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

From: Hopkins, Robert <>
Date: Mon, 12 Nov 2007 17:32:20 -0600

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. Please be aware that some
of the problems I encountered (or solutions below) might possibly be
machine specific (Windows XP on a HP laptop with AMD Athlon 64


1.) Begin with several GB of free space on your hard drive. Then, be
prepared that, as others have cautioned, this probably will be more
difficult than doing an install on a UNIX or Linux machine. Finally,
when a new error arises, be sure to *first* search the Amber Mailing
List Archives: <>

2.) Go to the Cygwin site, and also the following
<> to learn about the downloading process using the
setup.exe program in order to become familiar with the process/software.


3.) Choose a directory where you want set up Cygwin (e.g., I installed
it under C:\), however, avoid any directory that contains a blank space
in the name (e.g., Program Files). Create a folder there named, say,
Cygwin_Cache as a permanent repository for your downloaded Cygwin
installation files. Then go to the Cygwin site: <> , download and install
all of the following:

            a.) the basic Cygwin package plus, at minimum, the following
additional files or packages:

            b.) byacc

            c,) gcc (C and C++ compilers)

            d.) m4

            e.) make

            f.) patch

            g.) tcsh

            h.) util-linux

h.) the complete X11 package

            i.) any other files or packages of interest to you (e.g., a
text editor, etc.)


4.) Run cygwin and create two links in /bin:

            cd /bin

            ln -s byacc.exe yacc

            ln -s tcsh.exe csh


5.) Go to the g95 site <> and download
g95-x86-cygwin.tgz to your cygwin root directory (e.g., c:\cygwin in
DOS) and then install using the cygwin commands:

                        cd /

                        tar -xvzf g95-x86-cygwin.tgz


6.) You should now be ready to begin the installation of Amber9. First,
rather than just using the Amber9 User's Guide, print the README.TXT on
the Amber9 distribution cd-rom and follow the instructions (on my
machine, the cd-rom drive is /cygdrive/d/ rather than /mnt/cdrom/). I
found that 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. At this point, set the $AMBERHOME environment variable;
for example:

                        export AMBERHOME=/usr/local/amber9


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). Thus, in order to save some
potential grief later, it was important that this was changed to:


8.) The next step is to do the serial installation make serial.
However, in case things don't go well, you probably want to send both
the standard output and the error output to a log file named, say,
makeserial.log to review later. Thus, use the command:

                        make serial >makeserial.log 2>&1


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

Now you should be ready to test your Amber9 installation. Once again,
you probably want to save the output information to a log file (e.g.,
mktstser.log) for review later and to compare with the file called
TEST_FAILURES.diff that is generated by the test procedure. Thus, you
might use:

                        make test.serial >mktstser.log 2>&1


10.) Finally, before running the tutorials, you need to be able to
start your CygwinX server. You can get information on various
possibilities at
<> .html .


11.) Success!


For anyone new to Cygwin and Amber9, I hope this information may be of
some value.


Bob Hopkins



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Received on Wed Nov 14 2007 - 06:07:34 PST
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