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CESM2 with SPCAM (Jun 2018 or later): instructions to download yourself
CESM1.1.1 with SPCAM (Feb 2013) is downloaded in ~pchan/spcam2_0-cesm1_1_1/
CESM1.2.2 (Jun 2014) is downloaded in /n/holylfsholystore01/INTERNAL_REPOS/CLIMATE_MODELS/cesm1_2_2/
SPCAM3.5.0 (Feb 2009) is downloaded in ~kuang/Model/origSPCAM/

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Register in http://www.cesm.ucar.edu/models/register/register.html

Edit ~/.bashrc to include following lines (for If you do not yet have "huce file access", request it from RC. If you see groups=...10047(huce)... when you run id, then you already have the access.

Edit ~/.bashrc to include following lines (May 2018, also known as CentOS7):

module load intel/17.0.4-fasrc01 impi/2017.2.174-fasrc01 netcdf/4.1.3-fasrc02

module load perl-modules/5.10.1-fasrc13

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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 after May 2018 (the CentOS7 update)

2. Edit create_new_build.sh

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Partition is default to be huce_amd, which works in most of the case. For more about HUCE(huce_amd decomissioned, 2/3/2020) For more about HUCE's partitions, see Harvard cluster job queues.

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4. Run create_new_build.sh (~12 mins)

Make sure you are not in nx nodes (not in rcnx01 or holynx01).Make sure you have modules loaded as step 1.

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echo -n `date +%FT%T` TEST-ONLY-; sbatch --test-only ${CASE}.run

6. Submit the model

Make sure you are not in nx nodes (not in rcnx01 or holynx01).Make sure you have modules loaded as step 1.

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OUTPUT is the path of large file storage where all Build/Run and Short Term Archive will be located. Default is kuanglfs, which works only for Kuang's group. "/n/regal$SCRATCH/`id -gn`/$USER/cesm_output/${CASE}" will work well if you want to use regal$SCRATCH.

Partition is default to be huce_amd. To use huce_intel, uncomment the 3rd-4th lines.

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The above figure is adapted from http://www.cesm.ucar.edu/events/tutorials/2016/practical1-bertini.pdf p.48.

CESM1.1.1 (with SPCAM) is downloaded in ~pchan/spcam2_0-cesm1_1_1/

CESM1.2.2 is downloaded in ~leiw/cesm1_2_2/

There is no need There is no need to copy the CESM download folder. (for CESM1, which someone already downloaded for you)

The inputdata directory is located in /n/holystore01/kuanglfs/pchan/CAM_input. Packard INTERNAL_REPOS/CLIMATE_MODELS/cesm_2_1/inputdata. Seb has opened write access so everyone should be able to download inputdata when needed. Please only download data that you need, as the whole data set is >20T in size.

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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. ./xmlchange SSTICE_DATA_FILENAME=/path/to/new_sst.nc

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

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1. grep -Ev '^\s*$|^\s*!' user_nl_*
   can display all non-empty uncommented lines in user_nl_*

2. ./preview_namelists can update namelists (and input_data_list)

3. grep '' Buildconf/*.input_data_list
   can list out all input data.
   

4. DIN_LOC_ROOT=`./xmlquery -valonly -silent DIN_LOC_ROOT`
   ./check_input_data -inputdata $DIN_LOC_ROOT -check
   can check input data

5. Section &seq_infodata_inparm in drv_in can be checked in $RUNDIR/cpl.log.$LID

6. Always compare default namelist and new namelist

7. 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.

8. Never edit namelist in CaseDocs/ or Buildconf/, they are overwritten every time and NOT read by Fortran program.

References:

http://jules-lsm.github.io/vn4.2/namelists/intro.html

http://www.lahey.com/docs/lfpro73help/f95arnameliststmt.htm

http://www.codezone.co.uk/fortran/namelist.shtml

http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/c1128.html

http://www.cesm.ucar.edu/events/tutorials/2016/practical4-hannay.pdf

Compset

Compset is a short form for "component set", which specifies component models, forcing scenarios and physics options for those models.

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https://docs.google.com/document/d/1pev8G4OmJGacKhtK8Bh3t_B4yh4DFc_pvGc6I6BtWl8/edit?usp=sharing

Bugs and technical notes

Technical notes on how the model is ported to Harvard cluster: https://github.com/PackardChan/spcam2_0-cesm1_1_1-port

Starting CESM1.2.2, cesm_postrun_setup is problematic.

CESM1.2.2 obtained from NCAR is missing a few directories since google apps no longer works.  If you are running in to this problem:

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Unconfirmed: aquaplanet - src.aquap do not take effect.

References

http://www.cesm.ucar.edu/events/tutorials/2016/coursework.html (look for practical sessions)

spcam-workshop-jul2013.pdf

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/n/holylfs & /n/kuanglfs are near end of life. Both disks store inputdata. Please transition to /n/holystore01/INTERNAL_REPOS/CLIMATE_MODELS/cesm_2_1.
For CESM1, the command is ./xmlchange DIN_LOC_ROOT="/n/holystore01/INTERNAL_REPOS/CLIMATE_MODELS/cesm_2_1/inputdata"
For CESM2 (who follows our GoogleDoc instructions), the command is ln -sfT /n/holystore01/INTERNAL_REPOS/CLIMATE_MODELS/cesm_2_1/inputdata $CESMDATAROOT/inputdata
A temporary link has been created pointing from /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS to /n/holystore01/INTERNAL_REPOS/CLIMATE_MODELS. This temporary link will be removed when /n/holylfs decommission. Please run the above commands before the decommission.
The new place is limited to huce group. Updates (if any) will be posted here.
(last update: 7/30/2020)

Technical notes on how the model is ported to Harvard cluster: https://github.com/PackardChan/spcam2_0-cesm1_1_1-port

Starting CESM1.2.2, cesm_postrun_setup is problematic.

CESM1.2.2 obtained from NCAR is missing a few directories since google apps no longer works.  If you are running in to this problem:

1. Missing pio directory in /models/utils/pio
Solution:
svn checkout https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio ./cesm1_2_2/models/utils/pio

2. Missing genf90.pl file
Solution:
svn checkout https://github.com/PARALLELIO/genf90/tags/genf90_140121 ./cesm1_2_2/tools/cprnc/genf90

Unconfirmed: aquaplanet - src.aquap do not take effect.

References

http://www.cesm.ucar.edu/events/tutorials/2016/coursework.html (look for practical sessions)

spcam-workshop-jul2013.pdf