6 - Create snapshots of CAM

Configure and set-up CAM snapshot

Make a normal CAM (not CAM-SIMA) run using cam_snapshot to capture before and after files using a compset which exercises the parameterization being converted.

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 file numbers (offset by 1 as they are in CAM).
- The cam_take_snapshot_before and cam_take_snapshot_after are usually set to the same parameterization to capture the variables before and after the named parameterization.
  - 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 parameterizations 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'll add user_set snapshot calls to physpkg.F90 in the following way:

For tphysbc in physics/cam7/physpkg.F90:

if (trim(cam_take_snapshot_before) == "user_set") then
   call cam_snapshot_all_outfld_tphysbc(cam_snapshot_before_num, state, tend, cam_in, cam_out, pbuf, &
       cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, net_flx)
end if

<call to parameterization run phase>

if ( (trim(cam_take_snapshot_after) == "user_set") .and. &
     (trim(cam_take_snapshot_before) == trim(cam_take_snapshot_after))) then
        call cam_snapshot_ptend_outfld(ptend, lchnk)
end if

<call to physics_update and/or ptend outfld calls>

if (trim(cam_take_snapshot_after) == "user_set") then
   call cam_snapshot_all_outfld_tphysbc(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf, &
       cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, net_flx)
end if

For tphysac:

if (trim(cam_take_snapshot_before) == "user_set") then
   call cam_snapshot_all_outfld_tphysac(cam_snapshot_before_num, state, tend, cam_in, cam_out, pbuf, &
           fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
end if

<call to parameterization run phase>

if ( (trim(cam_take_snapshot_after) == "user_set") .and.      &
     (trim(cam_take_snapshot_before) == trim(cam_take_snapshot_after))) then
   call cam_snapshot_ptend_outfld(ptend, lchnk)
end if

<call to physics_update and/or ptend outfld calls>

if (trim(cam_take_snapshot_after) == "user_set") then
   call cam_snapshot_all_outfld_tphysac(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf, &
            fh2o, surfric, obklen, flx_heat, cmfmc, dlf, det_s, det_ice, net_flx)
end if

Note

The above calls may vary if your physpkg.F90 exists in a different directory within $CAM/src/physics (not cam7)

To enable cam_snapshot, add the following to your user_nl_cam file:

cam_snapshot_before_num=6
cam_snapshot_after_num=7
cam_take_snapshot_before='<parameterization>_tend' ! or 'user_set'
cam_take_snapshot_after='<parameterization>_tend' ! or 'user_set'
nhtfrq = 0,0,0,0,0,1,1
ndens = 2,2,2,2,2,1,1

The “before” file will be used for input for testing; “after” file will be used for comparisons
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

Warning

With short NUOPC runs, you may need to change ROF_NCPL and/or GLC_NCPL to the same size at ATM_NCPL to get them to run properly (./xmlchange ROF_NCPL=\$ATM_NCPL and ./xmlchange GLC_NCPL=\$ATM_NCPL)

Create CAM snapshots

Run CAM normally with

./case.setup
./case.build
./case.submit

Upon a successful completion, you will see a cam.h5i.xxx.nc and cam.h6i.xxx.nc in your run directory (assuming you used before and after of 6 and 7)

Save snapshot files

The generated snapshot files should be saved on derecho here:

/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots

with the naming convention cam_<resolution>_<parameterization>_snapshot_derecho_<compiler>_before_cYYYYMMDD.nc and cam_<resolution>_<parameterization>_snapshot_derecho_<compiler>_after_cYYYYMMDD.nc

Be sure to run

chmod u=rw,g=r,o=r <snapshot_files>

or

chmod 644 <snapshot_files>

on every file you copy over so that it is readable by everyone

On izumi, save your converted snapshot files in:

/project/amp02/cam_snapshot_files/<parameterization>

CAM snapshot run tips

Try to use the lowest resolution grid possible in order to keep the snapshot file size small (e.g. ne3pg3_ne3pg3_mg37).
We generally recommend running with debug flags on (./xmlchange DEBUG=True), as this way errors that can occur when you bring the CCPP-ized code back into CAM are easier to catch.
- However, if you decide not to, then do make sure that all of your other CAM runs also have debug flags off, as otherwise you can get differences in the results that are solely due to compiler settings, and not your code changes.
You should generate at least one set of snapshot files using GNU on derecho with DEBUG=TRUE, as these will be saved for use in the CAM-SIMA physics testbed to prevent unexpected answer changes.

Once you have created your snapshot files, proceed to 7 - Run CAM-SIMA