PS - The 'prefix' install was 328MB, compared to 2.5 GB for a full
Amber 16 install. Very nice.
On Thu, Feb 2, 2017 at 1:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Got a chance to try this today. I haven't tested thoroughly but it
> seems to work well. Nice work Hai!
>
> I hit a brief hiccup during my initial attempt with python stuff:
> ```
> Checking .pth file support in
> /u/droe/Amber/TEMP/prefix/lib/python2.7/site-packages/
> /mnt/local/droe/anaconda2/bin/python -E -c pass
> TEST FAILED: /u/droe/Amber/TEMP/prefix/lib/python2.7/site-packages/
> does NOT support .pth files
> error: bad install directory or PYTHONPATH
> ```
> It went on to describe the problem and potential solutions which was
> really nice, but the real issue was I had forgotten to source amber.sh
> - that fixed the problem. So maybe that could be the first thing you
> suggest for potential solutions?
>
> -Dan
>
>
> On Wed, Jan 25, 2017 at 3:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> Oops, no "="
>>
>> ./configure --prefix $HOME/try_another_folder gnu
>>
>> On Wed, Jan 25, 2017 at 3:31 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>>> > If I happen to get free time before
>>> now and the code freeze maybe I'll take another crack at making this
>>> happen.
>>>
>>> .Dan: I have working code in amber_prefix_Hai branch. Feel free to try and
>>> update that.
>>>
>>> ./configure --prefix=$HOME/try_another_folder gnu
>>>
>>> Hai
>>>
>>> On Thu, Dec 22, 2016 at 9:44 AM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>
>>> On Wed, Dec 21, 2016 at 10:04 PM, David Case
>>> <dacase.scarletmail.rutgers.edu> 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
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>>
>>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 02 2017 - 10:30:03 PST
