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Build failure on Fedora #5422

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joeltay opened this issue Jan 16, 2014 · 29 comments
Closed

Build failure on Fedora #5422

joeltay opened this issue Jan 16, 2014 · 29 comments
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building Build system, or building Julia or its dependencies system:linux Affects only Linux

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@joeltay
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joeltay commented Jan 16, 2014

Building master in latest Fedora gives the below error:

    LINK usr/bin/julia-readline
    CC ui/repl-basic.o
    LINK usr/bin/julia-basic
osutils.jl
/bin/sh: line 1: 23115 Illegal instruction     (core dumped) /home/joel/julia/usr/bin/julia-readline --build /home/joel/julia/usr/lib/julia/sys0 sysimg.jl
make[1]: *** [/home/joel/julia/usr/lib/julia/sys0.bc] Error 132
make: *** [release] Error 2

GCC version:

gcc (GCC) 4.8.2 20131212 (Red Hat 4.8.2-7)

Also happened with clang.

@IainNZ

@ivarne
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ivarne commented Jan 16, 2014

These kind of problems are often resolved by make clean or make cleanall. You seem to have tried that in order to use clang and gcc, but I hope it is okay that I ask anyway.

@joeltay
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joeltay commented Jan 16, 2014

I did make clean. And also from a fresh clone.

@StefanKarpinski
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What the architecture?

@joeltay
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joeltay commented Jan 16, 2014

Fedora 19, 3.12.7-200.fc19.x86_64
Memory: 3.8 GiB
Processor: Pentium(R) Dual-Core CPU T4200 @ 2.00GHz × 2
OS Type: 64-bit
Graphics: Mobile Intel® GM45 Express Chipset
GNOME: Version 3.8.4

Also, I did subsequently manage to build and run the release version successfully.

@staticfloat
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Can you post the output of cat /proc/cpuinfo? Also, is this running inside of a virtual machine?

@joeltay
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joeltay commented Jan 16, 2014

Not a VM.

Output requested:

processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 23
model name  : Pentium(R) Dual-Core CPU       T4200  @ 2.00GHz
stepping    : 10
microcode   : 0xa0b
cpu MHz     : 1200.000
cache size  : 1024 KB
physical id : 0
siblings    : 2
core id     : 0
cpu cores   : 2
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm xsave lahf_lm dtherm
bogomips    : 3987.04
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:

processor   : 1
vendor_id   : GenuineIntel
cpu family  : 6
model       : 23
model name  : Pentium(R) Dual-Core CPU       T4200  @ 2.00GHz
stepping    : 10
microcode   : 0xa0b
cpu MHz     : 1200.000
cache size  : 1024 KB
physical id : 0
siblings    : 2
core id     : 1
cpu cores   : 2
apicid      : 1
initial apicid  : 1
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm xsave lahf_lm dtherm
bogomips    : 3987.04
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:

@staticfloat
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You've got xsave present but not avx in your CPU flags. That's probably confusing some CPU capabilities checker, as they often assume that if you have xsave then you have avx as well.

Can you show us the output of <julia_source_dir>/deps/openblas-v0.2.8/config_last.h:

$ cat deps/openblas-v0.2.8/config_last.h
#define OS_DARWIN       1
#define ARCH_X86_64     1
#define C_CLANG 1
#define __64BIT__       1
#define FUNDERSCORE     _
#define PTHREAD_CREATE_FUNC     pthread_create
#define BUNDERSCORE     _
#define NEEDBUNDERSCORE 1
#define SANDYBRIDGE
#define L2_SIZE 262144
#define L2_ASSOCIATIVE 6
#define L2_LINESIZE 64
#define DTB_SIZE 4096
#define DTB_ASSOCIATIVE 4
#define DTB_DEFAULT_ENTRIES 64
#define HAVE_CMOV
#define HAVE_MMX
#define HAVE_SSE
#define HAVE_SSE2
#define HAVE_SSE3
#define HAVE_SSSE3
#define HAVE_SSE4_1
#define HAVE_SSE4_2
#define HAVE_AVX
#define HAVE_FMA3
#define HAVE_CFLUSH
#define NUM_SHAREDCACHE 1
#define NUM_CORES 1
#define CORE_SANDYBRIDGE
#define SLOCAL_BUFFER_SIZE      32768
#define DLOCAL_BUFFER_SIZE      16384
#define CLOCAL_BUFFER_SIZE      32768
#define ZLOCAL_BUFFER_SIZE      24576
#define USE64BITINT
#define GEMM_MULTITHREAD_THRESHOLD      4
#define EXPRECISION

@joeltay
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joeltay commented Jan 17, 2014

Output requested:

#define OS_LINUX    1
#define ARCH_X86_64 1
#define C_GCC   1
#define __64BIT__   1
#define PTHREAD_CREATE_FUNC pthread_create
#define BUNDERSCORE _
#define NEEDBUNDERSCORE 1
#define PENRYN
#define L1_CODE_SIZE 32768
#define L1_CODE_ASSOCIATIVE 8
#define L1_CODE_LINESIZE 64
#define L1_DATA_SIZE 32768
#define L1_DATA_ASSOCIATIVE 8
#define L1_DATA_LINESIZE 64
#define L2_SIZE 1048576
#define L2_ASSOCIATIVE 4
#define L2_LINESIZE 64
#define ITB_SIZE 4096
#define ITB_ASSOCIATIVE 4
#define ITB_ENTRIES 128
#define DTB_SIZE 4096
#define DTB_ASSOCIATIVE 4
#define DTB_DEFAULT_ENTRIES 256
#define HAVE_CMOV
#define HAVE_MMX
#define HAVE_SSE
#define HAVE_SSE2
#define HAVE_SSE3
#define HAVE_SSSE3
#define HAVE_CFLUSH
#define HAVE_HIT 1
#define NUM_SHAREDCACHE 1
#define NUM_CORES 1
#define CORE_PENRYN
#define SLOCAL_BUFFER_SIZE  32768
#define DLOCAL_BUFFER_SIZE  16384
#define CLOCAL_BUFFER_SIZE  32768
#define ZLOCAL_BUFFER_SIZE  16384
#define USE64BITINT
#define GEMM_MULTITHREAD_THRESHOLD  4
#define EXPRECISION

@staticfloat
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@vtjnash Reading through Makefile it looks like I should be able to just ../usr/bin/julia-readline --build output sysimg.jl within base, but that doesn't seem to be working, I get:

$ ../usr/bin/julia-readline --build output sysimg.jl
array.jl
error during bootstrap: LoadError(at "sysimg.jl" line 52: LoadError(at "array.jl" line 7: ErrorException("DenseArray not defined")))

Is there something else I need to do first?

@vtjnash
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vtjnash commented Jan 17, 2014

that's it. might even be worth documenting it

@staticfloat
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hrrmmm.. Any idea why I'm getting that error?

@staticfloat
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Anyway, maybe it's something weird with my machine. @joeltay, can you please try:

$ make debug
$ cd base
$ gdb ../usr/bin/julia-debug-basic
...
(gdb) r --build output sysimg.jl
...
(gdb) bt

The output could give us an idea as to where you're running into the illegal exception.

@joeltay
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joeltay commented Jan 17, 2014

[joel@localhost julia]$ make debug
    CC src/jltypes.do
    CC src/gf.do
    CC src/ast.do
    CC src/builtins.do
    CC src/module.do
    CC src/codegen.do
    CC src/interpreter.do
    CC src/alloc.do
    CC src/dlload.do
    CC src/sys.do
    CC src/init.do
    CC src/task.do
    CC src/array.do
    CC src/dump.do
    CC src/toplevel.do
    CC src/jl_uv.do
    CC src/jlapi.do
    CC src/profile.do
    CC src/gc.do
    LINK usr/lib/libjulia-debug.so
    CC ui/repl.do
    CC ui/repl-readline.do
    LINK usr/bin/julia-debug-readline
    CC ui/repl-basic.do
    LINK usr/bin/julia-debug-basic
[joel@localhost julia]$ cd base
[joel@localhost base]$ gdb ../usr/bin/julia-debug-basic
GNU gdb (GDB) Fedora 7.6.1-46.fc19
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/joel/julia/usr/bin/julia-debug-basic...done.
(gdb) r --build output sysimg.jl
Starting program: /home/joel/julia/base/../usr/bin/julia-debug-basic --build output sysimg.jl
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
[New Thread 0x7fffee23a700 (LWP 16649)]
ERROR: unknown option: --build
 in process_options at client.jl:306
 in _start at client.jl:389

[Thread 0x7fffee23a700 (LWP 16649) exited]
[Inferior 1 (process 16645) exited with code 01]
Missing separate debuginfos, use: debuginfo-install glibc-2.17-20.fc19.x86_64 libgcc-4.8.2-7.fc19.x86_64 libgfortran-4.8.2-7.fc19.x86_64 libquadmath-4.8.2-7.fc19.x86_64 libstdc++-4.8.2-7.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb) bt
No stack.

@staticfloat
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What version of julia are you compiling?
On Jan 17, 2014 1:53 PM, "joeltay" notifications@github.com wrote:

[joel@localhost julia]$ make debug
CC src/jltypes.do
CC src/gf.do
CC src/ast.do
CC src/builtins.do
CC src/module.do
CC src/codegen.do
CC src/interpreter.do
CC src/alloc.do
CC src/dlload.do
CC src/sys.do
CC src/init.do
CC src/task.do
CC src/array.do
CC src/dump.do
CC src/toplevel.do
CC src/jl_uv.do
CC src/jlapi.do
CC src/profile.do
CC src/gc.do
LINK usr/lib/libjulia-debug.so
CC ui/repl.do
CC ui/repl-readline.do
LINK usr/bin/julia-debug-readline
CC ui/repl-basic.do
LINK usr/bin/julia-debug-basic
[joel@localhost julia]$ cd base
[joel@localhost base]$ gdb ../usr/bin/julia-debug-basic
GNU gdb (GDB) Fedora 7.6.1-46.fc19
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/...
Reading symbols from /home/joel/julia/usr/bin/julia-debug-basic...done.
(gdb) r --build output sysimg.jl
Starting program: /home/joel/julia/base/../usr/bin/julia-debug-basic --build output sysimg.jl
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
[New Thread 0x7fffee23a700 (LWP 16649)]
ERROR: unknown option: --build
in process_options at client.jl:306
in _start at client.jl:389

[Thread 0x7fffee23a700 (LWP 16649) exited]
[Inferior 1 (process 16645) exited with code 01]
Missing separate debuginfos, use: debuginfo-install glibc-2.17-20.fc19.x86_64 libgcc-4.8.2-7.fc19.x86_64 libgfortran-4.8.2-7.fc19.x86_64 libquadmath-4.8.2-7.fc19.x86_64 libstdc++-4.8.2-7.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb) bt
No stack.


Reply to this email directly or view it on GitHubhttps://github.com//issues/5422#issuecomment-32652080
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@joeltay
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joeltay commented Jan 17, 2014

Ah. I got the release version running yesterday. Is there a way for me to help debug master without deleting that?

@staticfloat
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How did you download the release version?
On Jan 17, 2014 2:05 PM, "joeltay" notifications@github.com wrote:

Ah. I got the release version running yesterday. Is there a way for me to
help debug without deleting that?


Reply to this email directly or view it on GitHubhttps://github.com//issues/5422#issuecomment-32653551
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@joeltay
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joeltay commented Jan 17, 2014

git checkout release-0.2

@staticfloat
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Just git checkout master will move you back to master. You'll have to
recompile Julia, (make cleanall && make will do that for you) but that's
it.
-E

On Fri, Jan 17, 2014 at 2:13 PM, joeltay notifications@github.com wrote:

git checkout release-0.2


Reply to this email directly or view it on GitHubhttps://github.com//issues/5422#issuecomment-32654440
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@IainNZ
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IainNZ commented Jan 17, 2014

So what happened was:
@joeltay cloned master sometime yesterday, tried to build, failed
I then make cleanall'd his Julia folder
then git checkout'd release-0.2, which built

Joel, I recommend making a subfolder for master,e.g.
git clone https://githbub...julia julia-master

so you can keep your working 0.2 build

@joeltay
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joeltay commented Jan 18, 2014

Output:

    LINK usr/bin/julia-readline
    CC ui/repl-basic.o
    LINK usr/bin/julia-basic
osutils.jl
/bin/sh: line 1:  2786 Illegal instruction     (core dumped) /home/joel/julia/julia-master/usr/bin/julia-readline --build /home/joel/julia/julia-master/usr/lib/julia/sys0 sysimg.jl
make[1]: *** [/home/joel/julia/julia-master/usr/lib/julia/sys0.bc] Error 132
make: *** [release] Error 2
[joel@localhost julia-master]$ make debug
    CC src/jltypes.do
    CC src/gf.do
    CC src/ast.do
    CC src/builtins.do
    CC src/module.do
    CC src/codegen.do
    CC src/interpreter.do
    CC src/alloc.do
    CC src/dlload.do
    CC src/sys.do
    CC src/init.do
    CC src/task.do
    CC src/array.do
    CC src/dump.do
    CC src/toplevel.do
    CC src/jl_uv.do
    CC src/jlapi.do
    CC src/profile.do
    CC src/gc.do
    LINK usr/lib/libjulia-debug.so
    CC ui/repl.do
    CC ui/repl-readline.do
    LINK usr/bin/julia-debug-readline
    CC ui/repl-basic.do
    LINK usr/bin/julia-debug-basic
osutils.jl
/bin/sh: line 1:  3347 Illegal instruction     (core dumped) /home/joel/julia/julia-master/usr/bin/julia-debug-readline --build /home/joel/julia/julia-master/usr/lib/julia/sys0 sysimg.jl
make[1]: *** [/home/joel/julia/julia-master/usr/lib/julia/sys0.bc] Error 132
make: *** [debug] Error 2
[joel@localhost julia-master]$ cd base
[joel@localhost base]$ gdb ../usr/bin/julia-debug-basic
GNU gdb (GDB) Fedora 7.6.1-46.fc19
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/joel/julia/julia-master/usr/bin/julia-debug-basic...done.
(gdb) r --build output sysimg.jl
Starting program: /home/joel/julia/julia-master/base/../usr/bin/julia-debug-basic --build output sysimg.jl
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
osutils.jl

Program received signal SIGILL, Illegal instruction.
0x00007ffff03e9e54 in ?? ()
Missing separate debuginfos, use: debuginfo-install glibc-2.17-20.fc19.x86_64 libgcc-4.8.2-7.fc19.x86_64 libstdc++-4.8.2-7.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb) bt
#0  0x00007ffff03e9e54 in ?? ()
#1  0x0000000000000001 in ?? ()
#2  0x0000000000000001 in ?? ()
#3  0x0000000000000002 in ?? ()
#4  0x00007ffffff3adf0 in ?? ()
#5  0x0000000004de0070 in ?? ()
#6  0x0000000000a0a350 in ?? ()
#7  0x00007ffff715785f in jl_compile_hint (f=0x7ffffff3adf0, types=0x2)
    at gf.c:1314
#8  0x0000000000665050 in ?? ()
#9  0x00007ffffff3acc0 in ?? ()
#10 0x00007ffff715c5f9 in jl_apply (f=0x48e8458b48e0558b, 
    args=0x48c031f845894800, nargs=10277) at julia.h:1045
Backtrace stopped: previous frame inner to this frame (corrupt stack?)

@staticfloat
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Could you try installing the debug symbols for glibc as it suggests? (Via
debuginfo-install, as it says) then do the gdb stuff again, the backtrace
might be more helpful.
On Jan 17, 2014 6:03 PM, "joeltay" notifications@github.com wrote:

Output:

LINK usr/bin/julia-readline
CC ui/repl-basic.o
LINK usr/bin/julia-basic

osutils.jl
/bin/sh: line 1: 2786 Illegal instruction (core dumped) /home/joel/julia/julia-master/usr/bin/julia-readline --build /home/joel/julia/julia-master/usr/lib/julia/sys0 sysimg.jl
make[1]: *** [/home/joel/julia/julia-master/usr/lib/julia/sys0.bc] Error 132
make: *** [release] Error 2
[joel@localhost julia-master]$ make debug
CC src/jltypes.do
CC src/gf.do
CC src/ast.do
CC src/builtins.do
CC src/module.do
CC src/codegen.do
CC src/interpreter.do
CC src/alloc.do
CC src/dlload.do
CC src/sys.do
CC src/init.do
CC src/task.do
CC src/array.do
CC src/dump.do
CC src/toplevel.do
CC src/jl_uv.do
CC src/jlapi.do
CC src/profile.do
CC src/gc.do
LINK usr/lib/libjulia-debug.so
CC ui/repl.do
CC ui/repl-readline.do
LINK usr/bin/julia-debug-readline
CC ui/repl-basic.do
LINK usr/bin/julia-debug-basic
osutils.jl
/bin/sh: line 1: 3347 Illegal instruction (core dumped) /home/joel/julia/julia-master/usr/bin/julia-debug-readline --build /home/joel/julia/julia-master/usr/lib/julia/sys0 sysimg.jl
make[1]: *** [/home/joel/julia/julia-master/usr/lib/julia/sys0.bc] Error 132
make: *** [debug] Error 2

[joel@localhost julia-master]$ cd base
[joel@localhost base]$ gdb ../usr/bin/julia-debug-basic
GNU gdb (GDB) Fedora 7.6.1-46.fc19
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/...
Reading symbols from /home/joel/julia/julia-master/usr/bin/julia-debug-basic...done.
(gdb) r --build output sysimg.jl
Starting program: /home/joel/julia/julia-master/base/../usr/bin/julia-debug-basic --build output sysimg.jl
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
osutils.jl

Program received signal SIGILL, Illegal instruction.
0x00007ffff03e9e54 in ?? ()
Missing separate debuginfos, use: debuginfo-install glibc-2.17-20.fc19.x86_64 libgcc-4.8.2-7.fc19.x86_64 libstdc++-4.8.2-7.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb) bt
#0 0x00007ffff03e9e54 in ?? ()
#1 0x0000000000000001 in ?? ()
#2 0x0000000000000001 in ?? ()
#3 0x0000000000000002 in ?? ()
#4 0x00007ffffff3adf0 in ?? ()
#5 0x0000000004de0070 in ?? ()
#6 0x0000000000a0a350 in ?? ()
#7 0x00007ffff715785f in jl_compile_hint (f=0x7ffffff3adf0, types=0x2)
at gf.c:1314
#8 0x0000000000665050 in ?? ()
#9 0x00007ffffff3acc0 in ?? ()
#10 0x00007ffff715c5f9 in jl_apply (f=0x48e8458b48e0558b,
args=0x48c031f845894800, nargs=10277) at julia.h:1045
Backtrace stopped: previous frame inner to this frame (corrupt stack?)


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@JeffBezanson
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@loladiro do you think we should try disabling some CPU features in LLVM here?

@Keno
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Keno commented Jan 18, 2014

Possibly. @joeltay Can I see a disassembly of that location?

@joeltay
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joeltay commented Jan 18, 2014

@loladiro I'm new to Linux. What commands exactly would you like me to execute?

@Keno
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Keno commented Jan 18, 2014

Just the same as above, but with disassemble instead of bt.

@joeltay
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joeltay commented Jan 18, 2014

bt: Exactly the same as before:

(gdb) bt
#0  0x00007ffff03e9e54 in ?? ()
#1  0x0000000000000001 in ?? ()
#2  0x0000000000000001 in ?? ()
#3  0x0000000000000002 in ?? ()
#4  0x00007ffffff3adf0 in ?? ()
#5  0x0000000004de0070 in ?? ()
#6  0x0000000000a0a350 in ?? ()
#7  0x00007ffff715785f in jl_compile_hint (f=0x7ffffff3adf0, types=0x2)
    at gf.c:1314
#8  0x0000000000665050 in ?? ()
#9  0x00007ffffff3acc0 in ?? ()
#10 0x00007ffff715c5f9 in jl_apply (f=0x48e8458b48e0558b, 
    args=0x48c031f845894800, nargs=10277) at julia.h:1045
Backtrace stopped: previous frame inner to this frame (corrupt stack?)

disassemble:

(gdb) r --build output sysimg.jl
Starting program: /home/joel/julia/julia-master/base/../usr/bin/julia-debug-basic --build output sysimg.jl
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
osutils.jl
^G
Program received signal SIGILL, Illegal instruction.
0x00007ffff03e9e54 in ?? ()
(gdb) disassemble
No function contains program counter for selected frame.

@staticfloat
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Unfortunately these errors can be really hard to track down, as it looks like the stack frame is getting smashed somehow. We should have packages for Fedora created in the next few weeks (Thanks to @nalimilan!) so perhaps once we get that packaging ready, we can provide a build of master for you to test.

@ViralBShah
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Please reopen if still relevant. Lots of work in the last few months related to Fedora, and we also have nightlies for Fedora and such.

@tkelman
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tkelman commented Nov 22, 2014

Non-collaborators can't reopen issues, but add a comment if needed and someone else can do it.

@ViralBShah ViralBShah added the system:linux Affects only Linux label Nov 23, 2014
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