Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6

From: David A Case <>
Date: Tue, 12 Jul 2011 08:09:11 -0400

On Tue, Jul 12, 2011, Daniel Sindhikara wrote:

> I am trying to run AMBER11 on a mac. I have been using Ambertools
> successfully, but when I try to make serial in the $AMBERHOME/src/ directory
> I get some undefined symbols when trying to make sander (from command sudo
> make serial).

What version of AmberTools are you using? If it is 1.5, be sure to run the
python script before compiling amber11 itself, as instructed in the output
from configure.

Is it also possible that you have some old netcdf compiled files lying around
(maybe from a different compiler)? You could try a "make clean" (in
amber11/src) before the "make install" step.

Note that (1) you really should not use "sudo" to install Amber. Find a
directory where you have permissions as an ordinary user. I don't know that
Amber installation could do bad things to your system, but running complex
scripts like our installation procedure as root is needlessly dangerous;
(2) you should not be invoking the "serial" target of the Makefile directly,
but should rather type "make install". If there are instructions someplace
that indicate otherwise, please point them out, and we will get them updated.


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Received on Tue Jul 12 2011 - 05:30:04 PDT
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