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Illegal instruction (julia package on Ubuntu 13.04 on EC2 t1.micro) #3263

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cmey opened this Issue Jun 1, 2013 · 26 comments

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@cmey
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cmey commented Jun 1, 2013

Hi, just reporting a problem,

I tried to run julia on Ubuntu 13.04 on a free EC2 instance (t1.micro) and got an Illegal instruction just after typing julia.

I tried both 32 and 64 bit Ubuntu.
Haven't tried this on a non-free instance.

Steps to reproduce:

  • create a t1.micro instance running the OS : Ubuntu server 13.04 (32 or 64 bits) ;
  • sudo apt-get install julia
  • execute 'julia'
  • "Illegal instruction (core dumped)"
@arnim

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arnim commented Jun 1, 2013

Just gave @staticfloat s PPA a shot
(on a fresh 64 bit Ubuntu 13.04 on a t1.micro EC2 instance)

sudo add-apt-repository ppa:staticfloat/julia-deps -y
sudo add-apt-repository ppa:staticfloat/julianightlies -y
sudo apt-get update -qq -y
sudo apt-get install -y libpcre3-dev
sudo apt-get install julia -y

julia

resulting (as above) in
Illegal instruction (core dumped)

Version seems to be as in Setting up julia (0.2.0+nightly20130531~raring1)

Buildlog on launchpad
https://launchpadlibrarian.net/141163597/buildlog.txt.gz

@cmey

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cmey commented Jun 1, 2013

I tried compiling julia from source on this instance (it took 12h).
It gets to the point where is calls julia on several .jl files, and again, I get the dreaded "Illegal instruction (core dumped)" error message.

end of compilation output log:

CC src/jlapi.o
CC src/gc.o
LINK usr/lib/libjulia-release.so
PERL base/pcre_h.jl
PERL base/errno_h.jl
PERL base/build_h.jl
PERL base/file_constants.jl
PERL base/uv_constants.jl
CC ui/repl.o
CC ui/repl-basic.o
LINK usr/bin/julia-release-basic
CC ui/repl-readline.o
LINK usr/bin/julia-release-readline
JULIA usr/lib/julia/sys.ji
int.jl
Illegal instruction (core dumped)
*** This error is usually fixed by running 'make clean'. If the error persists, try 'make cleanall'. ***

This error is not fixed by running 'make clean' or 'make cleanall' ;-)

@staticfloat

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staticfloat commented Jun 1, 2013

This is likely a problem with virtualization. I've run into this on Virtualbox, so I would not be surprised if other virtualization technologies have similar issues.

Can you run cat /proc/cpuinfo for me so I can get a look at what kind of features your box is advertising it has? My guess is we may need to artificially reduce the number of instructions julia is attempting to use because the virtualization software can't support it, even though the cpu can. (For example, virtualbox doesn't allow AVX code to pass through; so even though the CPU can run it, software trying to use it will fail)

@arnim

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arnim commented Jun 1, 2013

@staticfloat

The programs included with the Ubuntu system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
applicable law.

Welcome to Ubuntu 13.04 (GNU/Linux 3.8.0-19-generic x86_64)

 * Documentation:  https://help.ubuntu.com/

  System information as of Sat Jun  1 23:42:04 UTC 2013

  System load:  0.64             Processes:           70
  Usage of /:   9.1% of 7.75GB   Users logged in:     0
  Memory usage: 20%              IP address for eth0: 10.224.3.150
  Swap usage:   0%

  Graph this data and manage this system at https://landscape.canonical.com/

  Get cloud support with Ubuntu Advantage Cloud Guest:
    http://www.ubuntu.com/business/services/cloud

  Use Juju to deploy your cloud instances and workloads:
    https://juju.ubuntu.com/#cloud-raring

0 packages can be updated.
0 updates are security updates.

ubuntu@ip-10-224-3-150:~$ cat /proc/cpuinfo
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 45
model name  : Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz
stepping    : 7
microcode   : 0x70a
cpu MHz     : 1799.999
cache size  : 20480 KB
physical id : 0
siblings    : 1
core id     : 0
cpu cores   : 1
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good nopl nonstop_tsc pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes avx hypervisor lahf_lm
bogomips    : 3599.99
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

ubuntu@ip-10-224-3-150:~$ sudo add-apt-repository ppa:staticfloat/julia-deps -y
gpg: keyring `/tmp/tmpcgt2j3/secring.gpg' created
gpg: keyring `/tmp/tmpcgt2j3/pubring.gpg' created
gpg: requesting key 3D3D3ACC from hkp server keyserver.ubuntu.com
gpg: /tmp/tmpcgt2j3/trustdb.gpg: trustdb created
gpg: key 3D3D3ACC: public key "Launchpad PPA for Elliot Saba" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
OK
ubuntu@ip-10-224-3-150:~$ sudo add-apt-repository ppa:staticfloat/julianightlies -y
gpg: keyring `/tmp/tmppe3tly/secring.gpg' created
gpg: keyring `/tmp/tmppe3tly/pubring.gpg' created
gpg: requesting key 3D3D3ACC from hkp server keyserver.ubuntu.com
gpg: /tmp/tmppe3tly/trustdb.gpg: trustdb created
gpg: key 3D3D3ACC: public key "Launchpad PPA for Elliot Saba" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
OK
ubuntu@ip-10-224-3-150:~$ sudo apt-get update -qq -y
ubuntu@ip-10-224-3-150:~$ sudo apt-get install -y libpcre3-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  binutils cpp cpp-4.7 gcc gcc-4.7 libc-dev-bin libc6-dev libcloog-ppl1
  libgcc-4.7-dev libgmpxx4ldbl libgomp1 libitm1 libmpc2 libmpfr4 libpcrecpp0
  libppl-c4 libppl12 libquadmath0 linux-libc-dev manpages-dev
Suggested packages:
  binutils-doc cpp-doc gcc-4.7-locales gcc-multilib make autoconf automake1.9
  libtool flex bison gdb gcc-doc gcc-4.7-multilib libmudflap0-4.7-dev
  gcc-4.7-doc libgcc1-dbg libgomp1-dbg libitm1-dbg libquadmath0-dbg
  libmudflap0-dbg binutils-gold glibc-doc
The following NEW packages will be installed:
  binutils cpp cpp-4.7 gcc gcc-4.7 libc-dev-bin libc6-dev libcloog-ppl1
  libgcc-4.7-dev libgmpxx4ldbl libgomp1 libitm1 libmpc2 libmpfr4 libpcre3-dev
  libpcrecpp0 libppl-c4 libppl12 libquadmath0 linux-libc-dev manpages-dev
0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
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Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
ubuntu@ip-10-224-3-150:~$ sudo apt-get install julia -y
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  git git-man libamd2.2.0 libarpack2 libcholmod1.7.1 libcolamd2.7.1
  libdouble-conversion0 liberror-perl libfftw3-3 libfftw3-double3
  libfftw3-single3 libgfortran3 liblapack3 libopenblas-base libopenlibm-base
  librmath-base librmath-dev libumfpack5.4.0 libunwind8
Suggested packages:
  git-daemon-run git-daemon-sysvinit git-doc git-el git-arch git-cvs git-svn
  git-email git-gui gitk gitweb ess libfftw3-bin libfftw3-dev
The following NEW packages will be installed:
  git git-man julia libamd2.2.0 libarpack2 libcholmod1.7.1 libcolamd2.7.1
  libdouble-conversion0 liberror-perl libfftw3-3 libfftw3-double3
  libfftw3-single3 libgfortran3 liblapack3 libopenblas-base libopenlibm-base
  librmath-base librmath-dev libumfpack5.4.0 libunwind8
0 upgraded, 20 newly installed, 0 to remove and 16 not upgraded.
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Setting up libfftw3-3:amd64 (3.3.3-2ubuntu1) ...
Setting up libamd2.2.0 (1:4.2.0-juliadeps1~raring) ...
Setting up libcolamd2.7.1 (1:4.2.0-juliadeps1~raring) ...
Setting up libcholmod1.7.1 (1:4.2.0-juliadeps1~raring) ...
Setting up libumfpack5.4.0 (1:4.2.0-juliadeps1~raring) ...
Setting up libarpack2 (3.1.2-2~exp1) ...
Setting up libopenlibm-base (0.1~gitc9cf16d-juliadeps4~raring) ...
Setting up librmath-base (2.15.2-juliadeps2~raring) ...
Setting up librmath-dev (2.15.2-juliadeps2~raring) ...
Setting up julia (0.2.0+nightly20130531~raring1) ...
Setting up liberror-perl (0.17-1) ...
Setting up git-man (1:1.8.1.2-1) ...
Setting up git (1:1.8.1.2-1) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
ubuntu@ip-10-224-3-150:~$ julia
Illegal instruction (core dumped)
ubuntu@ip-10-224-3-150:~$ 
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ViralBShah commented Jun 2, 2013

That is odd. @amitmurthy and I have been using the nightlies on successfully on EC2, but it may have been on the small instances.

We will soon have an AMI and the ability to do addprocs_ec2(n).

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amitmurthy commented Jun 2, 2013

Yes, just to confirm, they have been 'small' instances - julia runs without any issues on them. As @staticfloat pointed out, maybe Amazon uses a different virtualization technology for the micro instances.

Also, apparently the micro instances do not come with any swap space configured. Which means that we have a total of 600MB RAM. I don't know how much memory the JIT compiler / LLVM requires at startup, but I wonder if this is just a out-of-memory situation.

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arnim commented Jun 2, 2013

Yes, I've been running julia on t1.micro (Amazon Linux AMI 2013.03.1) so it's possible. Seems to be related to Ubuntu.
Sadly I had to build there julia (in a very long build process) on my own / no apt-get availible just yum.
@ViralBShah If there would be an AMI ... that would be great ;)

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amitmurthy commented Jun 3, 2013

I just tried with the following AMIs on micro instances using the nightlies and and it worked fine. ami-d96015b0 (32 bit) and ami-9b691cf2(64 bit).

AWS region - N. Virginia (US East 1)

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ViralBShah commented Jun 4, 2013

Thanks @amitmurthy

I guess we are reaching a point where we should maintain AMIs going forward, especially since AWS.jl makes it so easy to use julia with EC2.

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staticfloat commented Jun 4, 2013

I'm going to try compiling from scratch on the default "free" AMI, and see if I can reproduce this error.

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cmey commented Jun 4, 2013

@arnim @amitmurthy I can't make it work on my default AMI micro instance OS (ami-ddc1d7a9, Ireland) by compiling from source. It's the same error. Thus it seems not related to Ubuntu.

[ec2-user@ip-172-31-0-220 julia]$ make
    LINK usr/bin/julia-release-readline
    JULIA usr/lib/julia/sys.ji
int.jl
/bin/sh: line 1:  8359 Instruction non permise /home/ec2-user/julia/usr/bin/julia-release-readline -bf sysimg.jl
*** This error is usually fixed by running 'make clean'. If the error persists, try 'make cleanall'. ***

I ended up with a french OS for some reason, but the error is the same "illegal instruction" and occurs at the same place (as my 1st report on Ubuntu).

[ec2-user@ip-172-31-0-220 julia]$ cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 45
model name      : Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz
stepping        : 7
microcode       : 0x70a
cpu MHz         : 1799.999
cache size      : 20480 KB
physical id     : 0
siblings        : 1
core id         : 0
cpu cores       : 1
apicid          : 0
initial apicid  : 0
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 13
wp              : yes
flags           : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht nx constant_tsc up nonstop_tsc pni pclmulqdq ssse3 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes avx hypervisor
bogomips        : 3599.99
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

Now trying on the exact same AMI ID as you guys report it worked.

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staticfloat commented Jun 4, 2013

The 0.1.2 binaries work fine for me on a 64-bit free tier Ubuntu machine I just instantiated. Similarly, my 0.2.0 nightlies work fine as well. I'm currently trying building from source, but I get the feeling that will probably work just fine as well.

My /proc/cpuinfo is also slightly different than yours:

$ cat /proc/cpuinfo                                                                                     [2/4]
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 44
model name      : Intel(R) Xeon(R) CPU           E5645  @ 2.40GHz
stepping        : 2
microcode       : 0x13
cpu MHz         : 2000.070
cache size      : 12288 KB
physical id     : 0
siblings        : 1
core id         : 0
cpu cores       : 1
apicid          : 0
initial apicid  : 36
fpu             : yes
fpu_exception   : yes
cpuid level     : 11
wp              : yes
flags           : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc re
p_good nopl nonstop_tsc pni ssse3 cx16 pcid sse4_1 sse4_2 popcnt hypervisor lahf_lm
bogomips        : 4000.14
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management:

The key thing to note is that @arnim's CPU advertises AVX, whereas mine does not. This blog post has a rather interesting view on this, their solution is to avoid a certain CPU family (The same CPU as reported by @cmey above). What would be ideal, is if we can somehow disable the CPU reporting AVX such that OpenBLAS chooses Nehalem kernels, instead of sandy bridge ones. I'll look into this.

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cmey commented Jun 4, 2013

@staticfloat I think you're on the right track!

So, it works in Virginia instances with this CPU :

ubuntu@ip-10-245-81-118:~$ cat /proc/cpuinfo
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 23
model name  : Intel(R) Xeon(R) CPU           E5430  @ 2.66GHz
stepping    : 10
microcode   : 0xa07
cpu MHz     : 2659.998
cache size  : 6144 KB
fdiv_bug    : no
hlt_bug     : no
f00f_bug    : no
coma_bug    : no
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht nx constant_tsc pni ssse3 sse4_1 hypervisor
bogomips    : 5319.99
clflush size    : 64
cache_alignment : 64
address sizes   : 38 bits physical, 48 bits virtual
power management:

But not in Ireland where I get my previously reported CPU.

Thanks for looking into this :-)

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staticfloat commented Jun 4, 2013

Got it! I had to start up a server in Ireland, but I finally got one with the same CPU type; a Xeon E5-2650, and the error occurs. I don't want to just recompile OpenBLAS without AVX instructions, because any other pieces of software that have this problem will then also start throwing errors like this. I'm investigating what I can do on the kernel side to get it to hide those avx flags.

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xianyi commented Jun 5, 2013

Hi @staticfloat ,

I think I fixed the AVX detection bug on VM in issue xianyi/OpenBLAS#124 . So far, OpenBLAS will detect whether OS supports it.

Xianyi

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ViralBShah commented Jun 5, 2013

@pao @staticfloat I think it would be useful to start using the vagrant file to run various VMs on julia.mit.edu, which is quite beefy. Would you guys be able to set it up? If so, email me your preferred usernames.

I believe that @loladiro and @vtjnash are already running Windows VMs there.

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Keno commented Jun 5, 2013

Yeah, in fact I was already using Vagrant to run a bunch of Julia VMs ;). Every user on the system should be able to use the existing installation, so email me if you want to talk about that.

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staticfloat commented Jun 6, 2013

Well, I figured out that the standard Amazon-provided Ubuntu 13.04 kernel has a noxsave parameter you can pass that will also disable AVX, which does indeed remove the avx flag from /proc/cpuinfo. This does not, however, stop the illegal instruction signal, and manually compiling OpenBLAS with OPENBLAS_TARGET_ARCH=Nehalem confirms that this isn't an AVX/OpenBLAS problem. I also compiled a test C program that links with OpenBLAS, and with the noxsave kernel parameter, OpenBLAS does automatically detect the lack of AVX support, as I was expecting.

Making a debug Julia and trying to build the system image inside of gdb results in a bogus stack trace;

Program received signal SIGILL, Illegal instruction.
0x00007ffff46d581e in ?? ()
(gdb) bt
#0  0x00007ffff46d581e in ?? ()
#1  0x0000000000000008 in ?? ()
#2  0x00007fffffffc7e0 in ?? ()
#3  0x00000000006373ad in ?? ()
#4  0x00000000009f6090 in ?? ()
#5  0x00000000007ff620 in ?? ()
#6  0xce780d24fece1700 in ?? ()
#7  0xce780d24fece1700 in ?? ()
#8  0x00000000007ff620 in ?? ()
#9  0x0000000000000077 in ?? ()
#10 0x00000000000002f2 in ?? ()
#11 0x000000000000007a in ?? ()
#12 0x00000000006373ad in ?? ()
#13 0x00007fffffffc740 in ?? ()
#14 0x00007ffff62fb836 in jl_apply (f=0x2f2, args=0x77, nargs=0)
    at julia.h:1021
Backtrace stopped: frame did not save the PC
(gdb) 

I'm doubting that there was actually a stack frame at 0x08, so my guess is somewhere along the way we jump into the great unknown. I can't imagine why that is the case on one CPU and not another, but I'm still investigating. Right now I'm trying to figure out where things start to go south; it seems to happen during compilation of int.jl, although that may be inaccurate.

It'd help if I could do some printf debugging before things like print() are defined..... it looks like there's some old debug printing code at the top of sysimg.jl that was if false'ed out of normal execution. Bringing it back just throws out some errors, I'm assuming because noone has used it for a while. How do I throw out simple strings to STDOUT before print()?

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ViralBShah commented Jun 7, 2013

That's some pretty impressive work!

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staticfloat commented Jun 12, 2013

Bumping this issue to see if anyone can tell me how to print stuff out to the console during sys.ji creation

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ViralBShah commented Jun 12, 2013

@JeffBezanson @loladiro @vtjnash ?

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vtjnash commented Jul 28, 2013

I think this is a duplicate of #3634 and will be fixed when llvm is bumped to 3.3

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cmey commented Jul 28, 2013

Agreed

Le 28 juil. 2013 à 10:05, Jameson Nash notifications@github.com a écrit :

I think this is a duplicate of #3634 and will be fixed when llvm is bumped to 3.3


Reply to this email directly or view it on GitHub.

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staticfloat commented Jul 31, 2013

Aha! Thank you @vtjnash! Updating to llvm 3.3 does indeed solve the problem. Compiling julia completely from scratch (including LLVM 3.3, OpenBLAS, etc...) took the better part of two days, but I've finally got a Julia running on an Ireland instance with the "naughty" CPU. I'm closing this, although it would be nice to have this in the documentation somewhere, I just don't know where it should go.

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vtjnash commented Jul 31, 2013

It can probably go in the README on the front page, although we should be moving to llvm 3.3 soon.

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staticfloat commented Jul 31, 2013

wlbksy pushed a commit to wlbksy/julia that referenced this issue Nov 19, 2013

Update README.md
Incorporate wisdom from JuliaLang#3263

garrison added a commit to garrison/julia that referenced this issue Apr 24, 2015

Remove note about AVX and LLVM 3.2 [ci skip]
I'm removing the note added in 6b0ccb4 regarding JuliaLang#3263, which seems
to be irrelevant now.  In particular, LLVM 3.2 is no longer supported,
so the note is misleading at best.  I think the best thing is to
remove it entirely, unless somebody objects.

garrison added a commit to garrison/julia that referenced this issue Apr 24, 2015

Remove note about AVX and LLVM 3.2 [ci skip]
Removing the portion of the note added in 6b0ccb4 (see JuliaLang#3263) about
LLVM 3.2, which is no longer supported.

carnaval added a commit that referenced this issue Apr 27, 2015

Remove note about AVX and LLVM 3.2 [ci skip]
Removing the portion of the note added in 6b0ccb4 (see #3263) about
LLVM 3.2, which is no longer supported.

mbauman added a commit to mbauman/julia that referenced this issue Jun 6, 2015

Remove note about AVX and LLVM 3.2 [ci skip]
Removing the portion of the note added in 6b0ccb4 (see JuliaLang#3263) about
LLVM 3.2, which is no longer supported.
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