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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Recheck the units for that last number ….<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Albert<br>
<b>Sent:</b> Friday, 6 January 2012 3:24 PM<br>
<b>To:</b> gromacs maillist<br>
<b>Subject:</b> [gmx-users] another question about performance<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"WenQuanYi WenQuanYi Bitmap Song","serif"">Hello:<br>
here is my log file for mdrun:<br>
Writing final coordinates.<br>
step 100000, remaining runtime: 0 s <br>
<br>
Average load imbalance: 10.8 %<br>
Part of the total run time spent waiting due to load imbalance: 4.3 %<br>
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 19 % Z 0 %<br>
Average PME mesh/force load: 0.665<br>
Part of the total run time spent waiting due to PP/PME imbalance: 5.7 %<br>
<br>
NOTE: 5.7 % performance was lost because the PME nodes<br>
had less work to do than the PP nodes.<br>
You might want to decrease the number of PME nodes<br>
or decrease the cut-off and the grid spacing.<br>
<br>
<br>
NOTE: 9 % of the run time was spent communicating energies,<br>
you might want to use the -gcom option of mdrun<br>
<br>
<br>
Parallel run - timing based on wallclock.<br>
<br>
NODE (s) Real (s) (%)<br>
Time: 2435.554 2435.554 100.0<br>
40:35<br>
(Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>
Performance: 409.701 22.103 7.095 3.383<br>
<br>
gcq#149: "It's Against the Rules" (Pulp Fiction)<br>
<br>
<br>
<br>
As we can see from the end of this log file, the performance is 7.1ns/day, 3.4ns/hour. I am very confused about this output. How could this happen? Is there only two hours something each day?<br>
<br>
<br>
THX</span><o:p></o:p></p>
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