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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Anyone developed a Gaussian mixture model (e.g. several normal distributions representing the length distribution for each age) in ADMB that has a linear mixed
effect for the mean (e.g. the mean length at age) and a linear mixed effect for the proportion that each Gaussian makes of the total (e.g. the proportion that age makes of the total population)?<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I would like to know if this is computationally feasible in ADMB (32,000 data points, 2500 realizations of one of the random effects, 240 realizations for another
random effect) or if TMB would be better.<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks,<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Mark <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>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> developers-bounces@admb-project.org [mailto:developers-bounces@admb-project.org]
<b>On Behalf Of </b>Jim Ianelli - NOAA Federal<br>
<b>Sent:</b> Monday, August 04, 2014 2:47 PM<br>
<b>To:</b> dave fournier<br>
<b>Cc:</b> developers@admb-project.org<br>
<b>Subject:</b> Re: [Developers] interfacing with openblas for large problems<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">Seems like a worthwhile enterprise. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">Looking at the site there are a number of interesting aspects of OpenBlas that could help with ideas for the Foundation, not least of which is their balance sheet and funding model:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif""><a href="https://docs.google.com/spreadsheet/ccc?key=0AghkTjXe2lDndE1UZml0dGpaUzJmZGhvenBZd1F2R1E&usp=sharing#gid=0">https://docs.google.com/spreadsheet/ccc?key=0AghkTjXe2lDndE1UZml0dGpaUzJmZGhvenBZd1F2R1E&usp=sharing#gid=0</a></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">also hadn't heard of:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif""><a href="https://www.bountysource.com/faq">https://www.bountysource.com/faq</a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">before, looks like something of interest.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">also an aside but a useful git-branching model...: <a href="http://nvie.com/files/Git-branching-model.pdf">http://nvie.com/files/Git-branching-model.pdf</a></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">so back to the question, how can we as a community help with the interface work? I suppose steps might be something like:</span><o:p></o:p></p>
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<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-family:"Trebuchet MS","sans-serif"">pick some example function sets</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-family:"Trebuchet MS","sans-serif"">map the variable types appropriately (so they will work with ADMB</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-family:"Trebuchet MS","sans-serif"">write adjoint code for dvar functions (?) </span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-family:"Trebuchet MS","sans-serif"">test against current ADMB implmentations</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="font-family:"Trebuchet MS","sans-serif"">...</span><o:p></o:p></li></ol>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">thanks for the interest dave.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Trebuchet MS","sans-serif"">jim</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Aug 4, 2014 at 12:31 PM, dave fournier <<a href="mailto:davef@otter-rsch.com" target="_blank">davef@otter-rsch.com</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">I wonder if there is any interest in doing a bit of work to interface some of the common<br>
function like ludecomp and choleski decomp with the openblas versions.<br>
<br>
this is not too difficult once one figures out the boring stuff like the fact that matrices are strored<br>
by column in contiguous arrays.<br>
<br>
we are now looking at ever larger problems. I compared the admb lu decomp of a 2,000x2,000 matrix<br>
from numerical recipes with the openblas version.<br>
<br>
Time for openblas lu decomp 172.05 ms<br>
Time for numerical recipes lu decomp 22102.9 ms<br>
<br>
which is about 125 times faster<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p><a name="SafeHtmlFilter_SafeHtmlFilter_SafeHtmlFi"><span style="font-family:"Trebuchet MS","sans-serif"">James Ianelli<br>
</span></a><span style="font-family:"Trebuchet MS","sans-serif"">NMFS/NOAA Building 4<br>
7600 Sand Pt Way NE<br>
Seattle WA 98115</span><o:p></o:p></p>
<p><span style="font-family:"Trebuchet MS","sans-serif""> 206 526 6510</span><o:p></o:p></p>
<p>Visit the ADMB project <a href="http://admb-project.org/" target="_blank"><span style="color:#1155CC">http://admb-project.org/</span></a><o:p></o:p></p>
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