On Tue, 7 Aug 2018, Jan van der Laan wrote:
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?
If you are not opening files through R connections then this is not relevant.
If you are opening files on your own via C or C++ level calls then it
is a good idea to run gc if there is a failure -- that is what the
connections code does. I would put this logic at a low level, inside
lvec and such, before signaling an error. But this should be a
fall-back. You might be starving other libraries of file handles
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.
Have you done enough profiling to be sure this is true, in particular
for realistic usage, not small toy examples? This would be the
cleanest design. You could also maintain a small cache of open files,
but that is more work to implement.
Best,
luke
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
______________________________________________
r-package-de...@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
