RE: AMBER: configure question

From: Ross Walker <>
Date: Thu, 28 Jun 2007 10:06:40 -0700

Hi Steve,

> my issues I couldn't help but ask myself why isn't there a ./configure
> script for this just like most of all the other open source
> applications

This is more a philosophical point than anything else. The issue is one of
the fact that the Amber developers are scientists first and programmers
second. We do not get any funding from NSF or NIH specifically to develop
the software, and it is very hard to get such development included in grant
requests. The science always has to come first. Thus the issue is one of
maintenance. If you know how to build an autoconfigure script that will work
on all platforms imaginable and all MPI implementations imaginable, and I
mean from this everything from cygwin under windows to every flavour of
linux, to AIX, to IRIX then by all means feel free to create it and send it
to the developers we will be very grateful although it will have to be
simple enough that the average graduate student contributing to the code can
understand and maintain the script.

The issue at heart is that Amber is significantly more complicated than most
packages that use auto configure scripts and significant flexibility is
required with regards to what code gets compiled on what platforms, which
math libraries get linked in etc. If it was just a serial program running on
Linux platforms then this might be somewhat possible but when you throw in
both serial and MPI compilation + multiple platforms + multiple languages
(F77, F95, c, c++, perl etc) + multiple packages with multiple dependencies
(sander, sander.LES, sander.MPI, sander.PIMD, sander.PIMD.MPI, pmemd, ptraj,
ambpdb, xleap, tleap etc etc...) such an effort to produce an all
encompasing auto configure script gets out of hand very very quickly. Trust
me I have tried it myself and after a day or so I gave up since I didn't
have any more free time to work on it.

An alternative would be to provide binaries for certain platforms but again
this requires a significant amount of maintenance and testing that we simply
don't have the manpower or funding to do.

So, while I fully support what you are saying and agree that yes it really
would help things there really isn't sufficient money, people and expertise
to do this, maintain it, test it and teach everybody else how it works and
how to add to it. I wish it was different but this is largely a function of
the current funding climate in the US with regards to scientific software.

Just my 2c...

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Jul 01 2007 - 06:07:24 PDT
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