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

-----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 ()

On 19 January 2017 at 01:26, Klint Gore wrote:
| >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.

Sorry, what part of '14.04' is current?

Ubuntu is at 16.10. And release 16.04, which as a LTS replaces the LTS 14.04
you use, also passes.  Can you upgrade?

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 12:41 PM
To: Klint Gore
Cc: Dirk Eddelbuettel; r-sig-debian at r-project.org
Subject: RE: [R-sig-Debian] Taking determinant of a matrix of NAs results in
intermittent memory corruption


On 19 January 2017 at 01:26, Klint Gore wrote:
| >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.
> Sorry, what part of '14.04' is current?
>
> Ubuntu is at 16.10. And release 16.04, which as a LTS replaces the LTS
14.04 you use, also passes.  Can you upgrade?
That version of the openblas package is the latest currently available for 14.04
LTS from the official ubuntu repository.  14.04 LTS is "supported" by
Canonical until 2019.

Also, I'm just confirming that I can repeat it.  It's not an issue for
me as it's never happened other than the contrived example.  If someone
brought it to my attention, I'd probably follow your original though and ask
them if they really wanted the determinant of an unassigned matrix as it sounds
like not a useful thing to do.  Using rnorm to initialise the matrix works fine.

I'd suggest the OP pursue it with the linux mint people as it's directly
affecting him and it occurs in their "supported" version.

Klint.