generating 15km - 3km initial condition
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Wei Huang
Aug 31, 2018, 5:05:30 PM8/31/18
to MPAS-Atmosphere Help
Michael helped me to generate the static.nc file for 15km - 3km mesh.
I am following the instruction at:
15-km – 3-km mesh
This mesh contains 6488066 horizontal grid cells, with the circular refinement region spanning approximately 60 degrees of latitude/longitude. When using this mesh, there are several crucial changes that must be made to pre-processing steps and to the model configuration:
(1) The 3-d fields that exist in the model at higher resolution can easily exceed the 4 GB limit imposed by the classic netCDF format. When creating atmospheric initial conditions (i.e., the "init.nc" file), and when writing output streams from the model with 3-d fields, it is necessary to use an "io_type" that supports large variables, such as "pnetcdf,cdf5" or "netcdf4". For more information on selecting the "io_type" of a stream, refer to Chapter 5 in the Users' Guide.
(2) Depending on the amount of memory available, it may be necessary to interpolate the static, geographical fields in parallel. In the v5.0 release, doing this properly requires the use of a special, convex mesh decomposition file -- a regular METIS partition file will not give correct results! In order to process static fields in parallel, one must:
(a) comment-out the code between lines 199 and 204 in src/core_init_atmosphere/mpas_init_atm_cases.F that ordinarily prevents the parallel processing of static fields; and
(b) ensure that the "cvt" partition file prefix (e.g., x5.6488066.cvt.part.) is specified in the config_block_decomp_file_prefix variable in namelist.init_atmosphere.
to generate the initial condition:
Here is my namelist.init_atmosphere:
[whuang@cy001 run.6488066]$ cat namelist.init_atmosphere
&nhyd_model
config_init_case = 7
config_start_time = '2017-10-25_00:00:00'
config_stop_time = '2017-10-25_00:00:00'
config_theta_adv_order = 3
config_coef_3rd_order = 0.25
/
&dimensions
config_nvertlevels = 41
config_nsoillevels = 4
config_nfglevels = 38
config_nfgsoillevels = 4
/
&data_sources
config_geog_data_path = '/lustre/whuang/data4wrf/pre_geog/'
config_met_prefix = 'FILE'
config_sfc_prefix = 'SST'
config_fg_interval = 86400
config_landuse_data = 'USGS'
config_topo_data = 'GTOPO30'
config_use_spechumd = false
/
&vertical_grid
config_ztop = 30000.0
config_nsmterrain = 1
config_smooth_surfaces = true
config_dzmin = 0.3
config_nsm = 30
config_tc_vertical_grid = true
/
&interpolation_control
config_extrap_airtemp = 'linear'
/
&preproc_stages
config_static_interp = false
config_native_gwd_static = false
config_vertical_grid = true
config_met_interp = true
config_input_sst = false
config_frac_seaice = true
/
&io
config_pio_num_iotasks = 0
config_pio_stride = 1
/
&decomposition
config_block_decomp_file_prefix = '../data/../data/x5.6488066.cvt.part.'
/
! config_block_decomp_file_prefix = '../data/x5.6488066.graph.info.part.'
And my streams.init_atmosphere:
[whuang@cy001 run.6488066]$ cat streams.init_atmosphere
<streams>
<immutable_stream name="input"
type="input"
filename_template="../data/x5.6488066.static.nc"
input_interval="initial_only" />
<immutable_stream name="output"
type="output"
io_type="netcdf4"
filename_template="x5.6488066.init.nc"
x4ckages="initial_conds"
output_interval="initial_only" />
<immutable_stream name="surface"
type="output"
io_type="netcdf4"
filename_template="x5.6488066.sfc_update.nc"
filename_interval="none"
packages="sfc_update"
output_interval="86400" />
</streams>
After I run the "init_atmosphere_model", it generated an initial condition file:
[whuang@cy001 run.6488066]$ lsl x5*
-rw-r--r-- 1 whuang users 88887265816 Aug 31 09:43 x5.6488066.init.nc
without any error.
But check this file with a simple NCL script:
f = addfile("x5.6488066.init.nc", "r")
u = f->u
w = f->w
print("min u:" + min(u) + ", max u:" + max(u))
print("min w:" + min(w) + ", max w:" + max(w))
We have print-out:
(0) min u:-90.82411123645161, max u:90.61303594806952
(0) min w:-7.096226984411968e+46, max w:7.458973904421555e+46
The range of "u" looks reasonable, but not "w".
With such "w" we won't expect any reasonable forecast.
When I tried to run using this initial file, it gave error:
[whuang@cy001 run.6488066]$ cat atmosphere_model.80s-83853,r1i1n12.btr
atmosphere_model:83853 terminated with signal 11 at PC=2aaab0b80724 SP=7ffffffd87d8. Backtrace:
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(H5F_has_feature+0x4)[0x2aaab0b80724]
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(+0xa2100)[0x2aaab0b47100]
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(H5D__select_read+0x763)[0x2aaab0b63c83]
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(+0x94547)[0x2aaab0b39547]
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(H5D__read+0x7a5)[0x2aaab0b56915]
/lustre/whuang/impi.sw/18/lib/libhdf5.so.10(H5Dread+0x1b3)[0x2aaab0b55ee3]
/lustre/whuang/impi.sw/18/lib/libnetcdf.so.11(nc4_get_vara+0x1220)[0x2aaaab51a420]
/lustre/whuang/impi.sw/18/lib/libnetcdf.so.11(NC4_get_vara+0x5a)[0x2aaaab5248aa]
/lustre/whuang/impi.sw/18/lib/libnetcdf.so.11(NC_get_vara+0x6a)[0x2aaaab472a3a]
/lustre/whuang/impi.sw/18/lib/libnetcdf.so.11(nc_get_vara_double+0x40)[0x2aaaab470c20]
/lustre/whuang/impi.sw/18/lib/libnetcdff.so.6(nf_get_vara_double_+0x2ce)[0x2aaaaace8d1e]
/lustre/whuang/impi.sw/18/lib/libnetcdff.so.6(netcdf_mp_nf90_get_var_1d_eightbytereal_+0x1186)[0x2aaaaad60aec]
../executables/atmosphere_model[0xbff313]
../executables/atmosphere_model[0xbe4979]
../executables/atmosphere_model[0xa00bd3]
../executables/atmosphere_model[0xa0429a]
../executables/atmosphere_model[0xaad7e2]
../executables/atmosphere_model[0xa248f2]
../executables/atmosphere_model[0xa23d02]
../executables/atmosphere_model[0x51b8c4]
../executables/atmosphere_model[0x423362]
../executables/atmosphere_model[0x4208e9]
../executables/atmosphere_model[0x42089e]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaab02c8b35]
../executables/atmosphere_model[0x4207a9]
How can I fix such error?
Thanks,
Wei
MPAS-Atmosphere Help
Sep 4, 2018, 5:44:40 PM9/4/18
to MPAS-Atmosphere Help
Hi, Wei.
Can you take a look at some of the fields from your x5.6488066.init.nc file? One easy way to do this is with the 'convert_mpas' program, which you can download from https://github.com/mgduda/convert_mpas/. In particular, you may want to check the uReconstructZonal and uReconstructMeridional fields.
Kind regards,
Michael
Wei Huang
Sep 13, 2018, 6:46:04 PM9/13/18
to MPAS-Atmosphere Help
Michael,
I tried the convert_mpas program, run as:
Reading MPAS mesh information from file '../run.6488066/x5.6488066.init.nc'
Reading target domain specification from file 'target_domain'
Setting nlat = 1800
Setting nlon = 3600
Computing remapping weights
Time to compute remap weights: 57.695612 s
Created a new output file
Reading list of fields to include in remapped output
Found 2 lines in 'include_fields' file
Reading list of fields to exclude in remapped output
Found 121 lines in 'exclude_fields' file
Remapping MPAS fields from file '../run.6488066/x5.6488066.init.nc'
Input file has 1 records
Defining fields in output file
Remapping field u, frame 1
read: 574.727177 s
remap: 10.570400 s
write: 4.256009 s
Remapping field w, frame 1
read: 198.864747 s
remap: 8.383455 s
write: 4.089444 s
Total runtime: 881.299131
[whuang@cy001 convert_mpas]$ cat include_fields
u
w
[whuang@cy001 convert_mpas]$ cat chkinit.ncl
f = addfile("latlon.nc", "r")
u = f->u
w = f->w
print("min u:" + min(u) + ", max u:" + max(u))
print("min w:" + min(w) + ", max w:" + max(w))
printVarSummary(u)
printVarSummary(w)
dims = dimsizes(w)
lvl = dims(3)
do n = 0, lvl-1
print("Level: " + n + "min w:" + min(w(0,:,:,n)) + ", max w:" + max(w(0,:,:,n)))
end do
[whuang@cy001 convert_mpas]$ ncl chkinit.ncl
Copyright (C) 1995-2015 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.3.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) min u:-108.5282555376375, max u:108.904405467703
(0) min w:-5.598212796568182e+46, max w:5.221938861306397e+46
Variable: u
Type: double
Total Size: 2125440000 bytes
265680000 values
Number of Dimensions: 4
Dimensions and sizes: [Time | 1] x [latitude | 1800] x [longitude | 3600] x [nVertLevels | 41]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
Variable: w
Type: double
Total Size: 2177280000 bytes
272160000 values
Number of Dimensions: 4
Dimensions and sizes: [Time | 1] x [latitude | 1800] x [longitude | 3600] x [nVertLevelsP1 | 42]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
(0) Level: 0min w:0, max w:0
(0) Level: 1min w:-4.570939902329671e+45, max w:5.825969526936195e+45
(0) Level: 2min w:-4.74182119161955e+45, max w:6.269488288831202e+45
(0) Level: 3min w:-5.022927525009682e+45, max w:6.862101995361405e+45
(0) Level: 4min w:-5.280586915241106e+45, max w:7.465197043533117e+45
(0) Level: 5min w:-6.555982789109286e+45, max w:7.919177289252104e+45
(0) Level: 6min w:-8.005884963235175e+45, max w:8.235460786485164e+45
(0) Level: 7min w:-9.434785085932521e+45, max w:8.259634491158653e+45
(0) Level: 8min w:-1.077859503200933e+46, max w:7.80134708205267e+45
(0) Level: 9min w:-1.118051102013704e+46, max w:9.669106692224682e+45
(0) Level: 10min w:-1.14957136335454e+46, max w:1.267534598303824e+46
(0) Level: 11min w:-1.205371555944554e+46, max w:1.443855962522924e+46
(0) Level: 12min w:-1.830457081631015e+46, max w:1.960820931006962e+46
(0) Level: 13min w:-2.41525541288762e+46, max w:2.679056772772586e+46
(0) Level: 14min w:-2.283440952996701e+46, max w:2.810558946066765e+46
(0) Level: 15min w:-1.767980112794011e+46, max w:2.264415735907145e+46
(0) Level: 16min w:-2.336400052574338e+46, max w:2.288769013918737e+46
(0) Level: 17min w:-3.103131470116961e+46, max w:3.102689718461472e+46
(0) Level: 18min w:-4.079027826765615e+46, max w:4.024176474810659e+46
(0) Level: 19min w:-5.011864851617055e+46, max w:4.847107841155443e+46
(0) Level: 20min w:-5.598212796568182e+46, max w:5.221938861306397e+46
(0) Level: 21min w:-5.465279201581274e+46, max w:4.959948017299643e+46
(0) Level: 22min w:-4.546909738998896e+46, max w:4.210177536548558e+46
(0) Level: 23min w:-3.757433586534406e+46, max w:3.451789263743356e+46
(0) Level: 24min w:-3.712557497290637e+46, max w:3.035629475831722e+46
(0) Level: 25min w:-3.366384647479295e+46, max w:3.029530419986619e+46
(0) Level: 26min w:-3.051670785307675e+46, max w:3.254344990809085e+46
(0) Level: 27min w:-2.879929542215019e+46, max w:3.428645854578188e+46
(0) Level: 28min w:-2.727352350471598e+46, max w:3.580827005344161e+46
(0) Level: 29min w:-2.67683922054426e+46, max w:3.703160910824905e+46
(0) Level: 30min w:-2.898237097619185e+46, max w:3.795756366237386e+46
(0) Level: 31min w:-3.146075364003542e+46, max w:3.978047110813694e+46
(0) Level: 32min w:-3.379690721019053e+46, max w:4.273643902591571e+46
(0) Level: 33min w:-3.61497225466307e+46, max w:4.560725411068023e+46
(0) Level: 34min w:-3.733934213542434e+46, max w:4.684973554396754e+46
(0) Level: 35min w:-3.725173315644628e+46, max w:4.624674247613614e+46
(0) Level: 36min w:-3.70995203335566e+46, max w:4.550838720002478e+46
(0) Level: 37min w:-4.13867116341756e+46, max w:4.491000896498565e+46
(0) Level: 38min w:-4.320128936979583e+46, max w:4.453700878964591e+46
(0) Level: 39min w:-4.764285522062427e+46, max w:4.609823205844233e+46
(0) Level: 40min w:-5.569622992595342e+46, max w:4.766358114147098e+46
(0) Level: 41min w:0, max w:0
So, the "w" value is totally out of range.
Thanks,
Wei
Wei Huang
Oct 8, 2018, 1:34:57 PM10/8/18
to MPAS-Atmosphere Help
Tried convert zgrid and theta, as below:
(0) min w:-5.598212796568182e+46, max w:5.221938861306397e+46
(0) min zgrid:-227.3863862040193, max zgrid:30000.00153668225
Variable: u
Type: double
Total Size: 2125440000 bytes
265680000 values
Number of Dimensions: 4
Dimensions and sizes: [Time | 1] x [latitude | 1800] x [longitude | 3600] x [nVertLevels | 41]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
Variable: theta
Type: double
Total Size: 2125440000 bytes
265680000 values
Number of Dimensions: 4
Dimensions and sizes: [Time | 1] x [latitude | 1800] x [longitude | 3600] x [nVertLevels | 41]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
Variable: w
Type: double
Total Size: 2177280000 bytes
272160000 values
Number of Dimensions: 4
Dimensions and sizes: [Time | 1] x [latitude | 1800] x [longitude | 3600] x [nVertLevelsP1 | 42]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
Variable: zgrid
Number of Dimensions: 3
Dimensions and sizes: [latitude | 1800] x [longitude | 3600] x [nVertLevelsP1 | 42]
Coordinates:
latitude: [-89.94999..89.95]
longitude: [-179.95..179.95]
(0) Level: 0, min u:-40.9095120520588, max u:41.84523467937552
(0) Level: 1, min u:-43.36821241661917, max u:44.08226946202097
(0) Level: 2, min u:-45.73023118691846, max u:46.13555717362274
(0) Level: 3, min u:-47.92215350799295, max u:48.60150100116108
(0) Level: 4, min u:-49.69891039257573, max u:50.16631476858592
(0) Level: 5, min u:-51.08035837997937, max u:51.32150833623712
(0) Level: 6, min u:-52.37102399233424, max u:52.38524501009553
(0) Level: 7, min u:-53.205001893389, max u:52.63599161972577
(0) Level: 8, min u:-53.22657941447742, max u:50.76786106206795
(0) Level: 9, min u:-50.5365849343555, max u:49.13639529933761
(0) Level: 10, min u:-49.07133365077485, max u:50.54595150507087
(0) Level: 11, min u:-52.84377739216832, max u:52.23090067135246
(0) Level: 12, min u:-57.46569950521387, max u:58.33457043816229
(0) Level: 13, min u:-64.28854976858112, max u:67.34697865920167
(0) Level: 14, min u:-74.14174801376225, max u:76.74457221074728
(0) Level: 15, min u:-82.27768817310042, max u:83.56678418337707
(0) Level: 16, min u:-99.31881144765674, max u:101.8394195398674
(0) Level: 17, min u:-107.0011137701546, max u:106.8209210956658
(0) Level: 18, min u:-108.5282555376375, max u:108.904405467703
(0) Level: 19, min u:-106.5452308974767, max u:104.5756769081278
(0) Level: 20, min u:-102.484705940647, max u:99.74407632912296
(0) Level: 21, min u:-94.83473769636666, max u:92.29657128435827
(0) Level: 22, min u:-85.74566168497742, max u:83.52111372389882
(0) Level: 23, min u:-78.12285001699291, max u:76.2320486846202
(0) Level: 24, min u:-68.67066622955269, max u:67.35592568509169
(0) Level: 25, min u:-62.77287122038659, max u:60.12767852235751
(0) Level: 26, min u:-65.65385397257008, max u:62.81430793270454
(0) Level: 27, min u:-68.38989327208635, max u:66.25923716205926
(0) Level: 28, min u:-69.44040448044818, max u:68.31064676974744
(0) Level: 29, min u:-72.22193324908315, max u:73.40941632200143
(0) Level: 30, min u:-75.31199315026623, max u:75.42373254685535
(0) Level: 31, min u:-78.94075901104486, max u:78.18708365742009
(0) Level: 32, min u:-82.56974425079055, max u:81.4769989831275
(0) Level: 33, min u:-84.61446777729036, max u:83.5690721559171
(0) Level: 34, min u:-85.00899464329591, max u:83.35771286624335
(0) Level: 35, min u:-85.40352741813179, max u:83.14633369107962
(0) Level: 36, min u:-84.5284001987518, max u:82.07755647040948
(0) Level: 37, min u:-82.3146620316593, max u:79.36228888676062
(0) Level: 38, min u:-80.10092000109285, max u:78.04563374597419
(0) Level: 39, min u:-78.38382722854966, max u:77.68978395306446
(0) Level: 40, min u:-76.92366159891817, max u:77.33393303158032
(0) Level: 0, min theta:246.6136507207978, max theta:328.3178318944589
(0) Level: 1, min theta:247.7396201111839, max theta:328.3936119162924
(0) Level: 2, min theta:249.5598996516283, max theta:328.4534065325593
(0) Level: 3, min theta:252.1075989367, max theta:328.5661181513954
(0) Level: 4, min theta:253.4053349579328, max theta:328.7456200131811
(0) Level: 5, min theta:255.7304445854234, max theta:328.8469463495349
(0) Level: 6, min theta:258.528801686699, max theta:328.929167159814
(0) Level: 7, min theta:260.7032217902344, max theta:330.6012319758115
(0) Level: 8, min theta:264.3020460203171, max theta:332.4986480819966
(0) Level: 9, min theta:267.5218913870152, max theta:334.9676916291862
(0) Level: 10, min theta:270.0618273877405, max theta:337.3419102422978
(0) Level: 11, min theta:273.0307951675466, max theta:339.9744160760885
(0) Level: 12, min theta:277.8056644826423, max theta:341.9001355577284
(0) Level: 13, min theta:279.8179238313178, max theta:343.9578512151431
(0) Level: 14, min theta:283.4555931532375, max theta:346.0415895027085
(0) Level: 15, min theta:287.8930404054946, max theta:348.2048593538628
(0) Level: 16, min theta:295.3666137009136, max theta:350.4214714321715
(0) Level: 17, min theta:300.5838104644945, max theta:352.9528698071219
(0) Level: 18, min theta:304.2037542830785, max theta:356.3320072417086
(0) Level: 19, min theta:310.0216941282214, max theta:365.1441780871188
(0) Level: 20, min theta:318.0231842815896, max theta:378.8731192834602
(0) Level: 21, min theta:327.2101595014863, max theta:393.8552908946003
(0) Level: 22, min theta:337.4600934369292, max theta:408.8447732883026
(0) Level: 23, min theta:347.9599669249612, max theta:423.3459243884935
(0) Level: 24, min theta:356.2641622842751, max theta:438.9889248201507
(0) Level: 25, min theta:359.7432335535801, max theta:456.8705615889421
(0) Level: 26, min theta:368.8206205040221, max theta:475.3720887421499
(0) Level: 27, min theta:393.6712839544198, max theta:496.4484161959114
(0) Level: 28, min theta:410.7356940286377, max theta:516.0935521308146
(0) Level: 29, min theta:444.4687096532826, max theta:539.4841779641098
(0) Level: 30, min theta:473.5590319037833, max theta:562.3544976561046
(0) Level: 31, min theta:501.9674202118005, max theta:589.9029897492185
(0) Level: 32, min theta:530.2879397122688, max theta:623.0873426240728
(0) Level: 33, min theta:550.8801347206894, max theta:654.7140221875649
(0) Level: 34, min theta:572.1032089547402, max theta:687.9053156794502
(0) Level: 35, min theta:593.9004703444431, max theta:724.409374935762
(0) Level: 36, min theta:617.8982814501744, max theta:755.0363008177433
(0) Level: 37, min theta:645.7825938540003, max theta:788.5677078342536
(0) Level: 38, min theta:674.7765968552187, max theta:826.1978619994372
(0) Level: 39, min theta:704.654499354342, max theta:869.6898492857483
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On Friday, August 31, 2018 at 3:05:30 PM UTC-6, Wei Huang wrote:
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