Dear Luke,
Thanks. See below
On 07-08-18 17:07, luke-tier...@uiowa.edu wrote:
In R 3.5 and later you should not need to gc() -- that should happen
automatically within the connections code.
Could you elaborate on what has changed in R 3.5? As far as I can tell
my problem also occurs in R 3.5 (my computer is still on 3.4.4; but I
assume the solaris CRAN machine isn't). And what do you mean with 'the
connections code'? Is there something I can so/should do to have the
garbage collector be a bit more aggressive in cleaning up my mess?
Nevertheless, I would recommend redesigning your approach to avoid
hanging onto open file connections as these are a scarce resource.
You can keep around your temporary files without having them open and
only open/close them on access, with the close run in an on.exit or a
tryCatch/finally clause.
I am afraid that this will have a large performance penalty. The files
in question are memory mapped files from which code will reading and
writing continuously in most cases. Of course, there will probably
objects that are not used for large amounts of time that could be
temporarily closed , but it will be a bit difficult for the package to
detect which objects that will be. I would have to write my own 'garbage
collector'.
Best,
Uwe
Best,
luke
On Tue, 7 Aug 2018, Jan van der Laan wrote:
Dear Uwe,
(When replying to your message, I sent the reply to r-devel and not
r-package-devel, as Martin Meachler suggested that this thread would
be a better fit for r-devel.)
Thanks. In the example below I used rm() explicitly, but in general
users wouldn't do that.
One of the reasons for the large number of file handles is that
sometimes unnamed temporary objects are created. For example:
library(ldat)
libraty(lvec)
a <- lvec(10, "integer")
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214753f2af0'
b <- as_rvec(a[1:3])
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec32146a50f383'
OPENFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214484b652c'
print(b)
[1] 0 0 0
gc()
CLOSEFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec3214484b652c'
CLOSEFILE '/tmp/RtmpVqkDsw/file32145169fb06/lvec32146a50f383'
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 796936 42.6 1442291 77.1 1168576 62.5
Vcells 1519523 11.6 4356532 33.3 4740854 36.2
For debugging, I log when files are opened and closed. The call
a[1:3] (which creates a slice of a) creates two temporary objects
[1]. These are only deleted when I explicitly call gc() or on some
other random moment in time.
I hope this illustrates the problem better.
Best,
Jan
[1] One improvement would be to create less temporary files; often
these contain only very little information that is better kept in
memory. But that is only a partial solution.
On 07-08-18 15:24, Uwe Ligges wrote:
Why not add functionality that allows to delete object + runs
cleanup code?
Best,
Uwe Ligges
On 07.08.2018 14:26, Jan van der Laan wrote:
In my package I open handles to temporary files from c++, handles
to them are returned to R through vptr objects. The files are
deleted then the corresponding R-object is deleted and the garbage
collector runs:
a <- lvec(10, "integer")
rm(a)
Then when the garbage collector runs the file is deleted. However,
on some platforms (probably with lower limits on the maximum number
of file handles a process can have open), I run into the problem
that the garbage collector doesn't run often enough. In this case
that means that another package of mine using this package
generates an error when its tests are run.
The simplest solution is to add some calls to gc() in my tests. But
a more general/automatic solution would be nice.
I thought about something in the lines of
robust_lvec <- function(...) {
tryCatch({
lvec(...)
}, error = function(e) {
gc()
lvec(...) # duplicated code
})
}
e.g. try to open a file, when that fails call the garbage collector
and try again. However, this introduces duplicated code (in this
case only one line, but that can be more), and doesn't help if it
is another function that tries to open a file.
Is there a better solution?
Thanks!
Jan
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