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<div class="moz-cite-prefix">Hi,<br>
<br>
I think the hidden mdrun option -ddbondcomm should solve your
issues. Then the communication should always work up to 2x2x2.<br>
I don't know why I made this option hidden. We should probably
make this a normal option. We could also hint at the option in the
error message you quote.<br>
<br>
What will also help with your issue is the Verlet scheme. I
uploaded change <a class="moz-txt-link-freetext" href="https://gerrit.gromacs.org/#/c/2775/">https://gerrit.gromacs.org/#/c/2775/</a> which adds
support for LJ shift (through vdw-modifier=Force-switch) to the
Verlet scheme. This will make Martini run twice as fast and allows
you to use OpenMP only parallelization on a single node (which is
like PD, bu faster). On multiple nodes you can run MPI+OpenMP
parallelization, which will allow you to run less domains and
avoid the issue in many cases. Note that I have not (and will not)
implement shift functions for Coulomb, but I heard from Groningen
that reaction-field should work OK with Martini.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 11/18/2013 09:59 PM, XAvier Periole wrote:<br>
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<blockquote cite="mid:67042FD3-CD49-40CB-BB3C-E568E6703E76@rug.nl"
type="cite">
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<div>Dears,</div>
<div><br>
</div>
<div>Following on the issue of long range bonded terms preventing
the use of DD and before fixed using PD. </div>
<div><br>
</div>
<div>We have looked into the groupcoord.c solution but are
currently stuck. Our idea was to supplement at each step the
local atom list of each node with the atoms involved in those
long range bonded terms (total of six atoms). We have bypassed
the check on the minimum DD box size (15 nm) by forcing the code
to take the decomposition we choose. Here 2x2x2. </div>
<div><br>
</div>
<div>Of course now mdrun crashes when getting to calculate those
long range bonded interactions and complains that they are
missing. The error message is given bellow. We have trouble
finding where exactly the code determines which coordinates to
communicate to each domain. </div>
<div><br>
</div>
<div>Any suggestion or hint would be greatly appreciated.</div>
<div><br>
</div>
<div>XAvier and Manel.</div>
<div><br>
</div>
<div>…</div>
<div><span style="font-family: 'courier new', monospace; ">A list
of missing interactions:</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">
Bond of 60636 missing 1</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">
Improper Dih. of 12 missing 2</span><br
style="font-family: 'courier new', monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Molecule
type 'rhodimmer'</span><br style="font-family: 'courier new',
monospace; ">
<span style="font-family: 'courier new', monospace; ">the first
10 missing interactions, except for exclusions:</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">
Improper Dih. atoms 117 423 279 1066 global 117 423
279 1066</span><br style="font-family: 'courier new',
monospace; ">
<span style="font-family: 'courier new', monospace; ">
Bond atoms 279 1066 global 279 1066</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">
Improper Dih. atoms 279 1066 1210 904 global 279 1066
1210 904</span><br style="font-family: 'courier new',
monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">-------------------------------------------------------</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Program
mdrun, VERSION 4.6.3</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Source
code file: /src/gromacs-4.6.3/src/mdlib/domdec_top.c, line:
393</span><br style="font-family: 'courier new', monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Fatal
error:</span><br style="font-family: 'courier new', monospace;
">
<span style="font-family: 'courier new', monospace; ">3 of the
103492 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body
cut-off distance (1.4 nm) or the two-body cut-off distance
(1.4 nm), see option -rdd, for pairs and tabulated bonds also
see option -ddcheck</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">For more
information and tips for troubleshooting, please check the
GROMACS</span><br style="font-family: 'courier new',
monospace; ">
<span style="font-family: 'courier new', monospace; ">website
at </span><a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
style="font-family: 'courier new', monospace; ">http://www.gromacs.org/Documentation/Errors</a><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">-------------------------------------------------------</span><br
style="font-family: 'courier new', monospace; ">
</div>
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