Re: [AMBER] A9 tutorial problem

From: Robert Wohlhueter <>
Date: Sat, 20 May 2017 12:06:58 -0400

David, Hai,

Thanks for your responses. They were helpful, and I got ""

That my system python is "bad" is a relative statement: I have dozens
of programs that use python, some requiring version x, another version y
(and some, like amber which distributes their own version). And I admit
to a baroque set of scripts and aliases to try to satisfy each

The most expedient solution for me was simply to replace the
synaptic-distribution-numpy version of with the Amber16
version. (Hopefully, that won't break other numpy-dependent programs.
But is it does, I'm sensitized.)

Thanks again,

Bob W.

On 5/20/17 9:31 AM, David Case wrote:
> On Fri, May 19, 2017, Hai Nguyen wrote:
>> sounds like your system python is bad. Can you try to replace "python"
>> by "amber.python" (to use $AMBERHOME/miniconda python)?
> Sounds like this may already have been done:
>>> Using `find`, I also see an instance of this shared-lib in
>>> $AMBERHONE/miniconda/pkgs/numpy-1.12.0-py27_nomkl_0/lib/python2.7/site-packages/numpy/linalg/
>>> NONE of these instance defines the symbol
>>> "ATL_zttrsm" (as probed by `nm -Ca <lib-path-name> | grep ATL_zttrsm`)
> But if you haven't tried using amber.python, it's certainly worth a try.
>>> Any hints appreciated,
> I don't have any real hints, and I think this is the first time this problem
> has been reported.
> [Developers: we don't have any systematic way at all of keeping the
> tutorials in sync with the current code. Suggestions are welcome. Maybe
> new students/postdocs could be required to work through a tutorial,
> comment on problems or things that are difficult to understand, and post
> results to a wiki page? Other ideas might be better.
> It would be great if someone now could check tutorial A9.]
> ....dac
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Received on Sat May 20 2017 - 09:30:02 PDT
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