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<div class="moz-cite-prefix">On 11/19/2013 11:24 AM, XAvier Periole
wrote:<br>
</div>
<blockquote cite="mid:30268FCD-A255-494F-B4E5-D2C34DFFAAC3@rug.nl"
type="cite">
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charset=ISO-8859-1">
<div><br>
</div>
Hi,
<div><br>
</div>
<div>Indeed! I overlooked the dimensions associated with the
complain … the z dimension is shorter than the x/y (bilayer).</div>
<div><br>
</div>
<div>With a modified z dimension (unrealistically increased) it
all works fine with DD 2x2x2 … </div>
<div><br>
</div>
<div>Now:</div>
<div>- is it possible to get this to work with more CPUs? Any hint
on how to do this would be appreciated.</div>
</blockquote>
As I said, use master with the Verlet scheme, OpenMP threads and
this change for LJ shift:<br>
<a class="moz-txt-link-freetext" href="https://gerrit.gromacs.org/#/c/2775/">https://gerrit.gromacs.org/#/c/2775/</a><br>
<blockquote cite="mid:30268FCD-A255-494F-B4E5-D2C34DFFAAC3@rug.nl"
type="cite">
<div>- is it possible to overpass the check on the z dimension
without messing up other things? The distance/angle will never
make trouble in that direction.</div>
</blockquote>
Yes.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<blockquote cite="mid:30268FCD-A255-494F-B4E5-D2C34DFFAAC3@rug.nl"
type="cite">
<div><br>
</div>
<div>Thanks,</div>
<div>XAvier.</div>
<div><br>
<div>
<div>On Nov 19, 2013, at 9:28 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>
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">
<div><br>
</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; ">
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