<br><br><div class="gmail_quote">On Mon, Jun 28, 2010 at 4:32 AM, Carsten Kutzner <span dir="ltr"><<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</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">On Jun 28, 2010, at 10:23 AM, <a href="mailto:hess@sbc.su.se">hess@sbc.su.se</a> wrote:<br>
<br>
> Hi,<br>
><br>
> But does dlb get turned on at some point without -dlb?<br>
><br>
</div>Apparently not, at least not in the runs I just looked at.<br></blockquote><div><br></div><div>Does it crash immediately or after many steps?</div><div>If it is the later one: often it is possible to make it reproducible crash by setting GMX_DLB_FLOP to 1.</div>
<div><br></div><div>Roland</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Carsten<br>
<div><div></div><div class="h5"><br>
> Berk<br>
><br>
>> Hi,<br>
>><br>
>> there appears to be an issue with the -dlb flag when turned on<br>
>> from the very beginning in mdrun. For at least two different<br>
>> MD systems (incl. dppc with PME) I get errors like<br>
>><br>
>> Fatal error:<br>
>> 248 particles communicated to PME node 3 are more than 2/3 times the<br>
>> cut-off out of the domain decomposition cell of their charge group in<br>
>> dimension y.<br>
>><br>
>> when started with<br>
>> mpirun -np 4 mdrun -s ../tpr/ap_1ps.tpr -dlb yes.<br>
>><br>
>> With -dlb no everything works fine.<br>
>><br>
>> Carsten<br>
>><br>
>> --<br>
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>><br>
><br>
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<br>
<br>
</div></div>--<br>
Dr. Carsten Kutzner<br>
Max Planck Institute for Biophysical Chemistry<br>
Theoretical and Computational Biophysics<br>
Am Fassberg 11, 37077 Goettingen, Germany<br>
Tel. +49-551-2012313, Fax: +49-551-2012302<br>
<a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne" target="_blank">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>