On Thu, May 19, 2011, Daniel Roe wrote:
> I think that we should...
> split AmberTools completely from Sander/Pmemd, meaning
> that both AmberTools and Sander/Pmemd should each have their own
> directory and configure scripts.
Well, sander/pmemd and AmberTools already *do* have separate directories;
it might make good sense to give them separate config.h files.
> presence of AmberTools (for netcdf/sqm/rism/whatever other libs) via
> AMBERHOME (since sander/pmemd dont need AMBERHOME set anyway). I feel
> that separating them physically would ultimately simplify things like
> updates, and also would make the code separation make more sense to
> the user.
But even a more full separation doesn't solve the problem we have: if
we upgrade AmberTools (and hence sqm, pbsa & rism) more frequently than
we upgrade sander/pmemd, we have people trying to compile sander/pmemd
alongside both old and newer versions of AmberTools. This is what causes
the headaches.
> > The problem I'm having is a patch warning at stage 6:
> >
> > patching file test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_SPDP
> > patching file AmberTools/src/configure
> > Reversed (or previously applied) patch detected! Skipping patch.
> > 2 out of 2 hunks ignored -- saving rejects to file
> > AmberTools/src/configure.rej
> > patching file src/pmemd/config_data/linux_em64t_cuda_DPDP.gfortran.mpi
We could certainly add a note to the bugfix page, telling users to expect this
particular patch error if they are using AT1.5. (Mark, Jason?)
> > On another point, I've discovered that I need
> > to run AT15_Amber11.py every time I create a new config.h (via
> > configure) if I want to compile AMBER. This also is going to catch a few
> > people out.
I think we should patch the configure script add instructions at the end to
run the AT15_Amber11.py script before compiling Amber11. We could even
explicitly say: "you need to run this script every time you create a new
config.h file".
....dac
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Received on Thu May 19 2011 - 05:00:03 PDT
