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--- noresm:modeldiagnostics [2020-12-22 12:44:09]
yanchun.he@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/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.
@@ Line 23: / Line 16: @@
-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/diagnostics/noresm/bin/diag_run
-Version: 2.1
--------------------------------------------------
-Short description:
-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/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)
-                                                clm    : land package (LMWG)
-                                                cice   : sea-ice package
-                                                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).
--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/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/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 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 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 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>
-A comprehensive technical summary of diag_run (pdf): {{ :noresm:diag_run_documentation.pdf |}}
-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.
-  * 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 * . $HOME/.bash_profile; /projects/NS2345K/noresm_diagnostics/bin/diag_run -m cam,cice -c N18_f19_tn11_080617 -s 21 -e 50 -o /scratch/$USER/noresm_diagnostics2 -w \
-/projects/NS2345K/www/test -t time_series >& /scratch/$USER/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/diagnostics/noresm/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/NordicESMhub/noresmdiagnostics]]
 ====== Aerosol and Chemistry, Clouds and Forcing Diagnostics ======