<div dir="ltr">Hi,<br><br><div class="gmail_quote"><div dir="ltr">On Tue, Sep 1, 2015 at 6:26 AM Xingcheng Lin <<a href="mailto:linxingcheng50311@gmail.com">linxingcheng50311@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>I have a further question also. It seems that the value of rlist is the scope of the increased cells apart from the home cell. In 2D and 3D domain decomposition, is this the same case? In other words, does the home node know the coordinates of all the particles within the rlist in 2D/3D domain decomposition?</div></div></blockquote><div><br></div><div>Yes, by design. Do check out the algorithm description in chapter 3 of the reference manual, including the flow chart.</div><div><br></div><div>Mark</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div>Thank you,</div><div>Xingcheng</div><div><br><div class="gmail_extra"><br><div class="gmail_quote"></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote">On Sun, Aug 30, 2015 at 5:00 AM, <span dir="ltr"><<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a>></span> wrote:<br></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send gromacs.org_gmx-developers mailing list submissions to<br>
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1. Re: Increase the scope of dd domains (Xingcheng Lin)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 29 Aug 2015 11:23:36 -0500<br>
From: Xingcheng Lin <<a href="mailto:linxingcheng50311@gmail.com" target="_blank">linxingcheng50311@gmail.com</a>><br>
To: <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers@maillist.sys.kth.se</a></blockquote></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Subject: Re: [gmx-developers] Increase the scope of dd domains<br>
Message-ID:<br></blockquote></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<CAPugp-EV_R-vs4cgBAyv_x3TXv=<a href="mailto:01UKex2GRjTcjv98Zxrq2vA@mail.gmail.com" target="_blank">01UKex2GRjTcjv98Zxrq2vA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"</blockquote></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
Even when I choose<br>
<br>
cutoff-scheme=Verlet<br>
cutoff-buffer-drift=-1<br>
rlist=1.5<br>
<br>
some pairs are still missing.<br>
<br>
I do print them out from different node and use MPI_Reduce to combine them<br>
together. That is where I found out it is not a problem if all pairs sit at<br>
one node, while it shows up when pairs starts to be distributed into two<br>
nodes.<br>
<br></blockquote></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
To be clear, I put this code at the end of *do_force* function, after the<br>
*post_process_forces* function. I think the coordinates have been</blockquote></div></div></div></div><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
communicated up to this point, am I correct?<br>
<br>
if (bDoForces)<br>
{<br>
post_process_forces(fplog, cr, step, nrnb, wcycle,<br>
top, box, x, f, vir_force, mdatoms, graph, fr, vsite,<br>
flags);<br>
}<br>
if(bNS)<br>
{<br>
if (DOMAINDECOMP(cr))<br>
{<br>
int my_rank;<br>
int npes;<br>
int globalQC;<br>
int localQC;<br>
MPI_Comm_size(MPI_COMM_WORLD, &npes);<br>
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);<br>
if (my_rank == 0)<br>
{<br>
globalQC = 0;<br>
}<br>
// Barrier for the initialization;<br>
MPI_Barrier(MPI_COMM_WORLD);<br>
<br>
localQC = calQ_dd( x, f, step, cr, inputrec, box );<br>
<br>
// Barrier for Qcontacts accumulation;<br>
MPI_Barrier(MPI_COMM_WORLD);<br>
MPI_Reduce(&localQC, &globalQC, 1, MPI_INT, MPI_SUM, 0,<br>
MPI_COMM_WORLD);<br>
<br>
...<br>
<br>
Then I print out globalQC, it shows some pairs are missing.<br>
<br>
The code for calQdd is same as before (struct data is known statically):<br>
<br>
int calQdd ( rvec x[], rvec f[], int step, t_commrec *cr, t_inputrec *ir,<br>
matrix box )<br>
{<br>
int Npairs = 0;<br>
int i, ai, aj;<br>
/* for domain decomposition ---------------*/<br>
int localai, localaj;<br>
int localcell;<br>
/* for domain decomposition ---------------*/<br>
real r_N, r_N2, dr, dr2 ;<br>
rvec dx ;<br>
/* Set the pbc ----------------------------*/<br>
t_pbc pbc;<br>
set_pbc(&pbc, ir->ePBC, box);<br>
<br>
FILE *fp;<br>
fp = fopen("pairs.dat","a");<br>
if(fp == NULL){<br>
fprintf(stderr, "Can't open input file !\n");<br>
exit(1);<br>
}<br>
<br>
if ( NP > 0 )<br>
{<br>
for (i=0; i<NP; ++i)<br>
{<br>
ai = data.first[i] ;<br>
<br>
if (ga2la_get_home(cr->dd->ga2la, ai, &localai))<br>
{<br>
aj = data.second[i] ;<br>
<br>
if (ga2la_get(cr->dd->ga2la, aj, &localaj, &localcell))<br>
{<br>
<br>
fprintf(fp, "%d\t%d\n", ai, aj);<br>
<br>
r_N = data.r_native[i] ;<br>
r_N2 = r_N * r_N;<br>
pbc_dx(&pbc, x[localai], x[localaj], dx) ;<br>
dr2 = iprod( dx, dx ) ;<br>
if (dr2 < r_N2)<br>
{<br>
Npairs += 1;<br>
}<br>
}<br>
}<br>
}<br>
}<br>
fclose(fp);<br>
return Npairs;<br>
}<br>
<br>
As you can see, here I also print out the pairs recognized. Though I<br>
increase rlist=1.5 still some pairs are missing (though their mutual<br>
distance is less than 6 angstroms).<br>
<br>
Thanks,<br>
Xingcheng<br>
<br>
On Sat, Aug 29, 2015 at 5:00 AM, <<br>
<a href="mailto:gromacs.org_gmx-developers-request@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-request@maillist.sys.kth.se</a>> wrote:<br>
<br>
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> 1. Re: Increase the scope of dd domains (Berk Hess)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Fri, 28 Aug 2015 20:35:50 +0200<br>
> From: Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>><br>
> To: <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
> Subject: Re: [gmx-developers] Increase the scope of dd domains<br>
> Message-ID: <<a href="mailto:55E0AA06.8020404@kth.se" target="_blank">55E0AA06.8020404@kth.se</a>><br>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
><br>
> Hi,<br>
><br>
> If rlist=1, you should have access to all pairs up to 1 nm.<br>
><br>
> One more question:<br>
> You do check/print the pairs on all ranks, not only on the master rank?<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 08/28/2015 08:15 PM, Xingcheng Lin wrote:<br>
> > Hi Berk,<br>
> ><br>
> > Yes, I think I was calling that after the coordinate communication.<br>
> > The place where I code it in is after the command:<br>
> ><br>
> > if (bDoForces)<br>
> > {<br>
> > post_process_forces(fplog, cr, step, nrnb, wcycle,<br>
> > top, box, x, f, vir_force, mdatoms, graph, fr, vsite,<br>
> > flags);<br>
> > }<br>
> ><br>
> > After that I use a<br>
> > if(bNS){<br>
> > if (DOMAINDECOMP(cr)){<br>
> ><br>
> > to make sure it is done every neighboring list step.<br>
> ><br>
> > Is this correct? BTW, I was coding that in gromacs4.6.3 version (this<br>
> > is for historical reason because I have coded other unrelated things<br>
> > in other files).<br>
> ><br>
> > I have checked that the ga2la_get_home in the first loop find all ai<br>
> > atoms, but the second loop ga2la_get missed some aj atoms. One of the<br>
> > reasons I guess is because the missing atom pairs are too far apart<br>
> > (but less than 6 angstroms) in Cartesian space from each other, so<br>
> > that even by including all cells of the home node it still could not<br>
> > find it. That could be a problem, but I don't know exactly how -dd<br>
> > find this pair partner in its neighboring cells.<br>
> ><br>
> > Thank you,<br>
> > Xingcheng<br>
> ><br>
><br>
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