NCAR to main 2024-03-19 #1621
NCAR to main 2024-03-19 #1621
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* Enhancements for adding land block elimination to NUOPC cap: - Add sum_across_PEs_int4_2d to the sum_across_PEs interface - Allow mask_table file to be placed in run directory (now, the first dir that is looked at). * Enhance NUOPC cap to support MOM_mask_table. - Determine masked blocks. - Evenly distribute eliminated cells. - Fill ESMF gindex array accordingly. - During Export phase, set fields of eliminated cells to zero. * set %label in register_netcdf_field and register_netcdf_axis * first working version of an automated mask table generator * While determining masked blocks, take reentrancy and tripolar stitch into account * apply tripolar stitch fix in auto mask_table generation * add AUTO_IO_LAYOUT_FAC parameter to control IO_LOAYUT when AUTO_MASKTABLE is on * Miscellaneous auto masking fixes to address reviews: - Dimensionalize topographic depth variables used to determine cell masks in auto masktable routine. - Raise error if the user provided PE layout is inconsistent with auto masktable generation. - Save the masktable parameter description to a string variable to avoid repetition. - Fix typos, whitespaces, use modern array syntax. * Disable FPEs in MacOS testing Due to poor handling of floating point in HDF5 1.14.3, it is currently not possible to use floating point exceptions (FPEs) whenever this version is present. The GitHub Actions CI nodes would randomly select either 1.14.2 or 1.14.3, and would raise an FPE error if 1.14.3 was selected. Additionally, the homebrew installation does not provide a clean method for selecting a different version of HDF5. Thus, for now we disable FPEs in the MacOS testing, and hope to catch any legitimate FP errors in the Ubuntu version. We will restore these tests as soon as this has been fixed in an easily-accessible version of HDF5. As part of this PR, I have also moved the FCFLAGS configuration to the platform specific Actions files, allowing for independent compiler configuration for each platform. --------- Co-authored-by: Marshall Ward <[email protected]>
* Fix biharmonic Leith
Biharmonic Leith uses Del omega at is-1 and js-1. This unavoidably requires
u at js-3 and v at is-3, which are unavailable. It also requires Del omega
at Ieq+1 and Jeq+1, which requires v at Ieq+3 and u at Jeq+3, which are
unavailable. This necessitates a halo update.
Fixes several bugs in Leith+E.
- Fixes indexing when computing smoothed vorticity and its gradient
- Crucially, computes `vert_vort_mag` when using Leith+E
- Fixes some logic in the smoothing code
- Other minor indexing fixes
* Leith+E Logic Update
Ah is required at h and q points. The original code computed Ah at
h points, then packed into Ah_h, then applied upper bounds to Ah.
If Ah_h is in the diag_table or if debug is true, then the value of
Ah with upper bounds get packed into Ah_h. Then, at q points the
code unpacks Ah_h. This update makes sure that the upper bound
gets applied to q points, not just h points.
* Leith+E halo updates
The main thing that this commit does is to perform smoothing of u and v
outside of the loop over layers. This swaps nz 2D blocking halo updates
for a single blocking 3D halo update.
* Leith+E smoothing
This commit adds a runtime flag, SMOOTH_AH. If True (default) then
`m_leithy` and `Ah` are both smoothed, which leads to many blocking
communications. If False then these fields are rougher, but there
is less communication.
* Leith+E eliminate pass-var
This commit removes one halo update in Leith+E. To achieve this
requires re-indexing two assignments. The value of Ah and Kh are
computed at h points, then re-used at q points. Without the halo
update it is necessary to offset the assignment at h and q
points, e.g. Kh(I,J) = Kh_h(i+1,j+1,k), to avoid accessing
values that have not been computed.
* Leith+E OBC
Adds code so that Leith+E works with OBC.
* Leith+E eliminate halo update
This commit eliminates one more halo update in Leith+E.
* *Correct rotational symmetry with USE_LEITHY
This commit revises the smoothing code used when USE_LEITHY = True to give
answers that respect rotational symmetry and it also corrects some horizontal
indexing bugs and problems with the staggering in some halo update and smooth_x9
calls and reduces some loop ranges to their minimal required values. The
specific changes include:
1. Corrected a horizontal indexing bug when interpolating Kh_h and Ah_h to
corner (q) points when USE_LEITHY = True. These had previously been
inappropriately copied from the thickness point to the southwest of the
corner point. This required symmetric-memory-mode calculations of the
thickness point viscosities whenever USE_LEITHY is true, but to avoid adding
complicated logic, the symmetric-memory loop bounds are used for the
calculation of Kh.
2. Revised smooth_x9 to give rotationally symmetric answers and split it into
the two routines smooth_x9_h and smooth_x9_uv to reduce the memory used by
this routine and reduce the use of optional arguments.
3. Eliminated 4 unneeded halo update calls, and added error handling for the
case where Leith options are used with insufficiently wide halos.
4. Added new integers to indicate the loop ranges over which the viscosities
and related variables should be calculated, depending on which options are
active, and then adjusted 91 do-loop extents horizontal_viscosity code to
reflect the loop ranges over which arrays are actually used.
5. Added a new 2-d variable for the squared viscosity for smoothing that can
be used for halo updates and to avoid having a variable with confusingly
inconsistent dimensions at various points in the code.
6. Corrected the position arguments on 2 smooth_x9 calls and 4 pass_var calls
that are used when USE_LEITHY=.true. and SMOOTH_AH=.true. As previously
written, these smooth_x9 and pass_var calls would work when in non-symmetric
memory mode but would give incorrect answers when in symmetric memory mode.
These revisions change answers when USE_LEITHY is true, but answers are
bitwise identical in all other cases.
---------
Co-authored-by: Robert Hallberg <[email protected]>
Merge latest main
Merge latest main (Feb 28, 2024)
alperaltuntas
requested review from
marshallward,
kshedstrom,
jiandewang,
sanAkel and
abozec
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1621 +/- ##
==========================================
- Coverage 37.45% 37.40% -0.05%
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Files 270 270
Lines 79765 79914 +149
Branches 14833 14860 +27
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+ Hits 29878 29894 +16
- Misses 44350 44471 +121
- Partials 5537 5549 +12 ☔ View full report in Codecov by Sentry. |
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This doesn't change answers for me, so I approve. However, it changed the MOM_domains_init interface which requires PR #207 to SIS2. Also, a case of mine which is coupled to ice, but has no ice, now needs to have TOPO_CONFIG and/or TOPO_FILE set in SIS_input.
This commit makes the unit_scale_type argument US to MOM_domains_init and gen_auto_mask_table optional and moves it to the end of the argument list, so that coupled or ice-ocean models using SIS2 will compile with the proposed updates to the main branch of MOM6 from dev/ncar. Because MOM6 and SIS2 use some common framework code but are managed in separate github repositories, we need to use optional argument to allow a single version of SIS2 to work across changes to MOM6 interfaces. Because the TOPO_CONFIG parameter as used in SIS2 has a default value, there is an alternative call to get_param for TOPO_CONFIG with a default when MOM_domains_init is called with a domain_name argument. Also added missing scale arguments to get_param calls for MINIMUM_DEPTH and MASKING_DEPTH. This commit also adds or corrects units in the comments describing 4 recently added or modified variables. All answers are bitwise identical in any cases that worked before (noting that some cases using SIS2 would not even compile).
Make the US argument to MOM_domains_init optional
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@alperaltuntas what's the highest (finest) resolution that has been tested for the |
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preliminary test shows no problem for UFS. However our main testing machine HERA is undergoing migration from CentOS to Rocky 8 which preveting me from doing clean test at this moment. Please bear me a bit delay for final testing. |
The highest I tried was 0.25 deg. If you are asking about the performance of the iteration, it's quite fast for both 0.66 and 0.25 degrees (on the order of 0.1sec). If we discover in the future that it is slow for finer resolutions (e.g., 1/12 deg), I have plans to speed up the iteration, but for now, I opted for a simpler implementation for ease of maintenance. Other than that, I have not encountered any performance issues. |
That ( |
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@alperaltuntas what is automatic mask table generation ? |
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@alperaltuntas if we use land mask, then the lat/lon information on masked domain will be written as undefined value, is that true ? See an example at |
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@alperaltuntas one more minor point: in restart file variable "h" are all 1e-10 on land points but using land mask approach pure land domian have some points (but not all of them) with value of zero. All ocean points have identical values which is what we expected. |
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Thank you all for the reviews and confirmations. I am merging the PR. |
This PR contains enhancements and bug fixes from NCAR fork as listed below. In summary, these include (1) automated runtime land block elimination based on automatically generating a mask_table during domain initialization at runtime, (2) rotational symmetry fixes and efficiency improvements in Leith+E, and misc bug fixes.
Since this PR includes changes in the NUOPC cap, I'd recommend EMC to first run their tests and approve, before others run their full test suites.