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<div class="moz-cite-prefix">Hi,<br>
<br>
Ah, I overlooked that the option is on by default, that explains a
lot.<br>
But with DD 2x2x2 I think everything should work. Your distance
can't be larger than half the box size, right?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 11/19/2013 09:08 AM, XAvier Periole wrote:<br>
</div>
<blockquote cite="mid:789CA60A-52D8-43A4-B041-1341D1BBD710@rug.nl"
type="cite">
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charset=ISO-8859-1">
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</div>
Hi Berk,
<div><br>
</div>
<div>Thank you for your comments.</div>
<div><br>
</div>
<div>I looked at the -ddbondcomm (in gmx4.6.1). It is a hidden
option and turned on by default. </div>
<div><br>
</div>
<div>- Adding this option explicitly to my command line did not
affect the complain concerning the minimum box size needing to
be ~15 nm.</div>
<div>- adding explicitly -dd 2 2 2 (as you email seemed to
suggest) did remove the complain but then we get to the same
point as when hacking the code which was a complain for missing
the long range bonded interactions.</div>
<div>- adding -rdd 17.0 did not help, then of course the box size
force by -dd 2 2 2 is smaller than the minimum allowed (17.0
nm).</div>
<div><br>
</div>
<div>I am not sure if I am missing something here?</div>
<div><br>
</div>
<div>Thanks again,</div>
<div>XAvier.</div>
<div><br>
<div>
<div>On Nov 19, 2013, at 7:50 AM, Berk Hess <<a
moz-do-not-send="true" href="mailto:hess@kth.se">hess@kth.se</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<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 moz-do-not-send="true"
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>
</div>
<blockquote
cite="mid:67042FD3-CD49-40CB-BB3C-E568E6703E76@rug.nl"
type="cite">
<div><br>
</div>
<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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