Differences

This shows you the differences between two versions of the page.

--- noresm:modeldiagnostics [2017-11-28 10:05:26]
johan.liakka@nersc.no [NorESM Diagnostic Packages]
+++ noresm:modeldiagnostics [2020-12-22 12:44:09]
yanchun.he@nersc.no [NorESM Diagnostic Packages]
@@ Line 1: / Line 1: @@
 ====== Model Diagnostic Tools======
-This page links to tools used for NorESM model evaluation.
+This page links to tools used for the NorESM model evaluation.
 ===== NorESM Diagnostic Packages =====
+Output from the latest NCAR diagnostic pages can be found on nird here:
+via the web:
+http://ns2345k.web.sigma2.no/diagnostics/noresm/
+via the filesystem on nird here:
+/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
+----
 The diagnostics packages are currently available on NIRD. Each package can be run/configured from the command line using the program diag_run:
@@ Line 10: / Line 28: @@
 -------------------------------------------------
 Program:
-/projects/NS2345K/noresm_diagnostics/bin/diag_run
+/projects/NS2345K/diagnostics/noresm/bin/diag_run
-Version: 2.0
+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).
                                               Valid arguments:
-                                                cam  : atmospheric package (AMWG)
+                                                cam    : atmospheric package (AMWG)
-                                                clm  : land package (LMWG)
+                                                clm    : land package (LMWG)
-                                                cice : sea-ice package
+                                                cice   : sea-ice package
-                                                all  : configure all available packages (currently cam, clm and cice; micom and pop are still in development).
+                                                blom   : 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).
@@ Line 38: / Line 58: @@
 -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) should be installed (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=/scratch/johiak/noresm_diagnostics
+                                              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 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 clm -c N1850_f19_tn11_exp1 -s 21 -e 50 -t climo # model-obs climatology diagnostics (no time series) for CLM:
+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 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 -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>
-Report any problems, comments or suggestions to Johan Liakka: [[mailto:johan.liakka@nersc.no|johan.liakka@nersc.no]]
+A comprehensive technical summary of diag_run (pdf): {{ :noresm:diag_run_documentation.pdf |}}
-=== Recent changes ===
+Report any problems, comments or suggestions to Yanchun He: [[mailto:yanchun.he@nersc.no|yanchun.he@nersc.no]]
-  * 28.11.17. Update to v2.0: included a set of time series plots in CAM diagnostics. These also have their own 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>
+=== 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.
+  * 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 and export the variable RUN_BY_CRON, e.g.:
+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; 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 \
+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 81: / 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 87: / 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 262: / 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]]