Re: [AMBER-Developers] [GIT] git repository for AMBER: RCW: Change -nopysander to -pysander - make skipping of pysander build default since it requires external libraries that are not installed by default on most systems. - Should fix CruiseControl builds.

From: Ross Walker <>
Date: Wed, 01 Oct 2014 13:06:25 -0700

ssh root.cc_int

cat /etc/redhat-release

Red Hat Enterprise Linux Server release 6.5 (Santiago)

yum install python-dev

Loaded plugins: product-id, subscription-manager
This system is not registered to Red Hat Subscription Management. You can
use subscription-manager to register.
Setting up Install Process
No package python-dev available.
Error: Nothing to do

python-devel exists... Is it this you want instead?

On 10/1/14, 11:44 AM, "Jason Swails" <> wrote:

>On Wed, 2014-10-01 at 11:21 -0700, Ross Walker wrote:
>> Hi Jason,
>> Again I reiterate my point. Why are we requiring lots of non-default
>> packages to be installed?
>> Note - a LOT of people have to build AMBER on machines they do not have
>> root for. They also have to build it on non-Linux systems - such as AIX.
>> Thus I would suggest getting a machine and doing a default install -
>> most Linux systems the packages needed for Xleap etc are there. If they
>> are not then right now they get a message asking them to specify -noX11.
>> With this setup they will then get another message telling them to
>> -nopysander - at this point the poor user is like - WTF?? what are all
>> these things I am turning off, do I need pysander? What will it break
>> etc etc... Bad news... Probably we should just have it automatically
>> non-core packages if it does not find the relevant libraries.
>> As you had it the configure script would fail with a FATAL error if one
>> did not have python-dev installed. This requires root access to install.
>> I would suggest changing this to be non-fatal - if it does not detect
>> python-dev it just skips the building of pysander. This removes the
>> dependency on the external package rather than requiring the user to
>> explicitly specify -nopysander.
>This comes back to the question of when is it better to find out you're
>missing a dependency -- at configure time or when you decide to run it?
>We (amber devs) had this discussion several years ago about xleap and
>the X11 headers, and the people that spoke said that configure-time
>notice was better. That's why Tyler implemented that change.
>Keep in mind that the "standard" Linux user is more likely to be using a
>machine that has the Python headers and development libraries installed
>than they are a machine that has gfortran installed... out of the box at
>least. And python is deployed via buildbots on all kinds of OSes (AIX
>included), so portability is not an issue here.
>All the best,
>Jason M. Swails
>Rutgers University
>Postdoctoral Researcher
>AMBER-Developers mailing list

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Received on Wed Oct 01 2014 - 13:30:02 PDT
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