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: Jason Swails <>
Date: Wed, 1 Oct 2014 17:26:58 -0400

On Oct 1, 2014, at 4:20 PM, David A Case <> wrote:

> On Wed, Oct 01, 2014, Ross Walker wrote:
>> Again I reiterate my point. Why are we requiring lots of non-default
>> packages to be installed?
> I don't agree with Ross here. What do you think "default" is? A stock
> Ubuntu system won't even have a fortran compiler, much less a C-shell, or all
> kinds of other things that Amber requires. Are you sure the CC server
> is really just the "default" OS?
> On the web page, we list the "non-default" packages that are needed: for
> Ubuntu:
> sudo apt-get install csh flex patch gfortran g++ make xorg-dev libbz2-dev
> Add to this recommended packages for xparmed and mdoutanalyzer:
> sudo apt-get install python-tk python-dev python-matplotlib python-numpy
> python-scipy
> This is a big list, but it does include python-dev. The big change in the
> development version is that the absence of python-dev now (as I understand
> it) breaks the build (at the configure stage?), rather than just ending up
> with a non-functional program. Is there some (reasonably easy)
> way that lack of python-dev could be made to be less fatal, and to still
> build the stuff that doesn't depend on it?

Yes, thatís what we have now. The main reason it was made fatal was because unlike other Python requirements, it canít be detected at runtime (and activated when itís installed). It has to be available at compile-time.

> Note that for Fedora and openSuSE, the list of non-default packages is also
> quite large (see the web page). Is it really true that (a) RedHat version
> ??.? has everything one needs *execpt* python-dev and (b) there are a
> significant number of users that use that exact version and don't have root
> access?

Thereís probably a lot of RHEL-based systems that are used by people that donít have root access, but I agree with your points above. No programs are devoid of dependencies, and I think that, in general, python-dev is a more common dependency than gfortranÖ And even if users canít install something as root, they would have to request that certain programs (like gfortran) be installed, anyway.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Wed Oct 01 2014 - 14:30:02 PDT
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