[R-sig-hpc] Embarrasingly parallel computation of models

[Stefan Lüdtke]

Hi Michael,

hope I  don't write to much nonsense, but after giving the index "i" to
the the list, it complains about the data object that is not found. what
is true since I do not have a object "selected"


> outputList <- foreach(i = 1:4) %dopar% glmer(formulaList[[i]], family
= binomial, data = selected)
Error in glmer(formulaList[[i]], family = binomial, data = selected) :
  task 1 failed - "object 'selected' not found"

HTH, 


Stefan



On 09/06/2013 01:34 PM, Michael Kubovy wrote:
> Dear HPC people,
> 
> I'm trying to leasrn how to run multiple independent models in parrallel. I have succesfully run parallel computations on different sets of data (using 12 of my 24 cores). But there's something (probably trivial) about the nature of formulae that is escaping me. Here is what I tried.
> 
> I store my formulae:
> 
> formulaList <- vector('list', length = 4)
> formulaList[[1]] <- 'resp ~ BAratio +dispDiff + (BAratio + dispDiff | subject)'
> formulaList[[2]] <- 'resp ~ BAratio * dispDiff + (BAratio * dispDiff | subject)'
> formulaList[[3]] <- 'resp ~ BA3Dratio + dispDiff + (BA3Dratio + dispDiff | subject)'
> formulaList[[4]] <- 'resp ~ BA3Dratio * dispDiff + (BA3Dratio * dispDiff | subject)'
> 
> I get workers:
> 
> require(foreach)
> require(doMC)
> registerDoMC()
> getDoParWorkers()
> 
> I try to run:
> 
> outputList <- foreach(i = 1:4) %dopar% glmer(formulaList, family = binomial, data = selected)
> 
> I get: Error: task 1 failed - "invalid formula"
> 
> FYI
> 
>> sessionInfo()
> R version 3.0.1 Patched (2013-09-02 r63805)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] splines   datasets  utils     stats     graphics  grDevices methods   base     
> 
> other attached packages:
>  [1] lme4_0.999999-2   Matrix_1.0-12     lattice_0.20-23   xtable_1.7-1      gamlss_4.2-6      nlme_3.1-111     
>  [7] gamlss.data_4.2-6 gamlss.dist_4.2-0 plyr_1.8          foreach_1.4.1     sos_1.3-7         brew_1.0-6       
> [13] ggplot2_0.9.3.1   car_2.0-18        nnet_7.3-7        MASS_7.3-29      
> 
> loaded via a namespace (and not attached):
>  [1] codetools_0.2-8    colorspace_1.2-2   compiler_3.0.1     dichromat_2.0-0    digest_0.6.3       grid_3.0.1        
>  [7] gtable_0.1.2       iterators_1.0.6    labeling_0.2       munsell_0.4.2      proto_0.3-10       RColorBrewer_1.0-5
> [13] reshape2_1.2.2     scales_0.2.3       stats4_3.0.1       stringr_0.6.2      survival_2.37-4    tools_3.0.1       
> 
> ______________________________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
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