Unfortunately Duncan's suggestion to restart is probably the only way to go here. I've done similar thing myself too. What I've learned was that it is clever to include a so called hot-patch mechanism in your code, which will load R source code found in a certain directory, say, "hot/", once in a while (easy if you have do interations) and at the end of the batch code. Here is the idea (typed out of my head):
patchCode <- function(path="hot", pattern="[.]R$", removeAfter=FALSE, ...) { files <- list.files(pattern=pattern, path=path, full.names=TRUE); for (file in files) { tryCatch({ # You don't want you patch code to kill you batch job, # if you for instance have a typo. cat("Hot-path file: ", file, "\n"); source(file); # Remove the file afterwards? Especially useful if you only # want to redefine functions, and patch once. This way you # can also see what files has successfully been source():ed. if (removeAfter) file.remove(file); }, error = function(ex) { cat("Ignored error when sourcing:\n"); print(ex); }) } } # patchCode() Then in your batch code something like this: while (!converged) { # Patch the code every iteration. patchCode(path="hot/", removeAfter=TRUE) # The rest of your code here } # Put the code you want to call at the end, in a directory # of its own. patchCode(path="hot/onFinally/", removeAfter=TRUE) # End of your batch code Cheers Henrik Duncan Murdoch wrote: > Jean Eid wrote: > >>This is probably a weird question but I need to know if there is a way... >> >>I run an R batch job without saving the variables at each step to the >>disk. Is there a way to invoke another session of R and link it to the >>same environment for read only. >> >>The problem is that I am running optim with every step getting the >>parameters into the global env using <<- However, I forgot to issue a >>save(list=ls(),...) right after so I can load and see how the parameters >>are changing. It's been couple of days and it is still running so I am >>hoping that I can invoke another session of R and link it to the >>environment of the batch session. Does this sound totally ridiculous ? >> >>it is a debian machine with R 2.1.1 > > > If you happened to have compiled R with debug information, you might be > able to use gdb or another debugger to examine variables in the running > process, but you probably didn't, and it's probably easier to kill the > job, fix it, and start it again, than it would be to learn how to see > the active variables using gdb. > > Duncan Murdoch > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html