Hello Justin, I forgot to say that with 16 nodes I am getting message below. I search the list and used -pd option but it takes much much loner than one processor!
------------------------------------------------------- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 4.56121 nm Change the number of nodes or mdrun option -rdd 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 ------------------------------------------------------- On 24 February 2011 16:21, Justin A. Lemkul <[email protected]> wrote: > > > Nick wrote: > >> Hello all, >> >> When I issue mdrun program for EM altough this is not a parallel >> simulation, 6 nodes are getting involved. >> >> I am using 4.5.3 and get the error: >> >> Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision) >> Starting 16 threads >> >> Does anyone have idea why is this happening? >> >> > mdrun now uses thread-based parallelization by default, using all available > nodes. To suppress this effect, use mdrun -nt 1. Otherwise, yes, it is a > parallel calculation :) > > -Justin > > Thanks >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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