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Hugh Parsonage

2020-Sep-08 08:08 UTC

[Rd] Operations with long altrep vectors cause segfaults on Windows

I can only reproduce on Windows, but reliably (both 4.0.0 and 4.0.2):

$> R --vanilla
x <- c(0L, -2e9:2e9)

# > Segmentation fault

Tried to reproduce on Linux but the above worked as expected. Not an
issue merely with the length of the vector; for example, x <-
rep_len(1:10, 1e10) works, though the altrep vector must be long to
reproduce:

x <- c(0L, -1e9:1e9)  #ok

Segmentation faults occur with the following too:

x <- (-2e9:2e9) + 1L

Martin Maechler

2020-Sep-08 08:40 UTC

head link

[Rd] Operations with long altrep vectors cause segfaults on Windows

>>>>> Hugh Parsonage 
>>>>>     on Tue, 8 Sep 2020 18:08:11 +1000 writes:
    > I can only reproduce on Windows, but reliably (both 4.0.0 and 4.0.2):

    > $> R --vanilla
    > x <- c(0L, -2e9:2e9)

    > # > Segmentation fault

    > Tried to reproduce on Linux but the above worked as expected. Not an
    > issue merely with the length of the vector; for example, x <-
    > rep_len(1:10, 1e10) works, though the altrep vector must be long to
    > reproduce:

    > x <- c(0L, -1e9:1e9)  #ok

    > Segmentation faults occur with the following too:

    > x <- (-2e9:2e9) + 1L

Your operation would "need" (not in theory, but in practice)
to go from altrep to regular vectors.
I guess the segfault occurs because of something like this :

 R asks Windows to hand it a huge amount of memory and Windows replies
 "ok, here is the memory pointer"
 and then R tries to write to there, but illegally (because
 Windows should have told R that it does not really have enough
 memory for that ..). 

I cannot reproduce the segmentation fault .. but I can confirm
there is a bug there that shows for me on Windows but not on
Linux:

"My" Windows is on a terminalserver not with too many GB of memory
(but then in a version of Windows that recognizes that it cannot
 get so much memory):

------------------------- Here some transcript (thanks to
                          using Emacs w/ ESS also on Windows) ------------------

R Under development (unstable) (2020-08-24 r79074) -- "Unsuffered
Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' f?r Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' f?r mehr Information und
'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden k?nnen.

Tippen Sie 'demo()' f?r einige Demos, 'help()' f?r on-line
Hilfe, oder
'help.start()' f?r eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.
> x <- (-2e9:2e9) + 1L
Fehler: kann Vektor der Gr??e 14.9 GB nicht allozieren> y <- c(0L, -2e9:2e9)
Fehler: kann Vektor der Gr??e 14.9 GB nicht allozieren> Sys.setenv(LANGUAGE="en")
> y <- c(0L, -2e9:2e9)
Error: cannot allocate vector of size 14.9 Gb> y <- -1e9:4e9
> .Internal(inspect(y))@0x00000000195a6808 14 REALSXP g0c0 [REF(65535)]  -1000000000 : -294967296
(compact)> .Machine$integer.max / 1e9
[1] 2.147484> y <- -1e6:2.2e9
> .Internal(inspect(y))@0x000000000a11a5d8 14 REALSXP g0c0 [REF(65535)]  -1000000 : -2094967296
(compact)> y <- -1e6:2e9
> .Internal(inspect(y))@0x000000000a13adf0 13 INTSXP g0c0 [REF(65535)]  -1000000 : 2000000000
(compact)> ------------------------- end of transcript -----------------------------------

So indeed, no seg.fault, R notices that it can't get 15 GB of
memory.

But the bug is bad news:  We have *silent* integer overflow happening
according to what  .Internal(inspect(y)) shows...

 .... less bad new: Probably the bug is only in the 'internal inspect'
code
 where a format specifier is used in C's printf() that does not work
 correctly on Windows, at least the way it is currently compiled ..

On (64-bit) Linux, I get
> y <- -1e9:4e9 ; .Internal(inspect(y))@7d86388 14 REALSXP g0c0 [REF(65535)]  -1000000000 : 4000000000 (compact)
> y <- c(0L, y)Error: cannot allocate vector of size 37.3 Gb

which seems much better ... until I do find a bug, may again
only in the C code underlying .Internal(inspect(.)) :
> y <- -1e9:2e9 ; .Internal(inspect(y))@7d86ac0 13 INTSXP g0c0 [REF(65535)] Error: long vectors not supported yet:
../../../R/src/main/altclasses.c:139>

Martin Maechler

2020-Sep-08 08:52 UTC

head link

[Rd] Operations with long altrep vectors cause segfaults on Windows

>>>>> Martin Maechler 
>>>>>     on Tue, 8 Sep 2020 10:40:24 +0200 writes:
>>>>> Hugh Parsonage 
>>>>>     on Tue, 8 Sep 2020 18:08:11 +1000 writes:
    >> I can only reproduce on Windows, but reliably (both 4.0.0 and
4.0.2):

    >> $> R --vanilla
    >> x <- c(0L, -2e9:2e9)

    >> # > Segmentation fault

    >> Tried to reproduce on Linux but the above worked as expected. Not
an
    >> issue merely with the length of the vector; for example, x <-
    >> rep_len(1:10, 1e10) works, though the altrep vector must be long to
    >> reproduce:

    >> x <- c(0L, -1e9:1e9)  #ok

    >> Segmentation faults occur with the following too:

    >> x <- (-2e9:2e9) + 1L

    > Your operation would "need" (not in theory, but in practice)
    > to go from altrep to regular vectors.
    > I guess the segfault occurs because of something like this :

    > R asks Windows to hand it a huge amount of memory and Windows replies
    > "ok, here is the memory pointer"
    > and then R tries to write to there, but illegally (because
    > Windows should have told R that it does not really have enough
    > memory for that ..). 
 
    > I cannot reproduce the segmentation fault .. but I can confirm
    > there is a bug there that shows for me on Windows but not on
    > Linux:

    > "My" Windows is on a terminalserver not with too many GB of
memory
    > (but then in a version of Windows that recognizes that it cannot
    > get so much memory):

    > ------------------------- Here some transcript (thanks to
    > using Emacs w/ ESS also on Windows) ------------------

    > R Under development (unstable) (2020-08-24 r79074) -- "Unsuffered
Consequences"
    > Copyright (C) 2020 The R Foundation for Statistical Computing
    > Platform: x86_64-w64-mingw32/x64 (64-bit)

    > R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
    > Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu
verbreiten.
    > Tippen Sie 'license()' or 'licence()' f?r Details dazu.

    > R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
    > Tippen Sie 'contributors()' f?r mehr Information und
'citation()',
    > um zu erfahren, wie R oder R packages in Publikationen zitiert werden
k?nnen.

    > Tippen Sie 'demo()' f?r einige Demos, 'help()' f?r
on-line Hilfe, oder
    > 'help.start()' f?r eine HTML Browserschnittstelle zur Hilfe.
    > Tippen Sie 'q()', um R zu verlassen.

    >> x <- (-2e9:2e9) + 1L
    > Fehler: kann Vektor der Gr??e 14.9 GB nicht allozieren
    >> y <- c(0L, -2e9:2e9)
    > Fehler: kann Vektor der Gr??e 14.9 GB nicht allozieren
    >> Sys.setenv(LANGUAGE="en")
    >> y <- c(0L, -2e9:2e9)
    > Error: cannot allocate vector of size 14.9 Gb
    >> y <- -1e9:4e9
    >> .Internal(inspect(y))
    > @0x00000000195a6808 14 REALSXP g0c0 [REF(65535)]  -1000000000 :
-294967296 (compact)
    >> .Machine$integer.max / 1e9
    > [1] 2.147484
    >> y <- -1e6:2.2e9
    >> .Internal(inspect(y))
    > @0x000000000a11a5d8 14 REALSXP g0c0 [REF(65535)]  -1000000 :
-2094967296 (compact)
    >> y <- -1e6:2e9
    >> .Internal(inspect(y))
    > @0x000000000a13adf0 13 INTSXP g0c0 [REF(65535)]  -1000000 : 2000000000
(compact)
    >> 
    > ------------------------- end of transcript
-----------------------------------

    > So indeed, no seg.fault, R notices that it can't get 15 GB of
    > memory.

    > But the bug is bad news:  We have *silent* integer overflow happening
    > according to what  .Internal(inspect(y)) shows...

    > .... less bad new: Probably the bug is only in the 'internal
inspect' code
    > where a format specifier is used in C's printf() that does not work
    > correctly on Windows, at least the way it is currently compiled ..


    > On (64-bit) Linux, I get

    >> y <- -1e9:4e9 ; .Internal(inspect(y))
    > @7d86388 14 REALSXP g0c0 [REF(65535)]  -1000000000 : 4000000000
(compact)

    >> y <- c(0L, y)
    > Error: cannot allocate vector of size 37.3 Gb

    > which seems much better ... until I do find a bug, may again
    > only in the C code underlying .Internal(inspect(.)) :

    >> y <- -1e9:2e9 ; .Internal(inspect(y))
    > @7d86ac0 13 INTSXP g0c0 [REF(65535)] Error: long vectors not supported
yet: ../../../R/src/main/altclasses.c:139
    >> 

Indeed, the purported "integer overflow" (above) does not
happen.
It is "only" a  'printf' related bug inside
.Internal(inspect(.)) on Windows.

*interestingly*, the above bug I've noticed on (64-bit) Linux
does *not* show on Windows (64-bit), at least not for that case:

On Windows, things are fine as long as they remain (compacted
aka 'ALTREP') INTSXP:

  > y <- -1e3:2e9 ;.Internal(inspect(y))
  @0x000000000a285648 13 INTSXP g0c0 [REF(65535)]  -1000 : 2000000000 (compact)
  > y <- -1e3:2.1e9 ;.Internal(inspect(y))
  @0x0000000019925930 13 INTSXP g0c0 [REF(65535)]  -1000 : 2100000000 (compact)

and here, y is correct, just the printing from
.Internal(inspect(y)) is bugous (probably prints the double as an integer):

  > y <- -1e3:2.2e9 ; .Internal(inspect(y))
  @0x00000000195c0178 14 REALSXP g0c0 [REF(65535)]  -1000 : -2094967296
(compact)
  > length(y)
  [1] 2200001001
  > tail(y)
  [1] 2.2e+09 2.2e+09 2.2e+09 2.2e+09 2.2e+09 2.2e+09
  > tail(y) - 2.2e9
  [1] -5 -4 -3 -2 -1  0
  >

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