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Tidy up Makefiles for framework and atmosphere core #151

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@mgduda mgduda commented Feb 6, 2019

This PR is a work-in-progress to clean up Makefiles by fixing automatic variables in implicit
rules and correcting dependencies. The commit messages will be improved after more careful
review and testing of the changes.

…Makefiles

This commit also removes unnecessary rules from shared Makefiles
…ere Makefiles

This commit also removes unnecessary rules from atmosphere Makefiles
In the top-level Makefile, we don't need PIO, netCDF, or parallel-netCDF
include paths in CPPINCLUDES, and we don't need -D options like -DUSE_PIO2
in the FCINCLUDES variable.
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This passes MPAS-O nightly regression suite on grizzly with gnu/optimized, is bfb with previous.

I am not able to compile with ifort on grizzly. It is not able to find the pio include path. I messed around with the include lines that were changed, but was not able to figure it out.

@mgduda it looks like this PR is not on your schedule for the 6.2 release, so I can ignore this problem for right now?

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mgduda commented Feb 28, 2019

@mark-petersen Thanks so much for taking a look! This PR is not slated for inclusion in the v6.2 release, and at the moment only serves as a collection place for some Makefile changes that had come up when working on out-of-source builds of MPAS-A for CESM. It would be no problem to ignore this PR for now, and once I've worked on it a bit more, I'll check-in with you, @matthewhoffman, and others.

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