[Rd] memory consumption of nested (un)serialize of sys.frames()

Andreas Kersting r-deve| @end|ng |rom @ker@t|ng@de
Wed Apr 7 11:28:35 CEST 2021


please consider the following minimal reproducible example:

Create a new R package which just contains the following two (exported) objects:

crash_dumps <- new.env()

f <- function() {
  x <- runif(1e5)
  dump <- lapply(1:2, function(i) unserialize(serialize(sys.frames(), NULL)))
  assign("last.dump", dump, crash_dumps)

WARNING: the following will probably eat all your RAM!

Attach this package and run:

for (i in 1:100) {

You will notice that with each iteration the execution of f() slows down significantly while the memory consumption of the R process (v4.0.5 on Linux) quickly explodes.

I am having a hard time to understand what exactly is happening here. Something w.r.t. too deeply nested environments? Could someone please enlighten me? Thanks!


In an R package I store crash dumps on error in a parallel processes in a way similar to what I have just shown (hence the (un)serialize(), which happens as part of returning the objects to the parent process). The first 2 or 3 times I do so in a session everything is fine, but afterwards it takes very long and I soon run out of memory.

Some more observations:
- If I omit `x <- runif(1e5)`, the issues seem to be less pronounced.
- If I assign to .GlobalEnv instead of crash_dumps, there seems to be no issue - probably because .GlobalEnv is not included in sys.frames(), while crash_dumps is indirectly via the namespace of the package being the parent.env of some of the sys.frames()!?
- If I omit the lapply(...), i.e. use `dump <- unserialize(serialize(sys.frames(), NULL))` directly, there seems to be no issue. The immediate consequence is that there are less sys.frames and - in particular - there is no frame which has the base namespace as its parent.env.
- If I make crash_dumps a list and use assignInMyNamespace() to store the dump in it, there also seems to be no issue. I will probably use this as a workaround:

crash_dumps <- list()

f <- function() {
  x <- runif(1e5)
  dump <- lapply(1:2, function(i) unserialize(serialize(sys.frames(), NULL)))
  crash_dumps[["last.dump"]] <- dump
  assignInMyNamespace("crash_dumps", crash_dumps)

More information about the R-devel mailing list