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Having some problems with scaling of GROMACS onto multiple boxes.
Just want to see if the system I am simulating is may be too small to
scale well, or if there are some settings with may be LAM or even default
GROMACS that I need to be adjusting.<br><br>
System:<br>
<x-tab> </x-tab>Intel P733
Dual Processor<br>
<x-tab> </x-tab>Linux
Redhat 7.3<br>
<x-tab> </x-tab>LAM
6.5.4<br>
<x-tab> </x-tab>100 base
Ethernet<br><br>
MD Simulation:<br>
<x-tab> </x-tab>7.5 nm
cube<br>
<x-tab> </x-tab>16
molecules, 16 Na, + water<br>
<x-tab> </x-tab>42,000
atoms<br>
<x-tab> </x-tab>500
steps<br>
<x-tab> </x-tab>0.002 ps
step<br>
<x-tab> </x-tab>PME<br><br>
grompp switches:<br>
<x-tab> </x-tab>-sort<br>
<x-tab> </x-tab>-shuffle<br>
<x-tab> </x-tab>-np
#<br><br>
Initiation of mdrun:<br>
<x-tab> </x-tab>mpirun C
mdrun -s .....<br><br>
Results (time to perform the mdrun calculation):<br>
<x-tab> </x-tab>1 CPU / 1
box - 480 seconds<br>
<x-tab> </x-tab>2 CPU / 1
box - 340 seconds<br>
<x-tab> </x-tab>2 CPU / 2
box - 400 seconds<br>
<x-tab> </x-tab>4 CPU / 2
box - 420 seconds<br><br>
Some suggestions and guidance would be greatly appreciated :-)<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy<br>
Monash University<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9076</html>