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<div class="moz-cite-prefix">Hi,<br>
<br>
That is not only a quick fix, but also the real fix.<br>
I field an issue:<br>
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org/issues/1273">http://redmine.gromacs.org/issues/1273</a><br>
and the fix:<br>
<a class="moz-txt-link-freetext" href="https://gerrit.gromacs.org/#/c/2432/">https://gerrit.gromacs.org/#/c/2432/</a><br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 06/03/2013 09:24 PM, francesco oteri wrote:<br>
</div>
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cite="mid:CAFQcp-NpirVcm3eKC0UXzw1HKMLC2sH0M0pt42=rwfyNthSDuA@mail.gmail.com"
type="cite">
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<div dir="ltr">A quick fix might be changing the lines:
<div><br>
</div>
<div>
<div> if ( (gs.set[eglsSTOPCOND] < 0 ) || (
(gs.set[eglsSTOPCOND] > 0 ) && ( bNS ||
ir->nstlist == 0)) )</div>
<div> {</div>
<div> bLastStep = TRUE;</div>
<div> }</div>
</div>
<div><br>
</div>
<div style="">in</div>
<div style=""> if ( (gs.set[eglsSTOPCOND] < 0 ) || (
(gs.set[eglsSTOPCOND] > 0 ) && ( bNStList ||
ir->nstlist == 0)) )<br>
</div>
<div style="">
<div>
<div> {<br>
</div>
<div> bLastStep = TRUE;</div>
<div> }</div>
</div>
<div><br>
</div>
</div>
<div style="">What do you think about?</div>
<div style=""><br>
</div>
<div style="">Francesco <br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/6/3 francesco oteri <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear gromacs developers,
<div><br>
</div>
<div>analyzing a hunging replica exchange simulation, I
might have figured out a problem (likely a bug).</div>
<div><br>
</div>
<div>Let's suppose I am running replica exchange with
-maxh, -replex 50 and neighbour searching frequence = 5
steps . </div>
<div><br>
</div>
<div>If I well understood, once the code run for maxh*0.99
it stops at the next neighbour searching step.</div>
<div><br>
</div>
<div>If the program reaches maxh*0.99 let's say at the
step 50, the next neighbour searching step is the 55.
But if 2 replicas exchange at step 50, it implies
rebuilding the neighbour searching </div>
<div>( because in the code bExchanged=TRUE implies bNS to
be TRUE). </div>
<div><br>
</div>
<div>These two replicas so stop at step 51 but the other
replicas continue until the 55th step. </div>
<div>Here the problem appears. In this case mdrun performs
global communication calling compute_global next to the
line commented as:</div>
<div> /* ############## IF NOT VV, Calculate globals HERE,
also iterate constraints ############ */<br>
</div>
<div><br>
</div>
<div>Since the 2 replicas that exchanged already ended,
mdrun hungs.</div>
<div>
<br>
</div>
<div>Maybe my analysis is incorrect and in this case I
apologize.</div>
<div>In any case, if nobody did, I am looking for a fix.</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Francesco</div>
<div><br>
</div>
<div><br>
</div>
</font></span></div>
</blockquote>
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<div><br>
</div>
-- <br>
Cordiali saluti, Dr.Oteri Francesco
</div>
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