Re: AMBER: sander on cygwin

From: David A. Case <>
Date: Mon, 15 Sep 2003 13:03:23 -0700

On Mon, Sep 15, 2003, David E. Konerding DSD Staff wrote:
> From time to time, I compile sander under cygwin to test it out.
> It runs just fine for me (I basically just use the defaults) *except* that I
> get a lot of numerical instability. I've confirmed this sort of behavior
> with other programs as well- the cygwin-provided Python tends to produce
> very weird numbers (even when just using basic operations like +, *, /).
> I think they are doing something wrong with the Intel floating point control
> words somewhere and the FP register stack is being corrupted. I would
> strongly avoid using cygwin to compile sander unless you are willing to
> debug this sort of problem (I am not).

This is a surprise to me, since I use cygwin a lot, both for code development
and for actual runs, and I have not seen this sort of behavior.

Does sander pass all of the tests for you? Are any of the errors
reproducible? Do you know that gcc on cygwin does something different with
FP registers, etc, than gcc on Linux would do? I would have thought that
identical assembly code would be generated....


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Sep 15 2003 - 21:53:01 PDT
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