I'm using version 4.5.3<div><br></div><div>Here's the output from the log file from DD initiation to the error:</div><div><br></div><div><div>Initializing Domain Decomposition on 8 nodes</div><div>Dynamic load balancing: auto</div>
<div>Will sort the charge groups at every domain (re)decomposition</div><div>Initial maximum inter charge-group distances:</div><div> two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996</div><div> multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997</div>
<div>Minimum cell size due to bonded interactions: 5.382 nm</div><div>Using 0 separate PME nodes</div><div>Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25</div><div>Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm</div>
<div>The maximum allowed number of cells is: X 0 Y 0 Z 1</div><div><br></div><div>-------------------------------------------------------</div><div>Program mdrun_mpi, VERSION 4.5.3</div><div>Source code file: domdec.c, line: 6428</div>
<div><br></div><div>Fatal error:</div><div>There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.72787 nm</div><div>Change the number of nodes or mdrun option -rdd or -dds</div>
<div>Look in the log file for details on the domain decomposition</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div>
<div><br></div><div>And here is my mdp file</div><div><br></div><div><div>title = BMIM+PF6</div><div>cpp = /lib/cpp</div><div>constraints = hbonds</div><div>integrator = md</div>
<div>dt = 0.002 ; ps !</div><div>nsteps = 75000 ; total 150 ps</div><div>nstcomm = 10</div><div>nstxout = 50000</div><div>nstvout = 50000</div><div>
nstfout = 0</div><div>nstlog = 5000</div><div>nstenergy = 5000</div><div>nstxtcout = 25000</div><div>nstlist = 10</div><div>ns_type = grid</div><div>
pbc = xyz</div><div>coulombtype = PME</div><div>vdwtype = Cut-off</div><div>rlist = 1.2</div><div>rcoulomb = 1.2</div><div>rvdw = 1.2</div>
<div>fourierspacing = 0.12</div><div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>; Berendsen temperature coupling is on in two groups</div><div>Tcoupl = berendsen</div><div>
tc_grps = BMI PF6 SOL </div><div>tau_t = 0.2 0.2 0.2</div><div>ref_t = 300 300 300</div><div>nsttcouple = 1</div><div>; Energy monitoring</div><div>energygrps = BMI PF6 SOL</div>
<div>; Isotropic pressure coupling is now on</div><div>Pcoupl = berendsen</div><div>pcoupltype = isotropic</div><div>;pc-grps = BMI PFF</div><div>tau_p = 2.0</div><div>
ref_p = 1.0</div><div>compressibility = 4.5e-5</div><div><br></div><div>; Generate velocites is off at 300 K.</div><div>gen_vel = yes</div><div>gen_temp = 300.0</div><div>gen_seed = 100000</div>
<div><br></div></div><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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?<br>
<br>
</blockquote>
<br></div>
Not without significantly more information. Please post:<br>
<br>
1. Your Gromacs version<br>
2. Any DD-related information that is printed to either the log file or stdout<br>
3. Your .mdp file<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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