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: David A Case <>
Date: Wed, 1 Oct 2014 16:20:24 -0400

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

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

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?

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

> Thus I would suggest getting a machine and doing a default install...

As noted above, this will fail to build Amber on most any kind of Linux I ever
have to deal with. So we are not talking about "default" vs "non-default":
we're comparing the cost of adding one more item in the apt-get/yum/zypper
list of needed packages.


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Received on Wed Oct 01 2014 - 13:30:03 PDT
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