Jan 6, 2012 at 12:49 PM, Albert <mailmd2...@gmail.com> wrote: > Hello: > I found that each time I would like to increase my nodes for MD run, my > job always failed. it said: > > Will use 192 particle-particle and 64 PME only nodes > This is a guess, check the performance at the end of the log file > > ------------------------------------------------------- > Program mdrun_mpi_bg, VERSION 4.5.5 > Source code file: ../../../src/mdlib/domdec.c, line: 6436 > > Fatal error: > There is no domain decomposition for 192 nodes that is compatible with the > given box and a minimum cell size of > 1.02425 nm > Change the number of nodes or mdrun option -rcon or -dds or your LINCS > settings > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden) > > > Does anybody have any idea for this? here is my scrips for submitting jobs; > # @ job_name = I213A > # @ class = kdm-large > # @ account_no = G07-13 > # @ error = gromacs.err > # @ output = gromacs.out > # @ environment = COPY_ALL > # @ wall_clock_limit = 12:00:00 > # @ notification = error > # @ notify_user = alb...@icm.edu.pl > # @ job_type = bluegene > # @ bg_size = 64 > # @ queue > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v > -s npt.tpr" -mode VN -np 256 > > > if I change the bg_size=32 and -np=128, everything goes well.... > > > THX > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
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