Re: [AMBER-Developers] another amber 14 compile problem netcdf

From: Scott Brozell <>
Date: Sat, 28 Sep 2013 19:45:01 -0400


On Fri, Sep 27, 2013 at 09:58:17PM -0400, case wrote:
> On Fri, Sep 27, 2013, Daniel Roe wrote:
> > I'm not 100% sure but I think mdgx may require '-lnetcdf' since it can
> > be built as a shared library. Probably we will need to have
> > 'netcdf_flag' in configure2 set as a separate variable in config.h
> > (e.g. NETCDF_FLAG) instead of having it just be part of FLIBS, and
> > have programs that require '-lnetcdf' (like nab and mdgx) use that.
> The real solution is to figure out why some environments have trouble with
> netcdf. I'm not sure it's related to the FC, CC, etc. flags, since configure2
> explicitly sets all of those at configure time.
> Some ideas:
> (1) maybe the current version of netcdf will configure in a more reliable
> fashion.
> (2) require the user to have a gnu compiler, and only support intel compilers
> for pmemd, maybe sander. It would be nice to reduce the number of options
> available at configure time--as Mike found out, people don't test things
> like -nobintraj very often.

No doubt there is fat to be trimmed from configure, but the two features in
2 are useful. -nobintraj was used by me in May 2013. There are important
programs in AmberTools that do not involve trajectories and it is easy to
imagine someone installing with the '-no options' to quickly build for
example antechamber.

The intel compilers are important. Supporting only a few programs with them
could easily introduce more complexity into the build process.
In addition, even though gnu fortran seems to be closing the gap with intel
fortran with respect to performance, intel is still generally faster:

> The real solution is to figure out why some environments have trouble with
> netcdf.
and not to restrict Amber users that do not use NetCDF.

(3) maybe someone can make contact with the NetCDF developers to get help.


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Received on Sat Sep 28 2013 - 17:00:03 PDT
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