<div dir="ltr">Dear Prof. Snijders,<div><br></div><div>I see the error, -markeForkCluster- is meaningless in windows, that's why the error. I've change it to -makeCluster- which "is cross platform" so the error shouldn't show up again. Plus, I've included details in siena07.Rd (the function manual) about it:<br></div><div><br></div><div>> <font color="#000000" face="sans-serif">In the case of using multiple processors, there are two options for telling siena07 to use them. By specifying the options useCluster, nbrNodes, clusterString and initC, siena07 will create a cluster object that will be used by the parallel package. After finishing the estimation procedure, siena07 will automatically stop the cluster. Alternatively, instead of having the function to create a cluster, the user may provide its own by specifying the option cl, similar to what the boot function does in the boot package. By using the option cl the user may be able to create more complex clusters (see examples below).</font></div><div><br></div><div>Furthermore, I've included a couple of examples in the manual siena07.Rd:</div><div><br></div><div><div># Running in multiple processors -----------------------------------------------</div><div>## Not run: </div><div><br></div><div># Using 8 processors</div><div>ans2 <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE,</div><div> useCluster=TRUE, nbrNodes=8, initC=TRUE)</div><div><br></div><div># Loading the parallel package and creating a cluster</div><div># with 8 processors (this should be equivalent)</div><div><br></div><div>library(parallel)</div><div>cl <- makeCluster(8)</div><div><br></div><div>ans3 <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE,</div><div> cl = cl)</div><div><br></div><div># Notice that now -siena07- won't stop the cluster for you.</div><div>stopCluster(cl)</div><div><br></div><div># You can create even more complex clusters using several computers. In this</div><div># example we are creating a cluster with 3*8 = 24 processors on three</div><div># different machines.</div><div>cl <- makePSOCKcluster(</div><div> rep(c('localhost', '<a href="http://machine2.website.com">machine2.website.com</a>' , '<a href="http://machine3.website.com">machine3.website.com</a>'), 8),</div><div> user='myusername', rshcmd='ssh -p PORTNUMBER')</div><div><br></div><div>ans4 <- siena07(myalgorithm, data=mydata, effects=myeff, batch=TRUE,</div><div> cl = cl)</div><div>stopCluster(cl)</div></div><div><br></div><div>I've already pushed the new changes and the R CMD check is OK now.</div><div><br></div><div>Best,</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>George G. Vega Yon<br>+1 (626) 381 8171<br><a href="http://cana.usc.edu/vegayon" target="_blank">http://cana.usc.edu/vegayon</a></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Oct 14, 2016 at 12:01 AM, Tom Snijders <span dir="ltr"><<a href="mailto:tom.snijders@nuffield.ox.ac.uk" target="_blank">tom.snijders@nuffield.ox.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear George,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">As you may have seen, your update to RSiena at R-Forge failed. The windows-devel toolchain ended with the error:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> > library(parallel)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> > cl <- makeForkCluster(2)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> Error in makeForkCluster(2) : fork clusters are not supported on Windows<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">
</span><span lang="NL" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Execution halted<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">What are the platforms for which this makeForkCluster command works? If Windows is not included but, e.g., Linux is, then the solution is to drop this test
from tests/parallel.R, make sure by your own test that it works on other platforms, and leave the rest as it is.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Further, can you please send a longer description to me of how this works, understandable for R users whose knowledgeof computer science is limited? Then I
can see how I incorporate this somewhere in the manual. You can do this in an email directly to me; for the current message, I thought it is better to report this also to rsiena-help.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best wishes,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Tom<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">==============================<wbr>==============================<wbr>====<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Tom A.B. Snijders<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Professor of Statistics and Methodology<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dept. of Sociology, University of Groningen<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Emeritus Fellow, Nuffield College, University of Oxford<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Associate Member, Dept. of Statistics, University of Oxford<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://www.stats.ox.ac.uk/~snijders/" target="_blank">http://www.stats.ox.ac.uk/~<wbr>snijders/</a><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:rsiena-help-bounces@lists.r-forge.r-project.org" target="_blank">rsiena-help-bounces@lists.r-<wbr>forge.r-project.org</a> [mailto:<a href="mailto:rsiena-help-bounces@lists.r-forge.r-project.org" target="_blank">rsiena-help-bounces@<wbr>lists.r-forge.r-project.org</a>]
<b>On Behalf Of </b>Tom Snijders<br>
<b>Sent:</b> 05 October 2016 13:43<br>
<b>To:</b> <a href="mailto:rsiena-help@lists.r-forge.r-project.org" target="_blank">rsiena-help@lists.r-forge.r-<wbr>project.org</a><br>
<b>Subject:</b> Re: [Rsiena-help] More flexibility on using Clusters<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear George,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">That’s wonderful. This will be great for some users! I look forward to see these changes.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I suppose that you are indeed talking about RSiena and not RSienaTest.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">For committing the new version to R-Forge, there is a file "\RSienaTest\doc\HowToCommit.<wbr>pdf" (with the corresponding .tex) that gives the brief rules to follow;
there is a larger file in the same directory called SienaDeveloper. This tells about the versions to use. Currently indeed the next version will be 1.1-301; if you happen to wait until I’ll have committed my next changes (could be next week), this will have
changed to 1.1-302. To be safe, I always first do Tortoise-update before Tortoise-commit.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">There are no currently active plans to replace siena07 by sienacpp. Some options are different between the two. Evidently it is unpleasant to maintain two different
functions that do almost the same. I copy in Felix Schoenenberger who wrote sienacpp and still is working on elaborating the GMM estimator.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Changing the printing of warnings and messages to using R functions would be great indeed.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Tom<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">==============================<wbr>==============================<wbr>====<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Tom A.B. Snijders<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Professor of Statistics and Methodology<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dept. of Sociology, University of Groningen<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Emeritus Fellow, Nuffield College, University of Oxford<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Associate Member, Dept. of Statistics, University of Oxford<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://www.stats.ox.ac.uk/~snijders/" target="_blank">http://www.stats.ox.ac.uk/~<wbr>snijders/</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> George Vega Yon [mailto:<a href="mailto:g.vegayon@gmail.com" target="_blank">g.vegayon@gmail.com</a>]
<br>
<b>Sent:</b> 04 October 2016 23:58<br>
<b>To:</b> Tom Snijders<br>
<b>Cc:</b> Christian Steglich (<a href="mailto:c.e.g.steglich@rug.nl" target="_blank">c.e.g.steglich@rug.nl</a>) (<a href="mailto:c.e.g.steglich@rug.nl" target="_blank">c.e.g.steglich@rug.nl</a>)<br>
<b>Subject:</b> Re: [Rsiena-help] More flexibility on using Clusters<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Dear Prof. Snijders,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I've just finished adding the new feature in -siena07- allowing to pass a cluster object (cl) directly. I've included a simple example in tests/parallel.R and added the new argument in the documentation of siena07.r without changing the
sienacpp function. Before pushing my changes, I wanted to ask you something: In the ChangeLog file, what revision number should I include (currently 300)? Should I change the version number as well? If so, what versioning system do you use?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">About the sienacpp parallelization method, are you planning to replace siena07 with sienacpp? I get that using OpenMP for parallelization might better but, as user, I think it is nice to have the option of using parallel::makeCluster since
it can be useful for some (as myself). Ideally one could have both options: Split the work into C computers and latter use OpenMP within each computer to speed up things even more.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Finally, looking around I realized that you have a lot of lines creating warnings and printing messages on the screen. While those do the work it might be useful to use R's warning() and message() built in functions instead since the former
allows R keeping track of warnings internally and both allow using the functions suppressWarnings() and suppressMessages(). Perhaps I might be able to change those some time if you are OK with that (not a big change but makes it nicer with R... warnings show
with different color in RStudio for example).<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
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<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
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<p class="MsoNormal">George G. Vega Yon<br>
<a href="tel:%2B1%20%28626%29%20381%208171" value="+16263818171" target="_blank">+1 (626) 381 8171</a><br>
<a href="http://www.its.caltech.edu/~gvegayon/" target="_blank">http://www.its.caltech.edu/~<wbr>gvegayon/</a><u></u><u></u></p>
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