Hi Simon, Sorry to be a bother, but is "disabling the Tcl/Tk event loop in the forked processes" something that a package maintainer should do? If so, how? Again, apologies if I've missed something obvious.
I maintain a package (Amelia) that has an optional tcltk GUI that folks can use and we are in the process of integrating the parallel package into the main algorithm. The package only loads tcltk if the user explicitly calls the GUI. There's no (obvious) way for a user to run the main amelia() function in parallel from the tcltk GUI, but the above bug can be triggered by opening the GUI (which loads tcltk), closing it, then attempting to run "amelia()" with multiple cores. To stop this, I've prevented anyone who has "tcltk" loaded from running amelia() with multiple cores. Obviously, I would prefer the status of tcltk in the user's environment not to matter, so if there is some way to disable tcltk in the forked processes, that would be great. Cheers, matt. ~~~~~~~~~~~ Matthew Blackwell Assistant Professor of Political Science University of Rochester url: http://www.mattblackwell.org On Sun, Feb 3, 2013 at 2:34 PM, Simon Urbanek <simon.urba...@r-project.org>wrote: > As Peter pointed out earlier, this is better addressed by disabling the > Tcl/Tk event loop in forked processes. > > Cheers, > Simon > > On Feb 2, 2013, at 5:02 PM, Paul Johnson wrote: > > > Dear R-devel friends: > > > > I'm back to bother you again about the conflict between mclapply and > > tcltk. I've been > > monitoring several packages that want to use mclapply to parallelize > > computations and > > need to figure out what should be done. > > > > It appears tcltk cannot be safely unloaded, so the best we can do is > > check for the presence of tcltk and stop if it is found before > > mclapply() is used. > > > > I wish you would please review my suggestion below. Maybe > checkForTcltk() > > could be used in the parallel package. Otherwise, we are letting > > people run with scissors. > > > > There's a warning about this in ?mclapply > > > > It is _strongly discouraged_ to use these functions in GUI or > > embedded environments, because it leads to several processes > > sharing the same GUI which will likely cause chaos (and possibly > > crashes). Child processes should never use on-screen graphics > > devices.(Warning in ?mclapply) > > > > Bug report: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15040) > > > > By the way, what is "embedded environments" in ?mclapply > > > > ## I don't want to crash your system, but if you want to see a freeze-up: > > ## change 0 to 1 and run this: > > if (0){ > > library(parallel) > > library(tcltk) > > example(mclapply) > > } > > > > ## What are packagers supposed to do if they want to call mclapply? > > ## It appears to me the best a package can do is scan for tcltk and > > ## stop. Here's a function that does so. > > > > checkForTcltk <- function(){ > > if ("tcltk" %in% loadedNamespaces()){ > > stop("This function cannot be used because the R tcltk > > package is loaded. It is necessary to Close R, and re-run > > the program making sure that tcltk is never loaded before > > this function is called.") > > } > > } > > > > ## put that to use. > > MCLApply <- function(){ > > if (!require(parallel)) stop ("parallel wouldn't load") > > checkForTcltk() > > example(mclapply) > > } > > > > ## test that: > > > > checkForTcltk() > > MCLApply() > > > > library(tcltk) > > checkForTcltk() > > > > > > ## Why can't tcltk just be unloaded? I don't understand, but it is a deep > > ## problem. > > > > ## Consider the ominous warnings in R detach's help: > > ## > > ## "Unloading some namespaces has undesirable side effects: e.g. > > ## unloading grid closes all graphics devices, and on most systems > > ## tcltk cannot be reloaded once it has been unloaded and may crash > > ## R if this is attempted." (Note: section of ?detach). > > ## > > ## To be fair, that does not say unloading tcltk is fatal, but > > ## reloading it is fatal. And I've seen plenty of times when > > ## unloading it is fatal. > > > > ## Example 1. Crash on library.dynam.unload() > > detach("package:tcltk", unload = TRUE) > > library.dynam.unload("tcltk", system.file(package = "tcltk")) > > > > ## Output > > ## > library.dynam.unload("tcltk", system.file(package = "tcltk")) > > ## > > > ## *** caught segfault *** > > ## address 0x7f69c9d99580, cause 'memory not mapped' > > > > ## Possible actions: > > ## 1: abort (with core dump, if enabled) > > ## 2: normal R exit > > ## 3: exit R without saving workspace > > ## 4: exit R saving workspace > > ## Selection: > > ## Process R segmentation fault at Sat Feb 2 13:55:08 2013 > > > > > > ## Example 2. > > library(tcltk) > > detach("package:tcltk", unload = TRUE) > > library.dynam.unload("tcltk", system.file(package = "tcltk")) > > example(mclapply) > > > > ## Output: > > > > ## > example(mclapply) > > > > ## *** caught segfault *** > > ## address 0x7f25ccbfe000, cause 'memory not mapped' > > > > ## Possible actions: > > ## 1: abort (with core dump, if enabled) > > ## 2: normal R exit > > ## 3: exit R without saving workspace > > ## 4: exit R saving workspace > > ## Selection: > > > > > > pj > > > > -- > > Paul E. Johnson > > Professor, Political Science Assoc. Director > > 1541 Lilac Lane, Room 504 Center for Research Methods > > University of Kansas University of Kansas > > http://pj.freefaculty.org http://quant.ku.edu > > > > ______________________________________________ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]]
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