On Wed, Oct 21, 2015 at 7:11 PM, Timothy J Giese <timothyjgiese.gmail.com>
wrote:
> On 10/21/2015 03:49 PM, Jason Swails wrote:
>
> > API is -lsander (rather than needing -lsander -lnetcdf -lnetcdff -lblas
> > -llapack -lsqm).
> >
>
> Don't get me wrong -- I really don't care
You don't have to qualify :). Your insights are helpful and appreciated.
> -- but I'm just going to point
> out the obvious: You already tell people to source a bash (or csh
> script), so you could just as easily define a variable in that script
>
> export SANDER_LIBS="-lsander -lsqm -lnetcdf -lnetcdff -lblas -llapack"
>
> So that people can just add
>
> LDFLAGS="-L${AMBERHOME}/lib" \
> CPPFLAGS="-I${AMBERHOME}/include \
> LIBS="${SANDER_LIBS}"
>
> to whatever they are compiling.
> But, you know, whatever.
>
The real reason things are the way they are is because that's simply how I
got them to work. sander is a *beast*, built from components scattered all
over the place (libsqm, libpbsa, librism, libfftw3, libnetcdf, libblas,
liblapack, ...) and most of these libraries are Amber-built, static
archives (and a lot of the libs are linked in multiple places, like RISM
and PBSA that go into their standalone programs, nab, and sander).
So I *started* from a mostly-statically-linked sander executable, adjusted
the linking command to create a .so, and then added -fPIC everywhere so I
could get libsander to work with other PIC code (the main target here being
Python). So libsander.so is just a small perturbation of how sander is
built (it was already a lot of wrangling to get it even that far).
I'd like to improve things, but I'm wary of breaking something that *just
works* (Ross's report was the first I'd gotten of this not working) and
getting stuck in a time sink.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 11:30:04 PDT
