Re: [AMBER-Developers] NetCDF Update

From: Jason Swails <>
Date: Thu, 31 Oct 2013 14:32:24 -0400

On Thu, Oct 31, 2013 at 1:14 PM, Daniel Roe <> wrote:

> Hi All,
> The NetCDF in GIT master has been updated from version 3 (several
> years out of date) to version 4. The build is completely backwards
> compatible, and no additional features/requirements (such as using the
> HDF5 libraries) have been added.
> After version 4.1 NetCDF has been split into separate interfaces for C
> and Fortran. Because of this, the NetCDF build process is now slightly
> different. Basically the Fortran interface requires that the C
> interface be compiled beforehand, so now both interfaces are
> configured and compiled one after the other during Amber's main
> configure. This increases initial configure time, but subsequent
> builds are faster since the NetCDF configure/build step can be
> skipped. The configure script is smart enough to recognize when the
> interface needs to be rebuilt (such as when switching compiler types
> etc). The '--with-netcdf' keyword has been re-enabled as well so you
> can specify a separate NetCDF build.
> NetCDF now uses an automake build which has some wrinkles when
> combined with versioning control software such as GIT. Basically when
> you switch branches, file timestamps are reset. This leads to the
> automake framework thinking certain files need to be rebuilt when they
> really dont. I've added a script that updates certain critical file
> timestamps if necessary to prevent this, so you may see this during
> configure:
> Warning: NetCDF build timestamps need to be updated. This should
> ONLY happen during development after switching branches
> in GIT. Fixing timestamps (this will take about 7 seconds).
> This will ONLY be necessary after you switch branches.

A minor clarification here. This will only be necessary when you switch
from a branch with the old NetCDF to a branch with the new NetCDF. Once
you merge the master branch into your other development branches, this
should never occur again.

Thanks Dan for all the hard work!


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Thu Oct 31 2013 - 12:00:03 PDT
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