Fix bad gotm path in ocean build #862
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This commit makes two changes necessary to get correct behavior with extended cells used by Albany. The extension of the mesh for Albany requires 3 to cover all geometric possibilities. The thermal minimum thickness is set to 0 to ensure reasonable values everywhere there is ice, which is needed for realistic behavior when using Albany due to the way temperature is handled in extended cells.
This merge makes two changes necessary to get correct behavior with extended cells used by Albany.
* The extension of the mesh for Albany requires 3 to cover all geometric possibilities to ensure bit reproducibility.
* The thermal minimum thickness is set to 0 to ensure reasonable values everywhere there
is ice, which is needed for realistic behavior when using Albany due to the way
temperature is handled in extended cells.
* landice/increase_halo:
Update halos to 3; set thermal thickness min to 0
Step therm1 used vertex ice velocity instead of cell ice velocity Fixed minor bug with testing system
Added a square test case Fixed vertexDegree = 4 runs
Added square test case
This is needed because in setting up the vertical diffusion solve, there is a choice of basal b.c. depending on whether the bed is frozen or thawed. In some situations that won't be treated properly if the basalTemperature field is not present on a restart.
This commit adjusts the Interface to only use MPAS temperatures values from grid cells where the thickness exceeds the thickness limit used by the thermal solver. This avoids inconsistencies between what are considered valid temperatures that can lead to bad temperature values. Note that this condition is followed even if the MPAS thermal solver is off. So config_thermal_thickness has meaning to the interface even if the thermal solver is not being used.
This merge fixes subtle issues with how temperature is handled: * Fixes a bug in basalThickness on restarts by adding it as a new restart field. * Forces the interface to use the same definition of which cells have valid temperatures as MPAS is using. * landice/thermal_consistency: In interface, only use temperatures where MPAS calculates them Add basalTemperature as restart variable
Added linear as well as quadratic ocean stress Added periodic velocity boundaries
…estcase Added one dimensional velocity testcase
Widen Redi halo in hmix, correct OpenMP private variables #780
Codes for a semi implicit barotropic mode solver #422
Added one dimensional velocity hex test case
This was a bug in bcc5907
…/develop This merge fixes a bug in the scaling of thermal thickness limit that was introduced in bcc5907 * landice/fix_thermal_thickness_scaling_bug: Correct scaling of thermal thickness limit
Merge PR #583 'vanroekel/ocean/addCosineBellTest' into ocean/develop
This is the first phase of a GPU implementation of all the baroclinic velocity tendencies. It contains a subset of the necessary changes for running on the GPU that retain bit-for-bit accuracy with the current version when running on the CPU
This merge fixes a few intel build errors in E3SM: * Adds missing RKIND specifications to variable declarations that Intel errs on * Adds missing update to cmake build system for the bedtopo module * matt/landice/intel_errors: Add missing mpas_li_bedtopo.F to cmake build Add missing (kind=RKIND) in variable declarations
FO velocity solver requires 3 halos. edgeMask calculation also requires it. Checks have been put in both routines so that if one of those restrictions is ever relaxed, the other will still be triggered. A previous commit changed the default num_halos but did not ensure the runtime namelist was actually set that way.
This merge adds checks in the code that the runtime namelist is using the correct number of halos. * landice/halo_check: Add error checks for required number of halos (3)
This merge updates MALI in e3sm/develop for the first time since 9/3/2020. This update serves two purposes: * Bring in recently added calving laws and some bug fixes with temperature * Bring E3SM up to date before transitioning from submodules to inline code * landice/develop: (197 commits) Add error checks for required number of halos (3) Add missing mpas_li_bedtopo.F to cmake build Add missing (kind=RKIND) in variable declarations Delint MALI files Fix quotation mark issue in Registry Call subroutine specified_calving_velocity Make calving_rate option use the damage threshold for calving to initiate Rename alpha to principalStrainRateRatio General cleanup Undo eigencalving hijack that was made for testing Cleanup related to config_damage_calving_method option Add additional comments about 2-back scheme for posterity Remove trailing whitespace Make damage summary stats work on multiple procs Correct usage of calvingFrontMask in damage_calving routine Remove unneeded code from damage routines Update Registry description of tauMin/Max to indicate they are deviatoric Move nstar calculation into where loop to avoid divide by zero Use grounding line instead of dynamic cell mask Fix asymmetry in calving at grounded margins ...
isnan() is not Fortran standard and causes an error on PGI. Also, this check was checking the wrong variable.
This merge removes an instance of isnan(). It is not Fortran standard and causes an error on PGI. * landice/remove_isnan: Switch ieee_isnan Remove isnan() from calving routine
Add fix for isnan error on PGI. * origin/landice/develop: Switch ieee_isnan Remove isnan() from calving routine
Merge PR #607 'nairita87/topographic_wave_drag' into ocean/develop
qingli411
approved these changes
May 4, 2021
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This looks good to me. Thanks, @philipwjones!
Just curious, why it was working fine with GNU and Intel?
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@qingli411 - Within core_ocean the paths appear in two places. In the Makefile they are added to OCEAN_SHARED_INCLUDES and these are used to build the dycore library and were set correctly. But for some reason, PGI was also looking for module files at the higher mpas_subdriver level, even though there are no explicit use statements for the modules. PGI seems to follow the recursive "use" statements down the call stack? In that case, the include paths added in the build_options are being used by the higher-level makefile and the correct path wasn't there. Apparently the other compilers are only going off the explicit use statements so this isn't an issue. It's probably not great to have these set in multiple places and the build system needs some work, but this fix works for now. |
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@philipwjones OK I see. Thanks! |
mark-petersen
added a commit
to mark-petersen/E3SM
that referenced
this pull request
May 8, 2021
Includes change in MPAS-Dev/MPAS-Model#862
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It looks like the change in this PR is no longer necessary, as the include path for GOTM within E3SM is already correct. This can be closed. |
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Yes, I added this change in the transplant, as I was messing with the makefiles anyway. Thanks for closing. |
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The current path in the ocean core build_options.mk for the gotm package points to the wrong directory for module files, causing build failures for PGI compiler. This PR points to the proper directory.
bit for bit
Fixes #861