Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Confirm you have reviewed the following documentation

• Contributing guidelines

New GCClassic feature or discussion

Dependabot found a security issue (https://github.com/geoschem/GCClassic/security/dependabot/1) caused by the version of jinja2 (used to generate ReadTheDocs documentation) having a security vulnerability.

The solution is to update the docs/requirements.txt from:

# Requirements for building the GCHP documentation
#
# NOTE: Use specific versions for Python packages instead of upper
# bounds.  Using an upper bound will not necessarily install the
# intended version if there already is a version that meets the
# criteria present in the Python environment.
#  -- Bob Yantosca and Lizzie Lundgren (30 Jun 2022)
#
# The following package versions have been proven to work together:
#
sphinx==3.5.4
sphinx-autobuild==2021.3.14
sphinx_rtd_theme==0.5.2
sphinxcontrib-bibtex==2.2.0
recommonmark
docutils==0.16
jinja2==3.0.3

to

# ======================================================================
# ReadTheDocs requirements file
#
# If you wish to install the dependencies for building the ReadTheDocs
# ReadTheDocs documentation from PyPI (the Python Package Index), use:
#
# $ pip install -r requirements.txt
# ======================================================================
sphinx==7.2.6
sphinx_rtd_theme==2.0.0
sphinxcontrib-bibtex==2.6.2
sphinx-autobuild==2021.3.14
recommonmark==0.7.1
docutils==0.20.1
jinja2==3.1.3

as we have already done for GCPy.

Name and Institution (Required)

Name: Gourav Saha
Institution: IIT Delhi

Confirm you have reviewed the following documentation

• Support guidelines
• User manuals
• Debugging GEOS-Chem and HEMCO errors
• Current and past Github issues

Description of your issue or question

After downloading all the necessary files for the benchmark 1 month simulation-20190701 to 20190801, this error is being shown:

HEMCO: Opening ./Restarts/GEOSChem.Restart.20190701_0000z.nc4

HEMCO ERROR: Cannot find field SPC_BUTDI. Please check variable name in the co
nfig. file

HEMCO ERROR: Error encountered in routine HCOIO_Read!

HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: SPC_BUTD
I
--> LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)

HEMCO ERROR: Error in called ReadList_Fill (7) from HEMCO ReadList_Read
--> L
OCATION: ReadList_Read (HCO_ReadList_Mod.F90)
Error in ReadList_Read called from hco_run

GEOS-Chem ERROR: Error encountered in "HCO_Run"!
-> at HCOI_GC_Run (in module GeosCore/hco_interface_gc_mod.F90)

THIS ERROR ORIGINATED IN HEMCO! Please check the HEMCO log file for
additional error messages!

===============================================================================
GEOS-Chem ERROR: Error encountered in "HCOI_GC_Run"!
-> at Emissions_Run (in module GeosCore/emissions_mod.F90)

===============================================================================
GEOS-CHEM ERROR: Error encountered in "Emissions_Run", Phase 0

This error can indicate a missing file. Please check the HEMCO log file for
additional error messages!

STOP at -> at GEOS-Chem (in GeosCore/main.F90)

Name and Institution (Required)

Name: Melissa Sulprizio
Institution: Harvard / GCST

Confirm you have reviewed the following documentation

• Contributing guidelines

New GCClassic feature or discussion

We should add a section to Read the Docs with tips for customizing your GEOS-Chem simulation. This can include things like:

• Switching between offline and online emissions: What's the difference between the two? What changes are needed in HEMCO_Config.rc and HEMCO_Diagn.rc?
• Turning on/off certain options (e.g. sea salt debromination, nitrate photolysis, Luo wet dep, etc).
• Nested-grid guide
• Add more here!

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

New GCClassic feature or discussion

I am testing a new meteorology source in GC-Classic. In order to do this I need to change code in HEMCO and GEOS-Chem repositories and recompile. This is in addition to changing settings in geoschem_config.yml, HEMCO_Config.rc, and HEMCO_Config.rc.gmao_metfields, some of which are redundant. This is much more complicated than in GCHP which simply requires changing paths in ExtData.rc and rerunning.

I suggest that we take a look at how we handle meteorology inputs in GEOS-Chem Classic to see if we can make it a run-time option and with more flexibility and simplicity. I'll think about how to do this in preparation for adding GEOS-IT as a standard option in the model.

Name and Institution (Required)

Name:
zhaohongyan
Institution:
School of Environment , Beijing Normal University

Confirm you have reviewed the following documentation

• Support guidelines
• User manuals
• Debugging GEOS-Chem and HEMCO errors
• Current and past Github issues

Description of your issue or question

1. Build required software with Spack
   a. GCClassic version : 14.3.1, build from master
   b.
2. spack find

3. env file

4. cmake errors
   a.
   b. FailedCompile.txt log info

Name and Institution (Required)

Name: Lee Murray
Institution: University of Rochester

Line 71 of CMakeLists.txt (second line below) is missing the dash before the "g" compilation option, which makes ifort fail during compile time, as it is looking for a non-existent file named "g".

set(GEOSChem_Fortran_FLAGS_DEBUG_Intel
    g -O0 "SHELL:-check arg_temp_created" "SHELL:-debug all" -fpe0 -ftrapuv -check,bounds
    CACHE STRING "GEOSChem compiler flags for build type Debug with Intel compilers"
)

Once #4 is merged, "install" can be readded to the make step in the CI pipelines. Re-enabling "install" will help catch issues related to builds without run directories in the future.

Brief Description

There are two related submodule PRs for retiring use of input meteorology field land-water-ice (LWI) index and GEOS-Chem and HEMCO state arrays it is stored in. We are removing LWI as a dependency because it will not be included in the GEOS-IT dataset and determining whether a grid cell is over ocean, ice, or land is possible through other input meteorology fields. It is currently only used for computation in (1) dry deposition if using optional Luo wet deposition, and (2) HEMCO extensions.

Related Issues

Feature request to retire LWI:
geoschem/geos-chem#1413

Submodule Pull Requests

• geoschem/geos-chem#1435
• geoschem/HEMCO#170

Currently we test GEOS-Chem Classic with Azure. This will no longer work with the release of 13.0.0 since GEOS-Chem will be built inside of GEOS-Chem-Classic (this new repository). We will need to update the CI pipeline prior to that transition.

When I configure GEOS-Chem Classic to turn off OpenMP parallelization:

$ cd build
$ cmake ../CodeDir -DRUNDIR=.. -DOMP=n

I get this (non-fatal) error message:

-- The Fortran compiler identification is GNU 10.2.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-9.2.0/gcc-10.2.0-mzf6cdco4v5z5srfzjd7nwasabojxpx5/bin/gfortran - skipped
-- Checking whether /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-9.2.0/gcc-10.2.0-mzf6cdco4v5z5srfzjd7nwasabojxpx5/bin/gfortran supports Fortran 90
-- Checking whether /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-9.2.0/gcc-10.2.0-mzf6cdco4v5z5srfzjd7nwasabojxpx5/bin/gfortran supports Fortran 90 - yes
=================================================================
GCClassic 13.3.0 (superproject wrapper)
Current status: 13.3.0-alpha.12-4-g9c5f426
=================================================================
-- Found NetCDF: /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-mtuoejjcl3ozbvd6prgqm44k5jre3hne/lib/libnetcdff.so  
-- Useful CMake variables:
  + CMAKE_PREFIX_PATH:    /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-10.2.0/netcdf-c-4.7.4-22bkbtqledcaipqc2zrgun4qes7kkm5q
  ...             /net/seasasfs02/srv/export/seasasfs02/share_root/ryantosca/spack/opt/spack/linux-centos7-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-mtuoejjcl3ozbvd6prgqm44k5jre3hne
  + CMAKE_BUILD_TYPE:     Release
-- Run directory setup:
  + RUNDIR:       /local/ryantosca/GC/rundirs/partest_sp
-- Threading:
  * OMP:          ON  OFF
-- General settings:
  * CUSTOMMECH:   ON  OFF
  * BPCH_DIAG:    ON  OFF
  * USE_REAL8:    ON  OFF
-- Components:
  * TOMAS:        ON  OFF
  * TOMAS_BINS:   NA  15  40
  * APM:          ON  OFF
  * RRTMG:        ON  OFF
  * GTMM:         ON  OFF
  * HCOSA:        ON  OFF
  * LUO_WETDEP:   ON  OFF
=================================================================
HEMCO 3.2.0
Current status: 3.2.0-rc.0
=================================================================
=================================================================
GEOS-Chem 13.3.0 (science codebase)
Current status: 13.3.0-alpha.12-5-g8af9c9896
=================================================================
Creating /local/ryantosca/GC/rundirs/partest_sp/CodeDir/src/GEOS-Chem/Interfaces/GCClassic/gc_classic_version.H
CMake Warning at CMakeLists.txt:286 (message):
  Failed to compile a simple program that uses NetCDF-Fortran ! Could your
  NetCDF installation be broken?

  See "FailedCompile.txt" for more info.


-- Configuring done
-- Generating done
-- Build files have been written to: /local/ryantosca/GC/rundirs/partest_sp/build

CMake Warning at CMakeLists.txt:286 (message):
  Failed to compile a simple program that uses NetCDF-Fortran ! Could your
  NetCDF installation be broken?

The configuration completes and builds the Makefiles, but the try_compile.F90 program (which tests if you can write a netCDF file) dies with an error. It could be that this #ifdef block is not being applied properly:

#ifndef NO_OMP
    integer nthreads, tid, OMP_GET_THREAD_NUM

    write(*,*) 'About to start multiple threads'
    ! Try OpenMP
    !$OMP PARALLEL PRIVATE(nthreads, tid)
    TID = OMP_GET_THREAD_NUM()
    write(*,*) 'Hello from thread ', tid
    !$OMP END PARALLEL
#endif

A small bit of missing documentation...

The documentation page for HEMCO_DIagn.rc is missing a variable. In the numbered list of columns, "Dim" should be between "Hierarchy" and "Units".

In particular, I'd like to know if specifying "2" for a 3-D emission (e.g. aircraft) will provide the column sum of emissions in the diagnostic output, or just the first layer emission, or something else.

I really appreciate all the documentation that is there though!

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Confirm you have reviewed the following documentation

• Contributing guidelines](https://geos-chem.readthedocs.io/en/stable/help-and-reference/CONTRIBUTING.html)

New GCClassic feature or discussion

Intel has revealed that the icc/icpc/ifort compilers will be discontinued by late 2024 in favor of the newer icx/ifx LLVM compilers.

We will need to support both ifort and ifx compilers for a time, given that some users may not be able to convert right away. This will require updates to compilation options in CMakeLists.txt and CMakeScripts/ in this repository

Also we will need to benchmark with both ifort and ifx to make sure that the new compilers do not introduce any unexpected changes.

FASRC should have the Intel 2024 compilers and related libraries (MPI, netCDF, netCDF-Fortran, HDF5, etc) installed by March 2024 as part of the regular compiler update cadence. In the meantime I will leave this issue here as a reminder.