<font color="#000099"><font face="verdana,sans-serif">Not know. I will update the result tomorrow, as the 50000 steps take really long time :(<br></font></font><br><div class="gmail_quote">On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 29/09/2011 7:20 AM, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes, they are updated like:<br>
...<br>
Replica exchange at step 5700 time 11.4<br>
Repl ex 0 1 x 2 3 x 4 5 x 6 7 8 9 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49<br>
Repl pr 1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00<br>
<br>
Replica exchange at step 5750 time 11.5<br>
Repl 0 <-> 1 dE = -7.583e+00<br>
Repl ex 0 x 1 2 3 4 x 5 6 x 7 8 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49<br>
Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01<br>
<br>
Step Time Lambda<br>
5800 11.60000 0.00000<br>
<br>
Energies (kJ/mol)<br>
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br>
9.69806e+02 1.32207e+03 3.34938e+01 4.93171e+02 -3.91111e+03<br>
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.<br>
3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.00000e+00<br>
Potential Kinetic En. Total Energy Conserved En. Temperature<br>
-1.78987e+05 4.57462e+04 -1.33240e+05 1.23302e+10 5.62201e+02<br>
Pres. DC (bar) Pressure (bar) Constr. rmsd<br>
-2.12803e+02 -5.47109e+02 2.21484e-05<br>
...<br>
<br>
</blockquote>
<br>
Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling.<br>
</blockquote>
<br></div>
If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Thanks. currently what I see is the program runs very slowly,<br>
but get .log file for all the 50 replicas, does this mean all of<br>
them are running?<br>
<br>
<br>
Are the log files being updated, or do they all simply contain a<br>
fatal error message that there are insufficient nodes? I cannot<br>
think of a reason why 50 simulations could possibly run on 2 processors.<br>
<br>
-Justin<br>
<br>
On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Well, although this makes sense, why all the 50 replicas are<br>
running when I run "mpirun<br>
-np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on<br>
my own<br>
computer with only 2 cores?<br>
<br>
<br>
I can offer no explanation for this behavior, but I expect that<br>
either not all of them are actually running, or at the very least<br>
you will get horribly slow performance.<br>
<br>
<br>
By the way, would you please show me where I can find the<br>
reasonable replex number information in the literature?<br>
I did<br>
not find it in the link you posted and the manual either.<br>
<br>
<br>
A few minutes of real literature searching will be far more<br>
valuable<br>
than some random person on the Internet giving you a value<br>
that you<br>
blindly use ;)<br>
<br>
-Justin<br>
<br>
Thanks.<br>
<br>
<br>
-- Best,<br>
Liang Liu<br>
<br>
<br>
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</blockquote>
<br>
</blockquote>
<br>
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