[gmx-users] Regarding minimum size

[Justin Lemkul]

On 3/12/18 4:52 PM, Chhavi Yadav wrote:
> I wrote this code and was running the debugger:
>
>
> int main(int argc, char *argv[]) {
>
>
>      int rc;
>      MD mdrunner;
>      rc = mdrunner.mainFunction(argc, argv);
>      printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);
>
>      mdrunner.epot = 0;
>
>      t_state *t = mdrunner.globalState.get();
>      t->x[0][0] = 10.0;
>      t->x[0][1] = 10.0;
>      t->x[0][2] = 10.0;
>
>
>      rc = mdrunner.mainFunction(argc, argv);
>      printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);
>
>      return rc;
>
> }
>
> OUTPUT:
>
> Reading file 1aki/1AKI.tpr, VERSION
> 2018-dev-20180223-a989b355c-dirty-unknown (single precision)
>
> NOTE: disabling dynamic load balancing as it is not supported in reruns.
>
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> No option -multi
> Using 8 MPI threads
> starting md rerun 'LYSOZYME', reading coordinates from input trajectory
> '1aki/1AKI.gro'
>
> Reading frames from gro file 'LYSOZYME;', 1960 atoms.
>
> Reading frame       0 time    0.000
> WARNING: Some frames do not contain velocities.
>           Ekin, temperature and pressure are incorrect,
>           the virial will be incorrect when constraints are present.
>
>
> Last frame          0 time    0.000
>
>                 Core t (s)   Wall t (s)        (%)
>         Time:        0.961        0.120      800.0
>                   (ns/day)    (hour/ns)
> Performance:        0.719       33.377
> Potential Energy from integrator: -8519.961914
>
> NOTE: disabling dynamic load balancing as it is not supported in reruns.
>
>
> -------------------------------------------------------
> Program:     GROMACS, version 2018-dev-20180308-65a7ab86c-dirty-unknown
> Source file: src/gromacs/domdec/domdec.cpp (line 6571)
> MPI rank:    0 (out of 8)
>
> Fatal error:
> There is no domain decomposition for 8 ranks that is compatible with the
> given
> box and a minimum cell size of 5.81734 nm
> Change the number of ranks or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition

The minimum cell size for domain decomposition is a function of the 
topology of the system. A system that requires a minimum cell size of 
5.8 nm is very unusual and suggests atypical topological elements. 
Please see the mailing list archive for possible solutions to this 
error; it comes up frequently and there are more details on 
http://www.gromacs.org/Documentation/Errors?highlight=errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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