f05 and timing related questions in CESM2 beta version, and vertical level

[Joanna Liu]

Hi,
I recently tried to run cesm2_3_alpha17c/cesm2_3_alpha17d on a school server (Svante in MIT) and ran into the following problem:
1) I can't run FCnudge's f05_f05_mg17 grid resolution properly in CESM2.3, but it works fine in CESM2.2 version.CESM2.3 reports the following error after submitting the job:
vim ./run/cesm.log.224785.240424-003449

ERROR: surfdata_domain/ldomain lon/lat mismatch error 0.000000000000000E+000
0.117493472584783
ENDRUN:
ERROR: ERROR in surfrdMod.F90 at line 172

PS: the error report remains when I change to other compsets (any I or F compset).
2) CESM2.3 has no timing information on the Svante server, whereas CESM2.2 does.
After I run FCnudge f09_f09_mg17 normally, there is no timing output in the ./run/timing/. folder (even nothing in checkpoints), and no timing folder is generated in the case directory. I confirmed that the default setting of "CHECK_TIMING"=true in env_run.xml.

[zehui@fs03 FCnudged_GC-t2.1]$ ls ./run/timing/
checkpoints
[zehui@fs03 FCnudged_GC-t2.1]$ ls ./run/timing/checkpoints/
[zehui@fs03 FCnudged_GC-t2.1]$

I'm not sure if it has anything to do with the server compilation settings (config_machines.xml, config_batch.xml and config_compiler.xml), but I made samilar changes to the CESM2.3 and CESM2.2 on Svante.
3) Where can I see the vertical layer settings supported by the mode? I would like to add layers near ground level.
Looking forward to your answers!
Best, Zehui

 

[dbailey]

This sounds like some missing data files. I will move this to the CLM forum.

 

[oleson]

We don't have any answers for 2) and 3) in this forum. You could try the infrastructure/porting forum for 2), and the CAM forum for 3) (I assume you are talking about adding layers in the atmospheric model).
Regarding 1), I tried reproducing this with cesm2_3_alpha17d:

./create_newcase --case FCnudged_cesm23a17d_f05f05mg17_hist --compset FCnudged --res f05_f05_mg17 --run-unsupported

but got this error when I tried to generate the namelists:

out=CAM build-namelist - ERROR: No default value found for ncdata

So I couldn't reproduce your error. That error is pointing to a mismatch in latitude values between that given in the surface dataset and the domain (I think this would be the mesh in this version of the code) file.

 

[Joanna Liu]

We don't have any answers for 2) and 3) in this forum. You could try the infrastructure/porting forum for 2), and the CAM forum for 3) (I assume you are talking about adding layers in the atmospheric model).
Regarding 1), I tried reproducing this with cesm2_3_alpha17d:

./create_newcase --case FCnudged_cesm23a17d_f05f05mg17_hist --compset FCnudged --res f05_f05_mg17 --run-unsupported

but got this error when I tried to generate the namelists:

out=CAM build-namelist - ERROR: No default value found for ncdata

So I couldn't reproduce your error. That error is pointing to a mismatch in latitude values between that given in the surface dataset and the domain (I think this would be the mesh in this version of the code) file.

Hi Keith,
You can change to test IHistClm50Bgc or add ncdata pathway in user_nl_cam:
ncdata = .../camchem_2010-01-01_0.47x0.63_56L_c180613.nc' (It can be downloded in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/inic/fv/), in this case, you also need to change nlev=56;
I agree with you on that, but I checked the ./run/nuopc.runconfig(related seeting see below) and it looks fine.

mesh_atm = /net/fs01/data/cesm2/inputdata/share/meshes/fv0.47x0.63_141008_ESMFmesh.nc
mesh_glc = UNSET
mesh_ice = /net/fs01/data/cesm2/inputdata/share/meshes/fv0.47x0.63_141008_ESMFmesh.nc
mesh_lnd = /net/fs01/data/cesm2/inputdata/share/meshes/fv0.47x0.63_141008_ESMFmesh.nc
mesh_mask = /net/fs01/data/cesm2/inputdata/share/meshes/gx1v7_151008_ESMFmesh.nc
mesh_ocn = /net/fs01/data/cesm2/inputdata/share/meshes/fv0.47x0.63_141008_ESMFmesh.nc

Best, Zehui

 

[oleson]

Thanks for that. I tried this:

./create_newcase --case clm50_cesm23a17d_f05f05mg17_hist --compset IHistClm50Bgc --res f05_f05_mg17 --run-unsupported --project P93300641

but got this error:

ERROR: Command /glade/work/oleson/cesm2_3_alpha17d/components/clm/bld/build-namelist failed rc=255
out=
err=ERROR : CLM build-namelist::CLMBuildNamelist::add_default() : No default value found for flanduse_timeseries.
Are defaults provided for this resolution and land mask?

I'm just trying to get to the point where I can reproduce the error you get.

 

[Joanna Liu]

Thanks for that. I tried this:

./create_newcase --case clm50_cesm23a17d_f05f05mg17_hist --compset IHistClm50Bgc --res f05_f05_mg17 --run-unsupported --project P93300641

but got this error:

ERROR: Command /glade/work/oleson/cesm2_3_alpha17d/components/clm/bld/build-namelist failed rc=255
out=
err=ERROR : CLM build-namelist::CLMBuildNamelist::add_default() : No default value found for flanduse_timeseries.
Are defaults provided for this resolution and land mask?

I'm just trying to get to the point where I can reproduce the error you get.

Hi Keith, I forget mentiong you that you should also add flanduse in user_nl_clm:
fsurdat = '../surfdata_0.47x0.63_16pfts_Irrig_CMIP6_simyr1850_c170919.nc'
flanduse_timeseries = '../landuse.timeseries_0.47x0.63_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c171025.nc'

 

[oleson]

I replicated your error. I tried another mesh file I found:

fv0.47x0.63_141008_FIX102722_polemod_ESMFMesh.nc

and that got the model past your error.
However, I got another error:

ncd_inqvid: variable PCT_OCEAN is not on dataset
ENDRUN:
ERROR:
ERROR: PCT_OCEAN NOT on surfdata file but required when running ctsm5.2 or new
er; you are advised to generate a new surfdata file using the mksurfdata_esmf
tool ERROR in surfrdMod.F90 at line 421

and I realize now that the datasets you are using are not compatible with the newer code you are using.
Datasets are now created with the mksurfdata_esmf tool and are at:

inputdata/lnd/clm2/surfdata_esmf/ctsm5.2.0

However, 0.47x0.63 is not a resolution we have created datasets for so you'd have to create them yourself. Or switch to a resolution that is close to yours that we do have datasets for: 360x720cru

 

[Joanna Liu]

I replicated your error. I tried another mesh file I found:

fv0.47x0.63_141008_FIX102722_polemod_ESMFMesh.nc

and that got the model past your error.
However, I got another error:

ncd_inqvid: variable PCT_OCEAN is not on dataset
ENDRUN:
ERROR:
ERROR: PCT_OCEAN NOT on surfdata file but required when running ctsm5.2 or new
er; you are advised to generate a new surfdata file using the mksurfdata_esmf
tool ERROR in surfrdMod.F90 at line 421

and I realize now that the datasets you are using are not compatible with the newer code you are using.
Datasets are now created with the mksurfdata_esmf tool and are at:

inputdata/lnd/clm2/surfdata_esmf/ctsm5.2.0

However, 0.47x0.63 is not a resolution we have created datasets for so you'd have to create them yourself. Or switch to a resolution that is close to yours that we do have datasets for: 360x720cru

Hi Keith, Many thanks! How can I get fv0.47x0.63_141008_FIX102722_polemod_ESMFMesh.nc (It's not in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/share/meshes/ and https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/coords/ )?
Do you know where there is a tutorial on how to use mksurfdata_esmf tool? Also, what is the difference between this tool and the THESIS-CLM-Land-Use tool? I'm new to CLM and would really appreciate your help!

 

[oleson]

I've put it on our ftp site:

ftp://ftp.cgd.ucar.edu/pub/oleson

The mksurfdata_esmf tool creates surface/landuse timeseries files using "raw" high resolution input datasets, while the Land Use tool creates the raw datasets. The mksurdata_esmf tool would be here:

components/clm/tools/mksurfdata_esmf/

There is a README with instructions.