Re: [AMBER-Developers] More weirdness to do with netCDF

From: Ben Roberts <>
Date: Thu, 22 Oct 2009 10:57:45 -0400

Hi all,

> I was instructed (by the configure script) to do "make -f Makefile_at
> clean" and "Make -f Makefile_at parallel" after running ./configure
> -mpi. So I duly did so. That was what took out the netcdf libraries.

Further to my email last night, a colleague of mine (Jason Swails)
pointed out to me this morning that serial netCDF is built only by
serial ptraj. It also seems as though a "make clean" run using either
Makefile_at or Makefile removes serial netCDF. The upshot of all this is
that for either serial or parallel Amber to be built with netCDF
support, serial ptraj must have been built and neither Tools nor Amber
cleaned up afterward.

This brings to my mind a number of questions.

1. Should a "make serial" or "make parallel" automatically build serial
netCDF if the latter is missing for whatever reason?

2. I have added a rule, "clean_for_parallel", to the Makefile_at; this
rule will clean up sff, nab and ptraj serial versions, as these are the
ones that are rebuilt or otherwise changed during "make -f Makefile_at
parallel". I have not yet uploaded this change into CVS. Would such a
rule be useful (with a corresponding change to the configure script, to
better instruct users as to what needs to be done)?

3. Is it necessary to run "make -f Makefile_at clean" or "make (-f
Makefile) clean" between serial and parallel builds at all, or was this
a habit I had gotten into that relates to older versions of Amber and is
no longer applicable?


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Received on Thu Oct 22 2009 - 08:00:02 PDT
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