Thanks for you input Ben, sadly; no such luck.
Both the echo and env grep presents AMBERHOME as set correctly, but test still fails!
/usr/local/amber11
/usr/local/amber11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
VCN736:~ guolaa$ cd /usr/local/amber11/test/
VCN736:test guolaa$ env | grep PATH
PATH=/usr/local/packmol:/usr/local/amber11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
VCN736:test guolaa$ env | grep AMBERHOME
AMBERHOME=/usr/local/amber11
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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>
>
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Received on Fri Jan 21 2011 - 10:30:05 PST
