Ah, I see the problem! It is your use of sudo. I would strongly suggest
against installing amber in a location that requires root privileges to
access, for this very reason (amongst others). Using the sudo command
launches a root shell, which will not source your personal .profile/.bashrc
resource files. This is why all looks good when you test for the
environment variables, but fails when you try to do run the tests or bug fix
script with sudo.
My suggestion, change ownership of /usr/local/amber11 over to your user and
drop the sudo command from everything. This should fix your issues:
sudo chmod -R `whoami` /usr/local/amber11
cd $AMBERHOME/AmberTools/test
make test
cd ../../test
make test
Likewise, apply the bugfixes with the apply_bugfix.x patch WITHOUT the sudo
command.
Good luck!
Jason
On Fri, Jan 21, 2011 at 1:18 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Gustaf,
>
> On 21/1/2011, at 1:08 p.m., Gustaf Olsson wrote:
>
> > Thanks for you input Ben, sadly; no such luck.
> >
> > Both the echo and env grep presents AMBERHOME as set correctly, but test
> still fails!
> >
> > /usr/local/amber11
> >
> /usr/local/amber11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
> > VCN736:~ guolaa$ 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
>
> If you would, try running "cd /usr/local/amber11/test &&
> ./test_amber_serial.sh". That will test $AMBERHOME first thing, and if the
> latter is not defined it will fail.
>
> Also, where exactly are you setting $AMBERHOME? It may be that the test is
> starting up as a non-login shell. If it's doing that, setting AMBERHOME in
> bash_profile or its equivalent may be problematic; bash_profile files are
> ignored for non-login shells (I think).
>
> --
> For greater security, I support S/MIME encryption.
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jan 21 2011 - 11:00:03 PST
