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Update netCDF code (in src/Shared/NcdfUtil) to use the netCDF-F90 interface #226

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merged 2 commits into from
Jul 17, 2023
Merged

Update netCDF code (in src/Shared/NcdfUtil) to use the netCDF-F90 interface #226

merged 2 commits into from
Jul 17, 2023

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yantosca
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Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

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Describe the update

We have updated the HEMCO netCDF reading/writing routines in src/Shared/NcdfUtil from the netCDF-F77 interface to the netCDF-F90 interface. This is necessary to satisfy merging requirements for CESM.

The updates mainly involve:

  • Replacing INCLUDE "netcdf.inc" with USE netCDF
  • Replacing NF_ with NF90_ in netCDF parameters and function calls
  • Replacing obsolete netCDF-F77 routines with equivalent netCDF-F90 functionality
  • Also the hco_m_netcdf_io_read.F90 was indented according to F90 free-format.

Expected changes

This is a zero-diff update. No changes are expected.

Reference(s)

N/A

Related Github Issue(s)

Closes #225

Also tagging @jimmielin

yantosca added 2 commits July 14, 2023 18:17
@yantosca
HEMCO netCDF utilities now use netCDF-Fortran90 (aka NF90) interface
a032396 
src/Core/hcoio_write_std_mod.F90
- Set Compress=.FALSE. for the P0 variable.  This prevents a netCDF
  error when netCDF tries to compress a zero-dimension variable.

src/shared/NcdfUtil/hco_m_netcdf_*.F90
- Replaced"INCLUDE netcdf.inc" with "use netCDF"
- Now use the NF90_ function and variables

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Clean up logic in Ncdef_variable (in hco_m_netcdf_io_define.F90)
a695de5 
src/Shared/NcdfUtil/hco_m_netcdf_io_define.F90
- Eliminate ELSE blocks by using never-nesting techniques
- First execute the IF block in the #ifdef.  If COMPRESS is not
  passed, or is false, or if ndims == 0, then do not create the
  variable with netCDF compression.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca added category: Feature Request New feature or request category: Interface to External Model Related to HEMCO updates needed to interface with other models (GEOS, WRF, CESM, etc) topic: Structural Modifications Related to HEMCO structural modifications (as opposed to scientific updates) no-diff-to-benchmark This update will have no impact on benchmark simulations labels Jul 17, 2023
@yantosca yantosca added this to the 3.7.1 milestone Jul 17, 2023
@yantosca yantosca requested a review from lizziel July 17, 2023 14:39
@yantosca yantosca self-assigned this Jul 17, 2023
@yantosca yantosca linked an issue Jul 17, 2023 that may be closed by this pull request
Need to update HEMCO I/O routines to use the netCDF-F90 interface #225
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@yantosca
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Integration tests are running.

@yantosca
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When merged atop PR #1874 and PR #1876, GEOS-Chem Classic integration tests passed (except for TOMAS, which is a known issue that will be fixed later

==============================================================================
GEOS-Chem Classic: Execution Test Results

GCClassic #2c2dab8 GEOS-Chem submod updates: Merge PR #1874 and PR #1876 (GCHP updates)
GEOS-Chem #f9d697f18 Merge PR #1876 (Use standard format for AEIC monthly clim in ExtData.rc)
HEMCO     #725972f PR #226 post-merge fixes: Update CHANGELOG.md

Using 24 OpenMP threads
Number of execution tests: 26

Submitted as SLURM job: 63112103
==============================================================================

Execution tests:
------------------------------------------------------------------------------
gc_05x0625_NA_47L_merra2_CH4........................Execute Simulation....PASS
gc_05x0625_NA_47L_merra2_fullchem...................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem..........................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem_TOMAS15..................Execute Simulation....FAIL
gc_4x5_47L_merra2_fullchem_TOMAS40..................Execute Simulation....FAIL
gc_4x5_merra2_aerosol...............................Execute Simulation....PASS
gc_4x5_merra2_carbon................................Execute Simulation....PASS
gc_4x5_merra2_CH4...................................Execute Simulation....PASS
gc_4x5_merra2_CO2...................................Execute Simulation....PASS
gc_4x5_merra2_fullchem..............................Execute Simulation....PASS
gc_4x5_merra2_fullchem_aciduptake...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_APM..........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_benchmark....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA_SVPOA.............Execute Simulation....PASS
gc_4x5_merra2_fullchem_LuoWd........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_marinePOA....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_RRTMG........................Execute Simulation....PASS
gc_4x5_merra2_Hg....................................Execute Simulation....PASS
gc_4x5_merra2_metals................................Execute Simulation....PASS
gc_4x5_merra2_POPs_BaP..............................Execute Simulation....PASS
gc_4x5_merra2_tagCH4................................Execute Simulation....PASS
gc_4x5_merra2_tagCO.................................Execute Simulation....PASS
gc_4x5_merra2_tagO3.................................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers......................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers_LuoWd................Execute Simulation....PASS

Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 24
Execution tests failed: 2
Execution tests not yet completed: 0

Furthermore, most integration tests were identical to PR #1874 and PR #1876, except for APM (known issue) and RRTMG diagnostics (see #1869).

Checking gc_05x0625_NA_47L_merra2_CH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_05x0625_NA_47L_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem_TOMAS15
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem_TOMAS40
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_aerosol
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_carbon
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_CH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_CO2
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_aciduptake
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_APM
   -> 2 differences found in OutputDir
      * GCC_14.2.1_r10/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r11/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r10/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r11/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r10/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 
        GCC_14.2.1_r11/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 

Checking gc_4x5_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA_SVPOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_LuoWd
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_marinePOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_RRTMG
   -> 1 difference found in OutputDir
      * GCC_14.2.1_r10/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
        GCC_14.2.1_r11/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
   -> No differences in Restarts

Checking gc_4x5_merra2_Hg
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_metals
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_POPs_BaP
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagCH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagCO
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_TransportTracers
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_TransportTracers_LuoWd
   -> No differences in OutputDir
   -> No differences in Restarts

@jimmielin
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Thanks @yantosca for working on this! We will submit a PR to update it downstream in HEMCO-CESM when 3.7.1 is released.

@yantosca
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When merged atop PR #1874 and PR #1876, all GCHP integration tests passed (except for TOMAS, which is a known issue that will be fixed later).

==============================================================================
GCHP: Execution Test Results

GCClassic #baad1bd GEOS-Chem submod updates: Merge PR #1874 and PR #1876 (GCHP updates)
GEOS-Chem #f9d697f18 Merge PR #1876 (Use standard format for AEIC monthly clim in ExtData.rc)
HEMCO     #725972f PR #226 post-merge fixes: Update CHANGELOG.md

Number of execution tests: 5

Submitted as SLURM job: 63113136
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_merra2_fullchem................................Execute Simulation....PASS
gchp_merra2_fullchem_benchmark......................Execute Simulation....PASS
gchp_merra2_fullchem_RRTMG..........................Execute Simulation....PASS
gchp_merra2_tagO3...................................Execute Simulation....PASS
gchp_merra2_TransportTracers........................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 5
Execution tests failed: 0
Execution tests not yet completed: 0

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Furthermore, all GCHP integration tests were zero-diff w/r/t PR #1874 and PR #1876:

Checking gchp_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_RRTMG
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_TransportTracers
   -> No differences in OutputDir
   -> No differences in Restarts

lizziel
lizziel approved these changes Jul 17, 2023
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Looks good to merge. Thanks Bob!

yantosca added a commit that referenced this pull request Jul 17, 2023
@yantosca
PR #226 post-merge fixes: Update CHANGELOG.md
725972f 
CHANGELOG.md
- Now list the PR #226 (Update HEMCO netCDF I/O code to use the
netCDF-F90 interface) under version 3.7.1.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca merged commit f2b9d17 into dev/3.7.1 Jul 17, 2023
@yantosca yantosca deleted the feature/hco-netcdf-f90 branch July 17, 2023 19:04
This was referenced Jul 18, 2023
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yantosca added a commit that referenced this pull request Jul 20, 2023
@yantosca
Merge PR #227 (Fix several minor issues not addressed in PR #226)
599775d 
This merge brings PR #227 (Fix several minor issues not addressed in
PR #226, by @yantosca) into the HEMCO 3.7.1 development stream.

Important features added
- Convert hco_m_netcdf_io_write.F90 module to use netCDF-F90 interface
- Remove leftover calls to netCDF-F77 functions
- Updated comment headers

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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category: Feature Request New feature or request category: Interface to External Model Related to HEMCO updates needed to interface with other models (GEOS, WRF, CESM, etc) no-diff-to-benchmark This update will have no impact on benchmark simulations topic: Structural Modifications Related to HEMCO structural modifications (as opposed to scientific updates)
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Need to update HEMCO I/O routines to use the netCDF-F90 interface
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@yantosca @jimmielin @lizziel