[gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box
Seyed Mojtaba Rezaei Sani
s.m.rezaeisani at gmail.com
Wed May 6 09:01:02 CEST 2015
Thanks for your kind response. I didn't notice the point you mentioned. It
seems that grompp doesn't care the difference betwen vdwq and vdw-q.
however, I corrected the script. The error remains even in the case of
choosing 2 nodes. The only way to have a successful run is a serial
calculation. I attach the md.log file to this message. I would appreciate
any help you could provide.
On Tue, May 5, 2015 at 5:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 5/5/15 8:48 AM, Seyed Mojtaba Rezaei Sani wrote:
>> Dear gmx users,
>> Perhaps my problem is a repetitive question in the forum but I couldn't
>> find a trouble-shooter response for my case.
>> I am running a stochastic dynamics calculation for a solution of
>> doxorubicin. The following error occurs while the calculation runs:
>> Fatal error:
>> There is no domain decomposition for x nodes that is compatible with the
>> given box and a minimum cell size of 1.9433 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>> I have tried several numbers of nodes resulting in the same error. Here is
>> the mdp file:
>> integrator = sd
>> nsteps = 1000000
>> dt = 0.002
>> nstenergy = 1000
>> nstlog = 5000
>> ; turn off trajectory writing
>> nstxout = 0
>> nstvout = 0
>> ; cut-offs at 1nm
>> rlist = 1.0
>> nstlist = 10
>> coulombtype = pme
>> vdw-type = cut-off
>> rvdw = 1.0
>> constraints = all-bonds
>> ; set temperature to 300K
>> tcoupl = v-rescale
>> tc-grps = system
>> tau-t = 0.2
>> ref-t = 300
>> ; and pressure to 1 bar
>> pcoupl = parrinello-rahman
>> ref-p = 1
>> compressibility = 4.5e-5
>> tau-p = 5
>> ; and set the free energy parameters
>> free-energy = yes
>> couple-moltype = DOX
>> init-lambda = 0
>> ; these 'soft-core' parameters make sure we never get overlapping
>> ; charges as lambda goes to 0
>> sc-power = 1
>> sc-sigma = 0.3
>> sc-alpha = 1.0
>> ; we still want the molecule to interact with itself at lambda=0
>> couple-intramol = no
> This is what triggers the error. Note from the manual, for
> couple-intramol = no:
> "All intra-molecular non-bonded interactions for moleculetype
> couple-moltype are replaced by exclusions and explicit pair interactions.
> In this manner the decoupled state of the molecule corresponds to the
> proper vacuum state without periodicity effects."
> The added exclusions and pairs require larger DD cells to be constructed
> because these bonded interactions occur over larger distances than normal.
> This limits the size of the DD cells and hence how many processors/cores
> you can use. You haven't said how many you're trying to use, but the
> solution is simply to use fewer.
> couple-lambda1 = vdwq
> The option is "vdw-q" but I don't know if grompp magically translates it.
> Just check.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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Seyed Mojtaba Rezaei Sani
Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tel: +98 21 2310 (3069)
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