Duncan Murdoch wrote:
On 16/07/2009 5:06 PM, Hervé Pagès wrote:
Duncan Murdoch wrote:
On 7/16/2009 2:34 PM, Hervé Pagès wrote:
Duncan Murdoch wrote:
On 15/07/2009 10:15 PM, Hervé Pagès wrote:
I have to confess that I'm a little bit puzzled by how the
PROTECT/UNPROTECT mechanism is used in the C code of R.
Duncan, you say the problem you just fixed was an easy one.
I looked at the C code too and was able to recognize a pattern
that is indeed easy to identify as problematic:
an unprotected call to allocVector() followed by a call
that can trigger garbage collection (in that case another
call to allocVector())
It only took me 1 minute to find another occurrence of this pattern.
It's in the do_grep() function (src/main/character.c, line 1168):
> gctorture(TRUE)
> grep("b", c(A="aa", B="aba"), value=TRUE)
B
"B"
Given that the overhead of PROTECTing the SEXP returned by
allocVector() can really be considered 0 (or almost), I'm
wondering why this is not done in a more systematic way.
This is an explanation, not a justification:
If you look at the history of that file, you'll see a hint: line
1168 was written in 1998, the other lines were written later, by
other people. It is simply a matter of someone thinking something
was safe when it wasn't, and it's not clear who was wrong: it may
have been safe when written, but susceptible to later changes.
Even when nothing between PROTECT(allocVector()) and the
corresponding UNPROTECT could trigger garbage collection
(e.g. PROTECT(allocVector()) is close to the return statement).
Because making exceptions like this can make your code
really hard to maintain in the long term.
There are a lot of people who object to anything that slows R at
all. That puts pressure on anyone writing code to do it in a way
that wastes as few cycles as possible. That in turn makes it
harder for someone else to analyze the code. And overuse of
PROTECT also makes the code harder to read.
Most of the calls to allocVector() are currently protected. There is a
very small percentage of calls to allocVector() that are not. Most of
the times because people apparently decided that, at the time they
wrote
the code, it didn't seem necessary. It doesn't matter if they were
wrong
or write. My point is that this game is not worth it.
I bet if you protected all the calls to allocVector() you wouldn't
notice
any slow down in R. What is guaranteed though is that you end up
with code
that sooner or later will break because of some changes that are
made to
the function itself or to another function called by your function
(because
this other function is now calling gc and you were assuming that it
wouldn't
do that).
And this kind of breakage is one of the worst kinds: if you are lucky,
you get a segfault, but if you are not, you don't notice anything and
get the wrong answer, like in the length<-() and grep() examples (and
you can safely assume that there are many other places like this in R).
I guess 99.999% of R users would happily trade a 0.001% slow down for
a correct result.
First make it right, then make it fast. And sorry, but you're not going
to make it fast by saving a few calls to PROTECT() here and here.
As I said, I gave you an explanation, not a justification. I
generally agree with you, but not everyone does. For example, after
posting the first patch I received a private email suggesting that
the following PROTECT on xnames could be removed. I didn't remove
it, because I think it is mostly harmless, and it's not worth my time
to analyze whether any particular PROTECT is unneeded.
I generally agree with you, but I don't totally agree with you. The
protection stack is not infinite, so any time you add a PROTECT you
have to be sure it will be removed in a relatively short time. You
can't have something like
for (i=0; i < n; i++) { PROTECT( ans <- allocVector(...) ) ; ... }
UNPROTECT(n);
because you are likely to blow the stack when n is large. You need
the UNPROTECTs within the loop, but still after ans stops being
vulnerable to garbage collection.
Indeed, putting the UNPROTECT out of the loop would be a bad idea.
The only reason I see people would do this is because they have
some continue, break or return statements inside the loop and they
don't want to put the UNPROTECT before each of them.
But most of the times, it should be clear where to put the UNPROTECT,
and, if this is not the case, then that means that it was not clear
either that ans didn't need to be protected in the first place!
It's hard to place them automatically. And every extra
function/macro call adds to the obscurity of the code, so it's harder
to read it and know whether it really does what you wanted it to. My
inclination is to over-PROTECT things, but not to PROTECT everything.
I didn't say everything should be protected. Just that
PROTECT(allocVector()) could be used in a more systematic way.
Tell me the system.
OK, the system is the following. Here "you" is not you Duncan, but
the developer that is facing a protect-or-not-protect dilemma.
Every time you are tempted to write
x = allocVector();
think about what will happen the day someone will come and
add the following line right after your line:
y = allocVector();
Then cross your finger that s/he will remember to fix your code.
Alternatively you have the option to anticipate and make your
code safer in the long run. It's easy and at the same time you
show that you care more about long term maintainability than
saving an insignificant number of CPU cycles.
It's easy to imagine that people will be reluctant to change
things like:
ans_elt = allocVector();
SET_VECTOR_ELT(ans, i, ans_elt);
but I still think that the following is as good and not a lot
harder to read:
PROTECT(ans_elt = allocVector());
SET_VECTOR_ELT(ans, i, ans_elt);
UNPROTECT(1);
But maybe you can have a short list of authorized exceptions
to the rule for these very simple cases.
Otherwise, when you see code like
/* No protection needed as ExtractSubset does not allocate */
result = allocVector(mode, n);
PROTECT(result = ExtractSubset(x, result, indx, call));
it's nice to have a comment, but since 'result' gets finally
protected (ExtractSubset returns the same 'result' that was
passed to it), then why not just do:
PROTECT(result = allocVector(mode, n));
result = ExtractSubset(x, result, indx, call);
so you don't need to comment anything and the day someone
decides to allocate in ExtractSubset you are still good.
More generally, when a function is changed from being
non-allocating to be allocating, is the person in charge of
this change also supposed to come to every place where the
function is called and add the missing PROTECT/UNPROTECT?
Even worse, if it's a low-level routine that becomes an
allocating function, it could be that dozens or hundreds
of higher level functions now become allocating (being an
allocating function is a property that propagates to the
parents of the function), so the person can end up having to
check hundreds of places! The task might just become impossible.
H.
Duncan Murdoch
Thanks,
H.
Duncan Murdoch
Cheers,
H.
As an example: just below line 1168 there's another unprotected
allocVector of nm, but I think that one is safe, because it is
attached as an attribute to ans (which is now PROTECT'd) before
anything is done that could trigger gc. And a few lines below
that, on another branch of the if, another unprotected but
safe-looking allocation. Should I protect those? Then I'd also
need to call UNPROTECT again, or keep a counter of PROTECT calls,
and the code would be a little harder to read.
Thanks for tracking down these two bugs; I'll fix the grep bug
too. If you feel like looking for more, it would be appreciated.
(Writing an automatic tool to analyze code and determine where new
ones are needed and where existing ones could be eliminated might
be a fun project, but there are too many fun projects.)
Duncan Murdoch
Cheers,
H.
Hervé Pagès wrote:
murd...@stats.uwo.ca wrote:
On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote:
On 15/07/2009 8:08 PM, Hervé Pagès wrote:
Hi,
> x <- c(a=10, b=20)
> length(x) <- 1
> x
a
10
But with gctorture turned on, I get:
> gctorture(TRUE)
> x <- c(a=10, b=20)
> length(x) <- 1
> x
a
"a" <---- ???
> x <- c(a=10, b=20)
> length(x) <- 3
*** caught segfault ***
address (nil), cause 'unknown'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
This seems to have been around for a while (I get this with R
2.10,
2.9 and 2.8). Note that I don't get this with an unnamed vector.
This problem affects the methods package. I found it while
troubleshooting the "Protection stack overflow" I reported
earlier
(see
https://stat.ethz.ch/pipermail/r-devel/2009-July/054030.html)
but I can't tell yet whether the 2 issues are related or not.
That's clearly a bug (reproducible in today's R-devel build);
I've cc'd this reply to r-bugs. I'll take a look and see if I
can track it down.
That's got to be the easiest low-level bug I've worked on in a
while. Just a missing PROTECT. Now fixed, about to be committed
to R-devel.
Thanks Duncan! And the "Protection stack overflow" issue that was
affecting
the methods package is gone now :)
Cheers,
H.
Duncan Murdoch
It would be nice to see some reaction from the R developers
about these issues. Thanks in advance!
You should post them as bug reports if they are as clearly bugs
as this one; otherwise they can easily get lost in the noise.
I'm not going to offer to look into the other one; I don't know
the insides of the methods package.
Duncan Murdoch
H.
hpa...@fhcrc.org wrote:
Hi,
> gctorture(TRUE)
> setGeneric("foo", function(x, y) standardGeneric("foo"))
[1] "foo"
> setMethod("foo", c("ANY", "ANY"),
+ function(x, y) cat("calling foo,ANY,ANY method\n")
+ )
Error: protect(): protection stack overflow
Sorry this is something I already reported one week ago here
https://stat.ethz.ch/pipermail/r-devel/2009-July/053973.html
but I just had a 2nd look at it and realized that the problem
can in fact be reproduced out of the .onLoad() hook. So I'm
reporting it again with a different subject.
See my sessionInfo() below. Thanks!
H.
sessionInfo()
R version 2.10.0 Under development (unstable) (2009-06-26
r48837)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets
methods base
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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