On Thu, Feb 13, 2014 at 9:42 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Feb 13, 2014, Josh Berryman wrote:
>
> > Hello, I just built the head with these flags:
> >
> > ./configure -noX11 -nobintraj gnu
> > make -j 8 install
> >
> > and the mdgx build failed at link time with:
> >
> > /usr/bin/ld: cannot find -lnetcdf
> >
> > ...which is not surprising given that "-lnetcdf" (and -lfftw3) are
> > hard coded in the mdgx Makefile.
> >
> > I've just switched this to $(NETCDFLIB) and $(FLIBS_FFTW3) . Anyone
> > who knows more about (mdgx/AmberTools/life) should change it back
> > again quick if they think that I have only made things worse here.
>
> No...this won't work. The libmdgx.so target needs to have a relocatable
> netcdf (so that it can be linked to python code), but $(NETCDFLIB)
> generally
> points to libnetcdf.a.
>
> My vote would be to remove the -nobintraj option. We've been using bintraj
> for trajectories for years and now use it for restarts as well. I think
> features of REMD require it. So: why do you want to use that option?
>
> It's possible to add a lot of extra logic to configure2, and yet more
> defines in config.h. But you can see the problems that arise when there
> are flags (like -nobintraj) that are almost never used. Do you have no
> workaround?
>
Ick, more configure2 logic. :) The workaround is to specify -nofftw3 to
avoid building mdgx (and RISM) in the first place. I've reversed the mdgx
Makefile change and tied the -nobintraj option to disable the mdgx build
for now to avoid this problem.
I agree with Dave that unless a good use-case can be found for disabling
the best way we have to store trajectories (and restarts), -nobintraj
should be deep-sixed.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 13 2014 - 07:30:02 PST
