[gmx-users] RE: shake block problem

[David van der Spoel]

Jianhui Tian wrote:
>> Hi GMX-Users,
>>
>> Does anyone have any idea about the problem? Thanks a lot in advance.
>>
>> I got an error message when using gromacs on 2 processors on the same
>> computer.
>> The error message is like this:
>> _________________________________________________________________
>> splitting topology...
>> Walking down the molecule graph to make shake-blocks
>> There are 24390 charge group borders and 26054 shake borders
>> There are 24390 total borders
>> Division over nodes in atoms:
>>   21234   21234
>> -------------------------------------------------------
>> Program grompp_d, VERSION 3.3
>> Source code file: splitter.c, line: 121
>>
>> Fatal error:
>> Shake block crossing node boundaries
>> constraint between atoms (21226,21234)
>> -------------------------------------------------------
>> ________________________________________________________________
>> I used h-bonds constraints.  I tried not
>> to without constraints and the system can be ran on 2 processors well,
>> but the time-step is small then.
>>
> please submit a bugzilla and upload your input files (top, gro, mdp).
> 
> Hi David,
> 
> There are the mdp file and the errors in the following:

please go to http://bugzilla.gromacs.org and file a bug report.


> The mdp file:
> _________________________________________________________________
> title                    = ps md at 300 K, 1 bar
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   =
> integrator               = md
> tinit                    = 0.0
> dt                       = 0.001
> nsteps                   = 50000
> nstxout                  = 500
> nstvout                  = 500
> nstlog                   = 500
> nstenergy                = 500
> energygrps               = AOTs Cores ICTs
> nstlist                  = 1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> coulombtype              = pme
> rcoulomb                 = 1.0
> vdwtype                  = Cut-off
> rvdw                     = 1.0
> DispCorr                 = no
> tcoupl                   = Berendsen
> tc_grps                  = AOTs Cores ICTs
> tau_t                    = 0.5  0.5  0.5
> ref_t                    = 300.0   300.0 300.0
> pcoupl                   = berendsen
> pcoupltype               = isotropic
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = no
> constraints              = h-bonds
> constraint_algorithm     = shake
> ____________________________________________________
> Errors:
> _________________________________________________________________
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 72x72x72, spacing 0.119 0.119 0.119
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 24210 charge group borders and 25874 shake borders
> There are 24210 total borders
> Division over nodes in atoms:
>   21078   21078
> -------------------------------------------------------
> Program grompp_d, VERSION 3.3
> Source code file: splitter.c, line: 121
> 
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (21070,21078)
> -------------------------------------------------------
> 
> "You Think That You're Bigger When You Fill the Void" (Urban Dance Squad)
> 
> NNODES=2, MYRANK=0, HOSTNAME=compute-3-15.local
> NNODES=2, MYRANK=1, HOSTNAME=compute-3-15.local
> NODEID=1 argc=11
> NODEID=0 argc=11
> _____________
> _________________________________________________________________
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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