Re: [AMBER-Developers] [ Re: Amber 'configure' now forcing miniconda?]

From: Nhai <>
Date: Thu, 22 Dec 2016 10:09:52 -0500

Per --prefix stuff: i am still +1 for this and can help testing if you do that.

We are working on binary distribution and really want to get rid of AMBERHOME envs. :d


> On Dec 22, 2016, at 9:44 AM, Daniel Roe <> wrote:
> On Wed, Dec 21, 2016 at 10:04 PM, David Case
> <> wrote:
>>> On Wed, Dec 21, 2016, Dan Roe wrote:
>>> But I think it is important that these tests happen at 'configure'
>>> time, and it doesn't seem to me to be that difficult....
>> It may indeed be do-able, but it is not just a matter of seeing if "import
>> numpy" throws an error. The configure script would have to compile python
>> extensions in the same way the real code will (which is actually several
>> ways), and make sure they all work. And since only developers will decline
>> the miniconda download, and since they can find out by trial and error if
>> their system python works, writing and maintaining this functionality seems
>> like a lot of work for only a small payback.
> I think that some users (maybe installs at HPC sites etc) may also
> want to decline the miniconda download, but it does seem like python
> detection is problematic. As long as the '--with-python' flag works I
> think it's fine anyway. It would be nice to have configure be able to
> test the python ecosystem but if it's too much work then I'll just put
> it on my wishlist.
>> For those who want to play with this, configure2 alreay *has* a
>> check_compatible_python() function. We commented out the call to this
>> function (about line 935) since it was not reliable enough: having
>> configure say a python is OK when it is not is quite annoying and confusing.
> Agreed - that's worse from a user standpoint for certain.
>> Knowing I'm repeating myself: we *really* don't want users installing
>> packages into their existing python just to install Amber. There is too
>> much danger of creating incompatibilities with other things that require
>> python: that is, we increase the danger that installing Amber breaks
>> something else on the user's computer. [numpy, in particular, exists in
>> several incompatible releases; it is quite easy for program A to require
>> version 1.9 and program B to require version 1.10. We can't solve that
>> problem, but should not make it worse, either.]
> This is one of the gotchas of living in the python universe. Advanced
> users can just use the '--with-python' flag. "Normal" users can have a
> built-in miniconda. We just have to make it clear during configure
> time exactly why miniconda is a good idea instead of the vague "well,
> maybe stuff won't work" message of the past.
>>> I'll have to test '--with-python', but if it works there is not much
>>> of a downside that I can see other than that Amber installation is now
>>> the "python keystone", so I'd better not ever move it or I will break
>>> every Amber install based on it (and it's another configure flag that
>>> has to be specified each time).
> I was being a bit facetious about having to specify an extra flag :-)
> - that stuff doesn't come through in email sometimes. I think the
> '--with-python' flag is the correct solution.
>>>> [Next thing we know, people are going to want to be able to specify a build
>>>> directory, separate from the sources.....]
>>> I still want this :-). For separate installs the size can really add
>>> up, more because the Amber 16 source tree weighs in at 2.3 GB - the
>>> miniconda install adds 635 MB to that (sizable but not egregious).
>> Has anyone tried to just make a shadow directory (using "cp -as" or lndir),
>> with links to a clean amber tree, then build in the shadow directory?
> Unfortunately, this can't work for multiple parallel library/CUDA
> version builds (maybe I'm not understanding what you mean).
>> Realistically, I'd recommend bigger disks. You can get 500 Gb external
>> SSD drives with USB-3 or USB-C interconnects that are quite fast and will
>> allow you create all the Amber images you are ever likely to need....
> Just because disk space is cheap doesn't mean we should be wasteful. I
> would like to do with Amber what I can do with every other linux
> source code package: have one giant source directory that I can point
> to an install directory with '--prefix', and then that install
> directory contains only what I need to run that version of Amber.
> AMBERHOME can point to the common source, but PATH and LD_LIBRARY_PATH
> point to the install directory. If I happen to get free time before
> now and the code freeze maybe I'll take another crack at making this
> happen.
> -Dan
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> _______________________________________________
> AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Thu Dec 22 2016 - 07:30:03 PST
Custom Search