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<p class=MsoPlainText>Thanks Mark for your quick response and your suggestion.
I decreased <o:p></o:p></p>
<p class=MsoPlainText>the density of data points in each of my 274 table*.xvg
files <o:p></o:p></p>
<p class=MsoPlainText>(3 tables for each molecule and one table for all the
other atoms) by a factor of 10.<o:p></o:p></p>
<p class=MsoPlainText>I did notice a small increase in speed (1.584 ns/day to
1.590 ns/day), but obviously <o:p></o:p></p>
<p class=MsoPlainText>not as fast as without tables (~25ns/day). <o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>If there are other suggestions for speeding up the
simulations with a large number <o:p></o:p></p>
<p class=MsoPlainText>of tables (user-defined potentials), I would be more than
grateful. <o:p></o:p></p>
<p class=MsoPlainText>Again, thanks in advance for your help!<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Eli<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>>Musselman,
Eli D wrote:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
This works great but ***here’s the problem*** : *the simulations run <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
exceedingly slow when I use such a high number of defined
‘energygrps’*. <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
Without using the user defined potential functions I was getting <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
roughly 25 ns/day (which, as always with GROMACS, is amazingly fast!). <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
With the applied potential functions and ‘energygrps’ however I am
only <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
getting 1.5 ns/day. I thought one problem might be the number of
times <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
that ‘mdrun’ spends writing to the energy (.edr) file, but I have
ruled <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
this out as a possibility because when I increased my ‘nstenergy’
in my <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
*.mdp file by 100 fold ‘mdrun’ still runs at the same slow
rate. The <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
slowdown therefore appears to be directly related to the number of <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
‘energygrps.’. To confirm this, I decreased the number of
‘energygrps’ <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
to 3 (by lumping all ‘C1’ and ‘C2’ atoms together into
one ‘energygrp’ <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
and all ‘O1’ and ‘O2’ atoms into another
‘energygrp’) and this <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
accelerated the simulations dramatically; however, the same user <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
defined potential functions are then applied to both **intra** and <o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>><i>
**inter**molecular interactions, which is not what I want!<o:p></o:p></i></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>Good
diagnostics and description, thanks. It seems quite likely to me <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>that
this slowdown will be related to cache misses. 95 tables actually <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>uses
an appreciable amount of memory. More salient for the inner loops, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>however
is that each time a new table is being used in each integration <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>step,
the code will have to go and fetch locations from main memory, and <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>when
these hit the caches they won't be reused much.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>The
only simple work-around I can suggest is to decrease the density of <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>data
points in the table. That will degrade the accuracy, but possibly <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>lead
to fewer cache misses.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>>Mark<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
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