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

--
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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