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<div class="moz-cite-prefix">On 10/22/2014 04:31 AM, maren wrote:<br>
<br>
<br>
I found two memory leaks in df1b2lp8.cpp which were causing<br>
glmmadmb to run out of memory when doing mcmc. They would<br>
also affect other aspects of the analysis.<br>
<br>
The offending pointers are<br>
<br>
block_diagonal_re_list<br>
block_diagonal_fe_list<br>
<br>
In the code they should be checked to see if they are non zero
and<br>
deleted if they are. code is like that below.<br>
<br>
// check if already allocated<br>
if (block_diagonal_re_list)<br>
{<br>
delete block_diagonal_re_list;<br>
block_diagonal_re_list=0;<br>
}<br>
block_diagonal_re_list = new imatrix(1,num_separable_calls,<br>
1,itmp);<br>
if (block_diagonal_re_list ==0)<br>
{<br>
cerr << "error_allocating imatrix" << endl;<br>
ad_exit(1);<br>
}<br>
// check if already allocated<br>
if (block_diagonal_fe_list)<br>
{<br>
delete block_diagonal_fe_list;<br>
block_diagonal_fe_list=0;<br>
}<br>
block_diagonal_fe_list = new imatrix(1,num_separable_calls,<br>
1,itmpf);<br>
<br>
if (block_diagonal_fe_list ==0)<br>
{<br>
cerr << "error_allocating imatrix" << endl;<br>
ad_exit(1);<br>
}<br>
<br>
<br>
Thanks to valgrind for making this easy to find.<br>
<br>
So we need to get this into glmmadmb somehow.<br>
<br>
<br>
<br>
</div>
<blockquote cite="mid:54479577.1030303@avitec-research.de"
type="cite">
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<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Hi Dave,<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Thank you very
much for offering to look into the problem. I attached a
shortened version of my data set (the first 2000 lines out of
11195). I tried it out and the model is in principal running
with this shortened version. But please let me know if you
need a larger part of the data set.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Technically the
data set is not owned by us. Therefore, please don’t
distribute the data set further (without prior permission).
For the same reason I made all the variable names general. I
assumed that the details of what exactly is analysed here are
not important for the problem. But if you need more details
about the study or the variables please don’t hesitate to ask.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">I attached the
R-code to run the model below. In case it is of importance: I
am using the R version 3.1.0 and the glmmADMB version 0.8.0.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Thanks!<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Maren<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">#-----------------------------------------------------------------------------------------------------------------------#<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"># Here is the
R-code:<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">library(glmmADMB)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data <-
read.csv2("Rebke_Data_sample.csv", header=TRUE,
colClasses="character")<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Response<span
style="mso-spacerun:yes"> </span><-
as.numeric(Data$Response)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Fixed1<span
style="mso-spacerun:yes"> </span><span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Fixed1)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Fixed1 <-
relevel(Data$Fixed1, ref="Off")<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Fixed2<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Fixed2)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Fixed2 <-
relevel(Data$Fixed2, ref="1")<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Fixed3<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Fixed3)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Random1<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Random1)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Random2<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Random2)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Random3<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Random3)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Random4<span
style="mso-spacerun:yes"> </span><-
as.factor(Data$Random4)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Data$Offset<span
style="mso-spacerun:yes"> </span><-
as.numeric(Data$Offset)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">nsim <- 2000<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">thin <- 10<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Model <-
glmmadmb(Response ~ Fixed1 + Fixed2 + Fixed3 + (1|Random1) +
(1|Random2) + (1|Random3) + (1|Random4) + offset(log(Offset)),
data=Data, family="poisson", zeroInflation=TRUE,mcmc=TRUE,
mcmc.opts=mcmcControl(mcmc=nsim, mcsave=thin))<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-ansi-language:EN-GB"
lang="EN-GB">#-----------------------------------------------------------------------------------------------------------------------#<o:p></o:p></span></p>
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<div class="moz-cite-prefix">Am 22.10.2014 04:44, schrieb dave
fournier:<br>
</div>
<blockquote cite="mid:544719F8.90404@otter-rsch.com" type="cite">
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<div class="moz-cite-prefix">On 10/21/2014 02:48 PM, - - wrote:<br>
<br>
Hi,<br>
<br>
That sounds like a bug maybe. Maybe a memory leak. Don't
remember exactly how it is implemented, but<br>
I don't think the memory use of any of the MCMC stuff should
grow over time like that. If you send me <br>
what I need to run your model I'll take a look at it.<br>
<br>
Dave<br>
<br>
<br>
</div>
<blockquote
cite="mid:1499133270.34898.1413928121734.open-xchange@patina.store"
type="cite">
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charset=utf-8">
<div>
<p>Hi Dave,</p>
<p>Sorry, I guess I didn’t explain my problem correctly in
my original request due to translation issues. It is the
RAM and not the hard drive space that is reaching its
capacity. After running the MCMC chain for 24 hours
(approximately 2000 iterations for the model of my own
data) the allocated memory is already about 6 GB. </p>
<p>I will send a follow up to the mailing list to clarify
this.</p>
<p>Best wishes,<br>
Maren</p>
</div>
</blockquote>
<br>
</blockquote>
<br>
</blockquote>
<br>
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