Tutorial
These examples are for use on LCRC machines (e.g., Chrysalis). Some parameters
must be changed for use on other machines. These include the paths for
input, output, www, mapping_file, reference_data_path, obs_ts,
streamflow_obs_ts, and dc_obs_climo. Different machines also have different partition names, so
partition may need to be changed as well.
Example 1
Let’s say we want to post-process 100 years of an existing simulation.
Copy and paste the following into post.mysimulation.cfg
1[default]
2input = <input>
3input_subdir = archive/atm/hist
4output = <output>
5case = 20210122.v2_test01.piControl.ne30pg2_EC30to60E2r2-1900_ICG.chrysalis
6www = <www>
7partition = compute
8campaign = "water_cycle"
9
10# Regridded atmosphere climatologies every 20 and 50 years
11[climo]
12active = True
13years = "1:100:20", "1:100:50",
14# Use default vars
15
16 # Monthly climatology
17 [[ atm_monthly_180x360_aave ]]
18 mapping_file = /home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc
19 frequency = "monthly"
20
21 # Diurnal climatology (specifically, 3-hour increments of a day averaged over every day of a month)
22 [[ atm_monthly_diurnal_8xdaily_180x360_aave ]]
23 input_subdir = "archive/atm/hist"
24 input_files = "eam.h4"
25 mapping_file = /home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc
26 vars = "PRECT"
27 frequency = "diurnal_8xdaily"
28
29# Regridded atmosphere monthly time series files in 10 year chunks
30[ts]
31active = True
32years = "1:100:10",
33
34 # Monthly time series
35 [[ atm_monthly_180x360_aave ]]
36 input_subdir = "archive/atm/hist"
37 input_files = "eam.h0"
38 frequency = "monthly"
39 mapping_file = /home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc
40 # Use default vars
41
42 # Daily time series
43 [[ atm_daily_180x360_aave ]]
44 input_subdir = "archive/atm/hist"
45 input_files = "eam.h1"
46 frequency = "daily"
47 mapping_file = /home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc
48 vars = "PRECT"
49
50 # Monthly global time series
51 [[ atm_monthly_glb ]]
52 input_subdir = "archive/atm/hist"
53 input_files = "eam.h0"
54 frequency = "monthly"
55 mapping_file = "glb"
56 # Use default vars
57
58 # Monthly land time series
59 [[ land_monthly ]]
60 input_subdir = "archive/lnd/hist"
61 input_files = "elm.h0"
62 frequency = "monthly"
63 mapping_file = /home/ac.zender/data/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc
64 vars = "FSH,RH2M"
65
66 [[ rof_monthly ]]
67 input_subdir = "archive/rof/hist"
68 input_files = "mosart.h0"
69 frequency = "monthly"
70 mapping_file = ""
71 vars = "RIVER_DISCHARGE_OVER_LAND_LIQ"
72 extra_vars = 'areatotal2'
73
74[tc_analysis]
75active = boolean(default=True)
76years = "1:100:20", "1:100:50",
77scratch = <scratch directory>
78
79# E3SM Diags every 20 and 50 years
80[e3sm_diags]
81active = True
82years = "1:100:20", "1:100:50",
83ts_num_years = 10
84
85 # Monthly diagnostics
86 [[ atm_monthly_180x360_aave ]]
87 short_name = '20210122.v2_test01.piControl.ne30pg2_EC30to60E2r2-1900_ICG.chrysalis'
88 grid = '180x360_aave'
89 reference_data_path = '/lcrc/soft/climate/e3sm_diags_data/obs_for_e3sm_diags/climatology'
90 # These two lines need to be included if sets requiring time series files are being run.
91 obs_ts = '/lcrc/soft/climate/e3sm_diags_data/obs_for_e3sm_diags/time-series'
92 ref_start_yr = 1979
93 # This needs to be set for QBO Diags
94 ref_final_yr = 2016
95 # This needs to be set for streamflow diags
96 streamflow_obs_ts = '/lcrc/group/e3sm/public_html/diagnostics/observations/Atm/time-series/'
97 # These three lines need to be included if diurnal cycle diagnostics are being run.
98 dc_obs_climo = '/lcrc/group/e3sm/public_html/diagnostics/observations/Atm/climatology'
99 climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
100 climo_diurnal_frequency = "diurnal_8xdaily"
101 # This is for tropical cyclone diags
102 tc_obs = '/lcrc/group/e3sm/public_html/diagnostics/observations/Atm/tc-analysis/'
103
104# MPAS-Analysis
105[mpas_analysis]
106active = True
107walltime = "24:00:00"
108parallelTaskCount = 6
109ts_years = "1-50", "1-100",
110enso_years = "11-50", "11-100",
111climo_years = "21-50", "51-100",
112mesh = "EC30to60E2r2"
113
114# Global time series plots
115[global_time_series]
116active = True
117years = "1-100",
118ts_num_years = 10
119figstr=coupled_v2_test01
120moc_file=mocTimeSeries_0001-0100.nc
121experiment_name=20210122.v2_test01.piControl.chrysalis
122ts_years = "1-50", "1-100",
123climo_years = "21-50", "51-100",
Now we can run zppy -c post.mysimulation.cfg.
The [climo] subsections ([[ atm_monthly_180x360_aave ]] and
[[ atm_monthly_diurnal_8xdaily_180x360_aave ]]), the [ts] subsections
([[ atm_monthly_180x360_aave ]], [[ atm_daily_180x360_aave ]],
[[ atm_monthly_glb ]] and [[ land_monthly ]]), and
the [mpas_analysis] section will run first because they have
no dependencies.
Once the [climo] subsections and the [ts] subsection
[[ atm_monthly_180x360_aave ]] finish, [e3sm_diags] will run.
Once the [ts] subsection [[ atm_monthly_glb ]] and the [mpas_analysis]
section finish, [global_time_series] will run.
Post-processing results will be located in output and www. Some machines have
a web server. www should be pointed to that so that E3SM Diags, MPAS-Analysis, and
the global time series plots will be visible online.
Because we have specified campaign = "water_cycle", some parameters will
be automatically set. zppy/templates/water_cycle.cfg specifies what
[e3sm_diags] > sets, and
[mpas_analysis] > generate should be for the water cycle campaign.
Users may specify their own values for any of these parameters,
allowing for easy configuration changes. For example, a user could set
campaign = "water_cycle" but specify their own value for [e3sm_diags] > sets.
Example 2
This is another example of a configuration file, this time using a RRM simulation.
1[default]
2input = <input>
3input_subdir = archive/atm/hist
4output = <output>
5case = 20210603.v2rc3c.piControl.northamericax4v1pg2_WC14to60E2r3.chrysalis
6www = <www>
7partition = debug
8campaign = "water_cycle"
9
10[climo]
11active = True
12years = "1:60:20",
13
14 [[atm_monthly_180x360_aave]]
15 mapping_file = /home/ac.zender/data/maps/map_northamericax4v1pg2_to_cmip6_180x360_aave.20200401.nc
16
17 [[conus_0.23x0.31_aave]]
18 grid = 'conus_0.23x0.31_aave'
19 mapping_file = /home/ac.zender/data/maps/map_northamericax4v1pg2_to_conus_0.23x0.31_nco.20210301.nc
20
21[ts]
22active = True
23years = "1:60:10",
24mapping_file = /home/ac.zender/data/maps/map_northamericax4v1pg2_to_cmip6_180x360_aave.20200401.nc
25
26 [[ atm_monthly_180x360_aave ]]
27 input_subdir = "archive/atm/hist"
28 input_files = "eam.h0"
29 vars = "FSNTOA,FLUT,FSNT,FLNT,FSNS,FLNS,SHFLX,QFLX,TAUX,TAUY,PRECC,PRECL,PRECSC,PRECSL,TS,TREFHT,CLDTOT,CLDHGH,CLDMED,CLDLOW,U"
30
31 [[ atm_monthly_glb ]]
32 input_subdir = "archive/atm/hist"
33 input_files = "eam.h0"
34 mapping_file = "glb"
35 vars = "FSNTOA,FLUT,FSNT,FLNT,FSNS,FLNS,SHFLX,QFLX,TAUX,TAUY,PRECC,PRECL,PRECSC,PRECSL,TS,TREFHT,CLDTOT,CLDHGH,CLDMED,CLDLOW"
36
37 [[ land_monthly ]]
38 input_subdir = "archive/lnd/hist"
39 input_files = "elm.h0"
40 frequency = "monthly"
41 vars = "FSH,RH2M"
42
43[e3sm_diags]
44active = True
45reference_data_path = '/lcrc/soft/climate/e3sm_diags_data/obs_for_e3sm_diags/climatology'
46output_format_subplot = "pdf",
47short_name = '20210603.v2rc3c.piControl.naRRM'
48years = "1:60:20",
49
50 [[atm_monthly_180x360_aave]]
51 grid = '180x360_aave'
52 sets = "lat_lon","zonal_mean_xy","zonal_mean_2d","polar","cosp_histogram","meridional_mean_2d","enso_diags","qbo","area_mean_time_series",
53 ts_num_years = 10
54 obs_ts = '/lcrc/soft/climate/e3sm_diags_data/obs_for_e3sm_diags/time-series'
55 ref_start_yr = 1990
56 ref_end_yr = 1999
57 ref_final_yr = 2016
58
59 [[conus_0.23x0.31_aave]]
60 grid = 'conus_0.23x0.31_aave'
61 sets = 'lat_lon',
62 cfg = "e3sm_diags/lat_lon_conus.cfg"
63
64[mpas_analysis]
65active = False
66walltime = "24:00:00"
67parallelTaskCount = 6
68ts_years = "1-50",
69enso_years = "1-50",
70climo_years ="1-50",
71mesh = "WC14to60E2r3"
72partition = compute
73
74[global_time_series]
75active = False
Debugging failures
$ cd <output directory from cfg>/post/scripts $ grep -v "OK" *status # See what failed # Review `.o` files corresponding to failed `.status` files. # If an error is obvious, make a fix in the bash file and rerun: $ sbatch <failed job>.bash # If the error is not obvious, do the following: $ emacs <failed job>.bash # In this file, set `debug = True`. This will provide more information. # Note: another option is to set `debug = True` in your `cfg` and rerun `zppy`. $ sbatch <failed job>.bash