[datatable-help] Random segfaults

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Dec 15 16:50:03 CET 2011 

Hi,

Out of curiosity, is it impossible for you to upgrade R to the latest, or?

-steve


On Thu, Dec 15, 2011 at 10:42 AM, Chris Neff <caneff at gmail.com> wrote:
> I always use svn up. I'll reboot and reinstall just to make sure. As
> for reproducible, it still doesn't seem to crash in any consistent
> place but I'll give it a stronger try with a test data set.
>
> All 480 tests in test.data.table() completed ok in 7.395sec
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
> LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
> LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  grid
> methods   base
>
> other attached packages:
> [1] hexbin_1.26.0      lattice_0.19-33    RColorBrewer_1.0-5
> data.table_1.7.8   ggplot2_0.8.9      reshape_0.8.4
> [6] plyr_1.6
>
> On 15 December 2011 09:52, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>>
>> And you did an 'svn up' (or equivalent)? Grabbing daily tar.gz snapshot
>> from R-Forge won't include the fix yet. So svn up, then R CMD build, then
>> R CMD INSTALL, right? (Just checking quick basics first).
>>
>>> Result of test.data.table(), sessionInfo() and confirm it's a clean
>>> install after a reboot to make sure no old .so is still knocking around
>>> somehow please. Definitely installed to the right library? If it's
>>> crashing a lot then it should be reproducible?
>>> Still waiting for CRAN check results for 1.7.7 in old-rel. If it's not
>>> fixed there either that'll help to know....
>>>
>>>> Latest SVN version, no alloccol set, still crashing a lot.  I don't
>>>> use [<- or $<-, the only times I modify a data.table are with :=  or
>>>> by doing DT=merge(DT,blah).
>>>>
>>>> Any more info I can provide?
>>>>
>>>> On 15 December 2011 08:32, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>>>>> Great fingers and toes crossed. If you could unset alloccol option just
>>>>> to
>>>>> be sure please, that would be great. You're our best hope of confirming
>>>>> it's fixed since it was biting you several times an hour. If you use
>>>>> [<-
>>>>> or $<- syntax then R will copy via *tmp* and at that point the *tmp*
>>>>> data.table is similar to a data.table loaded from disk in that it isn't
>>>>> over-allocated anymore, I realised. Also a copy() will lose
>>>>> over-allocation until the next column addition.  That 'should' all be
>>>>> fine
>>>>> now in both <=2.13.2 and >=2.14.0, although the bug was something
>>>>> simpler.
>>>>>
>>>>> 1.7.7 is on CRAN now and been built for windows so if CRAN check
>>>>> results
>>>>> tick over from "ERROR" to "OK" later today (for both windows and mac
>>>>> old-rel), and, you're ok too, then it's fixed.
>>>>>
>>>>>
>>>>>> I've updated to the latest SVN version, and I'll be sure to let you
>>>>>> know if it still crashes (however I do have the alloccol option set to
>>>>>> 1000, so I shouldn't be bumping into reallocation very often). Thanks
>>>>>> for finding the bug so fast!
>>>>>>
>>>>>> On 14 December 2011 19:56, Matthew Dowle <mdowle at mdowle.plus.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hm. Sounds like it could be a different problem then if it was in R
>>>>>>> 2.14. There have been quite a few fixes since 1.7.4 so if you can
>>>>>>> reproduce with 1.7.7 would be great.  Or, we've sometimes seen that
>>>>>>> just
>>>>>>> after a package upgrade that a clean re-install can often fix things.
>>>>>>> Perhaps if the .so was in use by another R process or a zombie, or
>>>>>>> something. R seems to report data.table v1.7.4 (say) but it hasn't
>>>>>>> fully
>>>>>>> installed it properly and is still (perhaps partially) at 1.7.3. So
>>>>>>> quit
>>>>>>> all R (reboot to clear zombies too perhaps) and try reinstalling
>>>>>>> using
>>>>>>> R
>>>>>>> CMD INSTALL. Next time it happens I mean. Can also run
>>>>>>> test.data.table()
>>>>>>> to check the install.
>>>>>>>
>>>>>>> On Wed, 2011-12-14 at 17:40 +0000, Timothée Carayol wrote:
>>>>>>>> Hi --
>>>>>>>>
>>>>>>>> I have been having many unreproducible bugs with R 2.14, data.table
>>>>>>>> 1.7.4 and ubuntu 64 bits about 10 days ago. Data was getting
>>>>>>>> corrupted, and then R crashed. I had to go back to data.frame for
>>>>>>>> the
>>>>>>>> bits of code affected. I was doing a lot of rather unsafe
>>>>>>>> manipulations with row names, rbind and cbinds.
>>>>>>>> I didn't file a report, nor signal it, as it was occurring seemingly
>>>>>>>> at random, and I was doing operations which aren't really what
>>>>>>>> data.table was made for (tons of little manipulations on small
>>>>>>>> data);
>>>>>>>> still I guess I should now signal that 2.14 didn't fix everything
>>>>>>>> for
>>>>>>>> me. I do not know whether bugs subsist on post-1.7.4 versions.
>>>>>>>>
>>>>>>>> t
>>>>>>>>
>>>>>>>> On Wed, Dec 14, 2011 at 5:31 PM, Matthew Dowle
>>>>>>>> <mdowle at mdowle.plus.com>
>>>>>>>> wrote:
>>>>>>>> >
>>>>>>>> > Maybe, worth a try. Are you loading any data.table objects from
>>>>>>>> disk?
>>>>>>>> >
>>>>>>>> >> 64 bit 2.12.1 linux.
>>>>>>>> >>
>>>>>>>> >> Is there an option I can set in my session in order to work
>>>>>>>> around
>>>>>>>> the
>>>>>>>> >> truelength issue? I don't care if I lose some of the
>>>>>>>> over-allocation
>>>>>>>> >> niceties if it stops things from crashing. Looking at the
>>>>>>>> truelength
>>>>>>>> >> help, would just doing:
>>>>>>>> >>
>>>>>>>> >> options(datatable.alloc=quote(1000))
>>>>>>>> >>
>>>>>>>> >> stop this? I never have more than about 50 columns at a time.
>>>>>>>> >>
>>>>>>>> >> On 14 December 2011 11:43, Matthew Dowle <mdowle at mdowle.plus.com>
>>>>>>>> wrote:
>>>>>>>> >>>
>>>>>>>> >>> You're R < 2.14.0, right?  I'm really struggling in R < 2.14.0
>>>>>>>> to
>>>>>>>> make
>>>>>>>> >>> over-allocation work because R only started to initialize
>>>>>>>> truelength to
>>>>>>>> >>> 0
>>>>>>>> >>> in R 2.14.0+. Before that it's unitialized (random). Trouble is
>>>>>>>> my
>>>>>>>> >>> attempts in R < 2.14.0 to work around that work fine for me in
>>>>>>>> linux
>>>>>>>> >>> 32bit
>>>>>>>> >>> when I test in R 2.13.2, and I even test in 2.12.0 too. I test
>>>>>>>> on
>>>>>>>> 64bit
>>>>>>>> >>> too but just 2.14.0.  CRAN is also showing errors on 2.13.2
>>>>>>>> (old-rel)
>>>>>>>> >>> for
>>>>>>>> >>> both mac and windows.
>>>>>>>> >>>
>>>>>>>> >>> So, this is a pre-2.14.0 (only) problem that I'll continue to
>>>>>>>> try
>>>>>>>> and
>>>>>>>> >>> fix.
>>>>>>>> >>>
>>>>>>>> >>> Are you 64bit pre-2.14.0? Which OS?  If you are 64bit linux then
>>>>>>>> it
>>>>>>>> adds
>>>>>>>> >>> weight to me installing pre-2.14.0 on my 64bit instance in an
>>>>>>>> effort to
>>>>>>>> >>> reproduce.
>>>>>>>> >>>
>>>>>>>> >>>
>>>>>>>> >>>> This will be a crappy help request because I can't seem to
>>>>>>>> reproduce
>>>>>>>> >>>> it, but the past few days I've been getting a lot of segfaults.
>>>>>>>>  The
>>>>>>>> >>>> only common thing between every crash is that it happens when I
>>>>>>>> do
>>>>>>>> >>>>
>>>>>>>> >>>> DT[, z := x]
>>>>>>>> >>>>
>>>>>>>> >>>> where z was not a column that existed in DT before, and x is
>>>>>>>> either an
>>>>>>>> >>>> existing column of DT or a separate variable, doesn't matter.
>>>>>>>>  Beyond
>>>>>>>> >>>> that I can't reproduce a set of steps that gets R to crash.
>>>>>>>>  This
>>>>>>>> is
>>>>>>>> >>>> with the latest SVN version.
>>>>>>>> >>>>
>>>>>>>> >>>> Is there more information I can provide to help track this
>>>>>>>> down?
>>>>>>>> >>>> _______________________________________________
>>>>>>>> >>>> datatable-help mailing list
>>>>>>>> >>>> datatable-help at lists.r-forge.r-project.org
>>>>>>>> >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>>>>>>>> >>>>
>>>>>>>> >>>
>>>>>>>> >>>
>>>>>>>> >>
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > datatable-help mailing list
>>>>>>>> > datatable-help at lists.r-forge.r-project.org
>>>>>>>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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