GNU bug report logs - #21909
Segfault with eigen in R

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: <bug-guix <at> gnu.org>
Subject: Segfault with eigen in R
Date: Fri, 13 Nov 2015 10:53:42 -0500

Hello,

With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a
segfault when eigen is called with a matrix over some size.  I can
trigger the error with the following code [1]:

    > M <- 50
    > N <- 500
    > eigen(crossprod(matrix(rnorm(M * N), M, N)))

     *** caught segfault ***
    address 0xfb0, cause 'memory not mapped'

    Traceback:
     1: eigen(crossprod(matrix(rnorm(M * N), M, N)))

Can others reproduce this?

Thanks.


[1] This is a down-sized version of the snippet from an ATLAS bug report
    in 2011 for a similar error with R 2.14.

    http://sourceforge.net/p/math-atlas/support-requests/792/

--
Kyle

Message #8 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Kyle Meyer <kyle <at> kyleam.com>
Cc: 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Fri, 13 Nov 2015 21:26:34 +0100

Kyle Meyer <kyle <at> kyleam.com> writes:

> With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a
> segfault when eigen is called with a matrix over some size.  I can
> trigger the error with the following code [1]:
>
>     > M <- 50
>     > N <- 500
>     > eigen(crossprod(matrix(rnorm(M * N), M, N)))
>
>      *** caught segfault ***
>     address 0xfb0, cause 'memory not mapped'
>
>     Traceback:
>      1: eigen(crossprod(matrix(rnorm(M * N), M, N)))
>
> Can others reproduce this?

I can reproduce this running R 3.2.2 on GuixSD on a x86_64 machine.

~~ Ricardo

Message #11 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Wed, 18 Nov 2015 19:37:12 -0500

Ricardo Wurmus <rekado <at> elephly.net> writes:

> Kyle Meyer <kyle <at> kyleam.com> writes:
>
>> With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a
>> segfault when eigen is called with a matrix over some size.  I can
>> trigger the error with the following code [1]:
>>
>>     > M <- 50
>>     > N <- 500
>>     > eigen(crossprod(matrix(rnorm(M * N), M, N)))
>>
>>      *** caught segfault ***
>>     address 0xfb0, cause 'memory not mapped'
>>
>>     Traceback:
>>      1: eigen(crossprod(matrix(rnorm(M * N), M, N)))
>>
>> Can others reproduce this?
>
> I can reproduce this running R 3.2.2 on GuixSD on a x86_64 machine.

I haven't had any luck resolving this aside from just using R's internal
BLAS by removing "--with-blas=openblas" and "--with-lapack" from the
configure flags.

--
Kyle

Message #14 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kyle Meyer <kyle <at> kyleam.com>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Thu, 19 Nov 2015 10:39:12 +0100

I can reproduce the bug with:

   guix environment --pure --ad-hoc r -- R

and then typed “1” to get a core dump, which gives this:

--8<---------------cut here---------------start------------->8---
Core was generated by `/gnu/store/zci2lb9jlc9hlck3x3hc04ab3y86fzf9-r-3.2.2/lib/R/bin/exec/R'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f34616450e0 in dgemv_t_SANDYBRIDGE () from /gnu/store/hw9p1zyn1nh8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblas.so.0
[Current thread is 1 (Thread 0x7f34651307c0 (LWP 3399))]
(gdb) bt
#0  0x00007f34616450e0 in dgemv_t_SANDYBRIDGE () from /gnu/store/hw9p1zyn1nh8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblas.so.0
#1  0x00000000000000a2 in ?? ()

[...]

(gdb) disassemble
Dump of assembler code for function dgemv_t_SANDYBRIDGE:

[...]

   0x00007f34616450cf <+207>:   jle    0x7f3461645140 <dgemv_t_SANDYBRIDGE+320>
   0x00007f34616450d1 <+209>:   nopl   0x0(%rax,%rax,1)
   0x00007f34616450d6 <+214>:   nopw   %cs:0x0(%rax,%rax,1)
=> 0x00007f34616450e0 <+224>:   movsd  (%r9),%xmm0

[...]

(gdb) p $r9        
$1 = 4016
--8<---------------cut here---------------end--------------->8---

My CPU seems to be a Sandy Bridge:

--8<---------------cut here---------------start------------->8---
$ cat /proc/cpuinfo  | grep ^model | head -2
model           : 42
model name      : Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
--8<---------------cut here---------------end--------------->8---

Might be useful to report it upstream?

Thanks,
Ludo’.

Message #17 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Thu, 19 Nov 2015 19:05:07 -0500

ludo <at> gnu.org (Ludovic Courtès) writes:

> I can reproduce the bug with:
>
>    guix environment --pure --ad-hoc r -- R

[...]

> Might be useful to report it upstream?

Yes.  In preparing to do so, I figured that I should reproduce the issue
with a build outside of Guix.  However, when I tried with a manual build
on an Arch Linux system, the snippet ran fine.  This was with gcc
version 5.2.0, so I switched the gfortran input of openblas over to
gfortran-5, which seems to fix the issue.

While the issue should still be reported upstream, would it be OK to
update the gfortran input to gfortran-5?

--
Kyle

Message #20 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Kyle Meyer <kyle <at> kyleam.com>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Fri, 20 Nov 2015 10:58:41 +0100

Kyle Meyer <kyle <at> kyleam.com> skribis:

> ludo <at> gnu.org (Ludovic Courtès) writes:
>
>> I can reproduce the bug with:
>>
>>    guix environment --pure --ad-hoc r -- R
>
> [...]
>
>> Might be useful to report it upstream?
>
> Yes.  In preparing to do so, I figured that I should reproduce the issue
> with a build outside of Guix.  However, when I tried with a manual build
> on an Arch Linux system, the snippet ran fine.  This was with gcc
> version 5.2.0, so I switched the gfortran input of openblas over to
> gfortran-5, which seems to fix the issue.

Interesting.

> While the issue should still be reported upstream, would it be OK to
> update the gfortran input to gfortran-5?

The problem is that this leads to an R linked against GCC 4.9’s libgcc_s
and other run-time support libraries, and also against those of GCC 5.2,
via OpenBLAS.  I think we’d rather avoid it.

An additional data point:

--8<---------------cut here---------------start------------->8---
$ guix environment --pure --ad-hoc r valgrind -- R -d valgrind
/gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/bin/R: line 8: uname: command not found
==3198== Memcheck, a memory error detector
==3198== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==3198== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==3198== Command: /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/bin/exec/R
==3198== 

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-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.

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.

> M <- 50                                     
> N <- 500                                    
> eigen(crossprod(matrix(rnorm(M * N), M, N)))
==3198== Invalid read of size 8
==3198==    at 0x8E400E0: dgemv_t_SANDYBRIDGE (in /gnu/store/hw9p1zyn1nh8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblasp-r0.2.15.so)
==3198==    by 0x183AED48: dlatrd_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so)
==3198==    by 0x18461F92: dsytrd_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so)
==3198==    by 0x184B9540: dsyevr_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so)
==3198==    by 0x1B742D5E: La_rs (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so)
==3198==    by 0x1B745B96: mod_do_lapack (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so)
==3198==    by 0x4F35635: bcEval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==    by 0x4F432DF: Rf_eval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==    by 0x4F48F4B: Rf_applyClosure (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==    by 0x4F4345E: Rf_eval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==    by 0x4F6B0D9: Rf_ReplIteration (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==    by 0x4F6B430: R_ReplConsole (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so)
==3198==  Address 0xfb0 is not stack'd, malloc'd or (recently) free'd
==3198== 

 *** caught segfault ***
address 0xfb0, cause 'memory not mapped'
--8<---------------cut here---------------end--------------->8---

Here this suggests an R issue more than an OpenBLAS problem.

Ludo’.

Message #23 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Mon, 30 Nov 2015 18:25:50 -0500

I've opened an issue in the OpenBLAS repo [1].

  https://github.com/xianyi/OpenBLAS/issues/703

I'm trying to answer their questions, but, as is apparent in that
thread, I'm not really familiar with debugging these sorts of problems.
Since others are able to reproduce the error, any help over there would
be very appreciated.

[1] The last post suggested it may be an R issue rather than an OpenBLAS
    one, but I wanted to be more sure of that before going to R
    developers, especially given their comment about the --with-lapack
    flag:

    "Please do bear in mind that using --with-lapack is 'definitely not
    recommended': it is provided only because it is necessary on some
    platforms and because some users want to experiment with claimed
    performance improvements. Reporting problems where it is used
    unnecessarily will simply irritate the R helpers."

    https://cran.r-project.org/doc/manuals/r-release/R-admin.html#LAPACK

--
Kyle

Message #26 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: Kyle Meyer <kyle <at> kyleam.com>
Cc: Ludovic Courtès <ludo <at> gnu.org>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Wed, 2 Mar 2016 11:40:53 +0100

Kyle Meyer <kyle <at> kyleam.com> writes:

> I've opened an issue in the OpenBLAS repo [1].
>
>   https://github.com/xianyi/OpenBLAS/issues/703
>
> I'm trying to answer their questions, but, as is apparent in that
> thread, I'm not really familiar with debugging these sorts of problems.
> Since others are able to reproduce the error, any help over there would
> be very appreciated.
>
> [1] The last post suggested it may be an R issue rather than an OpenBLAS
>     one, but I wanted to be more sure of that before going to R
>     developers, especially given their comment about the --with-lapack
>     flag:
>
>     "Please do bear in mind that using --with-lapack is 'definitely not
>     recommended': it is provided only because it is necessary on some
>     platforms and because some users want to experiment with claimed
>     performance improvements. Reporting problems where it is used
>     unnecessarily will simply irritate the R helpers."
>
>     https://cran.r-project.org/doc/manuals/r-release/R-admin.html#LAPACK

We have since removed OpenBLAS from the inputs of R and just use the
internal BLAS instead.  Without OpenBLAS I cannot reproduce this bug
any more.

~~ Ricardo

Message #31 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
Cc: Kyle Meyer <kyle <at> kyleam.com>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Wed, 02 Mar 2016 22:09:52 +0100

Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de> skribis:

> We have since removed OpenBLAS from the inputs of R and just use the
> internal BLAS instead.  Without OpenBLAS I cannot reproduce this bug
> any more.

Nice.  So we can close?

Ludo'.

Message #34 received at 21909 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: Kyle Meyer <kyle <at> kyleam.com>, 21909 <at> debbugs.gnu.org
Subject: Re: bug#21909: Segfault with eigen in R
Date: Thu, 3 Mar 2016 21:54:44 +0100

Ludovic Courtès <ludo <at> gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de> skribis:
>
>> We have since removed OpenBLAS from the inputs of R and just use the
>> internal BLAS instead.  Without OpenBLAS I cannot reproduce this bug
>> any more.
>
> Nice.  So we can close?

I had already closed it in a subsequent email to
control <at> debbugs.gnu.org.

~~ Ricardo

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