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Stack Smashing Error (Read 3814 times)
Andrew_Roth
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Stack Smashing Error
Jun 22nd, 2009 at 4:22pm
 
I though I would post a quick fix for an error I was receiving after compiling HYPHY on Ubuntu 9.04.

Several batch analysis I was running were reporting some type of "Stack Smashing" errors. The problem is easily fixed by appending "-fno-stack-protector" in the C and C++ compiler flags and recompiling HYPHY.

This will turn off the GCC Stack-Smashing Protector which I take it is to stop some sort of buffer overflow problems.

Cheers,
Andrew
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Sergei
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Re: Stack Smashing Error
Reply #1 - Jun 22nd, 2009 at 5:36pm
 
Dear Andew,

Thanks for discovering this issue!

Could you post some the files needed to recreate the condition? I wonder if stack smashing has to do with poor behavior by HyPhy, or with too small a stack allocation made by gcc by default.

Sergei
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Andrew_Roth
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Re: Stack Smashing Error
Reply #2 - Jun 24th, 2009 at 10:51am
 
Hi Sergei,
This file seems to be crash HYPHY with the error when I load it through the GTK interface. I have also gotten the same error running analysis on this dataset using the command line version.

Cheers,
Andrew
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Andrew_Roth
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Re: Stack Smashing Error
Reply #3 - Jun 24th, 2009 at 10:54am
 
I should mention I am using the version of HYPHY available from the main website, not the SVN. I also get the problem using SP, MP or MP2 compilations.

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Andrew
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Sergei
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Re: Stack Smashing Error
Reply #4 - Jun 24th, 2009 at 11:43am
 
Dear Andrew,

Does HyPhy crash when you load the file into the data viewer, or during a specific analysis?

Sergei
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Andrew_Roth
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Re: Stack Smashing Error
Reply #5 - Jun 24th, 2009 at 11:56am
 
HYPHY crashes as soon as I load the data file.

Andrew
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Sergei
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Re: Stack Smashing Error
Reply #6 - Jun 26th, 2009 at 1:33pm
 
Dear Andrew,

I was able to load the file into a HyPhy GTK build using the current (SVN) source on Ubuntu 9.04. The SVN version also builds easily using instructions Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

I would recommend that you use the newer version.

Sergei
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Division of Biomedical Informatics
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