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
andcam_snapshot_after_num
are the output file numbers (offset by 1 as they are in CAM). - The
cam_take_snapshot_before
andcam_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 youruser_nl_cam
- If it's not there, you'll add
user_set
snapshot calls tophyspkg.F90
in the following way:
- If your parameterization is there, that will be your
- 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.
- To find the snapshot name, look in your source code checkout in
- The variables
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, &
flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, 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_tphysbc(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf, &
flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, det_s, det_ice, 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, &
flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, 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, &
flx_heat, cmfmc, cmfcme, zdu, rliq, rice, dlf, dlf2, rliq2, 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
andcam_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 resultingatm_in
file in the run directory. Look forfinclX
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.
- To check this, before you modify the
- 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
andcam_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