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

From: Gustaf Olsson <>
Date: Fri, 21 Jan 2011 19:08:39 +0100

Thanks for you input Ben, sadly; no such luck.

Both the echo and env grep presents AMBERHOME as set correctly, but test still fails!

        VCN736:~ guolaa$ cd /usr/local/amber11/test/
        VCN736:test guolaa$ env | grep PATH
        VCN736:test guolaa$ env | grep AMBERHOME
        VCN736:test guolaa$ sudo make test
        (find . -name '*.dif' -o -name 'profile_mpi' | \
                while read dif ;\
                do \
                    rm -f $dif ;\
                done ;\
        rm -f TEST_FAILURES.diff
        Error: AMBERHOME should be defined or else some tests will fail !
        make: *** [is_amberhome_defined] Error 2
        VCN736:test guolaa$

Best regards Gustaf

On Jan 21, 2011, at 7:00 PM, Ben Roberts wrote:

> Hi Gustav,
> On 21/1/2011, at 12:46 p.m., Gustaf Olsson wrote:
>> Thank you Jason!
>> I should have been a bit more detailed with my question.
>>> Small comment here: use bin rather than exe, since the use of exe is being phased out.
>> Usually I use /bin. I just tried /exe to see if it made a difference, forgot to change back.
>>> No. AMBERHOME and PATH are different environment variables. Put the following in your .profile or .bashrc:
>>> export AMBERHOME=/usr/local/amber11
>>> export PATH=$AMBERHOME/bin:$PATH
>>> and retry.
>> This is what I have in my .profile and have also tried in .bashrc as well as global profile and bashrc
>> export AMBERHOME=/usr/local/amber11
>> export PATH=${AMBERHOME}/bin:$PATH
>> Tried the suggestion without {}, but it did not make a difference!
>> I just don't understand, I've tried exporting in all profiles on the mac and nothing solves this problem. I might also add that we've compiled AmberTools successfully in three iMac:s running Snow Leopard, and they all break during the "tests" with the same error.
>> Anything else anyone suggests I should try before starting to dissect the code?
> In your bashrc or bash_profile or wherever, try echoing $AMBERHOME and $PATH (with the dollar signs in this case) just after you've set them. It may be that some other resource file you're loading is messing your environment up.
> Also, run "env | grep PATH" and "env | grep AMBERHOME" just before you might run the tests, and see what you can see.
> Cheers,
> Ben
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Received on Fri Jan 21 2011 - 10:30:05 PST
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