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--- noresm:modeldiagnostics [2018-02-23 15:28:08]
johan.liakka@nersc.no [NorESM Diagnostic Packages]
+++ 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: 3.1
--------------------------------------------------
-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
-                                                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.
-</file>
-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).
-=== Update to NCL version 6.4.0 ===
-The diagnostics packages have been configured and developed using NCL version 6.4.0 (the most recent version on NIRD as of 23.11.17). The user is strongly recommended to use this version, as some bugs have been reported for older versions. To update NCL, add the following two lines of code to your $HOME/.bashrc on NIRD:
-<file>
-export NCARG_ROOT=/opt/ncl64
-export PATH=/opt/ncl64/bin/:${PATH}
-</file>
-===Using diag_run with cron===
-If you want to use diag_run with crontab, you first need to load $HOME/.bash_profile and export the variable RUN_BY_CRON, e.g.:
-<file>
-#---------------------------------------
-# Min Hour Day Month Weekday Command(s)
-#---------------------------------------
-09 23 11 * . $HOME/.bash_profile; export RUN_BY_CRON="TRUE"; /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 277: / 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]]