[gmx-users] Domain decomposition configuration
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 9 22:06:24 CET 2011
Denny Frost wrote:
> 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.
>
I'll venture a guess that there were broken molecules in the system you
concatenated? That would gel with a bond that stretches across a 5-nm box. You
have to deal with whole molecules in the input configuration.
-Justin
> On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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> <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 <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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