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

From: Ben Roberts <>
Date: Thu, 14 Jan 2010 11:45:51 -0500

Jason Swails wrote:
> Hello,
> 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.

I agree, though I didn't want to just unilaterally do that, in case
there's some reason why it had been taken out that I wasn't aware of. Is
there such a reason?

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Received on Thu Jan 14 2010 - 09:00:04 PST
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