CAM Snapshots functionality

[David]

What version of the code are you using?
git describe:
release-cesm2.2.2-0-g779b0a3



Have you made any changes to files in the source tree?
I added a new machine directly to the cime config on the source tree.

Describe every step you took leading up to the problem:

N/A



If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.

N/A


Describe your problem or question:
I want to use the new snapshots functionality (the fields in phys_ctl_nl: cam_snapshot_after_num, cam_snapshot_before_num, cam_take_snapshot_after, cam_take_snapshot_before).

Would it be possible to provide an example of how to use it?

 

[peverley]

Hi David,

Here's some information on the CAM snapshot functionality.

• The cam_snapshot feature dumps the entire state/tend/pbuf/cnst arrays to netCDF files.
• The variables cam_snapshot_before_num and cam_snapshot_after_num are the output history file numbers (offset by 1, meaning setting this to cam_snapshot_before_num=7 will lead to the before snapshot being output on history volume h6).
• The cam_take_snapshot_before and cam_take_snapshot_after are usually set to the same routine to capture the variables before and after the named routine.
  • To find the snapshot name, look in your source code checkout in bld/namelist_files/namelist_definition.xml.
    • Inside this file, find the “cam_take_snapshot_before” definition. In this definition, it lists all possible routines which can have a snapshot file created around.
      • If your parameterization is there, that will be your cam_take_snapshot_before and _after values in your user_nl_cam
      • If it's not there, you can use the user_set option - i can explain that further if you'd like
• Make sure to avoid using tape number one (h0) for cam_snapshot_before_num and cam_snapshot_after_num
• Check your namelist for any extra “fincl” settings added by use cases, as those will add variables that can conflict with the snapshot output.
  • To check this, before you modify the user_nl_cam file, run ./case.setup, run ./preview_namelists and then look at the resulting atm_in file in the run directory. Look for finclX where X is your possible “before” and “after” numbers. Choose a number that is not used.
    • You most likely will see fincl1 which is why it is not an option.
• Set nhtfrq to 1 so that data is written out on every time step. Note that the nhtfrq and ndens variables are arrays based off of the “tape” number specified in cam_snapshot_before and cam_snapshot_after. (i.e. 6 = the sixth number in these two arrays)
• Finally, as cam_snapshot writes out all of state, pbuf and other variables at every time step, it is suggested that a limited number of time steps be made in a cam_snapshot run.
  • The run must be at least 2 time steps in order to work in subsequent steps. We recommend 3 to at most 9 time steps. (Note a 3 timestep run using a 2 degree FV grid can produce snapshot files with sizes over 4 Gb each).
  • To change the number of timesteps to 3 use ./xmlchange STOP_OPTION=nsteps and ./xmlchange STOP_N=3

Here's a sample user_nl_cam that will take a snapshot each timestep before and after gravity waves is run. The before snapshot will end up on the h5 file; the after snapshot will be on the h6 file):

cam_snapshot_before_num=6
cam_snapshot_after_num=7
cam_take_snapshot_before='gw_tend'
cam_take_snapshot_after='gw_tend'
nhtfrq = 0,0,0,0,0,1,1
ndens = 2,2,2,2,2,1,1

Hope that helps!
Courtney