Bug #10779: occasional segmentation fault running ruby 2.1, doesn't appear with ruby 1.9

• Status: Closed
• Assignee: -
• Target version: -
• ruby -v: 2.1.3p242 r47630
• Backport: 2.0.0: UNKNOWN, 2.1: UNKNOWN, 2.2: UNKNOWN

[LMHmedchem (LMH medchem)]

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]

[normalperson (Eric Wong)]

[e-mail] wrote:

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

Please do, thank you.

-- 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

[LMHmedchem (LMH medchem)]

• File script_test_files.tar.bz2 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

[nobu (Nobuyoshi Nakada)]

• File bug-10779.log bug-10779.log added
• Description updated (diff)
• Status changed from Open to Feedback

LMH medchem wrote:

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.

What distribution are you using?
Probably the debug info package would be available.

[LMHmedchem (LMH medchem)]

Nobuyoshi Nakada wrote:

LMH medchem wrote:

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.

What distribution are you using?
Probably the debug info package would be available.

I'm not sure what you mean by distribution in this context. Do you mean the linux distribution or ruby? I thought I included that information in the original post. This was ruby 2.1.3p242 r47630 on opensuse 13.2 x86-64 installed through Yast.

Since Yast is now built on ruby 2.1, there was no easy way to revert to 1.9 and get my script running. I had to re-install an older opensuse (12.3) to get things running again. I don't have opensuse 13.2 installed anymore. I could put it up on a VM if you need more information.

Which ruby-debuginfo package would this be? My opensuse 12.2 VM lists 10 ruby-debuginfo packages available.

cmpi-bindings-ruby-debuginfo graphviz-ruby-debuginfo kdebindings3-ruby-debuginfo kross-ruby-debuginfo libcaca-ruby-debuginfo libstorage-ruby-debuginfo openwsman-ruby-debuginfo weechat-ruby-debuginfo xmms2-ruby-debuginfo
None of these stand out as what you are looking for.

LMHmedchem

[jeremyevans0 (Jeremy Evans)]

• Status changed from Feedback to Closed