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module load intel/23.0.0-fasrc01 intelmpi/2021.8.0-fasrc01
module load netcdf-fortran/4.6.0-fasrc03
module load netcdf-c/4.9.2-fasrc02
module load ncf/1.0.0-fasrc01 perl_modules/5.10.1-ncf
export UCX_TLS=ib

If you never use cpan (package manager for Perl) before, after loading perl-modules, enter cpan, respond: yes, blank, yes.., then exit cpan. (takes several minutes)

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export NETCDF=${NETCDF_HOME}

** **

cp /n/home05/pchan/spcam2_0-cesm1_1_1/scripts/create_new_build.sh ~/ #please copy a newer version after May 2018 (the CentOS7 update)

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How namelists are built in CESM?

$RUNDIR/*_in are namelists directly read by Fortran program. They are recommended NOT to be edited directly, but instead, indirectly through user_nl_* and env_*.xml. The processes of indirectly creating namelists are as follows:

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preview_namelists
- calls Buildconf/$comp.buildnml.csh
- copies *_in to CaseDocs/

Buildconf/$comp.buildnml.csh
- call $CCSMROOT/models/**/bld/build-namelist, which create namelist Buildconf/*conf/*_in
- copy *_in to $RUNDIR (overwrite)

build-namelist
- takes “infile” from user_nl_*
- writes out Buildconf/*conf/*_in and Buildconf/*.input_data_list

When job is submitted:

$CASE.submit submits $CASE.run
$CASE.run calls preview_namelists
Same things happen again.

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How to modify namelists in CESM?

If possible, always use user_nl_* and env_*.xml.

E.g. Change the path to an input data file: ./xmlchange SSTICE_DATA_FILENAME=/path/to/new_sst.nc (this can also be listed as a line in user_nl_cam).

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If impossible, manually change $RUNDIR/*_in, and disable copying (overwriting) in Buildconf/$comp.buildnml.csh

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grep -Ev '^\s*$|^\s*!' user_nl_*
can display all non-empty uncommented lines in user_nl_*
./preview_namelists can update namelists (and input_data_list)
grep '' Buildconf/*.input_data_list
can list out all input data.
DIN_LOC_ROOT=`./xmlquery -valonly -silent DIN_LOC_ROOT`
./check_input_data -inputdata $DIN_LOC_ROOT -check
can check input data
Section &seq_infodata_inparm in drv_in can be checked in $RUNDIR/cpl.log.$LID
Always compare default namelist and new namelist
Sometimes, user_nl_* are not interpreted literally. E.g. specifying prescribed_ozone_file could remove lines for prescribed_ozone_cycle_yr, prescribed_ozone_name, etc.
Never edit namelist in CaseDocs/ or Buildconf/, they are overwritten every time and NOT read by Fortran program.