Re: amber-developers: Testing Amber Tools

From: David A. Case <>
Date: Tue, 6 May 2008 14:49:11 -0700

On Tue, May 06, 2008, Wei Zhang wrote:
> Regarding boost, to my best knowledge, the following modules of
> boost have been used by gleap:
> (5) vector: numerical vector class of boost. This part seems to be
> causing the compilation problem.

Is this the "valarray" stuff? That seemed like a pretty nice feature,
although I still have to learn more about how/if one can use these to
communicate to and from "C" code.

> Only (1) maybe (2) are absolute needs. All the others can be replaced.
> especially (5), which seems to be the root of all problems according to the
> error messages people posted.

I'll leave this to your judgment. I don't have any problem requiring point
(5) if it genuinely leads to better code. If it *is* valarray, then I would
not want to give it up casually, just so someone with gcc 3.2 can compile
sleap. We would just have to make it clear that it is indeed the requirement,
and try to have the configure script test for that.

Also, if it takes a week's work to undo this, that's a strong argument against
making the change.

On another point: is there code in amber11/src/gleap/freelib/boost that we are
*not* using? There are directories there that don't seem to correspond
to things you don't list above. If so, I'd like to clean that out so that we
only distribute the things we are using. (New code can always be added later
if you want to add new boost features.)

> (1) I have wrote a short paper (about 8 pages) which explains the basic idea
> of gleap, currently it is in MS word format, I will convert it to pdf and
> put it to CVS.
> (2) keep working on the programmers' guide.
> (3) I am now cleaning up the code and adding more comments to it.

Great...I really appreciate this.

> BTW, Eric Peterson, developer of Chimera, is work on a Makefile
               ^^^^^^^^^ = Pettersen, actually

> which will allow AmberTools to be compile under various platform: Mac,
> Window, HP-UX and IRIX. He plans to include AmberTools in Chimera
> distributions. Therefore, in the future, maybe we can instruct user who have
> problem compiling AmberTools to download and use the one come with Chimera.

Should we try to set up a meeting sometime with you, Scott, me and Eric (plus
others?). It might be a UCSF. I'd like to learn more about how the Chimera
connection will work, and how to build on the gleap foundation you have built.
If we can truly get a functional graphics connection going, that would really
be great.

...thanks again for your contributions here....dave
Received on Wed May 07 2008 - 06:07:49 PDT
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