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@axel-lauer axel-lauer commented Jan 18, 2023

Description

This technical PR increases the flexibility of the cloud diagnostics stored in diag_script/clouds to allow for:

  • analyzing single model datasets, i.e. dropping the requirement for having multiple datasets and
  • splitting a variable in a recipe into two sections (e.g. "clt" and "clt_icon") in case two different preprocessors are required. Two different preprocessors are required e.g. for ICON data (unstructured data) as the same regridder cannot be applied (yet) to data on regular grids such as observations.

Test recipes

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New or updated recipe/diagnostic

@axel-lauer axel-lauer requested a review from schlunma January 18, 2023 13:58
@axel-lauer axel-lauer changed the title Increase flexibility of cloud diagnostics Improve flexibility of cloud diagnostics Jan 19, 2023
@axel-lauer axel-lauer marked this pull request as ready for review January 19, 2023 05:40
@schlunma
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Thanks for expanding your diagnostics @axel-lauer!

I tested both recipes, both ran successfully! 🎉 However, there were a couple of warnings from the NCL scripts:

  1. recipe_test_cmip.yml:
WARNING [2341674] NCL: warning:Dimension (0) has not been defined                                                                                                                                                                                                         
WARNING [2341674] There were warnings during the execution of NCL script clouds/clouds.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_cmip_20230120_083422/run/clouds_clim_cmip5/avgclt/log.txt

WARNING [2341674] NCL: INFO    warning: cannot calculate t-test for dataset ERA5; need at least 3 years, dataset length = 2 years; disabling t-test                                                                                                                       
WARNING [2341674] There were warnings during the execution of NCL script clouds/clouds_zonal.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_cmip_20230120_083422/run/clw_cmip5/zonal/log.txt

WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
...
WARNING [2341674] NCL: warning:ContourPlotInitialize: no valid values in scalar field; ContourPlot not possible:[errno=1101]                                                                                                                                              
WARNING [2341674] NCL: ^Mwarning:ContourPlotSetValues: Data values out of range of levels set by EXPLICITLEVELS mode                                                                                                                                                      
WARNING [2341674] NCL: ^Mwarning:ContourPlotInitialize: no valid values in scalar field; ContourPlot not possible:[errno=1101]                                                                                                                                            
WARNING [2341674] NCL: ^Mwarning:ContourPlotInitialize: no valid values in scalar field; ContourPlot not possible:[errno=1101]                                                                                                                                            
WARNING [2341674] NCL: ^Mwarning:ContourPlotSetValues: Data values out of range of levels set by EXPLICITLEVELS mode                                                                                                                                                      
WARNING [2341674] There were warnings during the execution of NCL script clouds/clouds_dyn_matrix.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_cmip_20230120_083422/run/clouds_dynmatrices_cmip5_ocean/dynclt/log.txt

WARNING [2341674] NCL: warning:TransformDataPolyline, not enough points for a line                                                                                                                                                                                        
WARNING [2341674] There were warnings during the execution of NCL script clouds/clouds_pdf.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_cmip_20230120_083422/run/pdf_clt_djf_cmip5/southernocean/log.txt
  1. recipe_test_single.yml:
WARNING [2339113] NCL: warning:TransformDataPolyline, not enough points for a line                                                                                                                                                                                        
WARNING [2339113] There were warnings during the execution of NCL script clouds/clouds_pdf.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_single_20230120_083154/run/pdf_clt_djf_cmip5/southernocean/log.txt

WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
WARNING [2339109] NCL: warning:avg: Entire input array contains missing values, can't compute average
...
WARNING [2339109] There were warnings during the execution of NCL script clouds/clouds_dyn_matrix.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_single_20230120_083154/run/clouds_dynmatrices_cmip5_ocean/dynclt/log.txt

WARNING [2339107] NCL: warning:Dimension (0) has not been defined                                                                                                                                                                                                         
WARNING [2339107] There were warnings during the execution of NCL script clouds/clouds.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_single_20230120_083154/run/clouds_clim_cmip5/avgclt/log.txt    

WARNING [2339101] NCL: INFO    warning: cannot calculate t-test for dataset ERA5; need at least 3 years, dataset length = 2 years; disabling t-test                                                                                                                       
WARNING [2339101] There were warnings during the execution of NCL script clouds/clouds_zonal.ncl, for details, see the log /home/b/b309141/scratch/esmvaltool_output/recipe_test_single_20230120_083154/run/cl_cmip5/zonal/log.txt
  1. In addition, all dyn_matrix plots that involve ICON are empty, e.g.,

grafik

  1. I am currently also running other cloud recipes to test if anything is broken. So far I found a problem with recipe_clouds_ipcc.yml in the diagnostic clouds_ipcc_lwcre/clim:
  6 INFO    Loading settings from /home/b/b309141/scratch/esmvaltool_output/recipe_clouds_ipcc_20230120_084545/run/clouds_ipcc_lwcre/clim/settings.ncl                                                                                                                        
  7 INFO    Loading input data description from /home/b/b309141/scratch/esmvaltool_output/recipe_clouds_ipcc_20230120_084545/preproc/clouds_ipcc_lwcre/lwcre/lwcre_info.ncl                                                                                                   
  8 INFO    ++++++++++++++++++++++++++++++++++++++++++                                                                                                                                                                                                                        
  9 INFO    clim (var: lwcre)                                                                                                                                                                                                                                                 
 10 INFO    ++++++++++++++++++++++++++++++++++++++++++                                                                                                                                                                                                                        
 11 fatal:syntax error: line 211 in file /home/b/b309141/repos/ESMValTool/esmvaltool/diag_scripts/clouds/clouds_ipcc.ncl before or near delete                                                                                                                                
 12     delete                                                                                                                                                                                                                                                                
 13 ---------^                                                                                                                                                                                                                                                                
 14                                                                                                                                                                                                                                                                           
 15 ^Mfatal:error in statement                                                                                                                                                                                                                                                
 16 ^Mfatal:Syntax Error in block, block not executed                                                                                                                                                                                                                         
 17 ^Mfatal:error at line 780 in file /home/b/b309141/repos/ESMValTool/esmvaltool/diag_scripts/clouds/clouds_ipcc.ncl

@valeriupredoi
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@axel-lauer this looks very useful indeed (to my untrained NCL and sciencey eye), you should add the Milestone 2.8 to it, I reckon! @ESMValGroup/tech-reviewers can we have one NCL expert look at this please? 🍺

@axel-lauer
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axel-lauer commented Jan 20, 2023

Thanks @schlunma for taking a look! I found out that I made a mistake in the test recipes so only part of the functionality was actually tested. I updated the test recipes (sorry about this):

I think the NCL warnings about entire input arrays containing missing values resulting in the dyn_matrix plots for ICON being empty are caused by a problem with the extract_levels preprocessor. I use the preprocessor to select the 500 hPa level of wap, which results in an empty output field (containing only nan values). The preprocessor gives the following warning:

WARNING [1425940] There were warnings in variable wap:
 Cannot check requested values of 3D coordinate plev since it is not 1D
loaded from file /work/bd0854/b309141/icon_eval/data/cool014/cool014_atm_3d_ml_1979-2014.nc
WARNING [1425940] There were warnings in variable wap:
 Cannot check requested values of 3D coordinate plev since it is not 1D
loaded from file

This problem can be reprocuded with this test recipe: recipe_test_wap.yml.txt

If you think this could indeed be a more general problem, I would open an issue. In any case, I think the empty ICON plot and the many related NCL warnings are not a problem of the changes introduced in this PR.

@axel-lauer axel-lauer added this to the v2.8.0 milestone Jan 20, 2023
@schlunma
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Thanks for the update Axel! I will test this again with the new recipe versions.

Regarding the preprocessor for wap: I think you need a coordinate: air_pressure for the extract_levels preprocessor since ICON does not have a 1D but 3D air_pressure field. The warning is not related to that. I fix that when testing the recipes; if it works I will update the corresponding ICON documentation!

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The adapted recipes (additional coordinate: air_pressure) both ran fine now and I get plots for all CMIP models. However, the dyn_matrix plots for ICON look a bit weird and very different to the other models:

clouds_dyn_matrix_prob_ts_wap 000001

clouds_dyn_matrix_ts_wap_clt 000001

but this is probably related to the data itself, not the changes in this PR. I still get the NCL warnings though, even with the fixed wap field for ICON.

The recipe that failed before now also runs fine 👍 Thanks!!

@axel-lauer
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However, the dyn_matrix plots for ICON look a bit weird and very different to the other models:

I think there might be something strange going on with the unit conversion for ICON data.

    convert_units:
      units: "Pa min-1"

The first time step in the preprocessed files for ICON contains only very low values (in contrast to the other time steps). This seems wrong to me and might explain the "line" around wap=0 in the plot. Here an example of the first two time steps of the preprocessed files to illustrate what I mean (left = ERA5 and right = ICON). Btw, the other time steps also look strange. The values seem rather noisy and quite high compared to what I would expect.

era5-icon_wap

@schlunma
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I don't think this is an issue with the convert_units preprocessor. This is the raw data for January 2004:

> cdo infon -seldate,2004-01-31 -selvar,wap cool014_atm_3d_ml_1979-2014.nc                                                                                                                                                                                       407ms 
cdo(1) seldate: Process started                                                                                                                                                                                                                                               
cdo(2) selname: Process started                                                                                                                                                                                                                                               
    -1 :       Date     Time   Level Gridsize    Miss :     Minimum        Mean     Maximum : Parameter name                                                                                                                                                                  
     1 : 2004-01-31 23:45:00       1    20480       0 : -7.1167e-09  2.9211e-13  7.7118e-09 : wap                                                                                                                                                                             
     2 : 2004-01-31 23:45:00       2    20480       0 : -3.1761e-08 -4.9191e-11  3.0903e-08 : wap                                                                                                                                                                             
     3 : 2004-01-31 23:45:00       3    20480       0 : -6.5397e-08 -5.7341e-11  7.3015e-08 : wap                                                                                                                                                                             
     4 : 2004-01-31 23:45:00       4    20480       0 : -1.3055e-07 -5.4905e-11  1.0615e-07 : wap                                                                                                                                                                             
     5 : 2004-01-31 23:45:00       5    20480       0 : -2.9226e-07  1.7382e-10  2.1725e-07 : wap                                                                                                                                                                             
     6 : 2004-01-31 23:45:00       6    20480       0 : -6.8148e-07  4.0211e-10  3.0572e-07 : wap                                                                                                                                                                             
     7 : 2004-01-31 23:45:00       7    20480       0 : -6.7034e-07  4.4165e-10  6.1205e-07 : wap                                                                                                                                                                             
     8 : 2004-01-31 23:45:00       8    20480       0 : -7.8983e-07  8.1892e-10  7.2386e-07 : wap                                                                                                                                                                             
     9 : 2004-01-31 23:45:00       9    20480       0 : -7.0851e-07  9.1138e-10  7.4135e-07 : wap                                                                                                                                                                             
    10 : 2004-01-31 23:45:00      10    20480       0 : -9.2007e-07  9.0179e-10  9.1854e-07 : wap                                                                                                                                                                             
    11 : 2004-01-31 23:45:00      11    20480       0 : -1.2227e-06  7.9684e-10  9.8680e-07 : wap                                                                                                                                                                             
    12 : 2004-01-31 23:45:00      12    20480       0 : -1.5929e-06  2.7547e-10  1.2892e-06 : wap                                                                                                                                                                             
    13 : 2004-01-31 23:45:00      13    20480       0 : -2.2430e-06 -1.6896e-10  1.3992e-06 : wap                                                                                                                                                                             
    14 : 2004-01-31 23:45:00      14    20480       0 : -2.4143e-06 -5.5042e-10  2.0248e-06 : wap                                                                                                                                                                             
    15 : 2004-01-31 23:45:00      15    20480       0 : -3.7398e-06 -1.9255e-09  2.4443e-06 : wap                                                                                                                                                                             
    16 : 2004-01-31 23:45:00      16    20480       0 : -5.6178e-06 -3.6629e-09  4.0683e-06 : wap                                                                                                                                                                             
    17 : 2004-01-31 23:45:00      17    20480       0 : -4.1424e-06 -5.8895e-09  4.2739e-06 : wap                                                                                                                                                                             
    18 : 2004-01-31 23:45:00      18    20480       0 : -6.0425e-06 -9.0078e-09  6.2628e-06 : wap                                                                                                                                                                             
    19 : 2004-01-31 23:45:00      19    20480       0 : -1.1072e-05 -1.3541e-08  6.6932e-06 : wap                                                                                                                                                                             
    20 : 2004-01-31 23:45:00      20    20480       0 : -1.6428e-05 -1.6153e-08  1.1556e-05 : wap                                                                                                                                                                             
    21 : 2004-01-31 23:45:00      21    20480       0 : -3.0966e-05 -1.9117e-08  1.2874e-05 : wap                                                                                                                                                                             
    22 : 2004-01-31 23:45:00      22    20480       0 : -3.2487e-05 -2.0433e-08  1.6764e-05 : wap                                                                                                                                                                             
    23 : 2004-01-31 23:45:00      23    20480       0 : -3.2672e-05 -2.9051e-08  3.7560e-05 : wap                                                                                                                                                                             
    24 : 2004-01-31 23:45:00      24    20480       0 : -0.00011018 -4.5185e-08  8.6546e-05 : wap                                                                                                                                                                             
    25 : 2004-01-31 23:45:00      25    20480       0 : -0.00024596 -5.7868e-08  0.00012716 : wap                                                                                                                                                                             
    26 : 2004-01-31 23:45:00      26    20480       0 : -0.00034678 -6.3702e-08  0.00013203 : wap                                                                                                                                                                             
    27 : 2004-01-31 23:45:00      27    20480       0 : -0.00041334 -4.1644e-08  0.00016758 : wap                                                                                                                                                                             
    28 : 2004-01-31 23:45:00      28    20480       0 : -0.00044360 -3.1704e-09  0.00015490 : wap                                                                                                                                                                             
    29 : 2004-01-31 23:45:00      29    20480       0 : -0.00044274  3.6188e-08  0.00021983 : wap                                                                                                                                                                             
    30 : 2004-01-31 23:45:00      30    20480       0 : -0.00043368  6.6305e-08  0.00027186 : wap                                                                                                                                                                             
    31 : 2004-01-31 23:45:00      31    20480       0 : -0.00051028  8.3887e-08  0.00028731 : wap                                                                                                                                                                             
    32 : 2004-01-31 23:45:00      32    20480       0 : -0.00054055  9.7393e-08  0.00031635 : wap                                                                                                                                                                             
    33 : 2004-01-31 23:45:00      33    20480       0 : -0.00054955  1.0517e-07  0.00032663 : wap                                                                                                                                                                             
    34 : 2004-01-31 23:45:00      34    20480       0 : -0.00053920  1.0675e-07  0.00030782 : wap                                                                                                                                                                             
    35 : 2004-01-31 23:45:00      35    20480       0 : -0.00054621  1.0248e-07  0.00027728 : wap                                                                                                                                                                             
    36 : 2004-01-31 23:45:00      36    20480       0 : -0.00055896  9.3676e-08  0.00024290 : wap                                                                                                                                                                             
    37 : 2004-01-31 23:45:00      37    20480       0 : -0.00055081  1.0464e-07  0.00026969 : wap                                                                                                                                                                             
    38 : 2004-01-31 23:45:00      38    20480       0 : -0.00051664  1.3339e-07  0.00029790 : wap                                                                                                                                                                             
    39 : 2004-01-31 23:45:00      39    20480       0 : -0.00046242  1.6843e-07  0.00028879 : wap                                                                                                                                                                             
    40 : 2004-01-31 23:45:00      40    20480       0 : -0.00040076  2.2412e-07  0.00024659 : wap                                                                                                                                                                             
    41 : 2004-01-31 23:45:00      41    20480       0 : -0.00033678  3.1324e-07  0.00025553 : wap                                                                                                                                                                             
    42 : 2004-01-31 23:45:00      42    20480       0 : -0.00028845  4.7916e-07  0.00031654 : wap                                                                                                                                                                             
    43 : 2004-01-31 23:45:00      43    20480       0 : -0.00030098  8.0699e-07  0.00039933 : wap                                                                                                                                                                             
    44 : 2004-01-31 23:45:00      44    20480       0 : -0.00031034  1.4062e-06  0.00048213 : wap                                                                                                                                                                             
    45 : 2004-01-31 23:45:00      45    20480       0 : -0.00032026  2.3831e-06  0.00058814 : wap                                                                                                                                                                             
    46 : 2004-01-31 23:45:00      46    20480       0 : -0.00030654  3.1999e-06  0.00063805 : wap                                                                                                                                                                             
    47 : 2004-01-31 23:45:00      47    20480       0 : -0.00029163  3.3656e-06  0.00066832 : wap                                                                                                                                                                             
cdo(2) selname: Processed 415825920 values from 13 variables over 432 timesteps                                                                                                                                                                                               
cdo(1) seldate: Processed 962560 values from 1 variable over 302 timesteps

This is the data for February 2004:

> cdo infon -seldate,2004-02-29 -selvar,wap cool014_atm_3d_ml_1979-2014.nc                                                                                                                                                                                      1161ms
cdo(1) seldate: Process started
cdo(2) selname: Process started
    -1 :       Date     Time   Level Gridsize    Miss :     Minimum        Mean     Maximum : Parameter name
     1 : 2004-02-29 23:45:00       1    20480       0 : -2.1174e-05  8.6242e-10  2.2940e-05 : wap
     2 : 2004-02-29 23:45:00       2    20480       0 : -9.4485e-05 -1.4635e-07  9.1931e-05 : wap
     3 : 2004-02-29 23:45:00       3    20480       0 : -0.00019453 -1.7060e-07  0.00021722 : wap
     4 : 2004-02-29 23:45:00       4    20480       0 : -0.00038835 -1.6339e-07  0.00031578 : wap
     5 : 2004-02-29 23:45:00       5    20480       0 : -0.00086941  5.1721e-07  0.00064632 : wap
     6 : 2004-02-29 23:45:00       6    20480       0 :  -0.0020274  1.1968e-06  0.00090943 : wap
     7 : 2004-02-29 23:45:00       7    20480       0 :  -0.0019942  1.3146e-06   0.0018208 : wap
     8 : 2004-02-29 23:45:00       8    20480       0 :  -0.0023497  2.4369e-06   0.0021536 : wap
     9 : 2004-02-29 23:45:00       9    20480       0 :  -0.0021078  2.7117e-06   0.0022054 : wap
    10 : 2004-02-29 23:45:00      10    20480       0 :  -0.0027371  2.6831e-06   0.0027326 : wap
    11 : 2004-02-29 23:45:00      11    20480       0 :  -0.0036374  2.3709e-06   0.0029359 : wap
    12 : 2004-02-29 23:45:00      12    20480       0 :  -0.0047377  8.1947e-07   0.0038348 : wap
    13 : 2004-02-29 23:45:00      13    20480       0 :  -0.0066719 -5.0325e-07   0.0041623 : wap
    14 : 2004-02-29 23:45:00      14    20480       0 :  -0.0071829 -1.6383e-06   0.0060240 : wap
    15 : 2004-02-29 23:45:00      15    20480       0 :   -0.011125 -5.7302e-06   0.0072727 : wap
    16 : 2004-02-29 23:45:00      16    20480       0 :   -0.016713 -1.0901e-05    0.012105 : wap
    17 : 2004-02-29 23:45:00      17    20480       0 :   -0.012325 -1.7528e-05    0.012716 : wap
    18 : 2004-02-29 23:45:00      18    20480       0 :   -0.017976 -2.6806e-05    0.018631 : wap
    19 : 2004-02-29 23:45:00      19    20480       0 :   -0.032936 -4.0296e-05    0.019913 : wap
    20 : 2004-02-29 23:45:00      20    20480       0 :   -0.048872 -4.8070e-05    0.034375 : wap
    21 : 2004-02-29 23:45:00      21    20480       0 :   -0.092113 -5.6895e-05    0.038296 : wap
    22 : 2004-02-29 23:45:00      22    20480       0 :   -0.096644 -6.0815e-05    0.049871 : wap
    23 : 2004-02-29 23:45:00      23    20480       0 :   -0.097209 -8.6459e-05     0.11172 : wap
    24 : 2004-02-29 23:45:00      24    20480       0 :    -0.32778 -0.00013447     0.25749 : wap
    25 : 2004-02-29 23:45:00      25    20480       0 :    -0.73171 -0.00017222     0.37828 : wap
    26 : 2004-02-29 23:45:00      26    20480       0 :     -1.0317 -0.00018956     0.39279 : wap
    27 : 2004-02-29 23:45:00      27    20480       0 :     -1.2297 -0.00012390     0.49854 : wap
    28 : 2004-02-29 23:45:00      28    20480       0 :     -1.3198 -9.4015e-06     0.46081 : wap
    29 : 2004-02-29 23:45:00      29    20480       0 :     -1.3172  0.00010774     0.65397 : wap
    30 : 2004-02-29 23:45:00      30    20480       0 :     -1.2901  0.00019737     0.80877 : wap
    31 : 2004-02-29 23:45:00      31    20480       0 :     -1.5180  0.00024969     0.85475 : wap
    32 : 2004-02-29 23:45:00      32    20480       0 :     -1.6080  0.00028986     0.94114 : wap
    33 : 2004-02-29 23:45:00      33    20480       0 :     -1.6348  0.00031300     0.97170 : wap
    34 : 2004-02-29 23:45:00      34    20480       0 :     -1.6040  0.00031771     0.91573 : wap
    35 : 2004-02-29 23:45:00      35    20480       0 :     -1.6249  0.00030501     0.82489 : wap
    36 : 2004-02-29 23:45:00      36    20480       0 :     -1.6629  0.00027881     0.72265 : wap
    37 : 2004-02-29 23:45:00      37    20480       0 :     -1.6386  0.00031143     0.80220 : wap
    38 : 2004-02-29 23:45:00      38    20480       0 :     -1.5370  0.00039697     0.88614 : wap
    39 : 2004-02-29 23:45:00      39    20480       0 :     -1.3757  0.00050125     0.85904 : wap
    40 : 2004-02-29 23:45:00      40    20480       0 :     -1.1922  0.00066700     0.73351 : wap
    41 : 2004-02-29 23:45:00      41    20480       0 :     -1.0019  0.00093226     0.76024 : wap
    42 : 2004-02-29 23:45:00      42    20480       0 :    -0.85839   0.0014260     0.94201 : wap
    43 : 2004-02-29 23:45:00      43    20480       0 :    -0.89565   0.0024016      1.1884 : wap
    44 : 2004-02-29 23:45:00      44    20480       0 :    -0.92349   0.0041850      1.4348 : wap
    45 : 2004-02-29 23:45:00      45    20480       0 :    -0.95296   0.0070924      1.7502 : wap
    46 : 2004-02-29 23:45:00      46    20480       0 :    -0.91213   0.0095231      1.8987 : wap
    47 : 2004-02-29 23:45:00      47    20480       0 :    -0.86773    0.010016      1.9888 : wap
cdo(2) selname: Processed 415825920 values from 13 variables over 432 timesteps
cdo(1) seldate: Processed 962560 values from 1 variable over 303 timesteps

The values differ by a factor of ~10e4! The February values look much more similar than the data from other models, although the maximum is considerably higher. The noise you describe is also in the raw input data:

ICON_ICON_cool014_atm_3d_ml_Amon_wap_20040201-20040301

@axel-lauer
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I don't think this is an issue with the convert_units preprocessor. This is the raw data for January 2004:

I agree. Thanks for checking! I think this is ready to be merged then.

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4 participants