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

-----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)
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

So this converges towards 'old versions bad, new versions fine' ?

Dirk

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

-----Original Message-----
From: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] On Behalf Of
Dirk Eddelbuettel
Sent: Thursday, 19 January 2017 11:21 AM
To: Klint Gore
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Taking determinant of a matrix of NAs results in
intermittent memory corruption
>So this converges towards 'old versions bad, new versions fine' ?
Probably.  Old version of what, I don't know.  Openblas is 0.2.8-6ubuntu1 on
14.04 lts which is current.

Here's a backtrace if it helps.
> det(matrix(nrow=10,n*** Error in `/usr/lib/R/bin/exec/R': malloc():
memory corruption: 0x0000000000c34090 ***
Program received signal SIGABRT, Aborted.
0x00007ffff720fc37 in __GI_raise (sig=sig at entry=6)
    at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
56      ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0  0x00007ffff720fc37 in __GI_raise (sig=sig at entry=6)
    at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1  0x00007ffff7213028 in __GI_abort () at abort.c:89
#2  0x00007ffff724c2a4 in __libc_message (do_abort=1,
    fmt=fmt at entry=0x7ffff735a6b0 "*** Error in `%s': %s: 0x%s
***\n")
    at ../sysdeps/posix/libc_fatal.c:175
#3  0x00007ffff7259e26 in malloc_printerr (ptr=0xc34090,
    str=0x7ffff7356882 "malloc(): memory corruption",
action=<optimized out>)
    at malloc.c:4996
#4  _int_malloc (av=0x7ffff7597760 <main_arena>, bytes=32) at
malloc.c:3447
#5  0x00007ffff725b6c0 in __GI___libc_malloc (bytes=32) at malloc.c:2891
#6  0x00007ffff54b7dd9 in xmalloc ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#7  0x00007ffff54acfde in rl_add_undo ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#8  0x00007ffff54af709 in rl_insert_text ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#9  0x00007ffff54b07cc in _rl_insert_char ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#10 0x00007ffff5497a5d in _rl_dispatch_subseq ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#11 0x00007ffff5497f1d in readline_internal_char ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#12 0x00007ffff54ae8ad in rl_callback_read_char ()
   from /lib/x86_64-linux-gnu/libreadline.so.6
#13 0x00007ffff79baec6 in ?? () from /usr/lib/libR.so
#14 0x00007ffff78f7ca1 in Rf_ReplIteration () from /usr/lib/libR.so
#15 0x00007ffff78f80f1 in ?? () from /usr/lib/libR.so
#16 0x00007ffff78f81af in run_Rmainloop () from /usr/lib/libR.so
#17 0x00000000004007eb in main ()
#18 0x00007ffff71faf45 in __libc_start_main (main=0x4007d0 <main>, argc=1,
    argv=0x7fffffffd548, init=<optimized out>, fini=<optimized out>,
    rtld_fini=<optimized out>, stack_end=0x7fffffffd538) at
libc-start.c:287
#19 0x000000000040081b in _start ()