[gmx-users] Domain decomposition configuration

Denny Frost dsfrost at cableone.net
Wed Feb 9 22:02:07 CET 2011


This run is actually a combination of two 5x5x5 nm boxes, one if which was
previously run in DD, and the other is water.  Since the length of that bond
is almost 5 nm, is it possible that the pbc's are not being recognized?
 There is no way I have a bond that long from my previous run.

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Denny Frost wrote:
>
>> I'm using version 4.5.3
>>
>> Here's the output from the log file from DD initiation to the error:
>>
>> Initializing Domain Decomposition on 8 nodes
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>    two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
>>  multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
>> Minimum cell size due to bonded interactions: 5.382 nm
>>
>
> Bonded interactions should normally not occur over such a length.  The
> information printed here points to the culprits.  What are these atoms, and
> why are they bonded if they are so far away?
>
> -Justin
>
>  Using 0 separate PME nodes
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm
>> The maximum allowed number of cells is: X 0 Y 0 Z 1
>>
>> -------------------------------------------------------
>> Program mdrun_mpi, VERSION 4.5.3
>> Source code file: domdec.c, line: 6428
>>
>> Fatal error:
>> There is no domain decomposition for 8 nodes that is compatible with the
>> given box and a minimum cell size of 6.72787 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>> 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
>>
>> And here is my mdp file
>>
>> title               =  BMIM+PF6
>> cpp                 =  /lib/cpp
>> constraints         =  hbonds
>> integrator          =  md
>> dt                  =  0.002   ; ps !
>> nsteps              =  75000   ; total 150 ps
>> nstcomm             =  10
>> nstxout             =  50000
>> nstvout             =  50000
>> nstfout             =  0
>> nstlog              =  5000
>> nstenergy           =  5000
>> nstxtcout           =  25000
>> nstlist             =  10
>> ns_type             =  grid
>> pbc                 =  xyz
>> coulombtype         =  PME
>> vdwtype             =  Cut-off
>> rlist               =  1.2
>> rcoulomb            =  1.2
>> rvdw                =  1.2
>> fourierspacing      =  0.12
>> pme_order           =  4
>> ewald_rtol          =  1e-5
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl              =  berendsen
>> tc_grps             =  BMI      PF6     SOL tau_t               =  0.2
>>  0.2  0.2
>> ref_t               =  300  300  300
>> nsttcouple          =  1
>> ; Energy monitoring
>> energygrps          =  BMI      PF6     SOL
>> ; Isotropic pressure coupling is now on
>> Pcoupl              =  berendsen
>> pcoupltype          =  isotropic
>> ;pc-grps             =  BMI      PFF
>> tau_p               =  2.0
>> ref_p               =  1.0
>> compressibility     =  4.5e-5
>>
>> ; Generate velocites is off at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  300.0
>> gen_seed            =  100000
>>
>>
>> On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Denny Frost wrote:
>>
>>        I am trying to start a run using domain decomposition on a
>>        5x5x10 nm box with about 26,000 atoms in it.  I've tried running
>>        8-16 pp nodes, but gromacs always throws an error saying that
>>        there is no domain decomposition compatible with this box and a
>>        minimum cell size of 6.728 nm.  I've tried many values for -dds
>>        and a few dd vectors, but with no luck.  Does anyone know to get
>>        domain decomposition working on a rectangular system like this?
>>
>>
>>    Not without significantly more information.  Please post:
>>
>>    1. Your Gromacs version
>>    2. Any DD-related information that is printed to either the log file
>>    or stdout
>>    3. Your .mdp file
>>
>>    -Justin
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> 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
>
> ========================================
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