Re: AMBER: sander on cygwin

From: David E. Konerding DSD Staff <>
Date: Mon, 15 Sep 2003 11:24:29 -0700

Lee, Matthew wrote:

>I am running CYGWIN_NT-5.0 under Windows 2000 and compiled AMBER7 without
>error, but I can't get sander to run. All other modules of AMBER work and
>pass all the tests in the $AMBERHOME/test directory.
>When I try to execute sander, I get no STDOUT or STDERR and no output files
>of any type are created, not even mdout.
>cygwin9% ls
>cygwin10% sander
>cygwin11% ls
>cygwin12% gibbs
>open: No such file or directory
>apparent state: unit 5 named PIN
>lately writing direct unformatted external IO
>Aborted (core dumped)
>cygwin13% ls
>Does anyone have any ideas on how I can get sander to work in this
>environment? If so, please e-mail me as well as the reflector, because I am
>unable to receive reflector mail and must go to the Jarrod Smith's archive
>in order to read it.

 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).


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Received on Mon Sep 15 2003 - 19:53:01 PDT
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