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--- noresm:modeldiagnostics [2018-04-10 07:07:17]
johan.liakka@nersc.no
+++ noresm:modeldiagnostics [2018-08-20 18:03:45]
yanchun.he@nersc.no
@@ Line 21: / Line 21: @@
 Program:
 /projects/NS2345K/noresm_diagnostics/bin/diag_run
-Version: 4.0
+Version: 5.1
 -------------------------------------------------
 Short description:
-diag_run is used to configure and run the NorESM diagnostic packages.
+A wrapper script for NorESM diagnostic packages.
 Basic usage:
@@ Line 38: / Line 38: @@
                                                 cice   : sea-ice package
                                                 micom  : ocean package
-                                                hamocc : geo-bio-chemistry package
+                                                hamocc : biogeochemistry package
                                                 all    : configure all available packages.
 -c, -c1, --case=CASE1, --case1=CASE1          Test case simulation (OPTIONAL).
@@ Line 51: / Line 51: @@
                                               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
+                                              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.
@@ Line 57: / Line 57: @@
 -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.
 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 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 clm -c N1850_f19_tn11_exp1 -s 21 -e 50 -t climo # model-obs climatology diagnostics (no time series) for CLM:
+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 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.
 </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 ===
+  * 29.08.10. 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.
@@ Line 84: / Line 92: @@
 # 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 99: / Line 107: @@
 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 272: / Line 279: @@
 JASMIN
 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]]