all 8 nodes are running at full capacity, though<br><br><div class="gmail_quote">On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Here&#39;s what I&#39;ve got:<br>
<br>
M E G A - F L O P S   A C C O U N T I N G<br>
<br>
RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy<br>
T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)<br>
NF=No Forces<br>
<br>
Computing:                               M-Number         M-Flops  % Flops<br>
-----------------------------------------------------------------------------<br>
Coul(T) + VdW(T)                   1219164.751609    82903203.109    80.6<br>
Outer nonbonded loop                 25980.879385      259808.794     0.3<br>
Calc Weights                         37138.271040     1336977.757     1.3<br>
Spread Q Bspline                    792283.115520     1584566.231     1.5<br>
Gather F Bspline                    792283.115520     4753698.693     4.6<br>
3D-FFT                              119163.856212      953310.850     0.9<br>
Solve PME                             2527.465668      161757.803     0.2<br>
NS-Pairs                             47774.705001     1003268.805     1.0<br>
Reset In Box                           371.386080        1114.158     0.0<br>
Shift-X                              24758.847360      148553.084     0.1<br>
CG-CoM                                1237.953600        3713.861     0.0<br>
Angles                               18569.135520     3119614.767     3.0<br>
Propers                              14855.308416     3401865.627     3.3<br>
Impropers                             3094.855920      643730.031     0.6<br>
Virial                                1242.417375       22363.513     0.0<br>
Stop-CM                               1237.953600       12379.536     0.0<br>
P-Coupling                           12379.423680       74276.542     0.1<br>
Calc-Ekin                            12379.436160      334244.776     0.3<br>
Lincs                                11760.476208      705628.572     0.7<br>
Lincs-Mat                           245113.083072      980452.332     1.0<br>
Constraint-V                         23520.928704      188167.430     0.2<br>
Constraint-Vir                       11760.452496      282250.860     0.3<br>
-----------------------------------------------------------------------------<br>
Total                                               102874947.133   100.0<br>
-----------------------------------------------------------------------------<br>
<br>
<br>
R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G<br>
<br>
Computing:         Nodes     Number     G-Cycles    Seconds     %<br>
-----------------------------------------------------------------------<br>
Neighbor search    1      99195     8779.027     3300.3       3.8<br>
Force                   1     991941   188562.885    70886.8    81.7<br>
PME mesh           1     991941    18012.830     6771.6      7.8<br>
Write traj.             1            41     16.835          6.3          0.0<br>
Update                 1     991941     2272.379      854.3       1.0<br>
Constraints           1     991941    11121.146     4180.8     4.8<br>
Rest                     1                    2162.628      813.0      0.9<br>
-----------------------------------------------------------------------<br>
Total                    1                  230927.730    86813.1   100.0<br>
-----------------------------------------------------------------------<br>
-----------------------------------------------------------------------<br>
PME spread/gather      1    1983882      17065.384    6415.4   7.4<br>
PME 3D-FFT               1    1983882      503.340       189.2     0.2<br>
PME solve                  1     991941       427.136       160.6     0.2<br>
-----------------------------------------------------------------------<br>
<br>
Does that mean it&#39;s only using 1 node?  That would explain the speed issues.<br>
<br>
</blockquote>
<br></div></div>
That&#39;s what it looks like to me.<div class="im"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div><div><div></div><div class="h5">
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don&#39;t post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>