[gmx-developers] EM with gmx4.0.2

[Berk Hess]

Hi,

The log file says:

Initial maximum inter charge-group distances:
    two-body bonded interactions: 5.894 nm
  multi-body bonded interactions: 5.894 nm
Minimum cell size due to bonded interactions: 6.483 nm
Using 8 separate PME nodes
Optimizing the DD grid for 8 cells with a minimum initial size of 6.483 nm
The maximum allowed number of cells is: X 2 Y 2 Z 1

-------------------------------------------------------
Program mdrun, VERSION 4.0
Source code file: /data/pckr59/hessb/gmx4.0/src/mdlib/domdec.c, line: 5651

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the 
given b
ox and a minimum cell size of 6.48325 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
-------------------------------------------------------

Thus you have bonded interactions over an enormous distance (5.9 nm).
Thus you can not run the system of more than 4 (2x2) nodes.

The fastest you can get is: mpirun -np 8 mdrun -npme 4
(for better performance you should decrease the relative pme load)

I assume that this is only an initial structure problem, since you can run
md without problems.

I will remove the confusing 0 grid error message for 4.0.3.

Berk


andrea spitaleri wrote:
> Hi there,
> we having trouble in EM using gmx-4.0.2. Basically the problem is that the run crash immediately
> complaining about the number of separate PME:
>
>   
>> mdrun -s box -v -deffnm boxem
>>     
>
> Program mdrun, VERSION 4.0.2
> Source code file: domdec_setup.c, line: 132
>
> Fatal error:
> Could not find an appropriate number of separate PME nodes. i.e. >= 0.727885*#nodes (11) and <=
> #nodes/2 (8) and reasonable performance wis
> e (grid_x=88, grid_y=88).
> Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the
> manual for details.
>
> while:
>
>   
>> mdrun -s box -npme 8 -v -deffnm boxem
>>     
> gives:
> Program mdrun, VERSION 4.0.2
> Source code file: domdec.c, line: 5860
>
> Fatal error:
> The size of the domain decomposition grid (0) does not match the number of nodes (8). The total
> number of nodes is 16
>
> We are able to minimize the system using gmx-3.3.3 and then run the MD with gmx-4.0.2 without troubles.
> our em.mdp is:
>
> define              =  -DFLEXIBLE
> integrator          =  steep
> dt                  =  0.002    ; ps
> nsteps              =  2000
> nstlist             =  5
> ns_type             =  grid
> pbc                 =  xyz
> rlist               =  0.9
> table-extension     =  2
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing      =  0.15
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft              =  yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000
> emstep              =  0.01
> lincs_iter          = 4
>
>
> any help is well accepted.
>
> thanks in advance
>
> andrea
>
>