Hi, You already asked this here (http://stackoverflow.com/questions/28357210/parallel-computing-in-r) and got some comments.
Regards, Pascal On Fri, Feb 6, 2015 at 11:58 AM, Zhenchuan Wang <zwan...@mtu.edu> wrote: > I usually need to compute P-values as following: > 1. generate one sample (usually it is a matrix) > 2. apply several methods (I already wrote a subfunction for each method, > and they are independent) to the generated sample to get pvalues. > 3. compare the pvalues. > Since each method mentioned above takes long time (always different length > of time) to compute the pvalue, I am try to computing the pvalues parallel. > I want to assign computation of each method to each cores (I have intel > i7). Do you have any suggestion? I put the four subfunctions together as > > main.fun=function(i,x,y,numper) > { > if (i==1) z=cca1(y,x,numper) > if (i==2) z=2 > if (i==3) z=2 > if (i==4) z=3 > z > } > > Each i indicates ith subfunction. > But I always get > > task 1 failed - "Lapack routine dgesv: system is exactly singular: > U[84,84] = 0" > > But when I only run `cca1` function (not using `foreach`), there is no > error. > The `foreach` is like this > > pvalue=foreach(i=1:4,.combine=c,.packages=c("MASS","base")) %dopar% > main.fun(i,x,y,500) > > The single computation is like this > > pvalue=cca1(y,x,500) > > I also put following in the top lines of my program > > library(foreach) > library(doSNOW) > library(MASS) > cl=makeCluster(4,type="SOCK") > registerDoSNOW(cl) > > **This looks like when I compute the `pvalue` separately not using > `foreach`, there is no error. But when I combine the subfuntions togeter > like `main.fun`, it has error.** > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.