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"lnd_import ERROR: Longwave down sent from the atmosphere model is negative or zero"

H

Han Lubin

Han Lubin
Member
Hello everyone,

I use release-cesm2.2.0 and try to get the outputs with 'GRAINC_TO_FOOD'. I run this case with CAM60+CLM%Bgc-Crop+initial file "b.e20.BHIST.f09_g17.20thC.297_01_v3.clm2.r.1979-01-01-00000.nc". Unfortunately, I encountered such error to stop the run.

"lnd_import ERROR: Longwave down sent from the atmosphere model is negative or zero"

I set another case with CAM60+CLM%Bgc-Crop+initial file "clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c181015.nc" for test, but also encountered the same error. Mr. Oleson suggest me to post this error to the CAM forum, so could you please give me some advice?

Exact steps are as follows.
Bash: 
./create_newcase --case maize_be20_irr_test --compset HIST_CAM60_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV --res f09_g17 --run-unsupported --compiler intel --mach bscca3

cd maize_be20_irr_test

./xmlchange NTASKS=-3
./xmlchange ROOTPE=192
./xmlchange NTHRDS=1

./xmlchange NTASKS_ATM=-3
./xmlchange ROOTPE_ATM=0
./xmlchange NTHRDS=1

./xmlchange NTASKS_IAC=1
./xmlchange ROOTPE_IAC=0
./xmlchange NTHRDS=1

./case.setup

vi user_nl_clm
hist_nhtfrq=0,0
hist_mfilt=1,12
hist_fincl2='GRAINC_TO_FOOD'
hist_dov2xy=.true.,.false.
irrigate=.true.
use_init_interp = .true.

./xmlchange RUN_TYPE=hybrid
./xmlchange RUN_REFDIR='/public1/home/sc93599/CESM/my_cesm_sandbox/inputdata/cesm2_init/b.e20.BHIST.f09_g17.20thC.297_01_v3/1979-01-01/b.e20.BHIST.f09_g17.20thC.297_01_v3.clm2.r.1979-01-01-00000.nc'
./xmlchange RUN_REFCASE=b.e20.BHIST.f09_g17.20thC.297_01_v3
./xmlchange RUN_REFDATE=1979-01-01
./xmlchange STOP_OPTION=nyears
./xmlchange STOP_N=1
./xmlchange RESUBMIT=35
./xmlchange RUN_STARTDATE=1979-01-01
./xmlchange DOUT_S=TRUE

./case.build

./check_input_data
./check_case

./case.submit

I attach the file with error message and look forward to your reply.
Thanks in advance!
 

Attachments

  • atm.log.3108057.221129-232400.txt
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  • cesm.log.3108057.221129-232400.txt
    272.2 KB · Views: 1
  • cpl.log.3108057.221129-232400.txt
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  • lnd.log.3108057.221129-232400.txt
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  • rof.log.3108057.221129-232400.txt
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O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
To add to this, I ran a simpler out of the box case on cheyenne than the one above and got the same error after nstep=37 according to the atmospheric log:

git describe
cesm2.2.0

cd cime/scripts
./create_newcase --case cesm220_FHISTClm50BgcCrop --compset HIST_CAM60_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV --res f09_g17 --run-unsupported
cd cesm220_FHISTClm50BgcCrop
./xmlchange STOP_OPTION=nmonths
./xmlchange STOP_N=1
./case.setup
qcmd -- ./case.build
./case.submit

Following a suggestion from @nusbaume , I output 'T' at each time step. As shown below for a grid cell near the equator, the lowest atmospheric layer temperature is decreasing until it drops abruptly to zero. I assume this is due to some instability in the atmospheric model, but I'm not sure what to suggest for a fix since this is basically an out of the box case.



Case and run directory are here:

/glade/work/oleson/release-cesm2.2.0/cime/scripts/cesm220_FHISTClm50BgcCrop
/glade/scratch/oleson/cesm220_FHISTClm50BgcCrop/run
 
H

Han Lubin

Han Lubin
Member
Hello Mr. Oleson,

After searching solutions in the forum, I realised there might be some problem for I set CAM but turned off sea ice and ocean module. So in order to confirm my suspicions, I used release-cesm2.2.0 to set a case with HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV and got the output "GRAINC_TO_FOOD" successfully. More details are as follows.

Bash: 
./create_newcase --case F_case --compset HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV --res f09_g17 --run-unsupported --compiler intel --mach bscca3

cd F_case

vi user_nl_clm
hist_nhtfrq=0,0
hist_mfilt=1,12
hist_fincl2='GRAINC_TO_FOOD'
hist_dov2xy=.true.,.false.
irrigate=.true.

./xmlchange RUN_TYPE=startup
./xmlchange STOP_OPTION=nyears
./xmlchange STOP_N=1
./xmlchange RESUBMIT=0
./xmlchange RUN_STARTDATE=1979-01-01
./xmlchange DOUT_S=TRUE

./case.setup
./case.build
./check_input_data
./check_data
./case.submit

I still have some doubts and would like to seek your advice.

(1) I want to compare the difference in outputs between CAM+CLM and DATM+CLM. If I set a CAM+CLM case with HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV, should I also set a DATM+CLM case with HIST_DATM%GSWP3_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV? Is it reasonable?

(2) The initial files used for CAM+CLM and DATM+CLM are clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c181015.nc and clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c190312.nc. I set RUN_STARTDATE=1970-01-01 and get crop yields in 1980-2010. Should I set both cases with same initial file "clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c181015.nc"?

(3) The resolution I used is f09_g17. Is there 0.5 degree surface and landuse timeseries datasets with 78 pfts available on the official website? hcru_hcru seems to work, but only for DATM+CLM.

Thanks in advance!
 
H

Han Lubin

Han Lubin
Member
One more question: Is it reasonable to get crop yields by setting HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV and HIST_DATM%GSWP3_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV?
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
Ok, sorry to the CAM people, I didn't notice that you were trying to use stub ice and ocean.
I'm moving this back to the CLM Forum.
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
(1) Use stub ice and ocean for the DATM+CLM case
(2) I would use the initial files provided, as they are suitable for CAM+CLM and DATM+CLM respectively. And you are allowing for 10 years of spinup.
(3) I don't think hcru_hcru datasets are actually available, you would have to create them, see this post for example:

bb.cgd.ucar.edu

Information required in the CLM5 Spinup procedure.

The compset and resolution you are using in release-cesm2.2.0: --compset HIST_CAM60_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV --res f09_g17 comes out of the box with START_DATE=1979-01-01 and this initial file...
bb.cgd.ucar.edu bb.cgd.ucar.edu

Regarding your last question, unless you are perturbing your simulations (i.e., making changes to the out of the box configurations), then you should be aware that there are a number of simulations that have already been run for which you could analyze crop yields. See:

CESM2 Experiments, Data & Diagnostic Output

Multi-decadal model runs of given component sets at the target resolution, followed by scientific review of the model output diagnostics
csegweb.cgd.ucar.edu csegweb.cgd.ucar.edu

Dataset: CLM land-only release

www.earthsystemgrid.org www.earthsystemgrid.org

You might also want to look at this paper if you haven't yet:

Lombardozzi, D.L., Y. Lu, P. Lawrence, D.M. Lawrence, S. Swenson, K.W. Oleson, W.R. Wieder, and E.A. Ainsworth, 2020: Simulating transient crop management in the Community Land Model version 5, J. Geophys. Res., doi: 10.1029/2019JG005529.
 
H

Han Lubin

Han Lubin
Member
Hello Mr.Oleson,

Many thanks for your patience and reply. By analyzing the differences in crop yields under CAM and DATM, I attempt to modify or add something in the model to achieve a perturbation of simulation. So I believe it would be better if I could run CESM2 by myself to get the results. Thanks again for your advice!
 
H

Han Lubin

Han Lubin
Member
Hello, Mr.Oleson,

Could you please share map_3x3min_MODIS-wCsp_to_0.47x0.63_nomask_aave_da_c170914.nc? I didn't find it in the /inputdata/lnd/clm2/mappingdata/maps/0.47x0.63/. Thanks a lot.
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
ftp://ftp.cgd.ucar.edu/pub/oleson/map_3x3min_MODIS-wCsp_to_0.47x0.63_nomask_aave_da_c170914.nc
 
H

Han Lubin

Han Lubin
Member
Hello Mr.Oleson,

(1) Could you share map_0.5x0.5_AVHRR_to_0.47x0.63_nomask_aave_da_c170914.nc? Many thanks.

(2) I created the 1850 surface file of 0.23x0.31 successfully, but when I ran the I-case with same resolution f02_g17 to get 1980-2010 crop yield, there are something wrong with file fatmlndfrc. The error is Model clm missing file fatmlndfrc = '$CESMROOT/inputdata/share/domains/UNSET'. Could I use domain.lnd.fv0.23x0.31_gx1v6.100517.nc or create a new domain file?
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
(1) I'd rather provide all of the files you need rather than file by file. Can you look at the namelist you are using and make sure this is now the only file you need?

(2) @erik , can you answer this?
 
H

Han Lubin

Han Lubin
Member
Sorry to bother you again. Actually, I couldn't find .namelist file after running ./mksurfdata.pl -res 0.47x0.63 -years 1850. I am also eager to provide all files I need, but the error message warned me that only one file doesn't exist every time. For example, mapping file for this resolution does NOT exist (/public1/home/sc93599/CESM/my_cesm_sandbox/inputdata/lnd/clm2/mappingdata/maps/0.47x0.63/map_0.5x0.5_AVHRR_to_0.47x0.63_nomask_aave_da_c170914.nc). So I have to disturb you for it file by file. I would like to seek your help to solve this problem and show all files I need. That will be more convenient for us. Many thanks.
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
You should be able to run that command with the "-debug" option to get the namelist.

./mksurfdata.pl -res 0.47x0.63 -years 1850 -debug

That should generate a namelist like this:

surfdata_0.47x0.63_hist_78pfts_CMIP6_simyr1850_c230102.namelist
 
H

Han Lubin

Han Lubin
Member
Hello Mr. Oleson,

Sorry for the long delay in responding to you. I only got mksurfdata_map.namelist, not surfdata_0.47x0.63_hist_78pfts_CMIP6_simyr1850_c230124.namelist after ran ./mksurfdata.pl -res 0.47x0.63 -years 1850 -debug on different machines.

It seems to set 10x15 as default resolution in the mksurfdata_map.namelist. I wonder if it is possible to change the default resolution to 0.47x0.63 to get the required namelist of input files. Is this possible? Or is there a better way?

The file mksurfdata_map.namelist seems to be already existed when I install CESM2.2.0, and I didn't get surfdata_0.47x0.63_hist_78pfts_CMIP6_simyr1850_c230124.namelist. When generating the fsurdat file with 0.23x0.31 resolution, I find it seems that I have to upload all the required input files to get surfdata_0.23x0.31_hist_78pfts_CMIP6_simyr1850_c221231.nc and surfdata_0.23x0.31_hist_78pfts_CMIP6_simyr1850_c221231.namelist
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
What error do you get when you run ./mksurfdata.pl -res 0.47x0.63 -years 1850 -debug?

I've attached the namelist I get when I run it.
 

Attachments

  • surfdata_0.47x0.63_hist_78pfts_CMIP6_simyr1850_c230124.namelist.txt
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H

Han Lubin

Han Lubin
Member
oleson said:
What error do you get when you run ./mksurfdata.pl -res 0.47x0.63 -years 1850 -debug?

I've attached the namelist I get when I run it.
Click to expand...
Hello Mr.Oleson,

Thank you so much for your kindness. It seems that the .namelist file corresponding to 0.47x0.63 resolution is not generated when I run ./mksurfdata.pl -res 0.47x0.63 -years 1850 -debug on differnet machines. It still reports an error about a specific file being missing. The following files I need are not found on the official website https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/mappingdata/maps/0.47x0.63/, could you please share them? Thanks.

map_0.5x0.5_AVHRR_to_0.47x0.63_nomask_aave_da_c170914.nc
map_10x10min_nomask_to_0.47x0.63_nomask_aave_da_c170914.nc
map_1km-merge-10min_HYDRO1K-merge-nomask_to_0.47x0.63_nomask_aave_da_c170914.nc
map_3x3min_GLOBE-Gardner_to_0.47x0.63_nomask_aave_da_c170914.nc
map_3x3min_LandScan2004_to_0.47x0.63_nomask_aave_da_c170914.nc
map_3x3min_USGS_to_0.47x0.63_nomask_aave_da_c170914.nc
map_5x5min_IGBP-GSDP_to_0.47x0.63_nomask_aave_da_c170914.nc
map_5x5min_ISRIC-WISE_to_0.47x0.63_nomask_aave_da_c170914.nc
map_5x5min_ORNL-Soil_to_0.47x0.63_nomask_aave_da_c170914.nc
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
I've placed all of the mapping files we have for that resolution on our ftp site under the subdirectory mapping_files:

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

Let me know if anything is missing.
 
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