Re: [AMBER-Developers] [david.case.rutgers.edu: Re: Amber 'configure' now forcing miniconda?]

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Wed, 28 Dec 2016 12:18:49 -0500

thanks Tyler,

I just wish if I knew this (lndir) earlier.

Hai

On Sat, Dec 24, 2016 at 2:30 PM, Tyler Luchko (Lists) <
tluchko.lists.gmail.com> wrote:

>
> > On Dec 23, 2016, at 6:27 AM, David Case <david.case.rutgers.edu> wrote:
> >
> > On Thu, Dec 22, 2016, Tyler Luchko (Lists) wrote:
> >>
> >>>> 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?
> >>>
> >> FWIW, I’ve been using this approach for years. I use it to build and
> >> test with different compilers using the same git repo. It also makes
> >> git status much cleaner. And, if you are careful, you can switching
> >> between branches with little or no recompiling.
> >
> > If you have time, can you say a little more?
> >
> > - What commands did you use to create the shadow directory?
> > - What happens when files get added/deleted from the real source
> > directory, or when you change branches there. What do you
> actually
> > do to "be careful"?
>
> The procedure is straightforward. For this example I’m keeping my Amber
> git repo in ‘../../code/‘.
>
> mkdir amber-gcc48
> lndir -silent ../../code/amber.git/
> export AMBERHOME=`pwd`
> ./configure -noX11 gnu && make -j 5
> cd ..
> sudo port select gcc mp-gcc6
> mkdir amber-gcc6
> cd amber-gcc6
> lndir -silent ../../code/amber.git/
> export AMBERHOME=`pwd`
> ./configure -noX11 gnu && make -j 5
>
> If you are using macports like me, you may need to switch compilers to
> make sure the right libraries are being used for different versions of the
> GNU compiler. If you are compiling with GNU and Intel side-by-side, as I
> do on my cluster, this is not an issue.
>
> When I use the same repo to compile different branches, I’ll use roughly
> the same procedure as above but I’ll switch branches instead of compilers.
> The important thing to remember is that when you switch branches, the
> shadow directory for the inactive branches should not be used. While the
> compiled executables will be fine, other files that aren’t compiled may be
> different. Plus, if you recompile, the shadow directory will use the
> active branch.
>
> If you add files to the repo, then you just need to rerun the lndir
> command. There isn’t an automatic solution I know of if files are deleted.
>
> Even if you don’t want to mess around with different compilers or branches
> from a single source, shadow directories keep the git repo and ‘git status’
> clean. For me, that is the greatest benefit.
>
> Finally, Emacs automatically recognizes that the files are linked and part
> of a Git repo. It doesn’t matter if you open the link or the original,
> Emacs will update the original.
>
> Tyler
>
>
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Received on Wed Dec 28 2016 - 09:30:02 PST
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