[Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows
Hugh Parsonage
hugh@p@r@on@ge @end|ng |rom gm@||@com
Tue Sep 8 16:48:29 CEST 2020
Unfortunately I only get
[Thread 21752.0x4aa8 exited with code 3221225477]
[Thread 21752.0x4514 exited with code 3221225477]
[Thread 21752.0x3f10 exited with code 3221225477]
[Inferior 1 (process 21752) exited with code 030000000005]
(I'm guessing I would need to build an instrumented version of R, or
can R be debugged using gdb with an off-the-shelf installation?)
On Wed, 9 Sep 2020 at 00:32, <luke-tierney using uiowa.edu> wrote:
>
> On Tue, 8 Sep 2020, Hugh Parsonage wrote:
>
> > Thanks Martin. On further testing, it seems that the segmentation
> > fault can only occur when the amount of obtainable memory is
> > sufficiently high. On my machine (admittedly with other processes
> > running):
> >
> > $ R --vanilla --max-mem-size=30G -e "x <- c(0L, -2e9:2e9)"
> > Segmentation fault
> >
> > $ R --vanilla --max-mem-size=29G -e "x <- c(0L, -2e9:2e9)"
> > Error: cannot allocate vector of size 14.9 Gb
> > Execution halted
>
> Unfortunately I don't have access to a Windows machine with enough
> memory to get to the point of failure. If you have rtools and gdb
> installed can you run in gdb and see where the segfault is happening?
>
> Best,
>
> luke
>
> >
> > On Tue, 8 Sep 2020 at 18:52, Martin Maechler <maechler using stat.math.ethz.ch> wrote:
> >>
> >>>>>>> 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()' für Details dazu.
> >>
> >> > R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
> >> > Tippen Sie 'contributors()' für mehr Information und 'citation()',
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> >>
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> >> > 'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
> >> > Tippen Sie 'q()', um R zu verlassen.
> >>
> >> >> x <- (-2e9:2e9) + 1L
> >> > Fehler: kann Vektor der Größe 14.9 GB nicht allozieren
> >> >> y <- c(0L, -2e9:2e9)
> >> > Fehler: kann Vektor der Größe 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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> >
>
> --
> Luke Tierney
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa Phone: 319-335-3386
> Department of Statistics and Fax: 319-335-3017
> Actuarial Science
> 241 Schaeffer Hall email: luke-tierney using uiowa.edu
> Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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