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noresm:modeldiagnostics [2018-04-10 06:46:44]
johan.liakka@nersc.no
noresm:modeldiagnostics [2018-08-20 18:03:45] (current)
yanchun.he@nersc.no
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 Program: Program:
 /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run
-Version: ​4.0+Version: ​5.1
 ------------------------------------------------- -------------------------------------------------
 Short description:​ Short description:​
-diag_run is used to configure and run the NorESM diagnostic packages.+A wrapper script for NorESM diagnostic packages.
    
 Basic usage: Basic usage:
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                                                 cice   : sea-ice package                                                 cice   : sea-ice package
                                                 micom  : ocean package                                                 micom  : ocean package
-                                                hamocc : geo-bio-chemistry ​package+                                                hamocc : biogeochemistry ​package
                                                 all    : configure all available packages.                                                 all    : configure all available packages.
 -c, -c1, --case=CASE1,​ --case1=CASE1 ​         Test case simulation (OPTIONAL). -c, -c1, --case=CASE1,​ --case1=CASE1 ​         Test case simulation (OPTIONAL).
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                                               Default is --input-dir=/​projects/​NS2345K/​noresm/​cases                                               Default is --input-dir=/​projects/​NS2345K/​noresm/​cases
 -o, --output-dir=DIR ​                         Specify the directory where the package(s) the climatology and time-series files should be stored (OPTIONAL). -o, --output-dir=DIR ​                         Specify the directory where the package(s) the climatology and time-series files should be stored (OPTIONAL).
-                                              Default is --output-dir=/​projects/​NS2345K/​noresm_diagnostics/​out/​johiak+                                              Default is --output-dir=/​projects/​NS2345K/​noresm_diagnostics/​out/​$USER
 -p, --passive-mode ​                           Run the script in passive mode: the diagnostic script will be configured but not executed (OPTIONAL). -p, --passive-mode ​                           Run the script in passive mode: the diagnostic script will be configured but not executed (OPTIONAL).
 -t, --type=TYPE ​                              ​Specify climatology or time series diagnostics (OPTIONAL): valid options are --type=climo and --type=time_series. -t, --type=TYPE ​                              ​Specify climatology or time series diagnostics (OPTIONAL): valid options are --type=climo and --type=time_series.
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 -w, --web-dir=DIR ​                            ​Specify the directory where the html should be published (OPTIONAL). -w, --web-dir=DIR ​                            ​Specify the directory where the html should be published (OPTIONAL).
                                               Default is --web-dir=/​projects/​NS2345K/​www/​noresm_diagnostics                                               Default is --web-dir=/​projects/​NS2345K/​www/​noresm_diagnostics
 +--no-atm ​                                     Run CLM diagnostics without CAM data. Must be used for offline CLM simulations.
    
 Examples: Examples:
-diag_run -m all -c N1850_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics of N1850_f19_tn11_exp1 ​for all (available) components. +diag_run -m all -c N1850_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics of case=N1850_f19_tn11_exp1 (climatology between yrs 21 and 50for all model components. 
-diag_run -m cam -c N1850_f19_tn11_exp1 -s 21 -e 50 -w /​path/​to/​my/​html # model-obs diagnostics ​for CAM, publish the html in /​path/​to/​my/​html. +diag_run -m cam -c N1850_f19_tn11_exp1 -s 21 -e 50 -w /​path/​to/​my/​html # model-obs diagnostics ​in CAM, publish the html in /​path/​to/​my/​html. 
-diag_run -m micom -c N1850_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics ​for MICOM+diag_run -m micom -c N1850_f19_tn11_exp1 -t time_series ​# model-obs ​time-series ​diagnostics ​in MICOM for all years represented in the model output directory (/​projects/​NS2345K/​noresm/​cases/​N1850_f19_tn11_exp1/​ocn/​hist/​).
 diag_run -m cice -c N1850_f19_tn11_exp1 -s 21 -e 50 -p # configure (but do not run) model-obs diagnostics for CICE. diag_run -m cice -c N1850_f19_tn11_exp1 -s 21 -e 50 -p # configure (but do not run) model-obs diagnostics for CICE.
 diag_run -m clm -c N1850_f19_tn11_exp1 -s 21 -e 50 -i /​input/​directory1 -c2 N1850_f19_tn11_exp2 -s2 21 -e2 50 -i2 /​input/​directory2 # model1-model2 diagnostics for CLM with user-specified history file directories diag_run -m clm -c N1850_f19_tn11_exp1 -s 21 -e 50 -i /​input/​directory1 -c2 N1850_f19_tn11_exp2 -s2 21 -e2 50 -i2 /​input/​directory2 # model1-model2 diagnostics for CLM with user-specified history file directories
-diag_run -m clm -c N1850_f19_tn11_exp1 -s 21 -e 50 -t climo # model-obs climatology diagnostics (no time series) for CLM:+diag_run -m micom -c N1850_f19_tn11_exp1 -s 21 -e 50 -t climo # model-obs climatology diagnostics (no time series) for MICOM:
 diag_run -m cam -o /my/dir # install CAM diagnostics in /my/dir with minimal configuration. diag_run -m cam -o /my/dir # install CAM diagnostics in /my/dir with minimal configuration.
-diag_run -m micom,​hamocc -c N1850OC_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics for micom and hamocc.+diag_run -m micom,​hamocc -c N1850OC_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics for MICOM and HAMOCC. 
 +diag_run -m clm -c N1850_f19_tn11_clmexp1 -s 71 -e 100 --no-atm # model-obs time-series diagnostics for an offline (uncoupled) CLM simulation. 
 +diag_run -m hamocc ​-c N1850OC_f19_tn11_exp1 -s 31 -e 100 -t time_series # model-obs time-series diagnostics in HAMOCC between yrs 31 and 100.
 </​file>​ </​file>​
-complete ​technical summary of diag_run (pdf): {{ :​noresm:​diag_run_documentation.pdf |}}+comprehensive ​technical summary of diag_run (pdf): {{ :​noresm:​diag_run_documentation.pdf |}}
  
-Report any problems, comments or suggestions to Johan Liakka: [[mailto:johan.liakka@nersc.no|johan.liakka@nersc.no]]+Report any problems, comments or suggestions to Yanchun He: [[mailto:yanchun.he@nersc.no|yanchun.he@nersc.no]]
  
 === Recent updates === === Recent updates ===
 +  * 29.08.10. Update to v5.1: update NCO/NCL versions to support efficient process of compressed netcdf-4 files.
 +  * 29.06.18. Update to v5.0: new fields to HAMOCC and MICOM diagnostics;​ minor fixes to other issues.
 +  * 20.04.18. Update to v4.3: added new fields to HAMOCC diagnostics.
 +  * 19.04.18. Update to v4.2: included ability to do time-series diagnostics between two user-specified years.
 +  * 18.04.18. Update to v4.1: improved climatology and time-series calculations in CLM, and introduction of the --no-atm option to enable diagnostics for offline CLM simulations.
   * 09.04.18. Update to v4.0: included the HAMOCC diagnostics package.   * 09.04.18. Update to v4.0: included the HAMOCC diagnostics package.
   * 23.02.18. Update to v3.1: added monthly MLD, seasonal SST/SSS and annual meridional heat/​salinity fluxes to the MICOM diagnostics.   * 23.02.18. Update to v3.1: added monthly MLD, seasonal SST/SSS and annual meridional heat/​salinity fluxes to the MICOM diagnostics.
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 # Min Hour Day Month Weekday Command(s) # Min Hour Day Month Weekday Command(s)
 #​--------------------------------------- #​---------------------------------------
-50 09 23 11 * . $HOME/​.bash_profile;​ /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run -m cam,cice -c N18_f19_tn11_080617 -s 21 -e 50 -o /scratch/johiak/​noresm_diagnostics2 -w \ +50 09 23 11 * . $HOME/​.bash_profile;​ /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run -m cam,cice -c N18_f19_tn11_080617 -s 21 -e 50 -o /scratch/$USER/​noresm_diagnostics2 -w \ 
-/​projects/​NS2345K/​www/​test -t time_series >& /scratch/johiak/cron_out+/​projects/​NS2345K/​www/​test -t time_series >& /scratch/$USER/cron_out
 </​file>​ </​file>​
  
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 The NorESM diagnostics packages and diag_run are included in the Git version control repository: The NorESM diagnostics packages and diag_run are included in the Git version control repository:
 [[https://​github.com/​johiak/​NoresmDiagnostics]] [[https://​github.com/​johiak/​NoresmDiagnostics]]
- 
 ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ====== ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ======
  
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 JASMIN JASMIN
 http://​www.jasmin.ac.uk/​services/​jasmin-analysis-platform/​ http://​www.jasmin.ac.uk/​services/​jasmin-analysis-platform/​
 +
 +====== Post analysis and workup of CAM diagnostics output tables ======
 +
 +A tool for post analysis of (multiple) CAM diagnostics ASCII tables can be found in 
 +the following repository:
 +
 +GitHub https://​github.com/​jgliss/​noresm_diag_postproc
 +
 +To get started, please follow the instructions in repository README (displayed in repository). Currently, the main 
 +analysis tool is a jupyter IPython notebook called ​
 +
 +//​**analysis_tool.ipynb**//​ (https://​github.com/​jgliss/​noresm_diag_postproc/​blob/​master/​analysis_tool.ipynb)
 +
 +which includes more detailed instructions about setup and options. ​
 +
 +Use the notebook ​
 +
 +https://​github.com/​jgliss/​noresm_diag_postproc/​blob/​master/​download_tables.ipynb
 +
 +to download local copies of result tables using a list of URL's.
 +
 +
 +**Short summary:​** ​
 +The notebook reads multiple diagnostics files (runs) into one long table and creates heatmap plots
 +of //Bias, RMSE and RMSE relative error// for a subset of variables (rows -> y-axis of heatmap) ​
 +vs. the individual runs (columns -> xaxis). ​
 +
 +**NOTE:** In the current version, you need to download all tables that you are interested in as csv or 
 +ascii into one directory, that is specified in the header of the notebook.
 +
 +Variable groups can be defined in this config file:
 +
 +https://​github.com/​jgliss/​noresm_diag_postproc/​blob/​master/​config/​var_groups.ini
 +
 +**NOTE:** If you add groups to this file in your local copy of the repository, please consider sending
 +the updated to [[mailto:​jonasg@met.no|jonasg@met.no]] or to submit a pull request, so that the remote repository ​
 +remains up to date.
 +
 +**Troubleshooting**
 +
 +If you run into problems, please raise an issue in the repository or contact [[mailto:​jonasg@met.no|jonasg@met.no]]
  
noresm/modeldiagnostics.1523342804.txt.gz · Last modified: 2018-04-10 06:46:44 by johan.liakka@nersc.no