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+
NorESM User Workshop
+ +

NorESM model output and post-processing

+

Yanchun He
+Nansen Environment and Remote Sensing Center
+20 November, 2024

+
20 November, 2024
+
+
+
NorESM User Workshop
+

Directories storing model output

+
    +
  1. On the Sigma2 HPC (Betzy):
    +NorESM will constantly dump output during the runtime and archive the data after the run is finished.
    2. +
+
    +
  • +

    Model output during runtime (the run folder):
    +/cluster/work/users/<username>/noresm/cases/$CASE_NAME
    +(including model build and executables, input and configurations, model output and log files, etc)

    +
    • +
  • +

    Short-term archive after model finishes successfully (the archive folder):
    +/cluster/work/users/<username>/archive/cases/$CASE_NAME
    +(simulated physical/biogeochemical fileds from all active model output)

    +
    • +
+
    +
  1. On Sigma2 storage platform (NIRD):
    +If the simulation results is satisfactory, they should be transferred to Sigma2 storage facility, NIRD for long-term data archive and analysis.
    2. +
+
    +
  • Medium/Long-term archive.
    +(NIRD project areas, e.g., /projects/NS9560K for INES project.)
    • +
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Structure of model output archive

+Archive structure of model output + +

Model output are usually transferred from the HPC (Betzy) to the storage (NIRD) with rsync or scp.

+
$ cd /cluster/work/users/$USER/archive
+$ rsync -vazu <your_case_name> $USER@login.nird.sigma2.no:/projects/NSxxxxK/<folder_to_case>/<your_case_name>/
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

File naming convention of model output

+
+
+ +model components +
    +
  • History files: <component>/hist, e.g, atm/hist,ocn/hist.
    • +
  • Restart files: rest/hist.
    • +
  • Log files: <component>.log.$pid.ddmmyy-hhmmss.gz
    • +
+
+
+
$ tree -L 2
+.
+├── archive.log.200921-151923
+├── atm
+│   └── hist
+├── cpl
+│   └── hist
+├── esp
+│   └── hist
+├── ice
+│   └── hist
+├── lnd
+│   └── hist
+├── logs
+│   ├── atm.log.781577.200921-144102.gz
+│   ├── cesm.log.781577.200921-144102.gz
+│   ├── cpl.log.781577.200921-144102.gz
+│   ├── ice.log.781577.200921-144102.gz
+│   ├── lnd.log.781577.200921-144102.gz
+│   ├── ocn.log.781577.200921-144102.gz
+│   └── rof.log.781577.200921-144102.gz
+├── ocn
+│   └── hist
+├── rest
+│   └── 0001-02-01-00000
+└── rof
+    └── hist
+
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Example history file names:

+

<compset name>_<resolution sname>_<opt_desc_string>_<component>.<frequency>_<date>.nc

+
+
+
    +
  • N1850frc2_f19_tn14_test.blom.hm.0001-01.nc
    • +
  • N1850frc2_f19_tn14_test.cam.h0.0001-01.nc
    • +
+

By default, h0,hm denotes that the time sampling frequency is monthly.
+Other frequencies are saved under the h1, h2, etc.
+Different time sampling frequencies have distinct tags in the file names.

+
+
+

A full list of the tags:

+
    - blom.hy    = blom yearly
+    - blom.hbgcy = blom/bgc yearly
+    - blom.hm    = blom monthly
+    - blom.hbgcm = blom/bgc monthly
+    - blom.hd    = blom daily
+    - blom.hbgcd = blom/bgc daily
+    - cice.h     = ice monthly
+    - cice.h1    = ice daily
+    - cam.h0     = cam monthly 
+    - cam.h1     = cam daily
+    - cam.h2     = cam 6-hourly average
+    - cam.h3     = cam 6-hourly instant
+    - cam.h4     = cam 3-hourly average
+    - cam.h5     = cam 3-hourly instant
+    - clm2.h4    = clm yearly
+    - clm2.h0    = clm monthly
+    - clm2.h1    = clm daily
+    - clm2.h2    = clm 3-hourly average
+    - clm2.h3    = clm 3-hourly instant
+
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Metadata of model output

+

Taking a peek on the metadata of the atmosphere and ocean components.

+
+
+

grid:f19_tn14, CAM 2°x2°

+
netcdf NHISTfrc2_f19_tn14_1950.cam.h0.2014-12 {
+dimensions:
+	lat = 96 ;
+	lon = 144 ;
+	zlon = 1 ;
+	nbnd = 2 ;
+	lev = 32 ;
+	ilev = 33 ;
+	time = UNLIMITED ; // (1 currently)
+	chars = 8 ;
+
+
variables:
+	double lat(lat) ;
+		lat:_FillValue = -900. ;
+		lat:long_name = "latitude" ;
+		lat:units = "degrees_north" ;
+	double lon(lon) ;
+		lon:_FillValue = -900. ;
+		lon:long_name = "longitude" ;
+		lon:units = "degrees_east" ;
+	double gw(lat) ;
+		gw:_FillValue = -900. ;
+		gw:long_name = "latitude weights" ;
+...
+	double lev(lev) ;
+		lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
+		lev:units = "hPa" ;
+		lev:positive = "down" ;
+		lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
+		lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
+	double hyam(lev) ;
+		hyam:long_name = "hybrid A coefficient at layer midpoints" ;
+	double hybm(lev) ;
+		hybm:long_name = "hybrid B coefficient at layer midpoints" ;
+	double P0 ;
+		P0:long_name = "reference pressure" ;
+		P0:units = "Pa" ;
+	double ilev(ilev) ;
+		ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
+		ilev:units = "hPa" ;
+		ilev:positive = "down" ;
+		ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
+		ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
+	double hyai(ilev) ;
+		hyai:long_name = "hybrid A coefficient at layer interfaces" ;
+	double hybi(ilev) ;
+		hybi:long_name = "hybrid B coefficient at layer interfaces" ;
+
+
...
+	TREFHT:cell_methods = "time: mean" ;
+	float TS(time, lat, lon) ;
+		TS:units = "K" ;
+		TS:long_name = "Surface temperature (radiative)" ;
+		TS:cell_methods = "time: mean" ;
+...
+
+
+
+

grid:f09_tn14, CAM 1°x1°

+
netcdf NHISTfrc2_f09_tn14_20191025.cam.h0.2014-12 {
+dimensions:
+        lat = 192 ;
+        lon = 288 ;
+        zlon = 1 ;
+        nbnd = 2 ;
+        time = UNLIMITED ; // (1 currently)
+        chars = 8 ;
+        lev = 32 ;
+        ilev = 33 ;
+
+
variables:
+	double lat(lat) ;
+		lat:_FillValue = -900. ;
+		lat:long_name = "latitude" ;
+		lat:units = "degrees_north" ;
+	double lon(lon) ;
+		lon:_FillValue = -900. ;
+		lon:long_name = "longitude" ;
+		lon:units = "degrees_east" ;
+	double gw(lat) ;
+		gw:_FillValue = -900. ;
+		gw:long_name = "latitude weights" ;
+...
+	double lev(lev) ;
+		lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
+		lev:units = "hPa" ;
+		lev:positive = "down" ;
+		lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
+		lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
+	double hyam(lev) ;
+		hyam:long_name = "hybrid A coefficient at layer midpoints" ;
+	double hybm(lev) ;
+		hybm:long_name = "hybrid B coefficient at layer midpoints" ;
+	double P0 ;
+		P0:long_name = "reference pressure" ;
+		P0:units = "Pa" ;
+	double ilev(ilev) ;
+		ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
+		ilev:units = "hPa" ;
+		ilev:positive = "down" ;
+		ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
+		ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
+	double hyai(ilev) ;
+		hyai:long_name = "hybrid A coefficient at layer interfaces" ;
+	double hybi(ilev) ;
+		hybi:long_name = "hybrid B coefficient at layer interfaces" ;
+	double time(time) ;
+		time:long_name = "time" ;
+		time:units = "days since 1850-01-01 00:00:00" ;
+		time:calendar = "noleap" ;
+		time:bounds = "time_bnds" ;
+
+
...
+	TREFHT:cell_methods = "time: mean" ;
+	float TS(time, lat, lon) ;
+		TS:units = "K" ;
+		TS:long_name = "Surface temperature (radiative)" ;
+		TS:cell_methods = "time: mean" ;
+...
+
+
+
+

grid:f19_tn14, BLOM nominal 1°x1°

+
netcdf NHISTfrc2_f19_tn14_1950.blom.hm.2014-12 {
+dimensions:
+	time = UNLIMITED ; // (1 currently)
+	sigma = 53 ;
+	depth = 70 ;
+	bounds = 2 ;
+	lat = 171 ;
+	region = 4 ;
+	slenmax = 50 ;
+	section = 17 ;
+	y = 385 ;
+	x = 360 ;
+
+
variables:
+	double time(time) ;
+		time:long_name = "time" ;
+		time:units = "days since 1800-01-01 00:00" ;
+		time:calendar = "noleap" ;
+	double sigma(sigma) ;
+		sigma:_FillValue = 9.96920996838687e+36 ;
+		sigma:long_name = "Potential density" ;
+		sigma:standard_name = "sea_water_sigma_theta" ;
+		sigma:units = "kg m-3" ;
+		sigma:positive = "down" ;
+	double depth(depth) ;
+		depth:_FillValue = 9.96920996838687e+36 ;
+		depth:long_name = "z level" ;
+		depth:units = "m" ;
+		depth:positive = "down" ;
+		depth:bounds = "depth_bnds" ;
+	double depth_bnds(depth, bounds) ;
+		depth_bnds:_FillValue = 9.96920996838687e+36 ;
+	double lat(lat) ;
+		lat:_FillValue = 9.96920996838687e+36 ;
+		lat:long_name = "Latitude" ;
+		lat:standard_name = "latitude" ;
+		lat:units = "degree_north" ;
+	char region(region, slenmax) ;
+		region:long_name = "Region name" ;
+	char section(section, slenmax) ;
+		section:long_name = "Section name" ;
+
+
...
+	float sst(time, y, x) ;
+		sst:_FillValue = 9.96921e+36f ;
+		sst:units = "degC" ;
+		sst:long_name = "Ocean surface temperature" ;
+		sst:coordinates = "plon plat" ;
+		sst:cell_measures = "area: parea" ;
+...
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM horizontal grid: CAM and CLM

+

The atmphere (CAM) and land (CLM) components share the same grid.

+
    +
  • NorESM2-LM (CAM) for CMIP6: 2x2 degree
    • +
  • NorESM2-MM (CAM) for CMIP6: 2x2 degree
    • +
  • NorESM2.5/3 (CAM-SE) for CMIP7: SE grid
    • +
+
+
+
CAM: 2x2 deg
+netcdf NHISTfrc2_f19_tn14_1950.cam.h0.2014-12 {
+dimensions:
+	lat = 96 ;
+	lon = 144 ;
+	zlon = 1 ;
+	nbnd = 2 ;
+	lev = 32 ;
+	ilev = 33 ;
+	time = UNLIMITED ; // (1 currently)
+	chars = 8 ;
+
+
+
+NorESM horizontal and vertical grid system +
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM horizontal grid: BLOM and CICE

+

The ocean (BLOM) and sea ice (CICE) components share the same grid.
+Bipolar (gx1v6) for CMIP5; Tripolar (tnx1v4) for CMIP6.

+

In case folder, Buildconf/blom.input_data_list:
+grid_file = /cluster/shared/noresm/inputdata/ocn/blom/grid/grid_tnx1v4_20170622.nc
+or in run folder, noresm/run/ocn_in:
+GRFILE = '/cluster/shared/noresm/inputdata/ocn/blom/grid/grid_tnx1v4_20170622.nc

+
+
+
netcdf grid_tnx1v4_20170622 {
+dimensions:
+	x = 360 ;
+	y = 385 ;
+	nv = 4 ;
+variables:
+...
+	double plon(y, x) ;
+		plon:units = "degrees_east" ;
+		plon:long_name = "Longitude at p-points" ;
+		plon:corners = "pclon" ;
+	double plat(y, x) ;
+		plat:units = "degrees_north" ;
+		plat:long_name = "Latitude at p-points" ;
+		plat:corners = "pclat" ;
+	double ulon(y, x) ;
+		ulon:units = "degrees_east" ;
+...
+
+
+
+NorESM horizontal and vertical grid system +
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM horizontal grid: BLOM and CICE

+

The ocean (BLOM) and sea ice (CICE) components share the same grid.
+Bipolar (gx1v6) for CMIP5; Tripolar (tnx1v4) for CMIP6.

+

In case folder, Buildconf/blom.input_data_list:
+grid_file = /cluster/shared/noresm/inputdata/ocn/blom/grid/grid_tnx1v4_20170622.nc
+or in run folder, noresm/run/ocn_in:
+GRFILE = '/cluster/shared/noresm/inputdata/ocn/blom/grid/grid_tnx1v4_20170622.nc

+
+
+
netcdf grid_tnx1v4_20170622 {
+dimensions:
+	x = 360 ;
+	y = 385 ;
+	nv = 4 ;
+variables:
+...
+	double plon(y, x) ;
+		plon:units = "degrees_east" ;
+		plon:long_name = "Longitude at p-points" ;
+		plon:corners = "pclon" ;
+	double plat(y, x) ;
+		plat:units = "degrees_north" ;
+		plat:long_name = "Latitude at p-points" ;
+		plat:corners = "pclat" ;
+	double ulon(y, x) ;
+		ulon:units = "degrees_east" ;
+...
+
+
+
+Arakawa-C (https://xgcm.readthedocs.io/en/latest/grids.html) +
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM vertical coordinates

+
    +
  • CAM: terrian-following sigma coordinate
    • +
  • BLOM: isopycnic (potential density ) coordinated vertical coordinate
    • +
+
+
+
float temp(time, sigma, y, x) ;
+        temp:_FillValue = 9.96921e+36f ;
+        temp:units = "degC" ;
+        temp:long_name = "Temperature" ;
+        temp:standard_name = "Ocean temperature" ;
+        temp:coordinates = "plon plat" ;
+        temp:cell_measures = "area: parea" ;
+
+float templvl(time, depth, y, x) ;
+        templvl:_FillValue = 9.96921e+36f ;
+        templvl:units = "degC" ;
+        templvl:long_name = "Temperature" ;
+        templvl:standard_name = "Ocean temperature" ;
+        templvl:coordinates = "plon plat" ;
+        templvl:cell_measures = "area: parea" ;
+
+BLOM sigma vertical coordinate +
+
+NorESM horizontal and vertical grid system +
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM time-dimension (time slices)

+

BLOM
+The time coordinate variable in ocean model BLOM history represents the middle of the averaging period for variables that are averages. Notime_bounds for the time axis.

+

BLOM output

+
$ ncdump -t -v time N1850frc2_f19_tn14_Workshop2020.blom.hm.0001-01.nc |tail -4
+data:
+
+ time = "0001-01-17" ;
+}
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM time-dimension (time slices)

+

CAM

+

The time coordinate variable in atmospheric model CAM history and timeseries files represents the end of the averaging period for variables that are averages (inherited from CESM). Its time_bnds attribute of time axis gives over which period the field is averaged.

+

Example File: N1850frc2_f19_tn14_Workshop2020.cam.h0.0001-01.nc
+When the time coordinate variable is translated, the time is 00Z Februray 1st 0001, even though the file holds averaged variables for January 0001.

+

CAM output

+
$ ncdump -v time,time_bnds -t NHISTfrc2_f19_tn14_1950.cam.h0.2014-12.nc
+data:
+
+ time = "2015-01-01" ;
+
+ time_bnds =
+  "2014-12-01", "2015-01-01" ;
+}
+}
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Summary:

+
    +
  • Different model resoltions
    • +
  • Different components have different model grids
    • +
  • Different vertical coordinats
    • +
  • Huge number of output files and variables (> 1000)
    • +
  • ...
    • +
  • Post-processing and analysis?
    • +
  • A way to quickly to validate my model simulation/experiment?
    • +
+
20 November, 2024
+
+
+
NorESM User Workshop
+

The NorESM Diagnostic Tool Package

+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM Diagnostic Package:

+
+

is a NorESM model evaluation tool written with a set of scripts and utilities (bash, NCL, NCO, CDO etc) to provide a general evaluation and quick preview of the model performance with only one command line.
+The results (tables, figures) are presented with generated web pages.

+
+

Components of the package:

+

The diagnostic tool package consists atmospheric/land components based on the NCAR package.

+
    +
  • CAM_DIAG: (NCAR's AMWG Diagnostics Package)
    • +
  • CLM_DIAG: (CESM Land Model Diagnostics Package)
    • +
  • CICE_DIAG: snow/sea ice volume/area
    • +
  • HAMOCC_DIAG: time series, climaotology, zonal mean, regional mean
    • +
  • BLOM_DIAG: time series, climatologies, zonal mean, fluxes, etc
    • +
  • CISM_DIAG: time series, climatologies, etc
    • +
+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM Diagnostic Package (cont.)

+

Code structure

+

code structure code languages

+
20 November, 2024
+
+
+
NorESM User Workshop
+

NorESM Diagnostic Package (cont.)

+

It has a one-line command interface, and is simple-to-use.

+
# run this wraper script without parameters shows basic usage
+$ diag_run
+-------------------------------------------------
+Program:
+/diagnostics/noresm/bin/diag_run
+Version: 2.x
+-------------------------------------------------
+Short description:
+A wrapper script for NorESM diagnostic packages.
+
+Basic usage:
+# model-obs comparison
+$ diag_run -m [model] -c  [test case name] -s  [test case start yr] -e  [test case end yr]
+
+# model-model comparison
+$ 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]
+...
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Two types of analysis

+

1. Compare model with observations

+ +
+
+
$ diag_run --model=cam,cice,blom \ 
+--case=CASENAME \ 
+--start_year=51 \ 
+--end_year=100 \ 
+--input-dir=/PATH/TO/MODEL/FOLDER \ 
+--output-dir=/PATH/TO/OUTPUT/DATA \ 
+--web-dir=/PATH/TO/GENERATED/WEBPAGES \
+
+# or its short version
+$ diag_run -m cam,cice,blom \
+  -c CASENAME \
+  -s 51 -e 100 \
+  -i /PATH/TO/MODEL/FOLDER \
+  -o /PATH/TO/OUTPUT/DATA \
+  -w /PATH/TO/GENERATED/WEBPAGES
+
+
+
+ + + + + + + + + + + + + +
2m Air temperatureSea surface temperature
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

2. Compare model with control (another simulation)

+

Sample plots: Historical simulation of atmosphere compared to PI control

+
+
+
$ diag_run --model=cam,cice,blom \ 
+--case1=CASENAME1 \
+--start_year1=51 \
+--end_year1=100 \
+--input-dir1=/PATH/TO/MODEL/FOLDER1 \
+--case2=CASENAME2 \
+--start_year2=2 \
+--end_year2=50 \
+--input-dir2=/PATH/TO/MODEL/FOLDER2 \
+--output-dir=/PATH/TO/OUTPUT/DATA \
+--web-dir=/PATH/TO/GENERATED/WEBPAGES \
+
+# or its short version
+$ diag_run -m cam,cice,blom \
+ -c1 CASENAME1 -s1 51 -e1 100 -i1 /PATH/TO/MODEL/FOLDER1 \
+ -c2 CASENAME2 -s2 1  -e2 50  -i2 /PATH/TO/MODEL/FOLDER2 \
+ -o /PATH/TO/OUTPUT/DATA \
+ -w /PATH/TO/GENERATED/WEBPAGES
+
+
+
+ + + + + + + + + + + + + +
2m Air temperatureSea surface temperature
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Sets of diagnostics

+
+
+

Atmospheric diagnostics
+(example plots)
+

+
+
+

Ocean diagnostics
+(Example plots)
+

+
+
+

Biogeochemistry diagnostics
+(Example plots)
+

+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Sets of diagnostics (cont.)

+
+
+

Land diagnostics
+(example plots)
+

+
+
+

Sea ice diagnostics
+(Example plots)
+

+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Browse plots online, while you enjoy the peace ☕ 🍵

+
    +
  1. http://ns2345k.web.sigma2.no/datapeak/diagnostics/noresm +
      +
    • most of CMIP6 diagnostics are stored under commom/
      • +
    +
    2. +
  2. http://ns2345k.web.sigma2.no/datalake/diagnostics/noresm
    3. +
  3. http://ns9560k.web.sigma2.no/datalake/diagnostics/noresm +
      +
    • personal diagnostics are store under $username/
      • +
    +
    4. +
+

Note

+

The dianostic tool will write the webpage output to NS9560K by default.
+If you don't have access to it, specify -w option to direct your webpage to a NIRD project area where you have write permission.
+You can then make a tarball (tar -cvzf casenme.tar.gz /path/to/the/weboutput)
+And download to your local computer to view with your browser.

+
20 November, 2024
+
+
+
NorESM User Workshop
+

Resources

+

Where is it?

+
    +
  • Github: https://github.com/NorESMhub/NorESM-Diagnostics
    • +
  • Normal NIRD login nodes (login.nird.sigma2.no): /projects/NS9560K/diagnostics/noresm
    • +
  • "IPCC" node of NIRD (ipcc.nird.sigma2.no): /diagnostics/noresm
    • +
  • Betzy (betzy.sigma2.no): /cluster/shared/noresm/diagnostics/noresm
    • +
+

Do NOT directly modify these installations

+

Find the full doocumentation:

+ +
20 November, 2024
+
+
+
NorESM User Workshop
+

Exercises

+
    +
  • Task 1: set up the tool
    • +
  • Task 2: model-obs comparison
    • +
  • Task 3: model-model comparison
    • +
  • Task 4: run the tool under passive mode
    • +
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Task 1. Set up the tool

+

option 1: on NIRD

+

Use pre-installed tool under NIRD (Recommended)

+
# Fist, logon NIRD
+$ ssh -l <your_username> ipcc.nird.sigma2.no
+
+# Next, add alias in '~/.bashrc' for diag_run
+if [ -f /diagnostics/noresm/bin/diag_run ];then
+    alias diag_run='/diagnostics/noresm/bin/diag_run'
+fi
+
+# Then, source the bash configuration to take effect
+$ source ~/.bashrc
+
+# check if diag_run is in your searching path
+$ which diag_run
+
+
+

(See https://noresm-docs.readthedocs.io/en/latest/output/archive_output.html on how to transfer the NorESM output from Betzy to NIRD.)

+
20 November, 2024
+
+
+
NorESM User Workshop
+

Task 1. Set up the tool

+

Option 2: on Betzy

+
# Fist, logon betzy
+$ ssh -l <your_username> betzy.sigma2.no
+
+# Next, add alias in '~/.bashrc' for diag_run
+if [ -f /cluster/shared/noresm/diagnostics/noresm/bin/diag_run ];then
+    alias diag_srun='/cluster/shared/noresm/diagnostics/noresm/bin/diag_srun'
+fi
+
+# Then, source the bash configuration to take effect
+$ source ~/.bashrc
+
+# check if diag_run is in your searching path
+$ which diag_srun
+
+

diag_run and diag_srun

+
    +
  • job with diag_run will run directly on the login nodes (both on NIRD and Betzy)
    • +
  • job with diag_srun will submit a job to the compute node (on Betzy).
    • +
+

It is important to use diag_srun on Betzy to avoid clogging the login nodes!

+
20 November, 2024
+
+
+
NorESM User Workshop
+

Get familiar with the diag_run (diag_srun)

+

diag_run

+
$ diag_run
+
+Short description:
+  A wrapper script for NorESM diagnostic packages.
+
+Basic usage:
+  # model-obs comparison
+  diag_run -m [model] -c [test case name] -s [test case start yr] -e [test case end yr]
+  # model-model comparison
+  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]
+...
+
+

diag_srun

+
$ diag_srun
+
+Short Description:
+  A wrapper script for submitting a preprocessing job on Betzy for the NorESM diagnostic packages.
+
+Command-Line Options (in addition to options as shown with diag_run -h):
+  --account=<project_account> (OPTIONAL)
+      Specify the project account for CPU hours.
+      Default: ns9560k
+
+  --time=<DD-HH:MM:SS> (OPTIONAL)
+      Specify CPU walltime.
+      Default: Automatically calculated based on the length of years and active components.
+
+  --remove-source-files-flag=true|false (OPTIONAL)
+      Set whether source files should be removed after transferring the webpage from Betzy (/cluster) to NIRD (/nird).
+      Default: false
+...
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Task 2. Model-obs comparison

+
## Compare model to observation
+# syntax:
+$ diag_run  -m MODEL -c CASENAEME -s START_YEAR -e  END_YEAR -i INPUT -o OUTPUT -w WEBPAGE
+
+# examples:
+# 1, compare NorESM2-LM historical run (years 1985 - 2014) with observations 
+$ diag_run -m blom -c NHIST_f19_tn14_20190710 -s 1985 -e 2014 -i /projects/NS9560K/noresm/cases \
+ -o /projects/NS2345K/diagnostics/noresm/out/$USER -w /projects/NS2345K/www/diagnostics/noresm/$USER
+
+# 2, compare NorESM2-LM piControl run (years 1735 - 1764, equivalent to 1985 - 2014),
+#    only diagnose the ocean component, and omit the -o and -w options (default to the above settings).
+$ diag_run -m blom -c N1850_f19_tn14_20190621 -s 1735 -e 1764 -i /projects/NS9560K/noresm/cases
+
+# 3, run on Betzy with `sbatch` job to backend.
+$ diag_srun -m blom -c <case_name> -s 2000 -e 2010 -i /cluster/work/users/$USER/archive \
+    -o /cluster/work/users/$USER/diagnostics/out -w /nird/datalake/NS9560K/www/diagnostics/noresm/$USER \
+    --account=nn9039k --time=0-00:59:00
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Task 3. Model-model comparison

+

Compare model to model

+
# Syntax:
+$ diag_run  -m cam -c1 CASENAEME1 -s1 START_YEAR1 -e1  END_YEAR1 \
+    -c2 CASENAME2 -s2 START_YEAR2 -e2 –END_YEAR2 -i1 INPUT1 -i2 INPUT2 -o OUTPUT –w WEBPAGE
+
+# example, compare NorESM2-LM historical run, years, 1985 to 2014 to piControl (years, 1735 - 1764)
+$ diag_run  -m cam -c1 NHIST_f19_tn14_20190710 -s1 1985 -e1 2014 -i1 /projects/NS9560K/noresm/cases \
+    -c2 N1850_f19_tn14_20190621 -s2 1735 -e2 1764 -i2 /projects/NS9560K/noresm/cases
+
+# run on Betzy with `sbatch` job to backend.
+$ diag_srun ....
+
+
+
20 November, 2024
+
+
+
NorESM User Workshop
+

Task 4

+

The wrapper script diag_run can be invoked but not really executed, so one can futher tweak the diagnostic scripts. This is called the passive mode (with -p or --passive-mode)

+
# Example
+$ diag_run -m cam -c NHIST_f19_tn14_20190710 -s 1985 -e 2014 -p
+
+

In the standard output, you can find lines like:

+
...
+CAM DIAGNOSTICS SUCCESSFULLY CONFIGURED in /cluster/work/users/$USER/diagnostics/out/CAM_DIAG
+...
+
+

Go the that directory and check the shell script there, amwg_template.csh

+

For example, to switch on/off some options:
+/cluster/work/users/$USER/diagnostics/out/CAM_DIAG/amwg_template.csh

+
set significance = 0   # (0=ON,1=OFF)  Turn on significance test
+...
+set all_waccm_sets = 0 # (0=ON,1=OFF)  Do all the WACCM sets
+set all_chem_sets  = 0 # (0=ON,1=OFF)  Do all the CHEM sets
+
+

then start the scripit ./amwg_template.csh.

+
20 November, 2024
+
+

table { + width: 100%; +}

\ No newline at end of file