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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> Stack Smashing Error http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1245712944 Message started by Andrew_Roth on Jun 22^nd, 2009 at 4:22pm

Title: Stack Smashing Error
Post by Andrew_Roth on Jun 22^nd, 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

Title: Re: Stack Smashing Error
Post by Sergei on Jun 22^nd, 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

Title: Re: Stack Smashing Error
Post by Andrew_Roth on Jun 24^th, 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

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=HCN_v6_fasta.zip (13 KB | )

Title: Re: Stack Smashing Error
Post by Andrew_Roth on Jun 24^th, 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.

Cheers,
Andrew

Title: Re: Stack Smashing Error
Post by Sergei on Jun 24^th, 2009 at 11:43am

Dear Andrew,

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

Sergei

Title: Re: Stack Smashing Error
Post by Andrew_Roth on Jun 24^th, 2009 at 11:56am

HYPHY crashes as soon as I load the data file.

Andrew

Title: Re: Stack Smashing Error
Post by Sergei on Jun 26^th, 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