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Edit ~/.bashrc to include following lines (**updated June 2023 for rocky8**):

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
export I_MPI_HYDRA_IFACE="ib0"

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)

If you need POP2 (e.g. compset B), enter cpan, key in: install Switch, then exit cpan.

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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** Cluster update May 2024: CESM1 had compilation issues. If you need to run CESM1, please email sweidman at g dot harvard dot edu for instructions (until I update this wiki page). **

**Rocky8 update**

The netcdf software is now in two locations (netcdf-c and netcdf-fortran). CESM will break unless you put them in the same folder. One option is to copy the files for netcdf-c and netcdf-fortran in /n/sw/ into one folder in your home directory and combine the files in bin, lib, and include into the same folder. You can also copy

/n/home04/sweidman/netcdffolder into your home directory.

Then, edit your .bashrc file to include the lines:

export NETCDF_HOME='/n/home04/sweidman/netcdffolder/' (replace with the location of your combined netcdf folder)

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)

2. Edit create_new_build.sh

Edit ~/create_new_build.sh # look at TODO’s. For details, see "about create_new_build.sh".

Partition should default to be huce_cascade or huce_ice. (huce_amd was decomissioned, 2/3/2020.) For more about HUCE's partitions, see Harvard cluster job queues.

3. (Advanced user): prepare namelist and SourceMods

If you already know what namelist (user_nl_*) or SourceMods you are going to use, cd to the directory with user_nl_* and/or SourceMods. create_new_build.sh

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Edit ~/should be run in this directory.

4. Run create_new_build.sh

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(~12 mins)

Make sure you have modules loaded as step 1.

~/create_new_build.sh ".

Partition should default to be huce_intel. (huce_amd was decomissioned, 2/3/2020.) For more about HUCE's partitions, see Harvard cluster job queues.

3. (Advanced user): prepare namelist and SourceMods

If you already know what namelist (user_nl_*) or SourceMods you are going to use, cd to the directory with user_nl_* and/or SourceMods. create_new_build.sh should be run in this directory.

4. Run create_new_build.sh (~12 mins)

Make sure you have modules loaded as step 1.

~/create_new_build.sh CASENAME RESOLUTION COMPSET NCORES

E.g. ~/create_new_build.sh c1test f19_f19 F_2000 64

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CASENAME RESOLUTION COMPSET NCORES

E.g. ~/create_new_build.sh c1test f19_f19 F_2000 64

5. Final check

**Update Rocky 8**

Open your $case.run file and comment out the line that looks like "srun --mpi=pmi2 --ntasks=64 --cpu_bind=sockets --cpu_bind=verbose --kill-on-bad-exit $EXEROOT/cesm.exe >&! ccsm.log.$LID"

Instead, uncomment the line that looks like "mpirun -np 64 $EXEROOT/cesm.exe >&! ccsm.log.$LID" just above it.

** **

You can modify SourceMods here, but if you do so, you will have to do $CASE.clean_build and rebuild the model with

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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.