Issues initializing sea ice biogeochemistry (z_bgc) in CICE 6.5 within CESM 2.3 alpha17f

[jiaqii123]

What version of the code are you using?
cesm2_3_alpha17f

Have you made any changes to files in the source tree?
no

Describe every step you took leading up to the problem:
module load cesm/2.3alpha17f_nuopc
export PROJECT=cesm2.3_nuopc
export CASE_ROOT=$HOME/cesm2.3alpha_cases/cesm2.3alpha_cases19
export OUTPUT_ROOT=$HOME/cesm2.3alpha_output/cesm2.3alpha_cases19
cd $CESM_ROOT/cime/scripts
./create_newcase --case $CASE_ROOT --compset GIAF_JRA --res TL319_g17 --driver nuopc --mach lenovo --compiler gnu --mpilib openmpi --run-unsupported
cd /share/home/cesm2.3alpha_cases/cesm2.3alpha_cases19
./xmlchange OCN_TRACER_MODULES=ecosys
./xmlchange CIME_OUTPUT_ROOT=$OUTPUT_ROOT
./xmlchange PROJECT=$PROJECT
./xmlchange JOB_QUEUE=$JOB_QUEUE
./xmlchange DOUT_S_ROOT=$OUTPUT_ROOT/archive
./xmlchange STOP_OPTION=nmonths,STOP_N=1
./xmlchange JOB_WALLCLOCK_TIME=12:00:00
./xmlchange NTASKS_ATM=10,NTASKS_CPL=10,NTASKS_OCN=220,NTASKS_ICE=10,NTASKS_LND=10,NTASKS_ROF=10,NTASKS_WAV=10,NTASKS_GLC=10,ROOTPE_OCN=20,ROOTPE_ICE=10
./case.setup
vi user_nl_cice
./case.build
./case.submit


Describe your problem or question:

Hello everyone,

I am currently trying to use CICE to couple with other components in CESM. I have a few questions regarding the initialization of the full sea ice biogeochemistry (z_bgc) in CICE 6.5.

My main questions are:

1. How can I properly initialize sea ice biogeochemistry (z_bgc) in CESM2_3_alpha17f?
2. Are there existing ice initial biogeochemical forcing files available for CICE 6.5?
3. Why do some variables documented in namelist_definition_cice.xml not get recognized when set in user_nl_cice?

What I have tried:

After setting up my case, I modified user_nl_cice and set the following variables to .true. (full configuration is attached in the file):

tr_brine = .true.
restart_hbrine = .true.
z_tracers = .true.
solve_zbgc = .true.
bgc_flux_type = 'Jin2006'
restore_bgc = .true.
restart_bgc = .true.
solve_zsal = .true.
restart_zsal = .true.

The problem:

I cannot run the case successfully. The error from cesm.log is attached below:

2026-05-18 10:45:52: model execution error
ERROR: Command: 'mpirun -np 240 --tag-output .../cesm.exe >> cesm.log.$LID 2>&1' failed with error '' from dir '.../run'

2026-05-18 10:45:52: case.run error
ERROR: RUN FAIL: Command 'mpirun ...' failed
See log file for details: .../cesm.log.13480.260518-104544
Additional observation:

When I tried to set dEdd_algae = .true. in user_nl_cice, I got the following error:

ERROR: Variable 'dedd_algae' from file 'user_nl_cice' is not in the namelist definition.

However, I did find this variable listed in namelist_definition_cice.xml. This makes me wonder why it is not being recognized. The same issue also occurs for tr_bgc_nit and several other variables.

Summary of my questions:

• What is the correct way to initialize full sea ice BGC (z_bgc) in CESM2_3_alpha17f?
• Are there default BGC initial forcing files for CICE 6.5, and if so, where can I find them?
• Why do some variables from namelist_definition_cice.xml (e.g., dedd_algae) cause "variable not in namelist definition" errors in user_nl_cice?

Any guidance or suggestions would be greatly appreciated. Thanks in advance!

 

[dbailey]

This tag is not supported and we have never run the ZBGC in CESM. I would try starting with the standalone CICE to see if you can get the ZBGC working there.

 

[jiaqii123]

This tag is not supported and we have never run the ZBGC in CESM. I would try starting with the standalone CICE to see if you can get the ZBGC working there.

Thank you for your reply! I was able to successfully initialize z_bgc in standalone CICE. However, when I tried to do the same in CESM (setting 'tr_brine', 'z_tracers', 'solve_zbgc', and 'tr_bgc_Nit' to true in 'user_nl_cice'), I encountered the following error:

ERROR: Variable 'tr_bgc_nit' from file 'user_nl_cice' is not in the namelist definition.

I have verified that 'tr_bgc_Nit' does exist in '/components/cice/cime_config/namelist_definition_cice.xml'. This suggests the issue may not be with CICE itself, but rather with how CIME reads or validates the namelist.

I noticed that standalone CICE directly uses 'ice_in', whereas CICE in CESM relies on additional files to read user-modified variables from 'user_nl_cice' and generate the namelist, including:
/components/cice/cime_config/buildnml
/components/cice/cime_config/namelist_definition_cice.xml
/cime/CIME/nmlgen.py

I have confirmed that 'nmlgen.py' does not skip any groups. I also tried copying the default 'namelist_definition_cice.xml' to 'SourceMods/src.cice', but the problem persists.

Could you please offer some suggestions on how to resolve this? Thank you again for your help!

 

[dbailey]

You can copy the namelist_definition_cice.xml file to SourceMods/src.cice and add these in your case.