Merge branch 'jayeshkrishna/add_e3sm_pio' into next (PR E3SM-Project#…

…3159)

Adding SCORPIO to E3SM

This PR brings in v1.0.0 of SCORPIO to E3SM and includes
CIME changes required to use SCORPIO
* Scorpio classic (derived from PIO1) is now the default I/O library
  used by E3SM.
* E3SM users can choose to use scorpio (derived from PIO2) by
  changing the PIO_VERSION, in env_build.xml, to 2.
* Scorpio and scorpio classic libraries are included as git submodules
* Adding a compile time switch to disable the BGET memory allocator,
  due to its poor performance, in SCORPIO.
* The default rearranger is set to BOX

[BFB]

Merge branch 'wadeburgess-patch-1' into master (PR E3SM-Project#3143)

Update config_machines.xml to add default test suite

[BFB]

* origin/wadeburgess-patch-1:
  Update config_machines.xml to add default test suite

Merge branch 'mark-petersen/ocean/nonlocalBugfixKPP' (PR E3SM-Project…

…#3056)

Update MPAS-O: bug fixes for KPP nonlocal source term

This PR fixes several bugs in the calculation of the nonlocal source
term in KPP. for temperature, we need to subtract off the contribution
from thickness fluxes that don't change buoyancy. for salinity, we need
to add virtual salinity fluxes that do change buoyancy.

These fixes have been tested in E3SM G-cases and behave as expected.

Fixes E3SM-Project#3102
[non-BFB]

Merge branch 'sarich/anvil-intel-add-gnu-53' PR E3SM-Project#3076

Allows homme to link with compatible glibc/libstdc++ libraries on anvil

[BFB]

Update CIME to ESMCI cime5.8.3 (PR E3SM-Project#3010)

Update CIME to ESMCI cime5.8.3

Squash merge of jgfouca/branch-for-to-acme-2019-06-24

Features:
* Update to the latest NCAR pio2 development version 2.4.4. pio1 still default.
* require ids in namelist definition files to be lower case
* Add logic to control activation of glcshelf_c2_ice

Bug fixes:
* None

[BFB]

Merge branch 'oksanaguba/eam/tests-ftypes2' (PR E3SM-Project#2955)

Add coupled dycore tests using shared execs

Add tests for coupling mechanisms in EAM and for SL transport with
theta dycore for coupled atmosphere. Tests re-use executables; only 2
builds are required, one for preqx dycore and another one for theta.

[Non-BFB] because new baselines are required.

* origin/oksanaguba/eam/tests-ftypes2:
  reducing dtime for all theta + ne4 tests, still need to try it on skybridge
  moving tests to integration
  change hires settings to lowres
  moving thetasl test to shared execs set
  start over with tests

 This is an archive tag for reduced precision paper submitted to JAMES.

The model is used for to test the impact of reduced precision on E3SM atmosphere model(EAM)'s simulation. In this model configuration, single precision was used for the turbulence and clouds parameterization CLUBB while double precision was used for the rest of the model.

The simulations include:
1. The convergence test simulations (1h - 5day)
2. 10-year climate simulations for E3SM atmosphere model (EAM).

 This is an archive tag for reduced precision paper submitted to JAMES.

The model is used for to test the impact of reduced precision on E3SM atmosphere model(EAM)'s simulation. In this model configuration, A "round down and up" procedure where the lower order mantissa of a double-precision number was truncated for all the prognostic variables used by the turbulence and clouds parameterization CLUBB. Thus, half-precision (with 10 significand bits) was used for the turbulence and clouds parameterization CLUBB while double precision was used for the rest of the model.

The simulations include:
1. The convergence test simulations (1h - 5day)
2. 10-year climate simulations for E3SM atmosphere model (EAM).

 This is an archive tag for reduced precision paper submitted to JAMES.

The model is used for:
1. The convergence test simulations (1h - 5day)
2. 10-year climate simulations for E3SM atmosphere model (EAM) with operational configuration.

The defalut arithmetics was implemented for the whole model (64-bit double-precision floating-point numbers).

This is an archive tag for reduced precision paper submitted to JAMES.

The model is used for the tests of SE dynamical core with the third-order and first-order numerical solutions. However, a "round down and up" procedure where the lower order mantissa of a double-precision number was truncated for the dynamical core's prognostic variables u, v, T, Ps filelds at the end of each dynamics time step.

Compset and namelist settings to active SE dynamical core with third-order numerical solution

SE dynamical core only (compset FADIAB, no sub-stepping)

se_ne              = 30
se_ftype           = 0
tstep_type         = 5
qsplit             = 1
rsplit             = 0
se_nsplit          = 1
hypervis_subcycle  = 3
nu                 = 0
nu_div             = 0
nu_p               = 0
nu_q               = 0
nu_top             = 0

Compset and namelist settings to active SE dynamical core with first-order numerical solution

SE dynamical core only (compset FADIAB, no sub-stepping)

se_ne              = 30
se_ftype           = 0
tstep_type         = 5,
qsplit             = 1,
rsplit             = 1,
se_nsplit          = 1,
hypervis_subcycle  = 3,
nu                 = 1.0e15
nu_div             = 2.5e15
nu_p               = 1.0e15
nu_q               = -1.0
nu_top             = 2.5e5