AMBER Archive (2007)

Subject: RE: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Tue Nov 13 2007 - 10:13:18 CST

Thanks for your sharing. I am wondering whether anybody succeed in
compiling a parallel version on Windows XP. I have a machine with 4 cpus
running WinXP.

Thanks,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Tuesday, November 13, 2007 9:55 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installing Amber9 in a Cygwin environment on a
MS-Windows XP machine

On Mon, Nov 12, 2007, Hopkins, Robert wrote:

> After searching the Amber Mailing List Archives, I didn't find
> anyone's full experience of trying to install Amber9 on a MS Windows
> XP system using the Cygwin environment. So, out of appreciation for
> the Amber professionals that provide so much support (in particular,
> in my case, Ross Walker), I summarize below (for what it's worth) my
> experience, so that it might save others a few frustrations.

Thanks for the detailed instructions. I have a few comments, based on
my Cygwin experience.

> ....when I tried to apply the bugfixes using the patch command, I had
> to first edit the file bugfix.all into separate files and run each one

> separately.

I don't think this should be necessary. I routinely use the bugfix.all
file, without change, on cygwin. So, try the instructions as written
first.

>
> 7.) When running the configuration script, use the cygwin option:
> ./configure -cygwin g95. Afterward, be sure to look at config.h. For

> example, in this file, an environment variable was defined as:
> AMBER_SRC=C:\cygwin\usr\local\amber9/src (later on, this mixed
> DOS/Posix format proved to be a problem for me).

You should not have such mixed formats. This looks like you somehow set
up the AMBERHOME variable with backslashes, even though your email
indicates that you did not do that. You really don't want things like
"C:\" in your variables, and this never happens to me.

>
> 9.) After reviewing the log file, if all has gone well, go to the
> $AMBERHOME/test directory and edit a file there named dacdif as
follow.
> First, save a copy of dacdif as, say, dacdif.txt. Then, in the first
> line, change the shell from sh to ash:
>
> #!/bin/sh -> #!/bin/ash

I have never had the need to do this. For me the test suite works
without any changes.

>
> For anyone new to Cygwin and Amber9, I hope this information may be of

> some value.

It should be very helpful. My advice is to first try things as in the
instructions, and if they fail, look at some of the fixes Bob lists
here.

...thanks...dac

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