parallel

[tom]

Hi Karl:

I'm running into an error message trying to run permutations using multiple processors.  I'm working on a windows 64 bit machine with a quad core with windows 7.  I previously had success using multiple cores with the snow/relcuyer implementation in r/qtl.  With the most recent version of rqtl I'm getting this error message:

Error in mclapply(rep(n.perm, n.cluster), scantwoPermInParallel, cross = cross,  :
  'mc.cores' > 1 is not supported on Windows

Any sidestep to the problem? os is this simply a limitation to parallel on a windows machine.
Let me know if you have any thoughts - and happy new year!
Best,
Tom

[Karl Broman]

Hi, Tom,

What versions of R and R/qtl are you using?

If you're not using the latest versions (R 3.0.2 and R/qtl 1.29-2), maybe upgrading to the latest versions will solve the problem.
karl

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[tom]

Hi Karl:

I'm working with R3.0.2 and 1.29-2 .....and still get the error message.
TJ

[Karl Broman]

Hi, Tom,

It seems that that the function I'm using for parallel analysis, mclapply, doesn't work on Windows. Oops!

http://www.r-bloggers.com/a-no-bs-guide-to-the-basics-of-parallelization-in-r/

I'll work on it.

regards,
karl

[Karl Broman]

I've fixed the problem but haven't yet tested it in Windows.

You could try installing the development version from Github, using Hadley Wickham's devtools package.

If you don't have devtools installed, install it with:

  install.packages("devtools")

Load the devtools package and then attempt to install R/qtl:

  library(devtools)

  install_github("qtl", "kbroman", "devel")

karl

[Karl Broman]

I've not been able to test the changes yet, but I was able to compile the package for windows:

  http://www.rqtl.org/download/devel/

Let me know if it works for you.

karl

[tom]

Hi Karl:

That runs on my 32-bit R installation.....
Thanks,
Tom