[AMBER] PATH/evironment problem on Mac OS X

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Fri, 21 Jan 2011 16:33:14 +0100

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:

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?

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

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:


echo $PATH returns:

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?

Best regards
// Gustaf

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Received on Fri Jan 21 2011 - 08:00:04 PST
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