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

From: Ben Roberts <roberts.qtp.ufl.edu>
Date: Thu, 14 Jan 2010 11:14:05 -0500

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.

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?


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Received on Thu Jan 14 2010 - 08:30:02 PST
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