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--- noresm:modeldiagnostics [2018-04-09 14:14:55]
johan.liakka@nersc.no
+++ noresm:modeldiagnostics [2022-05-31 09:29:32] (current)
@@ Line 5: / Line 5: @@
 ===== NorESM Diagnostic Packages =====
-Output from the latest NCAR diagnostic pages can be found on nird here:
-via the web:
+**NB: The wiki page for the NorESM diagnostic tools is moved!!**
-http://ns2345k.web.sigma2.no/noresm_diagnostics/
-via the filesystem on nird here:
+Last updated: 12-Dec-2020.
-/projects/NS2345K/www/noresm_diagnostics/
+Please go to the following NorESM documentation page for the latest description:
+https://noresm-docs.readthedocs.io/en/latest/diagnostics/diagnostics.html
+----
-The diagnostics packages are currently available on NIRD. Each package can be run/configured from the command line using the program diag_run:
-<file>
--------------------------------------------------
-Program:
-/projects/NS2345K/noresm_diagnostics/bin/diag_run
-Version: 4.0
--------------------------------------------------
-Short description:
-diag_run is used to configure and run the 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 : geo-bio-chemistry 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/johiak
--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
-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 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 micom -c N1850_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics for MICOM
-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 -t climo # model-obs climatology diagnostics (no time series) for CLM:
-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.
-</file>
-A complete technical summary of diag_run (pdf): {{ :noresm:noresm:diag_run_documentation.pdf |}}
-Report any problems, comments or suggestions to Johan Liakka: [[mailto:johan.liakka@nersc.no|johan.liakka@nersc.no]]
-=== Recent updates ===
-  * 23.02.18. Update to v3.1: added monthly MLD, seasonal SST/SSS and annual meridional heat/salinity fluxes to the MICOM diagnostics.
-  * 17.01.18. Update to v3.0: the first version of MICOM diagnostics has been included.
-  * 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.:
-<file>
-#---------------------------------------
-# Min Hour Day Month Weekday Command(s)
-#---------------------------------------
-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 \
-/projects/NS2345K/www/test -t time_series >& /scratch/johiak/cron_out
-</file>
-=== 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:
-<file>
-alias diag_run='/projects/NS2345K/noresm_diagnostics/bin/diag_run'
-</file>
-=== NorESM diagnostics on GitHub ===
-The NorESM diagnostics packages and diag_run are included in the Git version control repository:
-[[https://github.com/johiak/NoresmDiagnostics]]
 ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ======
@@ Line 273: / Line 189: @@
 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]]