Re: [AMBER-Developers] Python issues...

From: Ross Walker <>
Date: Thu, 18 Feb 2016 12:39:09 -0800

>> On Feb 18, 2016, at 2:01 PM, Ross Walker <> wrote:
>> Can we at least have a section in the document - and probably we'll ultimately need some detailed tutorials on the website on installing - that lists all of the dependencies needed for AMBER. For Redhat this would be a list of packages that should be installed with yum install.
>> I would argue that if a package needed to compile AMBER (just serial AMBER I am talking about here) is not available as part of the standard OS packages (or at stretch also epel for Redhat) then that module, library etc should really not be used and instead one should code around the need for it. Relying on lots of third party stuff by default is just going to make things massively fragile going forward.
> This doesn't hold water. By that argument we shouldn't use Fortran because it's not included with vanilla RHEL. Every program has dependencies. There's no getting around that.

Yes it is. A standard RHEL 6 or 7 Developer install will give you gfortran.

My point is that ideally it is best to try and come up with a lowest common denominator of features that are available for the commonly used OS's and then design the code as best as one can to use that.

> The has all the packages you need to install (including Python packages) as a simple "yum install", including the Python packages, that will avoid the need to download miniconda. Unless you mean we should avoid anything that's not "yum-installable" instead of parts of the "raw" OS?

Nice - can we add Redhat 6 and 7, since these are the most common in managed computing environments, to this please and perhaps rename the URL so it doesn't say Ubuntu. I.e. we should probably have a master page for installing AMBER on various OS's.

> If anything yum installable is ok, then you can yum install all components you need already on the latest RHEL.

Yes I would say that it is perfectly reasonable to say that if you can yum install a package, or apt-get install a package then it is fine to have that as a dependency. The main thing we need is a central point of reference that everyone knows to go to that lists what the required packages are for each OS. This way we make it as easy as possible for users to get everything built. If we refer to it from the manual and also perhaps somewhere on the website that says 'How to install AMBER' then it is a single location that we can keep up to date and avoid confusion.

> I am going to get the added Python docs in the manual done sometime this weekend.

Excellent. Thanks this will help a lot. Can you try to incorporate it in a single install section (or at least a cutdown version of it) for users who don't necessarily know anything about programming etc.

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
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| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Feb 18 2016 - 13:00:05 PST
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