When you're installing amber10 I would have AMBERHOME set to your
amber10 directory (it should do this automatically, but best to be safe).
For general use, I agree with Jason that it's probably more important to
have $AMBERHOME set to your amberTools directory (the amber11 one in the
case of AmberTools 1.3), since programs like leap will search for
parameter files etc using the $AMBERHOME variable.
One thing to keep in mind is that when you are running test cases you
need to have $AMBERHOME set to the amber distribution you are running
the tests for. For example, when you're running tests for amber10,
$AMBERHOME needs to point to the amber10 directory for everything to
work correctly. Same deal for amber11 tests.
-Dan
PS - General note to everyone: I know there have been a lot of changes
to the configure process lately, but since Amber and AmberTools are
essentially separate at this point should an $AMBERTOOLSHOME variable
introduced, or would that introduce more issues that it would solve?
Stefan weber wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Dan,
>
> will try so, but where should $AMBERHOME point to? Amber10 or like
> ambertools amber11?
> I'll try with both and tell you later on...
>
> Best
>
> Stef
>
> On 1/12/10 3:32 PM, Daniel Roe wrote:
>
>> Hi Stefan,
>>
>> I'm not 100% certain, but since AmberTools 1.3 contains many
>> updates to the configure/compile process (one of the reasons it
>> extracts to amber11) it's likely that it is not completely
>> compatible with the amber 10 install process. Try to keep the two
>> separate and see if you can do a fresh install of amber10 by
>> itself, in its own directory.
>>
>> -Dan
>>
>> Stefan weber wrote: Hello,
>>
>> just a complete newbie with amber. I tried to install amber10 on
>> ubuntu 9.10 64bit. and got follwing problem. compiling starts
>> (amber -- ambertools v 1.3 are already done and tests are fine),
>> running a while and stopping with error do not find lapack.a and
>> blas.a. Both files where created just before and moved to the
>> $AMBERHOME/lib directory. Any help?
>>
>> Ok there are some other strange things before. All documentation
>> telling me ambertools and amber should be unpacked in one
>> directory, trying to do so amber10 extracts in amber10 and
>> ambertools1.3 in amber11. So to put them in one directory I
>> unpacked amber10 (to /usr/local/amber10) renamed folder amber10 to
>> amber11; unpacked ambertools and renamed the stuff back to amber10,
>> setting environment ($AMBERHOME) and PATH pointing to
>> /usr/local/amber10, then I patched everything (first ambertools
>> then amber10 and then starting to compile. As said before
>> ambertools v 1.3 compiled fine, run ambertools tests fine and then
>> run into trouble compiling amber10.
>>
>> I attached the logfile from compiling amber10 ( make serial >>
>> make-serial.log 2>&1 )
>>
>> Any Help?
>>
>> -- Stefan Weber Tel: +497612034642
>>
>> Rechenzentrum der Universität Freiburg Hermann-Herder-Str. 10
>> D-79104 Freiburg
>>
>> ++ Das Leben -- so wie es wirklich ist -- ist nicht der Kampf
>> zwischen Gut und Böse, sondern zwischen Böse und noch Schlimmerem.
>> ++
>>
>
> - --
> Stefan Weber
> Tel: +497612034642
>
> Rechenzentrum der Universität Freiburg
> Hermann-Herder-Str. 10
> D-79104 Freiburg
>
> ++ Das Leben -- so wie es wirklich ist --
> ist nicht der Kampf zwischen Gut und Böse,
> sondern zwischen Böse und noch Schlimmerem. ++
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>
--
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741
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Received on Tue Jan 12 2010 - 07:30:05 PST
