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I am running plink software through a PBS batch job. This error occurs when I run the job:

 *** glibc detected *** /software/plink: double free or corruption (out): 0x000000018dfafca0 ***
 ======= Backtrace: =========
 [0x7d7691]
 [0x7d8bea]
 [0x45f5ed]
 [0x47bb11]
 [0x40669a]
 [0x7bdb2c]
 [0x400209]

However it only occur with one of my files (bw 30-60 gb files) and each rerun shows the exact same back trace map. I tried running it not through the batch scheduler and received the same error again, with the same backtrace map. I am just using the software (plink), and didn't write it, so most of the answers online are about writing and freeing memory in your program.

Any ideas on

  1. what is causing this error, and
  2. how I can fix it?
Mofi
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roserose
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  • I know this isn't likely what you want to hear, but you probably need to report the error to whoever supports plink for you. The fact that you get it with or without the batch system strongly suggests it is an error in plink itself. You can also search known bugs in plink and see if perhaps this has already been fixed. – dbeer Aug 04 '14 at 17:37

1 Answers1

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what is causing this error, and

A double-free or heap corruption in the plink

how I can fix it?

You can't. You can do one of two things, depending on how much you know and understand.

First, build the newest version of plink from source, and see if the problem persists.

If it does not, you are done (or at least you might hope that someone else found and fixed this problem).

If it does, you'll have to debug the problem sufficiently for either you, or plink developers to fix it. Some tools that should help: Valgrind and Address Sanitizer (note: in addition to Clang, Address Sanitizer is also included in GCC-4.8).

Once you have a good report (where the memory was allocated, and where it got corrupted), you should either fix it and submit your fix to plink developers, or give them a bug report with the allocation and corruption location and stack traces.

Employed Russian
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  • Thanks for the great explanation!! It had to be rebuilt as it only happened with a specific filter command. I ended up just doing the analysis and a manual filter befoer you answered but now I know more for later – roserose Aug 13 '14 at 16:10