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

From: Ben Roberts <>
Date: Wed, 21 Oct 2009 17:41:48 -0400

Hi Ross,

Ross Walker wrote:
> Hi Ben,
> We ran into this problem yesterday when we were switching compilers. The
> clean scripts were not cleaning properly hence you got all kinds of weird
> link behavior. Why do you need to do a make clean after building AMBERTools
> and before building AMBER - this should not be necessary, the dependencies
> should take care of this I hope.
> If you do make clean after ambertools then all that should happen is netcdf
> gets built again when you make amber. So you should probably look at why
> this is not happening.

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.

I have in the past been bitten by not doing a "make clean" between
serial and parallel builds of the same component, be it Tools or Amber.
So I saw the need for another make clean in that instance.

I suppose parallel tools is optional, and if I didn't build it I could
do away with that step, and just do "make clean" and "make parallel" to
get parallel Sander.

I suppose netcdf would be built again if I were building serial Amber.
It seems that the problem stems from some part of the need to remove
serial object files (hence the make clean), together with not all
"serial" bits being rebuilt when I've asked for a "parallel" build. I'll
look into it some more, probably not today though.


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Received on Wed Oct 21 2009 - 15:00:03 PDT
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