Recent mods from MPAS-JEDI

[snyderdad]

Here's a consolidated list of modifications from JCSDA-internal/MPAS-Model that we hope to merge with MPAS-Dev/MPAS-Model. All except cmake build are specific to core_atmosphere or core_init_atmosphere.

• [x] Enable core_init_atmosphere to use mpas_new_unit and mpas_release_unit instead of fixed file unit numbers. See JCSDA-internal#12. Handled by PR #988 .
• [x] Add optional parameters to the mpas_init signature, allowing the caller to pass in a namelist and/or streams filename, identical to the functionality already present when using the -n and -s command-line parameters. See JCSDA-internal#10. @svahl991 Handled by PR #990 .
• [x] Cloud fraction and cloud height diagnostics. See #733 from @jamiebresch.
• [x] "2-stream I/O". This splits input streams into static and time-varying variables, as in an earlier branch from Ha, Skamarock. Also reduces the number of variables for I/O relative to a restart file and includes logic to manage the I/O, both similarly (but not identical) to Ha, Skamarock branch. See https://github.com/JCSDA-internal/MPAS-Model/pull/5. @junmeiban, @liujake
• [x] adjoint of halo exchange. See https://github.com/JCSDA-internal/MPAS-Model/commit/b22c34081f438137171b39e062bbf6464d9d7c0f. @byoung-joo Handled by PR #1138
• [x] bug fixes in core_init_atmosphere for initializing rho_zz and xice. @liujake (#829 addresses part)
• [ ] optional cmake build process and dependence on the jedi-cmake repository. See https://github.com/JCSDA-internal/mpas-bundle/pull/64. @svahl991
• [ ] Modify cmake build procedure to disable OpenMP. See JCSDA-internal#11.

PR for 2nd through 5th changes on list into JCSDA-internal/MPAS-model is https://github.com/JCSDA-internal/MPAS-Model/pull/8. @jjguerrette (Edit: @mgduda changed the order, so 2nd through 5th may not correspond anymore...)

Aim is to merge these into MPAS-Dev.

[mgduda]

As PRs are created to handle the modifications listed in this issue, it might be helpful to reference this issue in the description of the PR.

[svahl991]

Here's a consolidated list of modifications from JCSDA-internal/MPAS-Model that we hope to merge with MPAS-Dev/MPAS-Model.

An addition to the list: Add optional parameters to the mpas_init signature, allowing the caller to pass in a namelist and/or streams filename, identical to the functionality already present when using the -n and -s command-line parameters. See JCSDA-internal#10.

[jjguerrette]

The cmake build procedure is modified to disable OpenMP in https://github.com/JCSDA-internal/MPAS-Model/pull/11.

[jjguerrette]

https://github.com/JCSDA-internal/MPAS-Model/pull/12 enables core_init_atmosphere to use mpas_new_unit and mpas_release_unit instead of fixed file unit numbers

[jjguerrette]

Additional JCSDA-internal PR's since the list was last updated are as follows...

• [ ] Three bug fix PR's for IAU (can be merged into one commit) @syha

  • https://github.com/JCSDA-internal/MPAS-Model/pull/31
  • https://github.com/JCSDA-internal/MPAS-Model/pull/32
  • https://github.com/JCSDA-internal/MPAS-Model/pull/33

• [ ] Very small change to cmake build to allow for single-precision in mpas-bundle @metdyn: https://github.com/JCSDA-internal/MPAS-Model/pull/27

• [ ] https://github.com/JCSDA-internal/MPAS-Model/pull/25 can be combined with @byoung-joo's previous 2D adjoint of halo exchanges in a single commit

• [ ] Another fix for cmake for Pnetcdf: https://github.com/JCSDA-internal/MPAS-Model/pull/23

• [ ] Bug fixes to cmake for ecbuild 3.5: https://github.com/JCSDA-internal/MPAS-Model/pull/21

• [ ] Update to 2-stream I/O to avoid error/warning messages: https://github.com/JCSDA-internal/MPAS-Model/pull/19

• [ ] https://github.com/JCSDA-internal/MPAS-Model/pull/13