Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more

From: David Watson <>
Date: Fri, 30 Apr 2010 09:29:35 -0500

On Apr 30, 2010, at 9:10 AM, Yu Chen wrote:

> Hi,
> I am trying to recompile Amber10/AmberTools1.2 since we have upgraded from OS X leopard to Snow Leopard. While everything worked on Leopard, now it doesn't compile on Snow leopard. Any help is greatly appreciated!
> System: OS X 10.6.2 with Xcode 3.2.2, Intel compiler 10.1.014, Amber 10, AmberTools 1.2:

It would probably be in your best interest to use gcc instead of icc.
That being said, you are getting undefined symbols, which means that your libraries are not being found.
You should probably uninstall icc/ifort, install and update Snow Leopard and XCode to the latest version, then reinstall the Intel compilers.

Following this, make sure that you "source" the environment scripts provided by Intel withing your ~/.bash_profile
You will need to do something like this:

# Additions for Intel compiler
 . /Library/Frameworks/Intel_MKL.framework/Versions/Current/tools/environment/
 . /opt/intel/Compiler/10.1/014/bin/ intel64
 . /opt/intel/Compiler/10.1/014/bin/ intel64
# End of ~/.bash_profile additions

Once you have done this, start a new bash shell and start all over with a clean Amber10 directory, applying all of the AmberTools patches and Amber10 patches first.

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Received on Fri Apr 30 2010 - 08:00:04 PDT
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