Re: [AMBER-Developers] Configure script and parallel build of sander

From: Jason Swails <>
Date: Thu, 14 Jan 2010 11:41:22 -0500


On Thu, Jan 14, 2010 at 11:14 AM, Ben Roberts <> wrote:
> Hi all,
> Recently when I was trying to build parallel sander, I would get a lot of
> errors regarding undefined references to netcdf functions.
> It turns out that the problem stemmed from the NETCDF and NETCDFLIB entries
> in config.h, which under the serial version are set to netcdf.mod and
> ../netcdf/lib/libnetcdf.a respectively, but under parallel are left blank.
> It turns out, however, that parallel sander still uses serial netcdf to
> write its netcdf format trajectory files.

I'm going to guess this is because only the master process writes
restarts, so it's still serial netcdf that's *really* used? I'm
guessing pnetcdf is really only used for ptraj.MPI, since it's
parallelizing file reads? I think it would probably be easiest to
just add serial netcdf back to config.h generated for mpi.

> Is there a reason, then, that the serial netcdf was removed from the
> config.h file for parallel builds?
> Moving forward, I can see two possible approaches. One is to rewrite sander
> (or even just the sander makefiles) to use parallel netcdf instead of
> serial. The other is to reinstate serial netcdf, alongside parallel netcdf,
> in the config.h. Is there an opinion on which would be the preferred option,
> or is there a third good one that hasn't occurred to me?
> Ben
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Jan 14 2010 - 09:00:01 PST
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