From hpages at fhcrc.org  Thu Jul 16 23:06:26 2009
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Thu, 16 Jul 2009 14:06:26 -0700
Subject: [Rd] Resizing a named vector crashes
	R	with	gctorture(TRUE)	(PR#13837)
In-Reply-To: <4A5F7771.70706@stats.uwo.ca>
References: <20090716004516.0A505282BE84@mail.pubhealth.ku.dk>
	<4A5E7E07.8040203@fhcrc.org> <4A5E8D3A.30206@fhcrc.org>
	<4A5EFD11.4000702@stats.uwo.ca> <4A5F72C9.5090402@fhcrc.org>
	<4A5F7771.70706@stats.uwo.ca>
Message-ID: <4A5F9652.1090300@fhcrc.org>

Duncan Murdoch wrote:
> On 7/16/2009 2:34 PM, Herv? Pag?s wrote:
>> Duncan Murdoch wrote:
>>> On 15/07/2009 10:15 PM, Herv? Pag?s 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.

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.
>>>>
>>>>
>>>> Herv? Pag?s wrote:
>>>>> murdoch at stats.uwo.ca wrote:
>>>>>> On 15/07/2009 8:30 PM, murdoch at stats.uwo.ca wrote:
>>>>>>> On 15/07/2009 8:08 PM, Herv? Pag?s 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.
>>>>>>>>
>>>>>>>>
>>>>>>>> hpages at 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
>>>>>>>>>
>>>>>>>>> ______________________________________________
>>>>>>>>> R-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>>> ______________________________________________
>>>>>>> R-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>> ______________________________________________
>>>>>> R-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>
> 

-- 
Herv? Pag?s

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)
=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=