Re: [AMBER] PATH/evironment problem on Mac OS X

From: Jason Swails <>
Date: Fri, 21 Jan 2011 11:48:35 -0500


On Jan 21, 2011, at 10:33 AM, Gustaf Olsson <> wrote:

> Hello everyone
> We are experiencing some frustrating problems when installing AmberTools 1.4 and Amber11 in Mac OS X 10.6.X (snow leopard), not when compiling but when applying bugfix:es and making tests.
> On mac, users can specify shell profiles by creating .profile, .bashrc and so on in the users local directory. There are also system wide profiles stored under the root directory. Now to the problem...
> Compilation works just fine by exporting amberhome to PATH in you local profile, it works just as well when setting amberhome in the global profile.
> echo $PATH returns:
> /usr/local/packmol:/usr/local/amber11/exe:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

Small comment here: use bin rather than exe, since the use of exe is being phased out.

> in both cases. So the PATH variables seems to work just fine. You can run xleap, ptraj, sander and so forth....
> Here's the issue. When trying to apply the bugfix script for amber11 apply_bugfix.x it complains that $AMBERHOME needs to be defined to /usr/local/amber11. It already is, isn't it?

No. AMBERHOME and PATH are different environment variables. Put the following in your .profile or .bashrc:

export AMBERHOME=/usr/local/amber11

and retry.

> However, if AmberTools and Amber11 bugfix is applied through: patch -p0 -N < bugfix.all
> Everything runs smoothly with no complaints!

Because paths uses relative file paths and doesn't explicitly use AMBERHOME

> Now, after compilation we cd into test for both AmberTools 1.4 and Amber11, try to run "make test", and this is the response:
> (find . -name '*.dif' -o -name 'profile_mpi' | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> rm -f TEST_FAILURES.diff
> Error: AMBERHOME should be defined or else some tests will fail !
> make: *** [is_amberhome_defined] Error 2
> It does not matter in which profile (global/local, profile/bashrc/cshrc) we export $AMBERHOME, the result is always the same. It does not change if we set $AMBERHOME directly to:

Don't export $AMBERHOME, export AMBERHOME.

> /usr/local/amber11
> echo $PATH returns:
> usr/local/packmol:/usr/local/amber11:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
> Manual export/setenv does not change the response either.
> Has anyone experienced the same issue and has a workaround for this so that we can run the tests?

This error should not crop up if the environment variables are properly set. You can disable the check, but I'd suggest against it.

Good luck!

> Best regards
> // Gustaf
> _______________________________________________
> AMBER mailing list

Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jan 21 2011 - 09:00:02 PST
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