<div>Hi,</div><div><br></div>4.5beta compiled without MPI uses by defaults all cores using threads. You can run it with "mdrun -nt 1" to run only on one core and thus avoid parallelization errors. Why the minimum cell size is 6.6nm (which is huge) I'm not sure. It should write in the log file why mdrun computed the minimum cell size to be that big.<div>
<br></div><div>Roland<br><br><div class="gmail_quote">On Wed, Aug 25, 2010 at 10:35 PM, zhongjin <span dir="ltr"><<a href="mailto:zhongjin1000@yahoo.com.cn">zhongjin1000@yahoo.com.cn</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit"><div><font style="background-color:#cce8cf">Hi,</font></div>
<div><font style="background-color:#cce8cf"> I am doing a minimization in GMX 4.5-beta3. The system includes 256 DPPC and 9899 SOL. I used a command:</font></div>
<div> mdrun -v -deffnm min </div>
<div>Then an error occured,</div>
<div>Program mdrun_mpi, VERSION 4.5-beta3<br>Source code file: domdec.c, line: 6428</div>
<div>Fatal error:<br>There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.62125 nm<br>Change the number of nodes or mdrun option -rdd<br>Look in the log file for details on the domain decomposition<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------</div>
<div> </div>
<div>And then I try another command :</div>
<div> mpiexec -n 8 mdrun_mpi -deffnm min </dev/null</div>
<div>The same error occured.</div>
<div> </div>
<div> What's wrong? I have never come across such a error in GMX 4.0.7. Anybody could help me ? Thanks!</div>
<div> Zhongjin He </div></td></tr></tbody></table><font color="#888888"><br>
</font><br>--<br>
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