Add profiling utilities

[micaeljtoliveira]

Add utilities to handle FMS and ESMF profiling information. These allow to easily generate plots for scaling studies.

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[micaeljtoliveira]

@dougiesquire Would you have time to look at this PR? It's quite large, but I would be more interested in general comments about structure and design, rather than a careful review of all the details.

[dougiesquire]

This looks great @micaeljtoliveira. My first thought is that these tools are sufficiently general and useful beyond OM3 to justify moving them into their own package. Something to do now, later or never?

Since you asked for it, here's an attempt at a proposed restructure that I think makes things clearer for users and developers. Of course, this is all a matter of opinion so feel free to ignore all or parts of it:

om3utils/
├── __init__.py
├── config_file
│   ├── __init__.py # import all read_*.py and write_*.py functions
│   ├── mom6_input.py
│   ├── nuopc_config.py
│   └── payu_config_yaml.py
├── profiling
│   ├── __init__.py
│   ├── parser
│   │   ├── __init__.py # import ESMFProfilingParser and FMSProfilingParser
│   │   ├── base.py # contains ProfilingParser from profiling.py
│   │   ├── esmf.py # contains all of esmf_profiling.py and esmf_trace.py
│   │   └── fms.py # contains all of fms_profiling.py
│   └── analysis.py # contains all of profiling_analyses.py and parse_profiling_data from profiling.py
└── utils.py

Then the profiling tools could be used as follows:

from om3utils.profiling.parser import ESMFProfilingParser
from om3utils.profiling.analysis import (
    parse_profiling_data, 
    scaling_efficiency
)

stats = parse_profiling_data(
    run_dirs,
    ESMFProfilingParser,
    varname,
    getvar
)
eff = scaling_efficiency(stats)

You could even import all the parsers and analysis functions in profiling.__init__.py so that one does not need to go through the parser and analysis subpackages.

(Note I'm not really sold on the name of the config_file subpackage)

[micaeljtoliveira]

@dougiesquire Thanks for the feedback, lots of good points. I now realize that this PR is probably not the best place to discuss these, as they are quite broad and general. I'll open an issue for this. In order not to stall development anymore, I'll merge this branch as is, unless you want to have a more detailed look.

[dougiesquire]

Happy to merge 🙂