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Add timers to EAM to provide context to SCORPIO timers

SCORPIO has introduced some new timers. Unfortunately, the existing
timers in EAM are not sufficient to localize where the SCORPIO calls
are coming from. Here new timers are added to provide the missing
context. A few timers are also added to provide context for these
added timers and for some of the already existing timers.

The logic for the timer physpkg_st1 is also changed, so that the
count during the initialization is '1' instead of '2', and the count
is halved in the run loop.

Also, some places have timer names in double quotes in calls to
t_startf/t_stopf and some have them in single quotes. Changed double
quotes to single quotes in some files, to impose consistency within
the file.

Finally, a timer name typo (prim_run_sybcycle) is corrected (to
prim_run_subcycle).

For an initial run, 28 new timers are introduced into the
initialization and 13 new timers are introduced into the run loop.
Comparing the number of lines in the process 0 timing file for
a watercycle case, there are 41 more lines of timer data after
implementing these modifications, in agreement with the new
timer count.

For a continuation run, 30 new timers are introduced into the
initialization and 13 new timers are introduced into the run loop.
Comparing the number of lines in the process 0 timing file for
a watercycle case, there are 43 more lines of timer data after
implementing these modifications, in agreement with the new
timer count.

Fixes #4469

BFB

* worleyph/eam/add_io-related_timers:
  Add timers to EAM to provide context to SCORPIO timers
812d1f6

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E3SM Logo

Energy Exascale Earth System Model (E3SM)

E3SM is a state-of-the-art fully coupled model of the Earth's climate including important biogeochemical and cryospheric processes. It is intended to address the most challenging and demanding climate-change research problems and Department of Energy mission needs while efficiently using DOE Leadership Computing Facilities.

DOI: 10.11578/E3SM/dc.20180418.36

Please visit the project website for further details.

Table of Contents

Quick Start

The Quick Start page includes instructions on obtaining the necessary code and input data for model setup and execution.

Supported Machines

E3SM is high-performance computing application and generally requires a cluster with several hundred nodes to run a scientifically validated case at a useful simulation speed.

To run E3SM, it is recommended that you obtain time on a Supported Machine.

Running

Please refer to Running E3SM for instructions on running the model.

Contributing

Please refer to Contributing for details on our code development process for submitting pull requests.

Acknowledgement

The Energy Exascale Earth System Model (E3SM) Project should be acknowledged in publications as the origin of the model using these guidelines.

In addition, the software should be cited. For your convenience, the following BibTeX entry is provided.

@misc{e3sm-model,
	title = {{Energy Exascale Earth System Model (E3SM)}},
	author = {{E3SM Project}},
	abstractNote = {{E3SM} is a state-of-the-art fully coupled model of the {E}arth's 
		climate including important biogeochemical and cryospheric processes.},
	howpublished = {[Computer Software] \url{https://dx.doi.org/10.11578/E3SM/dc.20180418.36}},
	url = {https://dx.doi.org/10.11578/E3SM/dc.20180418.36},
	doi = {10.11578/E3SM/dc.20180418.36},
	year = 2018,
	month = apr,
}

License

The E3SM model became open development at the time of first model and data release. Please see LICENSE for details.