[ruby-core:67800] [ruby-trunk - Bug #10779] occasional segmentation fault running ruby 2.1, doesn't appear with ruby 1.9

Issue #10779 has been updated by LMH medchem.

File script_test_files.tar.bz2 added

Eric Wong wrote:
> [e-mail] wrote:
>  > I can post the script and sample input files if that would help.
>  
>  Please do, thank you.

I have uploaded a tar.bz2 with a test directory setup. Extract the archive, cd to the test directory and run,

./get_cols_and_sort.ruby RI_7 13 > output.txt

The file expected_output.txt gives what the output should look like. The script is reasonably documented but has been revised a few times so the doc may not be completely up to date. This ruby is called out of a bash script and is run in sets of 4 iterations. I have run it several times on opensuse 13.2, ruby 2.1, and had a number of errors by the time the script had run 16 times. This happened multiple times, so I kept restarting the batch to see if it would persist. Last night I set it up on opensuse 12.3, ruby 1.9, and it has run at least 224 times so far without any errors.

>  > -- C level backtrace information
>  > -------------------------------------------
>  > /usr/lib64/libruby2.1.so.2.1(+0x18b827) [0x7f683ae86827]
>  > /usr/lib64/libruby2.1.so.2.1(+0x18b8f3) [0x7f683ae868f3]
>  > /usr/lib64/libruby2.1.so.2.1(+0x6e623) [0x7f683ad69623]
>  > /usr/lib64/libruby2.1.so.2.1(rb_bug+0xb3) [0x7f683ad69c93]
>  > /usr/lib64/libruby2.1.so.2.1(+0x122a0f) [0x7f683ae1da0f]
>  
>  It would also be helpful if you compiled with debug info enabled
>  (-ggdb3, the default) and/or did not strip your binaries.
>  There should be file names and line numbers in there.
>  Thanks again

I'm not sure what you are referring to with this. I don't have anything compiled. I am just running the ruby script from the Hash-Bang line.

**LMHmedchem**



----------------------------------------
Bug #10779: occasional segmentation fault running ruby 2.1, doesn't appear with ruby 1.9
https://bugs.ruby-lang.org/issues/10779#change-51211

* Author: LMH medchem
* Status: Open
* Priority: Normal
* Assignee: 
* ruby -v: 2.1.3p242 r47630
* Backport: 2.0.0: UNKNOWN, 2.1: UNKNOWN, 2.2: UNKNOWN
----------------------------------------
Hello, 

Below is the error output from a ruby script I have been running. I am reporting this for two reasons. The first is that the error is intermittent and the second is that I don't get this error with ruby 1.9. The script gets called over and over again from a bash script. Most of the time it runs fine and produces the appropriate output. Occasionally, I get the error report below and the output file is blank. I have run this script for quite a while under windows cygwin and opensuse 12.3. Both platforms use ruby 1.9. I recently set up a new install of opensuse 13.2 and started seeing this error.

I can post the script and sample input files if that would help.

**LMHmedchem**




./get_cols_and_sort.ruby:130: [BUG] Segmentation fault at
0x00000000000000
ruby 2.1.3p242 (2014-09-19 revision 47630) [x86_64-linux-gnu]

-- Control frame information
-----------------------------------------------
c:0008 p:---- s:0026 e:000025 CFUNC  :==
c:0007 p:---- s:0024 e:000023 CFUNC  :==
c:0006 p:0013 s:0020 e:000019 BLOCK  ./get_cols_and_sort.ruby:130
[FINISH]
c:0005 p:---- s:0017 e:000016 IFUNC
c:0004 p:---- s:0015 e:000014 CFUNC  :each
c:0003 p:---- s:0013 e:000012 CFUNC  :all?
c:0002 p:0074 s:0010 E:001c88 EVAL   ./get_cols_and_sort.ruby:130
[FINISH]
c:0001 p:0000 s:0002 E:001ff8 TOP    [FINISH]

-- Ruby level backtrace information
----------------------------------------
./get_cols_and_sort.ruby:130:in `<main>'
./get_cols_and_sort.ruby:130:in `all?'
./get_cols_and_sort.ruby:130:in `each'
./get_cols_and_sort.ruby:130:in `block in <main>'
./get_cols_and_sort.ruby:130:in `=='
./get_cols_and_sort.ruby:130:in `=='

-- C level backtrace information
-------------------------------------------
/usr/lib64/libruby2.1.so.2.1(+0x18b827) [0x7f683ae86827]
/usr/lib64/libruby2.1.so.2.1(+0x18b8f3) [0x7f683ae868f3]
/usr/lib64/libruby2.1.so.2.1(+0x6e623) [0x7f683ad69623]
/usr/lib64/libruby2.1.so.2.1(rb_bug+0xb3) [0x7f683ad69c93]
/usr/lib64/libruby2.1.so.2.1(+0x122a0f) [0x7f683ae1da0f]
/lib64/libc.so.6(+0x35200) [0x7f683a988200]

-- Other runtime information
-----------------------------------------------

* Loaded script: ./get_cols_and_sort.ruby

* Loaded features:

    0 enumerator.so
    1 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/encdb.so
    2 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/trans/transdb.so
    3 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/rbconfig.rb
    4 /usr/lib64/ruby/2.1.0/rubygems/compatibility.rb
    5 /usr/lib64/ruby/2.1.0/rubygems/defaults.rb
    6 /usr/lib64/ruby/2.1.0/rubygems/deprecate.rb
    7 /usr/lib64/ruby/2.1.0/rubygems/errors.rb
    8 /usr/lib64/ruby/2.1.0/rubygems/version.rb
    9 /usr/lib64/ruby/2.1.0/rubygems/requirement.rb
   10 /usr/lib64/ruby/2.1.0/rubygems/platform.rb
   11 /usr/lib64/ruby/2.1.0/rubygems/basic_specification.rb
   12 /usr/lib64/ruby/2.1.0/rubygems/stub_specification.rb
   13 /usr/lib64/ruby/2.1.0/rubygems/util/stringio.rb
   14 /usr/lib64/ruby/2.1.0/rubygems/specification.rb
   15 /usr/lib64/ruby/2.1.0/rubygems/exceptions.rb
   16 /usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_gem.rb
   17 thread.rb
   18 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/thread.so
   19 /usr/lib64/ruby/2.1.0/monitor.rb
   20 /usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_require.rb
   21 /usr/lib64/ruby/2.1.0/rubygems.rb

* Process memory map:

00400000-00401000 r-xp 00000000 08:12 532347
 /usr/bin/ruby
00600000-00601000 r--p 00000000 08:12 532347
 /usr/bin/ruby
00601000-00602000 rw-p 00001000 08:12 532347
 /usr/bin/ruby
01550000-08ac7000 rw-p 00000000 00:00 0
 [heap]
7f68397d4000-7f68397ea000 r-xp 00000000 08:12 1835120
 /lib64/libgcc_s.so.1
7f68397ea000-7f68399e9000 ---p 00016000 08:12 1835120
 /lib64/libgcc_s.so.1
7f68399e9000-7f68399ea000 r--p 00015000 08:12 1835120
 /lib64/libgcc_s.so.1
7f68399ea000-7f68399eb000 rw-p 00016000 08:12 1835120
 /lib64/libgcc_s.so.1
7f68399eb000-7f68399ee000 r-xp 00000000 08:12 527717
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/thread.so
7f68399ee000-7f6839bed000 ---p 00003000 08:12 527717
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/thread.so
7f6839bed000-7f6839bee000 r--p 00002000 08:12 527717
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/thread.so
7f6839bee000-7f6839bef000 rw-p 00003000 08:12 527717
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/thread.so
7f6839bef000-7f6839bf2000 r-xp 00000000 08:12 527661
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/trans/transdb.so
7f6839bf2000-7f6839df1000 ---p 00003000 08:12 527661
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/trans/transdb.so
7f6839df1000-7f6839df2000 r--p 00002000 08:12 527661
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/trans/transdb.so
7f6839df2000-7f6839df3000 rw-p 00003000 08:12 527661
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/trans/transdb.so
7f6839df3000-7f6839df5000 r-xp 00000000 08:12 527672
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/encdb.so
7f6839df5000-7f6839ff4000 ---p 00002000 08:12 527672
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/encdb.so
7f6839ff4000-7f6839ff5000 r--p 00001000 08:12 527672
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/encdb.so
7f6839ff5000-7f6839ff6000 rw-p 00002000 08:12 527672
 /usr/lib64/ruby/2.1.0/x86_64-linux-gnu/enc/encdb.so
7f6839ff6000-7f683a0f6000 r-xp 00000000 08:12 1835195
 /lib64/libm-2.19.so
7f683a0f6000-7f683a2f5000 ---p 00100000 08:12 1835195
 /lib64/libm-2.19.so
7f683a2f5000-7f683a2f6000 r--p 000ff000 08:12 1835195
 /lib64/libm-2.19.so
7f683a2f6000-7f683a2f7000 rw-p 00100000 08:12 1835195
 /lib64/libm-2.19.so
7f683a2f7000-7f683a303000 r-xp 00000000 08:12 1835105
 /lib64/libcrypt-2.19.so
7f683a303000-7f683a502000 ---p 0000c000 08:12 1835105
 /lib64/libcrypt-2.19.so
7f683a502000-7f683a503000 r--p 0000b000 08:12 1835105
 /lib64/libcrypt-2.19.so
7f683a503000-7f683a504000 rw-p 0000c000 08:12 1835105
 /lib64/libcrypt-2.19.so
7f683a504000-7f683a532000 rw-p 00000000 00:00 0
7f683a532000-7f683a535000 r-xp 00000000 08:12 1835171
 /lib64/libdl-2.19.so
7f683a535000-7f683a734000 ---p 00003000 08:12 1835171
 /lib64/libdl-2.19.so
7f683a734000-7f683a735000 r--p 00002000 08:12 1835171
 /lib64/libdl-2.19.so
7f683a735000-7f683a736000 rw-p 00003000 08:12 1835171
 /lib64/libdl-2.19.so
7f683a736000-7f683a74e000 r-xp 00000000 08:12 1835180
 /lib64/libpthread-2.19.so
7f683a74e000-7f683a94d000 ---p 00018000 08:12 1835180
 /lib64/libpthread-2.19.so
7f683a94d000-7f683a94e000 r--p 00017000 08:12 1835180
 /lib64/libpthread-2.19.so
7f683a94e000-7f683a94f000 rw-p 00018000 08:12 1835180
 /lib64/libpthread-2.19.so
7f683a94f000-7f683a953000 rw-p 00000000 00:00 0
7f683a953000-7f683aaf1000 r-xp 00000000 08:12 1835183
 /lib64/libc-2.19.so
7f683aaf1000-7f683acf1000 ---p 0019e000 08:12 1835183
 /lib64/libc-2.19.so
7f683acf1000-7f683acf5000 r--p 0019e000 08:12 1835183
 /lib64/libc-2.19.so
7f683acf5000-7f683acf7000 rw-p 001a2000 08:12 1835183
 /lib64/libc-2.19.so
7f683acf7000-7f683acfb000 rw-p 00000000 00:00 0
7f683acfb000-7f683af4a000 r-xp 00000000 08:12 527206
 /usr/lib64/libruby2.1.so.2.1.0
7f683af4a000-7f683b14a000 ---p 0024f000 08:12 527206
 /usr/lib64/libruby2.1.so.2.1.0
7f683b14a000-7f683b14f000 r--p 0024f000 08:12 527206
 /usr/lib64/libruby2.1.so.2.1.0
7f683b14f000-7f683b152000 rw-p 00254000 08:12 527206
 /usr/lib64/libruby2.1.so.2.1.0
7f683b152000-7f683b177000 rw-p 00000000 00:00 0
7f683b177000-7f683b197000 r-xp 00000000 08:12 1835122
 /lib64/ld-2.19.so
7f683b230000-7f683b331000 rw-p 00000000 00:00 0
7f683b331000-7f683b370000 r--p 00000000 08:12 1311625
 /usr/lib/locale/en_US.utf8/LC_CTYPE
7f683b370000-7f683b375000 rw-p 00000000 00:00 0
7f683b38a000-7f683b38b000 rw-p 00000000 00:00 0
7f683b38b000-7f683b38c000 ---p 00000000 00:00 0
7f683b38c000-7f683b38f000 rw-p 00000000 00:00 0
 [stack:6054]
7f683b38f000-7f683b396000 r--s 00000000 08:12 534452
 /usr/lib64/gconv/gconv-modules.cache
7f683b396000-7f683b397000 rw-p 00000000 00:00 0
7f683b397000-7f683b398000 r--p 00020000 08:12 1835122
 /lib64/ld-2.19.so
7f683b398000-7f683b399000 rw-p 00021000 08:12 1835122
 /lib64/ld-2.19.so
7f683b399000-7f683b39a000 rw-p 00000000 00:00 0
7fff6700e000-7fff6702f000 rw-p 00000000 00:00 0
7fff671a9000-7fff671ab000 r-xp 00000000 00:00 0
 [vdso]
7fff671ab000-7fff671ad000 r--p 00000000 00:00 0
 [vvar]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
 [vsyscall]


[NOTE]
You may have encountered a bug in the Ruby interpreter or extension
libraries.
Bug reports are welcome.
For details: http://www.ruby-lang.org/bugreport.html

---Files--------------------------------
script_test_files.tar.bz2 (3.31 MB)


-- 
https://bugs.ruby-lang.org/