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noresm:modeldiagnostics [2015-12-17 10:52:12]
michaels [MICOM Diagnostic Package (NEW 2015.04.23)]
noresm:modeldiagnostics [2019-08-09 07:46:23] (current)
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 ====== Model Diagnostic Tools====== ====== Model Diagnostic Tools======
 +This page links to tools used for the NorESM model evaluation.
 ===== NorESM Diagnostic Packages ===== ===== NorESM Diagnostic Packages =====
-Please, refer to GUIDE_ReadME_first and the ReadME files in each of the Model Components Diagnostic Tools (Packages) locations below for more details.+Output from the latest NCAR diagnostic pages can be found on nird here:
-<​file>​ +via the web: 
-Usagenohup [your work directory path]/[amwg/ice_diag]_template.csh >& out & +​noresm_diagnostics/​
-PurposeModel solution validation, evaluation, and analysis ​ +via the filesystem on nird here
-         compared to observations and reference model simulation.  ​+/​projects/​NS2345K/​www/​noresm_diagnostics/​
-Description:​ Automated diagnostic packages for each of the NorESM model components (atmosphere,​ sea ice, land, ocean) 
-             based on the NCAR CESM diagnostics packages. ​ 
-             ​Written in NCL, NCO and C-Shell. Output is in the form of: .ps or .png plots and web-pages. 
-The packages are installed and stored in 4 locations; please use them on Cruncher or Grunch when possible: 
-On in:+The diagnostics packages are currently available on NIRDEach package can be run/configured from the command line using the program diag_run:
 +Version: 6.0 
 +Short description:​ 
 +A wrapper script for NorESM diagnostic packages. 
 +Basic usage: 
 +diag_run -m [model] -c [test case name] -s [test case start yr] -e [test case end yr] # Run model-obs diagnostics 
 +diag_run -m [model] -c [test case name] -s [test case start yr] -e [test case end yr] -c2 [cntl case name] -s2 [cntl case start yr] -e2 [cntl case end yr] # Run model1-model2 diagnostics 
 +nohup /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run -m [model] -c [test case name] -s [test case start yr] -e [test case end yr] &> out & # Run model-obs diagnostics in the background with nohup 
 +Command-line options: 
 +-m, --model=MODEL ​                            ​Specify the diagnostics package (REQUIRED). 
 +                                              Valid arguments:​ 
 +                                                cam    : atmospheric package (AMWG) 
 +                                                clm    : land package (LMWG) 
 +                                                cice   : sea-ice package 
 +                                                micom  : ocean package 
 +                                                hamocc : biogeochemistry package 
 +                                                all    : configure all available packages. 
 +-c, -c1, --case=CASE1,​ --case1=CASE1 ​         Test case simulation (OPTIONAL). 
 +-s, -s1, --start_yr=SYR1,​ --start_yr1=SYR1 ​   Start year of test case climatology (OPTIONAL). 
 +-e, -e1, --end_yr=EYR1,​ --end_yr1=EYR1 ​       End year of test case climatology (OPTIONAL). 
 +-c2, --case2=CASE2 ​                           Control case simulation (OPTIONAL). 
 +-s2, --start_yr2=SYR2 ​                        Start year of control case climatology (OPTIONAL). 
 +-e2, --end_yr2=EYR2 ​                          End year of control case climatology (OPTIONAL). 
 +-i, -i1, --input-dir=DIR,​ --input-dir1=DIR ​   Specify the directory where the test case history files are located (OPTIONAL). 
 +                                              Default is --input-dir=/​projects/​NS2345K/​noresm/​cases 
 +-i2, --input-dir2=DIR ​                        ​Specify the directory where the control case history files are located (OPTIONAL). 
 +                                              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). 
 +                                              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). 
 +-t, --type=TYPE ​                              ​Specify climatology or time series diagnostics (OPTIONAL): valid options are --type=climo and --type=time_series. 
 +                                              Default is to run both. Note that the time series are computed over the entire simulation. 
 +-w, --web-dir=DIR ​                            ​Specify the directory where the html should be published (OPTIONAL). 
 +                                              Default is --web-dir=/​projects/​NS2345K/​www/​noresm_diagnostics 
 +--no-atm ​                                     Run CLM diagnostics without CAM data. Must be used for offline CLM simulations. 
 +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 50) for all model components. 
 +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 -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 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 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 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. 
 +A comprehensive technical summary of diag_run (pdf): {{ :​noresm:​diag_run_documentation.pdf |}}
-On in:+Report any problems, comments or suggestions to Yanchun He: [[mailto:​|]]
-/work-common/shared/noresm/diagnostics/Packages +=== Recent updates === 
- +  * 08.08.19. Note: NS2345K is recovered now, please use the normal ​/projects/NS2345K/noresm_diagnostics/bin/diag_run; put the webpage output to /​projects/​NS2345K/​ and view the results at: http://​
-On in: +  * 08.08.19. Update to v6.0: add support to TS-derived mltsglobal averages: tempga,salnga,sstga and sssgaupdated volume transports, support extend Atlantic-Arctic overturning ​(mmflxdfor the NorESM2 version. And other minor changes 
- +  * 29.08.18. Update to v5.1: update NCO/NCL versions to support efficient process of compressed netcdf-4 files. 
-/​work/​shared/noresm/diagnostics/​Packages +  * 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
-There are 6 diagnostic tools CAM_DIAG (ready for use)CICE_DIAG (ready for use)CLM_DIAG (in testing), +  * 19.04.18. Update to v4.2: included ability to do time-series diagnostics between two user-specified years. 
-POP_DIAG (in testing)MICOM_DIAG ​(in developmentand CVDP_DIAG (the new NCAR Climate Package, in testing) +  * 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. 
-Currently only the CAM (AMWG) and the CICE packages are ported ​and ready to use.  +  * 23.02.18. Update to v3.1: added monthly MLD, seasonal SST/​SSS ​and annual meridional heat/​salinity fluxes to the MICOM diagnostics. 
-You will find for each of those c-shell macroscript ​*_template.csh.[machine] +  * 17.01.18. Update to v3.0: the first version of MICOM diagnostics has been included. 
-Copy it in your working directorychange the paths and file names in the user-defined part of it and run.+  * 28.11.17. Update to v2.0: included a set of time series plots in CAM diagnostics,​ along with an html interface, which can be accessed from the index page (sets.htm)
 +===Using diag_run with cron===
 +If you want to use diag_run with crontab, you first need to load $HOME/​.bash_profile,​ i.e.:
 +# Min Hour Day Month Weekday Command(s)
 +50 09 23 11 * . $HOME/​.bash_profile;​ /​projects/​NS2345K/​noresm_diagnostics/​bin/​diag_run -m cam,cice -c N18_f19_tn11_080617 -s 21 -e 50 -o /​scratch/​$USER/​noresm_diagnostics2 -w \
 +/​projects/​NS2345K/​www/​test -t time_series >& /​scratch/​$USER/​cron_out
 </​file>​ </​file>​
-Report any problems or suggestions to Detelina Ivanova: [[mailto:​|]] 
-===== MICOM Diagnostic Package ​===== +=== Other tips === 
- +It is useful to add diag_run as an alias in $HOME/.bashrc, so that you do not need to write out the whole path every time you run it
- (NEW 2015.04.23) ​ +<​file>​ 
-First version of MICOM diagnostic package ​is available on grunch/norstore/​hexagon/​viljePlease find more details ​ {{:noresm:​detelinaivanova_noresm_diagnostics_rg1_032515.pdf|here}}. +alias diag_run='/projects/NS2345K/noresm_diagnostics/bin/diag_run'​ 
- +</file>
-===== SVN Repository for NorESM Diagnostic Packages (NEW 2015.04.23) ===== +
- +
-The NorESM Diagnostic Packages can be downloaded via svn using the command:  +
-  svn export svn:// +
- +
- +
- +
-A web-viewer is available at [[​8443/websvn/​wsvn/​NORESG-diagpacks]] (user: guestuser, passw: friendly).+
 +=== NorESM diagnostics on GitHub ===
 +The NorESM diagnostics packages and diag_run are included in the Git version control repository:
 ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ====== ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ======
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   * Example: ftp://​​projects/​noresmatm/​upload/​NorESM2Diagnostics/​ModIvsModII/​revision610inclSOA-Nudged_1984-12to1985-11_vs_CAM4-Oslo/​ModIvsModII.htm   * Example: ftp://​​projects/​noresmatm/​upload/​NorESM2Diagnostics/​ModIvsModII/​revision610inclSOA-Nudged_1984-12to1985-11_vs_CAM4-Oslo/​ModIvsModII.htm
 +===== Cloud water mass and number analysis (budgets) ======
 +===Configuring a run with more cloud diagnostics in NorESM2 ===
 +To switch on extra output for cloud diagnostics (mass and number tendencies for liquid water and mass) change the following namelist variable:
 +history_budget = .true.
 +A python script for plotting the mass and number budgets for the cloud microphysics can be found under:
 +models/​atm/​cam/​tools/​diagnostics/​ncl/​cloudBudgets ​
 +in the same branch. Copy the script to your local computer or lustre and edit the script to read the correct input file(s) (instructions inside the script). Run the script by typing:
 +in your terminal.
 ===== Automatic AEROCOM analysis ===== ===== Automatic AEROCOM analysis =====
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 <​ModelName>​_<​ExperimentName>:​ is the dataset identifier under which the plots appear on the AeroCom webinterface \\  <​ModelName>​_<​ExperimentName>:​ is the dataset identifier under which the plots appear on the AeroCom webinterface \\ 
-of the form NorESM-CAM5_svn{RevisionNumber}_YYMMDD{initials}_Freetext. \\ +in the required format  
-Example: "​NorESM-CAM5_svn1094_151201AG_CMIP6endelig"​ \\+**NorESM-CAM5_svn{RevisionNumber}_YYMMDD{initials}_Freetext**. \\ 
 +Example: ​ 
 +"**NorESM-CAM5_svn1094_151201AG_CMIP6endelig**" \\
 Initials AG: Alf Grini, AK: Alf Kirkevåg, DO: Dirk Olivie... Initials AG: Alf Grini, AK: Alf Kirkevåg, DO: Dirk Olivie...
 +Where the date YYMMDD corresponds to the time when the  AeroCom data preparation script has been executed. ​
 The script creates files named like The script creates files named like
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 http://​​services/​jasmin-analysis-platform/​ http://​​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://​​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://​​jgliss/​noresm_diag_postproc/​blob/​master/​analysis_tool.ipynb)
 +which includes more detailed instructions about setup and options. ​
 +Use the notebook ​
 +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:
 +**NOTE:** If you add groups to this file in your local copy of the repository, please consider sending
 +the updated to [[mailto:​|]] or to submit a pull request, so that the remote repository ​
 +remains up to date.
 +If you run into problems, please raise an issue in the repository or contact [[mailto:​|]]
noresm/modeldiagnostics.1450349532.txt.gz · Last modified: 2015-12-17 10:52:12 by michaels