RE: AMBER: configure question

From: Steve Young <>
Date: Fri, 29 Jun 2007 10:31:19 -0400

        By no means was I intending to create a flame war. I was just curious
if there was a reason =). I do understand that many are scientists first
and that Amber is complicated software. Coming from a computer science
background I have been amazed at how many of the popular chemistry
software packages can be difficult to build (not just amber). I can
imagine that for some people who just want to do the research and not
have the expertise of a computer person around that this kind of thing
could get very frustrating.
        Anyhow, it sounds like you all have had this discussion already ;). I
appreciate the response. Thanks,


On Thu, 2007-06-28 at 10:06 -0700, Ross Walker wrote:
> 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
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Jul 01 2007 - 06:07:33 PDT
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