R SIG Debian - Jan 2017 - Taking determinant of a matrix of NAs results in intermittent memory corruption

Greetings; I've posted the following to R's bug tracking system (at
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17210 ) and Martin Maechler
requested that I post to this list as well.
If I start R from the command line with --vanilla, then repeatedly execute the
following line:

det(matrix(nrow=10,ncol=10))

... I eventually get a crash, with error:

*** Error in `/usr/lib/R/bin/exec/R': malloc(): memory corruption:
0x0000000002399400 ***

The specific address in memory that is referenced varies. The number of times I
need to execute the above line before getting a crash also varies.

This occurs with a wide range of matrix dimensions; 10x10 is not the only size
that causes this issue.

output of R.version:
platform      x86_64-pc-linux-gnu
arch          x86_64
os            linux-gnu
system        x86_64, linux-gnu
status
major          3
minor          3.2
year          2016
month          10
day            31
svn rev        71607
language      R
version.string R version 3.3.2 (2016-10-31)
nickname      Sincere Pumpkin Patch

I am running Linux Mint 17.3; my CPU is an Intel Core i7-2620m (Sandy Bridge).
My RAM is non-ECC. My R binary is from the CRAN Ubuntu repository at
cran.cnr.berkeley.edu . (r-base and r-base-core versions 3.3.2-1trusty0 )

I also see this issue running R within Emacs, as well as Rstudio.

This issue may be related to
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16862 but I'm not
certain.

The output of La_version() for me is:
[1] "3.5.0"

The output of:
system(paste("lsof -p", Sys.getpid(), "| grep -iE
'(blas|lapack)'"))
is:
R      3636 <myusername>  mem    REG              252,0    39272 11930369
/usr/lib/R/modules/lapack.so
R      3636 <myusername>  mem    REG              252,0  5882272 11933488
/usr/lib/lapack/liblapack.so.3.0
R      3636 <myusername>  mem    REG              252,0 23108112 11929607
/usr/lib/openblas-base/libopenblas.so.0
Is anyone able to reproduce?

Thanks,

--Ian

On 19/01/17 11:54, Ian Erickson wrote:
> Greetings; I've posted the following to R's bug tracking system (at
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17210 ) and Martin Maechler
requested that I post to this list as well.
> If I start R from the command line with --vanilla, then repeatedly execute
the following line:
>
> det(matrix(nrow=10,ncol=10))
>
> ... I eventually get a crash, with error:
>
> *** Error in `/usr/lib/R/bin/exec/R': malloc(): memory corruption:
0x0000000002399400 ***
>
> The specific address in memory that is referenced varies. The number of
times I need to execute the above line before getting a crash also varies.
>
> This occurs with a wide range of matrix dimensions; 10x10 is not the only
size that causes this issue.
>
> output of R.version:
> platform      x86_64-pc-linux-gnu
> arch          x86_64
> os            linux-gnu
> system        x86_64, linux-gnu
> status
> major          3
> minor          3.2
> year          2016
> month          10
> day            31
> svn rev        71607
> language      R
> version.string R version 3.3.2 (2016-10-31)
> nickname      Sincere Pumpkin Patch
>
> I am running Linux Mint 17.3; my CPU is an Intel Core i7-2620m (Sandy
Bridge). My RAM is non-ECC. My R binary is from the CRAN Ubuntu repository at
cran.cnr.berkeley.edu . (r-base and r-base-core versions 3.3.2-1trusty0 )
>
> I also see this issue running R within Emacs, as well as Rstudio.
>
> This issue may be related to
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16862 but I'm not
certain.
>
> The output of La_version() for me is:
> [1] "3.5.0"
>
> The output of:
> system(paste("lsof -p", Sys.getpid(), "| grep -iE
'(blas|lapack)'"))
> is:
> R      3636 <myusername>  mem    REG              252,0    39272
11930369 /usr/lib/R/modules/lapack.so
> R      3636 <myusername>  mem    REG              252,0  5882272
11933488 /usr/lib/lapack/liblapack.so.3.0
> R      3636 <myusername>  mem    REG              252,0 23108112
11929607 /usr/lib/openblas-base/libopenblas.so.0
> Is anyone able to reproduce?

I can't.  I tried

for(i in 1:100000) det(matrix(nrow=10,ncol=10))

and got no crash.  I am running Ubuntu 16.04 (with Mate Desktop 1.12.1, 
if that matters).

Output of sessionInfo():

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8
  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8
  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] misc_0.0-16

loaded via a namespace (and not attached):
  [1] deldir_0.1-13       Matrix_1.2-7.1      tools_3.3.2
  [4] mgcv_1.8-15         abind_1.4-5         spatstat_1.48-0.010
  [7] rpart_4.1-10        nlme_3.1-128        grid_3.3.2
[10] polyclip_1.5-6      lattice_0.20-34     goftest_1.0-3
[13] tensor_1.5

cheers,

Rolf Turner

-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 18 January 2017 at 22:54, Ian Erickson wrote:
| Greetings; I've posted the following to R's bug tracking system (at
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17210 ) and Martin Maechler
requested that I post to this list as well.
| If I start R from the command line with --vanilla, then repeatedly execute the
following line:
| 
| det(matrix(nrow=10,ncol=10))

That is not reproducible code. While you a matrix with dimensions, you do not
have content in it. Did you mean something like

   set.seed(42)      # or any other seed
   det(matrix(rnorm(100), nrow=10, ncol=10))


Ok now I looked at your example in the BTS. You meant

   det(matrix( , nrow=10, ncol=10))

and I just don't know how meaningful that is.  It is random input. Sure, R
should never die...

But just like Martin Maechler, I can run

  r -e 'for(i in 1:100000) { d <- det(matrix(, 10,10));
stopifnot(identical(d, NA_real_)) }; cat("Alive\n")'

just fine on two different machines (which both happen to Ubuntu 16.04 using
OpenBLAS).

| ... I eventually get a crash, with error:
| 
| *** Error in `/usr/lib/R/bin/exec/R': malloc(): memory corruption:
0x0000000002399400 ***
| 
| The specific address in memory that is referenced varies. The number of times
I need to execute the above line before getting a crash also varies.
| 
| This occurs with a wide range of matrix dimensions; 10x10 is not the only size
that causes this issue.
| 
| output of R.version:
| platform      x86_64-pc-linux-gnu
| arch          x86_64
| os            linux-gnu
| system        x86_64, linux-gnu
| status
| major          3
| minor          3.2
| year          2016
| month          10
| day            31
| svn rev        71607
| language      R
| version.string R version 3.3.2 (2016-10-31)
| nickname      Sincere Pumpkin Patch
| 
| I am running Linux Mint 17.3; my CPU is an Intel Core i7-2620m (Sandy Bridge).
My RAM is non-ECC. My R binary is from the CRAN Ubuntu repository at
cran.cnr.berkeley.edu . (r-base and r-base-core versions 3.3.2-1trusty0 )
| 
| I also see this issue running R within Emacs, as well as Rstudio.
| 
| This issue may be related to
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16862 but I'm not
certain.
| 
| The output of La_version() for me is:
| [1] "3.5.0"
| 
| The output of:
| system(paste("lsof -p", Sys.getpid(), "| grep -iE
'(blas|lapack)'"))
| is:
| R      3636 <myusername>  mem    REG              252,0    39272
11930369 /usr/lib/R/modules/lapack.so
| R      3636 <myusername>  mem    REG              252,0  5882272
11933488 /usr/lib/lapack/liblapack.so.3.0
| R      3636 <myusername>  mem    REG              252,0 23108112
11929607 /usr/lib/openblas-base/libopenblas.so.0
| Is anyone able to reproduce?

I cannot as stated above.

Try one of the other blas implementations. On a .deb-based system, this is
just a an apt-get way. I keep forgetting whether atlas has higher priority
than openblas but you know enough to check this.

Dirk
 
| Thanks,
| 
| --Ian
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

-----Original Message-----
From: R-SIG-Debian [mailto:r-sig-debian-bounces at r-project.org] On Behalf Of
Rolf Turner
Sent: Thursday, 19 January 2017 10:11 AM
To: Ian Erickson
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] [FORGED] Taking determinant of a matrix of NAs
results in intermittent memory corruption
>On 19/01/17 11:54, Ian Erickson wrote:
>> Greetings; I've posted the following to R's bug tracking system
(at https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17210 ) and Martin
Maechler requested that I post to this list as well.
>> If I start R from the command line with --vanilla, then repeatedly
execute the following line:
>>
>> det(matrix(nrow=10,ncol=10))
>>
>> ... I eventually get a crash, with error:
>>
>> *** Error in `/usr/lib/R/bin/exec/R': malloc(): memory corruption: 
>> 0x0000000002399400 ***
>>
>> Is anyone able to reproduce?
>
>I can't.  I tried
>
>for(i in 1:100000) det(matrix(nrow=10,ncol=10))
I can.  It's repeatable as well. 
CPU is Intel Xeon E5-2630v3 
Ubuntu 14.04.5 LTS
R from deb http://cran.r-project.org/bin/linux/ubuntu trusty/

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>  La_version()
[1] "3.5.0"
> system(paste("lsof -p", Sys.getpid(), "| grep -iE
'(blas|lapack)'"))
R       25596 kgore4  mem    REG    8,4    39272 118292573
/usr/lib/R/modules/lapack.so
R       25596 kgore4  mem    REG    8,4  5882272 118096040
/usr/lib/lapack/liblapack.so.3.0
R       25596 kgore4  mem    REG    8,4 23058832 118129172
/usr/lib/openblas-base/libblas.so.3
>  det(matrix(nrow=10,ncol=10))
[1] NA
>  det(matrix(nrow=10,ncol=10))
[1] NA
>  det(matrix(nrow=10,ncol=10))
[1] NA
>  det(matrix(nrow=10,ncol=10))
[1] NA
>  det(matrix(nrow=10,ncol=10))
*** Error in `/usr/lib/R/bin/exec/R': malloc(): memory corruption:
0x0000000001393090 ***
Aborted (core dumped)

It doesn't seem to matter what happens after the 4th execution it throws it
out.  Eg I just started mashing the keyboard

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> det(matrix(nrow=10,ncol=10))
[1] NA
> det(matrix(nrow=10,ncol=10))
[1] NA
> det(matrix(nrow=10,ncol=10))
[1] NA
> det(matrix(nrow=10,ncol=10))
[1] NA
> sdfsdfjkjsdhfkjsdhfk*** Error in `/usr/lib/R/bin/exec/R': malloc():
memory corruption: 0x00000000025c4090 ***
Aborted (core dumped)
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