Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12

From: Jason Swails <>
Date: Tue, 28 Jan 2014 15:06:52 -0500

On Tue, 2014-01-28 at 13:53 -0500, Robyn Ayscue wrote:
> I've successfully compiled Amber12/AmberTools13 on my MacBookPro and I've
> found that you must activate the root account and compile as root.

I've never had to compile as root on my Mac (and I would strongly
encourage people not to). I have built Amber on OS X 10.5 through 10.9
without root. This sounds like an issue with file ownership or
permissions -- you need to make sure that AMBERHOME is owned
(recursively) by the user you are trying to install as, and that the
files have the appropriate permissions to allow reading, writing, and

sudo chown -R <user> /path/to/amber

> Logging
> in to a shell as yourself and trying to compile by typing "sudo" in front
> of every command doesn't seem to work well with Amber programs (even if you
> have full admin privileges). I would always get arcane errors, like the one
> about $AMBERHOME not being set (even when typing "echo $AMBERHOME" proved
> that it really was set)

This is a common stumbling block. AMBERHOME is in fact _not_ set when
you see complaints about AMBERHOME not being set... the key qualifier
being that AMBERHOME is not set in the shell being used to run the
commands. By default, "sudo" does not necessarily inherit the calling
shell's environment (you need to use the -E flag to do this). This is
actually not unique to Amber, although most other programs do not rely
so heavily on a particular environment variable as Amber does.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 28 2014 - 12:30:02 PST
Custom Search