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The custom TC4 Makefile has been added (oops), and the presumed Python Ubuntu packages have been added for Travis.
Simplified scaling factors in MOM_forcing_type or encapsulated groups of scaling factors in local variables. All answers are bitwise identical.
Rescaled the units of optional _rate variables returned by extractFluxes1d and simplified the calculations using these variables in applyBoundaryFluxesInOut. All answers are bitwise identical, but the units of arguments to a public type have changed.
Combined scaling factors in MOM_forcing_type including the introduction of some new local variables and the use of dt_in_T in place of dt. All answers are bitwise identical.
Rescaled the units of 3 surface salt flux elements to [R Z T-1] in the forcing type, including salt_flux, salt_flux_in, and salt_flux_added. Also added a unit_scaling_type arguments to insert_brine. All answers are bitwise identical, but the units of 3 elements of a widely used public type have changed and there is a new subroutine argument.
Simplified scaling factors in the solo_driver version of MOM_surface_forcing, including rescaling of FLUX_CONST and encapsulating groups of scaling factors in local variables and eliminating other local variables. All answers are bitwise identical.
Converted the units of FLUXCONST to [Z T-1] in eight modules for expanded dimensional consistency testing. All answers are bitwise identical.
Converted the units of RHO0 to [R] in four modules for expanded dimensional consistency testing. All answers are bitwise identical.
Removed unnecessary commented out code and an unused variable in MOM_barotropic.F90. All answers are bitwise identical.
Fixed a recently bug in insert_brine that was introduced yesteray with MOM6 commit 965c2c2. This bug is a double inclusion of US%s_to_T, so technically it does not change answers, just breaks dimensional consistency testing. For some reason the impacted code was not triggered by the MOM6-examples test cases.
Pass timestep to applyBoundaryFluxesInOut and insert_brine in units of [T]. All answers are bitwise identical, but the units of arguments to two public subroutines have rescaled dimensions.
Pass timestep to extractFluxes1d and extractFluxes2d in units of [T]. All answers are bitwise identical, but the units of arguments to two public subroutines have rescaled dimensions.
Pass timestep to thickness_diffuse and mixedlayer_restrat in units of [T]. All answers are bitwise identical, but the units of arguments to two public subroutines have rescaled dimensions.
Changed the name and units of the timestep element in the sum_output_CS to work with units of [T]. Also combined mass flux scaling factors into a local variable in accumulate_net_input for simplification. All answers are bitwise identical.
+Rescaled the units of the 9 fluxes%heat_content_... variables to units of [J kg-1 R Z T-1], and of tv%TempxPmE to units of [degC R Z] for greater dimensional consistency testing and for code simplification. All answers are bitwise identical.
A diagnostic ID was compared to floating point 0. to test if it had been set. This patch replaces this with an integer inequality test. This resolves GitHub Issue mom-ocean#1016. Thanks to Stephen Griffies for reporting.
Cleaned up code in insert_brine. However, this routine does not appear to be in use, and it does not appear to have ever been properly coded and tested. I think that this routine is a candidate for deletion, and the flag that triggers its use, ALT_REJECT_BELOW_ML, should be obsoleted. All answers are bitwise identical with these changes.
Pass timestep to step_forward_MEKE and calc_slope_functions in units of [T]. All answers are bitwise identical, but the units of arguments to two public subroutines have rescaled dimensions.
Corrected a dimensional rescaling factor in entrainment_diffusive, which would only impact buoyancy forced cases without temperature and salinity as state variables. All answers in the MOM6-examples test cases are bitwise identical.
Pass timestep to btstep in units of [T], and changed the internal units of CS%dtbt and CS%dtbt_max to [T] in barotropic_CS. All answers are bitwise identical, but the units of an arguments to a public subroutine has rescaled dimensions.
Pass timestep to btstep in units of [T], and changed the internal units of CS%dtbt and CS%dtbt_max to [T] in barotropic_CS. All answers are bitwise identical, but the units of an arguments to a public subroutine has rescaled dimensions.
Pass MLDdensityDifference to diagnoseMLDbyDensityDifference in units of [R]. All answers are bitwise identical.
Widespread cleanup of units in comments in vertical parameterizations. All answers are bitwise identical.
Cleanup of units in comments in MOM_hor_visc. All answers are bitwise identical.
+Rescaled the units of tv%salt_deficit to units of [ppt R Z] for greater dimensional consistency testing and for code simplification. This also required adding a unit_scale_type argument to MOM_thermo_chksum. All answers are bitwise identical, but there is a new subroutine argument.
ALE: Float ID inequality replaced with integer
This adds dimensional scaling to the vprec diagnostic, and resolves some variable name changes and additions to the OpenMP directives. This fixes some of the tests in GitHub PR 1019.
T scaling and OpenMP fixes
This patch fixes several issues with the current test suite Makefile: - the DO_REPRO_TEST flag is now available to disable the REPRO=1 test, which currently fails on older GCC compilers and Intel compilers. This may be expected, and needs further investigation. - Regression tests against PR targets had been inadvertently disabled due to a misnamed variable (TEST vs TESTS). This has been fixed. - OpenMP tests have been added to the suite. Success may vary... - We now report a full diff output for a failed cmp test of stats and diagnostic checksums - tab indentation was being used outside the context of rule definitions. This was not causing issues but has been replaced with space intents to avoid future problems. Note that OpenMP testing issues were observed on an older GCC compiler, but it's not clear if this will persist on Travis or more modern GCC compilers, and may be disabled (or perhaps even fixed) in a future commit.
Fix OMP race conditions and some chkcsum calls
Fix a bug in GM when using MEKE_GEOMETRIC
Following changes have been made: * add new argument (thickness_diffuse_CS) to horizontal_viscosity; this is needed so that the GM coeff can be called from MOM_hor_visc. * Deletes unnecessary calls to pass_vector * Simplifies GME by removing dependecy on MEKE. GME is now set to be some multiple of the GM coeff. A new runtime parameter (GME_efficiency) can be used to control the strength of GME.
Updates GME by removing dependency on MEKE
Fix thread-unsafe computations of advective tracer flux vertical sums
….com/gustavo-marques/MOM6 into gustavo-marques-dev-master-candidate-ncar-2020-03-27
solve conflice in mom_surface_forcing_nuopc.F90
Update to GFDL 20200401 dev/master
* cleanup of ESMF error handling Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu>
* allows control of MOM6 restarts and MOM6 intermediate restarts using nems.configure settings restart_n and restart_option. Fixes duplicate restart issue when running with CMEPS (#16). * when field dumping is turned on, all fields in import state and export state are written to single file with timestamped file name (#15) * moves call to data_override field lrunoff out of the enclosing do loop (#21 ) Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu>
pjpegion
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Feb 1, 2021
Bugfix: sign error on fprec for nuopc and mct caps
pjpegion
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Jul 13, 2022
Note that most of these commits are from previously squashed pull requests, and this PR is restoring them. - 6360dbb Merge branch 'main' into main_to_dev - bac8031 Merge pull request mom-ocean#1566 from jiandewang/EMC-FMS-mixed-mode-20220411 - e532d86 Merge pull request NOAA-EMC#88 from marshallward/missing_attrib_with_class_bugfix - d380f1d An alternate fix to class(*) issues with FMS 2022-01 - 8ecf333 Merge pull request NOAA-EMC#87 from jiandewang/feature/update-to-main-20220317 - ba37f94 Merge remote-tracking branch 'FSU/main' into feature/update-to-main-20220317 this is corresponding to MOM6 main 20220317 commit (hash # 399a7db) - 44313d9 Merge pull request NOAA-EMC#85 from jiandewang/feature/update-to-main-20220217 - 966707f Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217 this is corresponding to MOM6 main branch 20220217 commit (hash # 6f6d4d6), which originally based on GFDL-candidate-20220129 - 32c0e1e Merge pull request NOAA-EMC#81 from jiandewang/feature/update-to-main-20211220 - 9642b1d delete external/OCEAN_stochastic_phyiscs directory as Phil re-coded in external/stochastic_physics directory - e7c9ada solve minor conflict in mom_cap.F90 mom_ocean_model_nuopc.F90 and MOM_energetic_PBL.F90, add two new files: src/parameterizations/stochastic/MOM_stochastics.F90 and config_src/external/stochastic_physics/stochastic_physics.F90 - 90d5961 Merge pull request NOAA-EMC#78 from jiandewang/feature/update-to-GFDL-20211019 - fd02017 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20211019 - 36f17eb Merge pull request NOAA-EMC#72 from pjpegion/ocn_stoch_july2021 - a9a957e return a more accurate error message in MOM_stochasics - 56bb41e Merge branch 'ocn_stoch_july2021' of https://github.com/pjpegion/MOM6 into ocn_stoch_july2021 - ca2ae1c update to dev/emc - 14ca4a1 Merge pull request NOAA-EMC#76 from jiandewang/feature/update-to-GFDL-20210914 - 29016c2 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210914 merge GFDL main 20210914 commit (hash # c09e199) - a8577df Merge branch 'NOAA-EMC:dev/emc' into ocn_stoch_july2021 - f8a8e4c update to gfdl 20210806 (NOAA-EMC#74) - 16e6af0 update to dev/emc - 237a510 add comments - 1b4273d revert logic wrt increments - 5b2040e add logic to remove incrments from restart if outside IAU window - c5f2b72 add write_stoch_restart_ocn to MOM_stochastics - bdf2dc7 doxygen cleanup - 8bc4acc move stochastics to external directory - a3fa3a1 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch_july2021 - e4bc007 stochastic physics re-write - 202cbd4 update to dev/emc - 61717ee Merge remote-tracking branch 'origin/dev/emc' into ocn_stoch - 565e0bb remove debug statements - a4c0411 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 689a73f remove PE_here from mom_ocean_model_nuopc.F90 - 8afe969 clean up of mom_ocean_model_nuopc.F90 - 25ed4fc revert MOM_domains.F90 - b8d9888 place stochastic array in fluxes container and make SPPT specific arrays allocatable - d984a7e remove stochastics container - eb88219 clean up of code for MOM6 coding standards - 6e3ea1b correct coupled_driver/ocean_model_MOM.F90 and other cleanup - 0b99c1f make stochastics optional - 85023f8 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 80f9f44 clean up MOM_domains - 5443f8e remove blank link in MOM_diagnostics - 1727d9a re-write of stochastic code to remove CPP directives - 600ebf9 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch - 6bb9d0b fix non stochastic ePBL calculation - 1d7ffa3 clean up code - 040e1f1 Merge pull request #13 from NOAA-EMC/dev/emc - 2cba995 Merge branch 'dev/emc' into ocn_stoch - 1dc0f4f Merge remote-tracking branch 'upstream/dev/emc' into dev/emc - 4bd9b9e clean up debug statements - 25ed5ef additions for stochy restarts - a2a374b add stochy_restart writing to mom_cap - 0c15f4c Update MOM_diabatic_driver.F90 - 167a62e Merge pull request #12 from pjpegion/dev/emc - bd477a9 Update MOM_diabatic_driver.F90 - 7212400 Update MOM_diabatic_driver.F90 - 7de295c cleanup of code and enhancement of ePBL perts - cd06356 Merge pull request #11 from NOAA-EMC/dev/emc - 9896d61 Merge pull request #9 from pjpegion/dev/emc_merge - 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge - 3cad1ba Merge pull request #8 from NOAA-EMC/dev/emc - c2aa2a8 updates from dev/emc - 182ef34 additions for stochastic physics and ePBL perts - 671c714 Merge pull request #1 from NOAA-EMC/dev/emc
pjpegion
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Aug 25, 2022
* Autoconf: Fix makedep path The current path of makedep in the autoconf build assumes a directory tree as in .testing. This patch uses the generalized @srcdir@ to support more general autoconf builds. Other minor changes: * The `depend` rule was split into an explicit Makefile.dep rule and a phony rule to support `make depend` * SRC_DIRS shell assignment is replaced with an Autoconf macro. * A "self-generate" rule was added to `Makefile.in`, so that changes to `Makefile.in` do not trigger a full `./configure` run and regeneration of `.config.status`. This could possibly be extended to support `make depend` but let's first see how this one goes. * Autoconf: makedep uses autoconf var conventions This patch changes the makedep script to use autoconf environment variable conventions rather than mkmf ones: * FCFLAGS in place of FFLAGS * DEFS in place of CPPDEFS * LDFLAGS and LIBS rather than just LDFLAGS (NOTE: This differs from Makefile's LDLFLAGS/LDLIBS) This also allowed us to remove the custom build rule in the FMS build. Note that we now use an autoconf-friendly rule, rather than the default Makefile rule (which was arguably for fixed-format Fortran anyway). The description of autoconf->mkmf translation from the Makefile templates has also been removed, since they're no longer relevant. Some other minor changes in this build: * The `make depend` rule was added to the FMS Makefile template. * @srcdir@ is directly passed to FMS makedep, rather than identically re-defining it in a variable. * Testing: Resolve makedep paths This patch resolves some issues relating to finding the path to makedep in both .testing and more generalized autoconf builds. An explicit autoconf test for makedep has been added, with a default path which includes the `ac` directory relative to `deps`. The .testing directory, which does not lie within `ac`, instead modifies the PATH to allow autoconf to find makedep. The absolute path is determined and substituted into the appropriate Makefile.in template. Some redundant operations in .testing/Makefile have been removed, but I suspect there are even more. Much of the structure required to support mkmf and list_paths is probably no longer needed.
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