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Hello,
OK got it. Thanks a lot for help, I did like you advised me. Let
AmberTools in amber11 and amber10 in amber10 compiled AmberTools
(AMBERHOME pointing to amber11) after test set AMBERHOME to amber10
compile got an error looking for netcdf in src directory -- linked it
(softlink) from amber11/src/ to amber10/src compiled it -- and hu --
it works!:-) For daily use I will set AMBERHOME to amber11 and put
both bin directories into the PATH. Again thanks for help.
I agree an env.-variable AMBERTOOLS could help much. You may get rid
of the softlinked netcdf-directory.
One last thing (maybe somebody who could change or arrange it read
this): A documentation which is up to date and which describes how to
do would help much and I would not need to bother other people with
stupid problems. I do not expect this from free software but I do from
a piece of software I bought.
Stef
On 1/12/10 4:17 PM, Daniel Roe wrote:
> 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: 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. ++
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Received on Tue Jan 12 2010 - 23:00:02 PST
