From murdoch at stats.uwo.ca  Sun Jul 20 16:39:33 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Sun, 20 Jul 2008 10:39:33 -0400
Subject: [Rd] garbage collection, "preserved" variables,
 and different outcome depending on "--verbose" or not
In-Reply-To: <27d1e6020807200702sbb97febw96a4bbd7cf43b809@mail.gmail.com>
References: <27d1e6020807200601q41312608x7c1c2c5864c83068@mail.gmail.com>	<48834344.603@stats.uwo.ca>
	<27d1e6020807200702sbb97febw96a4bbd7cf43b809@mail.gmail.com>
Message-ID: <48834E25.2020602@stats.uwo.ca>

On 20/07/2008 10:02 AM, Laurent Gautier wrote:
> I tripped on that while crafting the example.
> 
> The problem still exists when moving the "releases" in the middle,
> and removing the last "release".

I can't spot any problems in the new version of your code, but I can't 
reproduce the problem, either.  So it appears to be system specific -- I 
was using the identical revision as you, but on Windows, not 
"x86_64-unknown-linux-gnu".  What exact Linux is that?  Can others using 
that system (or similar ones) reproduce it?

Duncan Murdoch

> 
> 
> #include <R.h>
> #include <Rdefines.h>
> 
> 
> SEXP createObject(void)
> {
>   SEXP x_R;
>   int len_x = 1000000;
>   PROTECT(x_R = allocVector(REALSXP, len_x));
>   Rprintf("Created 'x' at %p\n", x_R);
>   Rprintf("  (mode is %i, length is %i)\n", TYPEOF(x_R), LENGTH(x_R));
>   Rprintf("  (first element is %d)\n", REAL(x_R)[0]);
>   R_PreserveObject(x_R);
>   UNPROTECT(1);
>   return x_R;
> }
> 
> void printObject(SEXP sexp)
> {
>   Rprintf("object at %p\n", sexp);
>   Rprintf("  (mode is %i, length is %i, named is %i)\n",
> 	  TYPEOF(sexp), LENGTH(sexp), NAMED(sexp));
> }
> 
> SEXP lostobject(SEXP n_R)
> {
>   /*
>    * This function will:
>    * 1- create a numerical vector "x" and "preserve it"
>    * 2- make call "list(x)"
>    * 3- return "x" to R
>    */
> 
> 
>   SEXP x_R;
>   int i;
> 
>   int n = INTEGER(n_R)[0];
> 
>   /* Create a numerical vector "x_R" */
> 
>   for (i=0; i<n; i++) {
>     x_R = createObject();
>     printObject(x_R);
>     R_ReleaseObject(x_R);
>     R_gc();
>   }
> 
>   x_R = createObject();
>   printObject(x_R);
>   R_gc();
> 
>   Rprintf("Returning 'x' at %p\n", x_R);
>   Rprintf("  (first element is %d)\n", REAL(x_R)[0]);
>   return x_R;
> }
> 
> 
> 2008/7/20 Duncan Murdoch <murdoch at stats.uwo.ca>:
>> On 20/07/2008 9:01 AM, Laurent Gautier wrote:
>>> Dear list,
>>>
>>> While trying to identify the root of a problem I am having with
>>> garbage collected variables,
>>> I have come across the following oddity: depending on whether --verbose is
>>> set
>>> or not, I obtain different results.
>> You are working with variables without protecting them, so you just get
>> lucky whenever the code works.
>>
>> More below...
>>
>>> I have made a small standalone example to demonstrate it.
>>> The example is very artificial, but I had a hard time reproducing
>>> reliably the problem.
>>>
>>> So when I do: (the content of test.R is at the end of this email)
>>>
>>> R --no-save < test.R
>>>
>>> [The two last lines of the output are:]
>>>> x[1:3]
>>> [1] 0 0 0
>>>
>>> while with
>>>
>>> R --verbose --no-save < test.R
>>>
>>> [The two last lines of the output are:]
>>>> x[1:3]
>>> [1] 3.733188e-317 3.137345e-317 3.137345e-317
>>>
>>>
>>> The C code is compiled with:
>>> R CMD SHLIB test_lostobject.c
>>>
>>>
>>>> sessionInfo()
>>> R version 2.7.1 Patched (2008-07-19 r46081)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>>
>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>>
>>> ### -- file test.R
>>>
>>> dyn.load("test_lostobject.so")
>>>
>>> x = .Call("lostobject", as.integer(5))
>>>
>>> x[1:3]
>>>
>>>
>>> ### ---
>>>
>>> ###--- file lostobject.c
>>>
>>> #include <R.h>
>>> #include <Rdefines.h>
>>>
>>>
>>>
>>> SEXP createObject(void)
>>> {
>>>  SEXP x_R;
>>>  int len_x = 1000000;
>>>  PROTECT(x_R = allocVector(REALSXP, len_x));
>>>  Rprintf("Created 'x' at %p\n", x_R);
>>>  Rprintf("  (mode is %i, length is %i)\n", TYPEOF(x_R), LENGTH(x_R));
>>>  Rprintf("  (first element is %d)\n", REAL(x_R)[0]);
>>>  R_PreserveObject(x_R);
>>>  UNPROTECT(1);
>>>  return x_R;
>>> }
>>>
>>> void printObject(SEXP sexp)
>>> {
>>>  Rprintf("object at %p\n", sexp);
>>>  Rprintf("  (mode is %i, length is %i, named is %i)\n",
>>>          TYPEOF(sexp), LENGTH(sexp), NAMED(sexp));
>>> }
>>>
>>> SEXP lostobject(SEXP n_R)
>>> {
>>>  /*
>>>   * This function will:
>>>   * 1- create a numerical vector "x" and "preserve it"
>>>   * 2- make call "list(x)"
>>>   * 3- return "x" to R
>>>   */
>>>
>>>
>>>  SEXP x_R;
>>>  int i;
>>>
>>>  int n = INTEGER(n_R)[0];
>>>
>>>  /* Create a numerical vector "x_R" */
>>>
>>>  for (i=0; i<n; i++) {
>>>    x_R = createObject();
>>>    R_ReleaseObject(x_R);
>> At this point, the variable is unprotected, i.e. you have declared that  its
>> memory is free for the taking.  You should not try to do anything with it.
>>  printObject calls several functions, and one of those may have overwritten
>> the memory.  It's not surprising that different flags (--verbose or not)
>> result in different behaviour.
>>
>>>    printObject(x_R);
>>>    R_gc();
>>>  }
>>>
>>>  x_R = createObject();
>>>  printObject(x_R);
>>>  R_gc();
>>>  R_ReleaseObject(x_R);
>> Same thing here.  x_R is unprotected now, so you shouldn't use it.
>>
>> Duncan Murdoch
>>
>>>  Rprintf("Returning 'x' at %p\n", x_R);
>>>  Rprintf("  (first element is %d)\n", REAL(x_R)[0]);
>>>  return x_R;
>>> }
>>>
>>> ______________________________________________
>>> 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



[Rd] garbage collection, "preserved" variables, and different outcome depending on "--verbose" or not
Duncan Murdoch