Differences

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--- noresm:modeldiagnostics [2018-04-18 07:52:18]
johan.liakka@nersc.no
+++ noresm:modeldiagnostics [2020-12-22 12:44:09]
yanchun.he@nersc.no [NorESM Diagnostic Packages]
@@ Line 8: / Line 8: @@
 via the web:
-http://ns2345k.web.sigma2.no/noresm_diagnostics/
+http://ns2345k.web.sigma2.no/diagnostics/noresm/
 via the filesystem on nird here:
-/projects/NS2345K/www/noresm_diagnostics/
+/projects/NS2345K/www/diagnostics/noresm
+**NB: The following wiki page for the NorESM diagnostic tools is moved!!**
+Last updated: 12-Dec-2020.
+Please go to the following NorESM documentation page for the latest description:
+https://noresm-docs.readthedocs.io/en/latest/diagnostics/diagnostics.html
+----
@@ Line 20: / Line 28: @@
 -------------------------------------------------
 Program:
-/projects/NS2345K/noresm_diagnostics/bin/diag_run
+/projects/NS2345K/diagnostics/noresm/bin/diag_run
-Version: 4.1
+Version: 2.1
 -------------------------------------------------
 Short description:
-diag_run is used to configure and run the NorESM diagnostic packages.
+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
+nohup /projects/NS2345K/diagnostics/noresm/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).
@@ Line 37: / Line 45: @@
                                                 clm    : land package (LMWG)
                                                 cice   : sea-ice package
-                                                micom  : ocean package
+                                                blom   : ocean package
                                                 hamocc : biogeochemistry package
                                                 all    : configure all available packages.
@@ Line 51: / Line 59: @@
                                               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
+                                              Default is --output-dir=/projects/NS2345K/diagnostics/noresm/out/yanchun
 -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
+                                              Default is --web-dir=/projects/NS2345K/www/diagnostics/noresm/yanchun
 --no-atm                                      Run CLM diagnostics without CAM data. Must be used for offline CLM simulations.
 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 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 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 blom -c N1850_f19_tn11_exp1 -t time_series # model-obs time-series diagnostics in BLOM 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 blom -c N1850_f19_tn11_exp1 -s 21 -e 50 -t climo # model-obs climatology diagnostics (no time series) for BLOM:
 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 blom,hamocc -c N1850OC_f19_tn11_exp1 -s 21 -e 50 # model-obs diagnostics for BLOM and HAMOCC.
-diag_run -m clm -c N1850_f19_tn11_clmexp1 -t time_series --no-atm # model-obs time-series diagnostics for an offline (uncoupled) CLM simulation.
+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.
+*** NOTE: '-m micom' should be used for the ocean component of NorESM version 1 ***
 </file>
 A 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 ===
+  * 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://ns2345k.web.sigma2.no/noresm_diagnostics/
+  * 08.08.19. Update to v6.0: add support to TS-derived mlts, global averages: tempga,salnga,sstga and sssga, updated volume transports, support extend Atlantic-Arctic overturning (mmflxd) for 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.
+  * 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.
@@ Line 87: / Line 104: @@
 # 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 \
+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>
@@ Line 95: / Line 112: @@
 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'
+alias diag_run='/projects/NS2345K/diagnostics/noresm/bin/diag_run'
 </file>
@@ Line 101: / Line 118: @@
 === NorESM diagnostics on GitHub ===
 The NorESM diagnostics packages and diag_run are included in the Git version control repository:
-[[https://github.com/johiak/NoresmDiagnostics]]
+[[https://github.com/NordicESMhub/noresmdiagnostics]]
 ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ======
@@ Line 276: / Line 292: @@
 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]]