Using source() within parallel foreach loops

Here is a toy example to illustrate my problem.

library(foreach) library(doMC) registerDoMC(cores=2)  foreach(i = 1:2) %dopar%{   i + 2 } [[1]] [1] 3  [[2]] [1] 4 

So far so good...

But if the code i + 2 is saved in the file addition.R and that I call that file using source() then

> foreach(i = 1:2) %dopar%{ +   source("addition.R") + } Error in { : task 1 failed - "object 'i' not found" 

3 Answers

Answers 1

I cannot fully reproduce your toy, but I had a smiliar problem, which I was able to solve by:

source(file, local = TRUE) 

which should parse the source in the local environment, i.e. recognizing i.

Answers 2

I finally solved the problem by converting the source("addition.R") to a function and simply passing the variables into it. I don't know why but the suggested solutions based on source(file, local = TRUE) does not work.

Answers 3

The comment by NiceE and the answer by Sosel already address this; when calling source(file) it defaults to source(file, local = FALSE), which means that the code in the file sourced is evaluating in the global environment ("user's workspace") and there is, cf. ?source. Note that there is no variable i in the global environment. The solution is to make sure the file sourced in the environment that calls it, i.e. to use source(file, local = TRUE).

Solution:

library("foreach")  y <- foreach(i = 1:2) %dopar% {   i + 2 } str(y)  doMC::registerDoMC(cores = 2L) y <- foreach(i = 1:2) %dopar% {   source("addition.R", local = TRUE) } str(y) 

Example of the same problem with a for() loop:

The fact that source() is evaluated in the global environment which is different from the calling environment where i lives can also be illustrated using a regular for loop by running the for loop in another environment than the global, e.g. inside a function or by:

local({   for(i in 1:2) {     source("addition.R")   } }) 

which gives:

Error in eval(ei, envir) : object 'i' not found 

Now, the reason why the above foreach(i = 1:2) %dopar% { source("addition.R") } works with registerDoSEQ() if and only if called from the global environment, is that then the foreach iteration is evaluated in the calling environment, which is the global environment, which is the environment that source() uses. However, if one used local(foreach(i = 1:2) %dopar% { ... }) also this fails analoguously to the above local(for(i in 1:2) { ... }) call.

In conclusion: nothing magic happens, but to understand it is a bit tedious.

If You Enjoyed This, Take 5 Seconds To Share It

• Facebook
• Twitter
• Google+
• StumbleUpon
• Digg
• Delicious
• LinkedIn
• Reddit
• Technorati