From hb at maths.lth.se  Sat Aug 27 12:09:09 2005
From: hb at maths.lth.se (Henrik Bengtsson)
Date: Sat, 27 Aug 2005 12:09:09 +0200
Subject: [Rd] Memory leakage/violation?
In-Reply-To: <431034D8.5030008@statistik.uni-dortmund.de>
References: <430F3B7A.5020807@maths.lth.se>
	<Pine.A41.4.61b.0508261146090.87310@homer03.u.washington.edu>
	<431034D8.5030008@statistik.uni-dortmund.de>
Message-ID: <43103BC5.3040909@maths.lth.se>

Thank you Thomas and Uwe for this.

This is really odd, because today I can neither reproduce it myself (I 
rebooted my computer this morning).   I try to recall what I did 
yesterday: I did _not_ reboot my machine, but I did install the latest 
binaries of R 2.1.1 and 2.2.0dev from CRAN.  I did close all R sessions 
and restarted them by R --vanilla (only one at the time) and got the 
same errors over and over for hours (trust me, I was really frustrated 
with my analysis).   Maybe a reboot would have solved it - I should know 
better and try that first!  A worse scenario is that the hardware was 
overheated or starts to fall apart.

To answer you question Uwe, I don't know about the compiler settings 
since I got the pre-build binaries from CRAN.

Best wishes

Henrik

Uwe Ligges wrote:
> Thomas Lumley wrote:
> 
>> I can't reproduce this on R2.2.0dev on Windows XP (in a few hundred 
>> tries), or running under Valgrind on AMD64 Linux (in four or five tries).
> 
> 
> Cannot reproduce either (using R-2.1.1 and an older version of R-devel, 
> though). Maybe a compiler issue?
> Henrik, do you use exactly the compiler set up mentioned in the manuals? 
> Which version of gcc? Did your emember to replace the f771.exe?
> 
> Uwe
> 
> 
> 
>>      -thomas
>>
>>
>> On Fri, 26 Aug 2005, Henrik Bengtsson wrote:
>>
>>
>>> Hi,
>>>
>>> I've spotted a possible memory leakage/violation in the latest R v2.1.1
>>> patched and R v2.2.0dev on Windows XP Pro SP2 Eng.
>>>
>>> I first caught it deep down in a nested svd algorithm when subtracting a
>>> double 'c' from a integer vector 'a' where both had finite values but
>>> when assigning 'a <- a - c' would report NaNs whereas (a-c) alone would
>>> not.  Different runs with the identical data would introduce NaNs at
>>> random positions, but not all the time.
>>>
>>> Troubleshooting is after a couple of hours still at v0.5, but here is a
>>> script that generates the strange behavior on the above R setups.  I let
>>> the script speak for itself.  Note that both the script 'strange.R' and
>>> the data 'strange.RData' is online too, see code below.
>>>
>>> People on other systems (but also on Windows), could you please try it
>>> and see if you can reproduce what I get.
>>>
>>> Cheers
>>>
>>> Henrik
>>>
>>>
>>> # The following was tested on: Windows XP Pro SP2 Eng with
>>> #   i) R Version 2.1.1 Patched (2005-08-25)
>>> #  ii) R 2.2.0 Under development (unstable) (2005-08-25 r35394M)
>>>
>>> # Start 'R --vanilla' and source() this script, i.e.
>>> #  source("http://www.maths.lth.se/help/R/strange.R")
>>> # If you do not get any errors, retry a few times.
>>>
>>> foo <- function(x) {
>>>  print(list(
>>>    name=as.character(substitute(x)),
>>>    storage.mode=storage.mode(x),
>>>    na=any(is.na(x)),
>>>    nan=any(is.nan(x)),
>>>    inf=any(is.infinite(x)),
>>>    ok=all(is.finite(a))
>>>  ))
>>>  print(length(x))
>>>  print(summary(x))
>>> }
>>>
>>> # Load data from a complicated "non-reproducible" algorithm.
>>> # The below errors occur also when data is not
>>> # saved and then reloaded from file.  Data was generated in
>>> # R v2.1.1 patched (see above).
>>> if (file.exists("strange.RData")) {
>>>  load("strange.RData")
>>> } else {
>>>  load(url("http://www.maths.lth.se/help/R/strange.RData"))
>>> }
>>>
>>> # First glance at data...
>>> foo(a)
>>> foo(c)
>>>
>>> ## $name
>>> ## [1] "a"
>>> ##
>>> ## $storage.mode
>>> ## [1] "integer"
>>> ##
>>> ## $na
>>> ## [1] FALSE
>>> ##
>>> ## $nan
>>> ## [1] FALSE
>>> ##
>>> ## $inf
>>> ## [1] FALSE
>>> ##
>>> ## $ok
>>> ## [1] TRUE
>>> ##
>>> ## [1] 15000
>>> ##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
>>> ##    41.0    51.0    63.0   292.2   111.0 65170.0
>>> ## $name
>>> ## [1] "c"
>>> ##
>>> ## $storage.mode
>>> ## [1] "double"
>>> ##
>>> ## $na
>>> ## [1] FALSE
>>> ##
>>> ## $nan
>>> ## [1] FALSE
>>> ##
>>> ## $inf
>>> ## [1] FALSE
>>> ##
>>> ## $ok
>>> ## [1] TRUE
>>> ##
>>> ## [1] 1
>>> ##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
>>> ##   53.43   53.43   53.43   53.43   53.43   53.43
>>> ##
>>>
>>> # But, trying the following, will result in
>>> # no-reproducible error messages. Sometimes
>>> # it errors at kk==1, sometimes at kk >> 1.
>>> # Also, look at the different output for
>>> # different kk:s.
>>> for (kk in 1:100) {
>>>  cat("kk=",kk, "\n")
>>>  print(summary(a-c))
>>> }
>>>
>>> ## kk= 1
>>> ##       Min.     1st Qu.      Median        Mean     3rd Qu.        
>>> Max.
>>> ## -7.741e+307  -2.431e+00   9.569e+00               5.757e+01
>>> ## kk= 2
>>> ##     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
>>> ##   -12.430    -2.431     9.569   238.700    57.570 65120.000
>>> ## kk= 3
>>> ##     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
>>> ##   -12.430    -2.431     9.569              57.570 65120.000
>>> ## kk= 4
>>> ##     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
>>> ##   -12.430    -2.431     9.569   238.700    57.570 65120.000
>>> ## kk= 5
>>> ##     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
>>> ##   -12.430    -2.431     9.569   238.700    57.570 65120.000
>>> ## kk= 6
>>> ## Error in quantile.default(object) : missing values and NaN's
>>> ## not allowed if 'na.rm' is FALSE
>>>
>>>
>>> ## Comments: If you shorten down 'a', the bug occurs less frequently.
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>>
>> Thomas Lumley            Assoc. Professor, Biostatistics
>> tlumley at u.washington.edu    University of Washington, Seattle
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 
>



[Rd] Memory leakage/violation?
Henrik Bengtsson