Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

cleanup changes to nuopc branch #4

Merged
merged 13 commits into from
Jul 7, 2020
Merged

cleanup changes to nuopc branch #4

merged 13 commits into from
Jul 7, 2020

Conversation

mvertens
Copy link

@mvertens mvertens commented Jul 5, 2020 •
edited
Loading

For detailed information about submitting Pull Requests (PRs) to the CICE-Consortium,
please refer to: https://github.com/CICE-Consortium/About-Us/wiki/Resource-Index#information-for-developers

PR checklist

  • Short (1 sentence) summary of your PR:
    cleanup of #ifdefs and introduction of wrapper component that introduces stubs for nems
  • Developer(s):
    @mvertens, @DeniseWorthen
  • Suggest PR reviewers from list in the column to the right.
  • Please copy the PR test results link or provide a summary of testing completed below.
    ERS_Vnuopc_Ld5.T62_g37.DTEST.cheyenne_intel passed successfully (hash upcoming for nuopc_dev)
  • How much do the PR code changes differ from the unmodified code?
    • bit for bit (for just the simple test above)
    • different at roundoff level
    • more substantial
  • Does this PR create or have dependencies on Icepack or any other models?
    • Yes
    • No
  • Does this PR add any new test cases?
    • Yes
    • No
  • Is the documentation being updated? ("Documentation" includes information on the wiki or in the .rst files from doc/source/, which are used to create the online technical docs at https://readthedocs.org/projects/cice-consortium-cice/. A test build of the technical docs will be performed as part of the PR testing.)
    • Yes
    • No, does the documentation need to be updated at a later time?
      • Yes
      • No
  • Please provide any additional information or relevant details below:
    Carried out only very limited testing - but @DeniseWorthen also carried out tests with NEMS, CMEPS and CICE6 that showed that these changes were bit for bit.
    @dbailey - the following files came from changes introduced by @DeniseWorthen and were needed I believe to get cice6 working in NEMS with CMEPS - @DeniseWorthen could you please comment
cicecore/cicedynB/analysis/ice_history_shared.F90
cicecore/cicedynB/infrastructure/ice_read_write.F90
cicecore/cicedynB/infrastructure/ice_restart_driver.F90
cicecore/cicedynB/infrastructure/io/io_netcdf/ice_restart.F90

@mvertens mvertens requested a review from dabail10 July 5, 2020 04:33
DeniseWorthen
DeniseWorthen reviewed Jul 5, 2020
View reviewed changes
cicecore/cicedynB/infrastructure/ice_read_write.F90 Outdated
@@ -1106,14 +1106,15 @@ subroutine ice_read_nc_xy(fid, nrec, varname, work, diag, &
integer (kind=int_kind) :: &
varid , & ! variable id
status ! status output from netcdf routines
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

When uncommenting the 'optional diagnostics' in this routine, multiple declaration lines in this subroutine require adding an & at the end of the line.

I believe a better solution would be to add the additional variables as separate lines which could be cleanly uncommented when diagnostic output is desired, eg:

! integer (kind=int_kind) :: &
! ndim, vnvar, & ! sizes of netcdf file
! id, & ! dimension index
! dimlin & ! dimension size

DeniseWorthen
DeniseWorthen reviewed Jul 5, 2020
View reviewed changes
cicecore/cicedynB/infrastructure/io/io_netcdf/ice_restart.F90
@@ -228,9 +227,7 @@ subroutine init_restart_write(filename_spec)
call define_rest_field(ncid,'uvel',dims)
call define_rest_field(ncid,'vvel',dims)

#ifdef CESMCOUPLED
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Adding coszen to the restart files replicates EMC_CICE5 behaviour.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Great news. We will still need some sort of ifdef around this.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

In the EMC CICE5, there was originally no coszen present as a restart field so I didn't realize this is a coupled-only field. There is no NEMSCOUPLED; do we need one or could we use the exisiting "coupled" ifdef?

dabail10
dabail10 reviewed Jul 6, 2020
View reviewed changes
cicecore/cicedynB/infrastructure/ice_restart_driver.F90
@@ -58,9 +58,7 @@ subroutine dumpfile(filename_spec)
stressp_1, stressp_2, stressp_3, stressp_4, &
stressm_1, stressm_2, stressm_3, stressm_4, &
stress12_1, stress12_2, stress12_3, stress12_4
#ifdef CESMCOUPLED
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This still needs CESMCOUPLED around it as it is not used in the standalone CICE. Is there an equivalent ifdef for NEMS?

dabail10
dabail10 reviewed Jul 6, 2020
View reviewed changes
cicecore/cicedynB/infrastructure/io/io_netcdf/ice_restart.F90
@@ -84,7 +84,6 @@ subroutine init_restart_read(ice_ic)
endif
endif ! use namelist values if use_restart_time = F

write(nu_diag,*) 'Restart read at istep=',istep0,time,time_forc
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why are you deleting this line?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I saw that---I think this might have been an accidental delete.

dabail10
dabail10 requested changes Jul 6, 2020
View reviewed changes
Copy link
Collaborator

@dabail10 dabail10 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

There are a couple things changed in the standalone code here. These will still need to be wrapped in some sort of ifdef.

@mvertens
Copy link
Author

mvertens commented Jul 7, 2020

@dabail10 - @DeniseWorthen and I have addressed the issues you raised except for the cosine zenith angle being required on restart.

dabail10
dabail10 approved these changes Jul 7, 2020
View reviewed changes
Copy link
Collaborator

@dabail10 dabail10 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This will do for now. There is still a print statement being deleted in ice_restart.F90. Does EMC not use io_pio? Regardless, I am working on changes to add a "restart_coszen" flag.

@dabail10 dabail10 merged commit 8ebdda9 into ESCOMP:nuopc Jul 7, 2020
dabail10 added a commit that referenced this pull request Nov 8, 2022
@DeniseWorthen @apcraig
@dabail10 @eclare108213 @MinsukJi-NOAA @phil-blain
Add wave-ice coupling to nuopc/cmeps driver (CICE-Consortium#782)
251ca48 
* merge latest master (#4)

* Isotopes for CICE (CICE-Consortium#423)

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>

* updated orbital calculations needed for cesm

* fixed problems in updated orbital calculations needed for cesm

* update CICE6 to support coupling with UFS

* put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied

* Convergence on ustar for CICE. (CICE-Consortium#452) (#5)

* Add atmiter_conv to CICE

* Add documentation

* trigger build the docs

Co-authored-by: David A. Bailey <[email protected]>

* update icepack submodule

* Revert "update icepack submodule"

This reverts commit e70d1ab.

* update comp_ice.backend with temporary ice_timers fix

* Fix threading problem in init_bgc

* Fix additional OMP problems

* changes for coldstart running

* Move the forapps directory

* remove cesmcoupled ifdefs

* Fix logging issues for NUOPC

* removal of many cpp-ifdefs

* fix compile errors

* fixes to get cesm working

* fixed white space issue

* Add restart_coszen namelist option

* update icepack submodule

* change Orion to orion in backend

remove duplicate print lines from ice_transport_driver

* add -link_mpi=dbg to debug flags (#8)

* cice6 compile (#6)

* enable debug build. fix to remove errors

* fix an error in comp_ice.backend.libcice

* change Orion to orion for machine identification

* changes for consistency w/ current emc-cice5 (#13)

Update to emc/develop fork to current CICE consortium 

Co-authored-by: David A. Bailey <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: apcraig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>

* Fixcommit (#14)

Align commit history between emc/develop and cice-consortium/master

* Update CICE6 for integration to S2S


* add wcoss_dell_p3 compiler macro

* update to icepack w/ debug fix

* replace SITE with MACHINE_ID

* update compile scripts

* Support TACC stampede (#19)

* update icepack

* add ice_dyn_vp module to CICE_InitMod

* update gitmodules, update icepack

* Update CICE to consortium master (#23)

updates include:

* deprecate upwind advection (CICE-Consortium#508)
* add implicit VP solver (CICE-Consortium#491)

* update icepack

* switch icepack branches

* update to icepack master but set abort flag in ITD routine
to false

* update icepack

* Update CICE to latest Consortium master (#26)


update CICE and Icepack

* changes the criteria for aborting ice for thermo-conservation errors
* updates the time manager
* fixes two bugs in ice_therm_mushy
* updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases

* add cice changes for zlvs (#29)

* update icepack and pointer

* update icepack and revert gitmodules

* Fix history features

- Fix bug in history time axis when sec_init is not zero.
- Fix issue with time_beg and time_end uninitialized values.
- Add support for averaging with histfreq='1' by allowing histfreq_n to be any value
  in that case.  Extend and clean up construct_filename for history files.  More could
  be done, but wanted to preserve backwards compatibility.
- Add new calendar_sec2hms to converts daily seconds to hh:mm:ss.  Update the
  calchk calendar unit tester to check this method
- Remove abort test in bcstchk, this was just causing problems in regression testing
- Remove known problems documentation about problems writing when istep=1.  This issue
  does not exist anymore with the updated time manager.
- Add new tests with hist_avg = false.  Add set_nml.histinst.

* revert set_nml.histall

* fix implementation error

* update model log output in ice_init

* Fix QC issues

- Add netcdf ststus checks and aborts in ice_read_write.F90
- Check for end of file when reading records in ice_read_write.F90 for
  ice_read_nc methods
- Update set_nml.qc to better specify the test, turn off leap years since we're cycling
  2005 data
- Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data
- Add QC run to base_suite.ts to verify qc runs to completion and possibility to use
  those results directly for QC validation
- Clean up error messages and some indentation in ice_read_write.F90

* Update testing

- Add prod suite including 10 year gx1prod and qc test
- Update unit test compare scripts

* update documentation

* reset calchk to 100000 years

* update evp1d test

* update icepack

* update icepack

* add memory profiling (#36)


* add profile_memory calls to CICE cap

* update icepack

* fix rhoa when lowest_temp is 0.0

* provide default value for rhoa when imported temp_height_lowest
(Tair) is 0.0
* resolves seg fault when frac_grid=false and do_ca=true

* update icepack submodule

* Update CICE for latest Consortium master (#38)


    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision

* Use CICE-Consortium/Icepack master (CICE-Consortium#40)

* switch to icepack master at consortium

* recreate cap update branch (CICE-Consortium#42)


* add debug_model feature
* add required variables and calls for tr_snow

* remove 2 extraneous lines

* remove two log print lines that were removed prior to
merge of driver updates to consortium

* duplicate gitmodule style for icepack

* Update CICE to latest Consortium/main (CICE-Consortium#45)

* Update CICE to Consortium/main (CICE-Consortium#48)


Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics.
Refactored eap puny/pi lookups to improve scalar performance
Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp
Update for sea bed stress calculations

* fix comment, fix env for orion and hera

* replace save_init with step_prep in CICE_RunMod

* fixes for cgrid repro

* remove added haloupdates

* baselines pass with these extra halo updates removed

* change F->S for ocean velocities and tilts

* fix debug failure when grid_ice=C

* compiling in debug mode using -init=snan,arrays requires
initialization of variables

* respond to review comments

* remove inserted whitespace for uvelE,N and vvelE,N

* Add wave-cice coupling; update to Consortium main (CICE-Consortium#51)


* add wave-ice fields
* initialize aicen_init, which turns up as NaN in calc of floediam
export
* add call to icepack_init_wave to initialize wavefreq and dwavefreq
* update to latest consortium main (PR 752)

* add initializationsin ice_state

* initialize vsnon/vsnon_init and vicen/vicen_init

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: Minsuk Ji <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>
dabail10 added a commit that referenced this pull request Aug 30, 2023
@DeniseWorthen @apcraig
@dabail10 @eclare108213 @MinsukJi-NOAA @phil-blain @junwang-noaa
Add logging features to nuopc/cmeps cap; deprecates zsalinity in cap (C…
e8a69ab 
…ICE-Consortium#856)

* merge latest master (#4)

* Isotopes for CICE (CICE-Consortium#423)

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>

* updated orbital calculations needed for cesm

* fixed problems in updated orbital calculations needed for cesm

* update CICE6 to support coupling with UFS

* put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied

* Convergence on ustar for CICE. (CICE-Consortium#452) (#5)

* Add atmiter_conv to CICE

* Add documentation

* trigger build the docs

Co-authored-by: David A. Bailey <[email protected]>

* update icepack submodule

* Revert "update icepack submodule"

This reverts commit e70d1ab.

* update comp_ice.backend with temporary ice_timers fix

* Fix threading problem in init_bgc

* Fix additional OMP problems

* changes for coldstart running

* Move the forapps directory

* remove cesmcoupled ifdefs

* Fix logging issues for NUOPC

* removal of many cpp-ifdefs

* fix compile errors

* fixes to get cesm working

* fixed white space issue

* Add restart_coszen namelist option

* update icepack submodule

* change Orion to orion in backend

remove duplicate print lines from ice_transport_driver

* add -link_mpi=dbg to debug flags (#8)

* cice6 compile (#6)

* enable debug build. fix to remove errors

* fix an error in comp_ice.backend.libcice

* change Orion to orion for machine identification

* changes for consistency w/ current emc-cice5 (#13)

Update to emc/develop fork to current CICE consortium 

Co-authored-by: David A. Bailey <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: apcraig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>

* Fixcommit (#14)

Align commit history between emc/develop and cice-consortium/master

* Update CICE6 for integration to S2S


* add wcoss_dell_p3 compiler macro

* update to icepack w/ debug fix

* replace SITE with MACHINE_ID

* update compile scripts

* Support TACC stampede (#19)

* update icepack

* add ice_dyn_vp module to CICE_InitMod

* update gitmodules, update icepack

* Update CICE to consortium master (#23)

updates include:

* deprecate upwind advection (CICE-Consortium#508)
* add implicit VP solver (CICE-Consortium#491)

* update icepack

* switch icepack branches

* update to icepack master but set abort flag in ITD routine
to false

* update icepack

* Update CICE to latest Consortium master (#26)


update CICE and Icepack

* changes the criteria for aborting ice for thermo-conservation errors
* updates the time manager
* fixes two bugs in ice_therm_mushy
* updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases

* add cice changes for zlvs (#29)

* update icepack and pointer

* update icepack and revert gitmodules

* Fix history features

- Fix bug in history time axis when sec_init is not zero.
- Fix issue with time_beg and time_end uninitialized values.
- Add support for averaging with histfreq='1' by allowing histfreq_n to be any value
  in that case.  Extend and clean up construct_filename for history files.  More could
  be done, but wanted to preserve backwards compatibility.
- Add new calendar_sec2hms to converts daily seconds to hh:mm:ss.  Update the
  calchk calendar unit tester to check this method
- Remove abort test in bcstchk, this was just causing problems in regression testing
- Remove known problems documentation about problems writing when istep=1.  This issue
  does not exist anymore with the updated time manager.
- Add new tests with hist_avg = false.  Add set_nml.histinst.

* revert set_nml.histall

* fix implementation error

* update model log output in ice_init

* Fix QC issues

- Add netcdf ststus checks and aborts in ice_read_write.F90
- Check for end of file when reading records in ice_read_write.F90 for
  ice_read_nc methods
- Update set_nml.qc to better specify the test, turn off leap years since we're cycling
  2005 data
- Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data
- Add QC run to base_suite.ts to verify qc runs to completion and possibility to use
  those results directly for QC validation
- Clean up error messages and some indentation in ice_read_write.F90

* Update testing

- Add prod suite including 10 year gx1prod and qc test
- Update unit test compare scripts

* update documentation

* reset calchk to 100000 years

* update evp1d test

* update icepack

* update icepack

* add memory profiling (#36)


* add profile_memory calls to CICE cap

* update icepack

* fix rhoa when lowest_temp is 0.0

* provide default value for rhoa when imported temp_height_lowest
(Tair) is 0.0
* resolves seg fault when frac_grid=false and do_ca=true

* update icepack submodule

* Update CICE for latest Consortium master (#38)


    * Implement advanced snow physics in icepack and CICE
    * Fix time-stamping of CICE history files
    * Fix CICE history file precision

* Use CICE-Consortium/Icepack master (CICE-Consortium#40)

* switch to icepack master at consortium

* recreate cap update branch (CICE-Consortium#42)


* add debug_model feature
* add required variables and calls for tr_snow

* remove 2 extraneous lines

* remove two log print lines that were removed prior to
merge of driver updates to consortium

* duplicate gitmodule style for icepack

* Update CICE to latest Consortium/main (CICE-Consortium#45)

* Update CICE to Consortium/main (CICE-Consortium#48)


Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics.
Refactored eap puny/pi lookups to improve scalar performance
Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp
Update for sea bed stress calculations

* fix comment, fix env for orion and hera

* replace save_init with step_prep in CICE_RunMod

* fixes for cgrid repro

* remove added haloupdates

* baselines pass with these extra halo updates removed

* change F->S for ocean velocities and tilts

* fix debug failure when grid_ice=C

* compiling in debug mode using -init=snan,arrays requires
initialization of variables

* respond to review comments

* remove inserted whitespace for uvelE,N and vvelE,N

* Add wave-cice coupling; update to Consortium main (CICE-Consortium#51)


* add wave-ice fields
* initialize aicen_init, which turns up as NaN in calc of floediam
export
* add call to icepack_init_wave to initialize wavefreq and dwavefreq
* update to latest consortium main (PR 752)

* add initializationsin ice_state

* initialize vsnon/vsnon_init and vicen/vicen_init

* Update CICE (CICE-Consortium#54)


* update to include recent PRs to Consortium/main

* fix for nudiag_set

allow nudiag_set to be available outside of cesm; may prefer
to fix in coupling interface

* Update CICE for latest Consortium/main (CICE-Consortium#56)

* add run time info

* change real(8) to real(dbl)kind)

* fix syntax

* fix write unit

* use cice_wrapper for ufs timer functionality

* add elapsed model time for logtime

* tidy up the wrapper

* fix case for 'time since' at the first advance

* add timer and forecast log

* write timer values to timer log, not nu_diag
* write log.ice.fXXX

* only one time is needed

* modify message written for log.ice.fXXX

* change info in fXXX log file

* Update CICE from Consortium/main (CICE-Consortium#62)


* Fix CESMCOUPLED compile issue in icepack. (CICE-Consortium#823)
* Update global reduction implementation to improve performance, fix VP bug (CICE-Consortium#824)
* Update VP global sum to exclude local implementation with tripole grids
* Add functionality to change hist_avg for each stream (CICE-Consortium#827)
* Update Icepack to #6703bc533c968 May 22, 2023 (CICE-Consortium#829)
* Fix for mesh check in CESM driver (CICE-Consortium#830)
* Namelist option for time axis position. (CICE-Consortium#839)

* reset timer after Advance to retrieve "wait time"

* add logical control for enabling runtime info

* remove zsal items from cap

* fix typo

---------

Co-authored-by: apcraig <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: Mariana Vertenstein <[email protected]>
Co-authored-by: Minsuk Ji <[email protected]>
Co-authored-by: Tony Craig <[email protected]>
Co-authored-by: Philippe Blain <[email protected]>
Co-authored-by: Jun.Wang <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@DeniseWorthen DeniseWorthen DeniseWorthen left review comments

@dabail10 dabail10 dabail10 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@mvertens @dabail10 @DeniseWorthen