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POUbuntu R ForEach / DoMC not using multiple cores
 

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  1. POUbuntu R ForEach / DoMC not using multiple cores
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    <p>I have built a function in R (running on Ubuntu 12.04 LTS 64bit, 4 core i7 server with multithreading and 6gb ram) where I've installed R using the standard packages:</p> <pre><code>sudo apt-get install r-base r-recommended r-base-dev sudo apt-get install r-cran-multicore r-cran-iterators r-cran-foreach r-cran-domc </code></pre> <p>NB: I also installed <code>foreach</code> &amp; <code>doMC</code> inside R (which didn't help either), like I installed the <code>deldir</code> package:</p> <pre><code>install.packages(c("deldir"), dependencies = TRUE) </code></pre> <p>My function runs fine, but it does not use parallel cores (just maxes out 1 of the 8):</p> <pre><code>library(deldir) library(foreach) library(doMC) registerDoMC(cores=8) #getDoParWorkers() #getDoParName() #getDoParVersion() # loop through files inputfiles &lt;- dir(path="/home/geoadmin/data/objects/", pattern='.txt') for( inputfilenr in 1:length(inputfiles)) { # set file variables curinputfile = paste("/home/geoadmin/data/objects/",inputfiles[[inputfilenr]], sep = "", collapse = NULL) print (curinputfile) curoutputfile = paste("/home/geoadmin/data/objects/",substr(inputfiles[[inputfilenr]], start=1, stop=10), '.out', sep = "", collapse = NULL) # select the point x/y coordinates into a data frame... points &lt;- read.csv(curinputfile, header = TRUE, sep = ",", dec=".", fill = TRUE) # set calculation variables, precision on 3 digits only because of the RDW coordinate system voro = deldir(points$x, points$y, digits=3, list(ndx=2,ndy=2), rw=c(min(points$x)-abs(min(points$x)-max(points$x)), max(points$x)+abs(min(points$x)-max(points$x)), min(points$y)-abs(min(points$y)-max(points$y)), max(points$y)+abs(min(points$y)-max(points$y)))) tiles = tile.list(voro) poly = array() # start loop poly &lt;- foreach (i=1:length(tiles), .combine=cbind) %dopar% { # load tile info tile = tiles[[i]] # start with EWKB notation curpoly = "POLYGON((" # add list of coordinates by looping through the points in tile for (j in 1:length(tiles[[i]]$x)) { curpoly = sprintf("%s %.6f %.6f,",curpoly,tile$x[[j]],tile$y[[j]]) } # then again the first point to close the polygon and end the EWKB notation, adding that to the poly array sprintf("%s %.6f %.6f))",curpoly,tile$x[[1]],tile$y[[1]]) } write.csv(t(poly), file = curoutputfile, row.names = FALSE) } </code></pre> <p>So the results are good, but no parallelism... </p> <p><code>doMC</code> did register correctly:</p> <pre><code>&gt; getDoParWorkers() [1] 8 &gt; getDoParName() [1] "doMC" &gt; getDoParVersion() [1] "1.2.5" </code></pre> <p>If I look at the usage (with <code>top</code>):</p> <pre><code>top - 01:03:19 up 9 min, 3 users, load average: 1.02, 0.86, 0.45 Tasks: 131 total, 2 running, 127 sleeping, 0 stopped, 2 zombie Cpu(s): 12.5%us, 0.0%sy, 0.0%ni, 87.5%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 6104932k total, 1240512k used, 4864420k free, 16656k buffers Swap: 6283260k total, 0k used, 6283260k free, 141996k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1553 zzzzzzzz 20 0 913m 850m 3716 R 100 14.3 8:22.03 R </code></pre> <p>So just maxing out one core. Does anyone have any idea what could cause <code>foreach</code>/<code>doMC</code> to not use multiple cores?</p> <pre><code>&gt; sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doMC_1.2.5 multicore_0.1-7 iterators_1.0.6 foreach_1.4.0 [5] deldir_0.0-19 loaded via a namespace (and not attached): [1] codetools_0.2-8 </code></pre>
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    1. USJoshua Ulrich
    1. USCarst
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    1. COCan you post the output of `sessionInfo()`?
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      1. USDason
    2. COAdded it! thanks for your interest!
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      1. POUbuntu R ForEach / DoMC not using multiple cores
      1. USCarst
    3. COJust to confirm: foreach/mc does work on the computer itself (with the standard example). So something in the specific code stops the multiprocessor part. But thinking of it, it might be that the deldir package takes up 99% of the time in the whole procedure. I could also do the file loop in parallel but would take up a lot of memory...
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