Cant run WRF after Dataset Upgrade on 7/19/2017

Any issues with the actual running of the WRF.

Cant run WRF after Dataset Upgrade on 7/19/2017

Postby ngallia » Fri Feb 16, 2018 11:45 am

Hello,
We have (had) WRF running every 6 hours for a forecast service, however since 7/19/2017 it stopped working. I've seen the message in http://www2.mmm.ucar.edu/wrf/users/wpsv3.9/known-prob-3.9.html, and tried the solution proposed (both update WPS or ungrib only), I've successfuly recompiled completely WRF & WPS 3.7, 3.8, 3.9.0.1, 3.9, 3.9.1. Also tried many other things like getting brand new WPS_geog files, changed timestep, namelist files, sf_surface_physics parameter, and anything else I found on the forums, however the issue persists.
I'm running a single 7km domain, GFS border conditions

Basically, if I use data previous to 7/19 WRF executes flawlessly, with data from 7/19 or recent, wrf.exe presents the following sintoms:

CONSOLE:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7F5E6AF32E08
#1 0x7F5E6AF31F90
#2 0x7F5E6A2244AF
#3 0x1C4D972 in __module_cu_kfeta_MOD_kf_eta_para
#4 0x1C6269D in __module_cu_kfeta_MOD_kf_eta_cps
#5 0x1709D31 in __module_cumulus_driver_MOD_cumulus_driver._omp_fn.1 at module_cumulus_driver.f90:?
#6 0x7F5E6A9FB43D
#7 0x7F5E6A5C06B9
#8 0x7F5E6A2F641C
#9 0xFFFFFFFFFFFFFFFF
Violación de segmento (`core' generado)


WRF.LOG
(header looks fine, then hundred of lines like:)
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PLEASE help me in getting the service back online!

Find below the complete files obtained for a reduced execution using 7/20 data: (let me know if I should provide anything else)

namelist.input
&time_control
run_days = 0 ,
run_hours = 3 ,
run_minutes = 0 ,
run_seconds = 0 ,
start_year = 2017,2017,2017,2017 ,
start_month = 07,07,07,07 ,
start_day = 20,20,20,20 ,
start_hour = 12,12,12,12 ,
start_minute = 00,00,00,00 ,
start_second = 00,00,00,00 ,
end_year = 2017,2017,2017,2017 ,
end_month = 07,07,07,07 ,
end_day = 20,20,20,20,
end_hour = 15,15,15,15,
end_minute = 00,00,00,00,
end_second = 00,00,00,00,
interval_seconds = 10800 ,
history_interval = 60,
frames_per_outfile = 1000,1000,1000,
restart = .false.,
restart_interval = 0,
input_from_file = .T.,.T.,.T.,
io_form_history = 2 ,
io_form_restart = 2 ,
io_form_input = 2 ,
io_form_boundary = 2 ,
debug_level = 0 ,
/

&domains
use_adaptive_time_step = .true.
step_to_output_time = .true.
target_cfl = 1.2
max_step_increase_pct = 5
starting_time_step = -1
max_time_step = -1
min_time_step = -1
smooth_cg_topo = .false.
time_step = 28,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
s_we = 1,
e_we = 220,
s_sn = 1,
e_sn = 330,
s_vert = 1,
e_vert = 38,
p_top_requested = 5000,
num_metgrid_levels = 27,
dx = 7000,
dy = 7000,
grid_id = 1,
parent_id = 1,
i_parent_start = 1,
j_parent_start = 1,
parent_grid_ratio = 1,
parent_time_step_ratio = 1,
feedback = 0,
smooth_option = 0,
/

&physics
mp_physics = 6,
ra_lw_physics = 1,
ra_sw_physics = 1,
radt = 7,
sf_sfclay_physics = 2,
sf_surface_physics = 2,
bl_pbl_physics = 2,
bldt = 0,
cu_physics = 1,
cudt = 0,
isfflx = 1,
ifsnow = 1,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
num_land_cat = 24,
sst_update = 0,
/

&fdda
grid_fdda = 0, 0, 0,
obs_nudge_opt = 0, 0, 0,
/

&dynamics
w_damping = 1,
diff_opt = 1,
km_opt = 4,
diff_6th_opt = 0, 0, 0,
diff_6th_factor = 0.12, 0.12, 0.12,
base_pres = 100000.,
base_temp = 290.,
base_lapse = 50.,
damp_opt = 3,
zdamp = 5000., 5000., 5000.,
dampcoef = 0.2, 0.2, 0.2,
khdif = 0, 0, 0,
kvdif = 0, 0, 0,
non_hydrostatic = .true., .true., .true.,
/

&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .T., .F., .F.,
nested = .F., .T., .T.,
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/


namelist.wps
&share
wrf_core = 'ARW',
max_dom = 1,
start_date = '2017-07-20_12:00:00','2017-07-20_12:00:00','2017-07-20_12:00:00','2017-07-20_12:00:00'
end_date = '2017-07-20_15:00:00','2017-07-20_15:00:00','2017-07-20_15:00:00','2017-07-20_15:00:00'
interval_seconds = 10800
io_form_geogrid = 2,
opt_output_from_geogrid_path = '/home/wrf/WRF-OPERATIVO-3.9.1-B/corrida-12Z',
debug_level = 0,
/

&geogrid
parent_id = 1,
parent_grid_ratio = 1,
i_parent_start = 1,
j_parent_start = 1,
e_we = 220,
e_sn = 330,
geog_data_res = '30s',
dx = 7000,
dy = 7000,
map_proj = 'lambert',
ref_lat = -48,
ref_lon = -70,
truelat1 = -48,
truelat2 = -48,
stand_lon = -70,
ref_x = 110.0,
ref_y = 165.0,
geog_data_path='/home/wrf/WRF-OPERATIVO-3.9.1-B/WPS_geog',
opt_geogrid_tbl_path='/home/wrf/WRF-OPERATIVO-3.9.1-B/corrida-12Z',

/

&ungrib
out_format='WPS',
prefix='FILE',
/

&metgrid
fg_name= 'FILE' ,
constants_name= './SST:2017-07-19_00',
io_form_metgrid= 2,
opt_output_from_metgrid_path='/home/wrf/WRF-OPERATIVO-3.9.1-B/corrida-12Z',
opt_metgrid_tbl_path='/home/wrf/WRF-OPERATIVO-3.9.1-B/corrida-12Z',
/


real.log
--- WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero.
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: grid_fdda is 0 for domain 1, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 1, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: bl_pbl_physics /= 4, implies mfshconv must be 0, resetting
Need MYNN PBL for icloud_bl = 1, resetting to 0
--- NOTE: RRTMG radiation is not used, setting: o3input=0 to avoid data pre-processing
*************************************
No physics suite selected.
Physics options will be used directly from the namelist.
*************************************
--- NOTE: num_soil_layers has been set to 4
REAL_EM V3.9.1 PREPROCESSOR
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 2166190404 bytes allocated
Time period # 1 to process = 2017-07-20_12:00:00.
Time period # 2 to process = 2017-07-20_15:00:00.
Total analysis times to input = 2.

-----------------------------------------------------------------------------

Domain 1: Current date being processed: 2017-07-20_12:00:00.0000, which is loop # 1 out of 2
configflags%julyr, %julday, %gmt: 2017 201 12.0000000
metgrid input_wrf.F first_date_input = 2017-07-20_12:00:00
metgrid input_wrf.F first_date_nml = 2017-07-20_12:00:00
Timing for input 2 s.
flag_soil_layers read from met_em file is 1
Max map factor in domain 1 = 1.02. Scale the dt in the model accordingly.
Using sfcprs3 to compute psfc
Converged znw(kte) should be about 0.0 = -1.53362122E-03
Full level index = 1 Height = 0.0 m
Full level index = 2 Height = 56.6 m Thickness = 56.6 m
Full level index = 3 Height = 137.9 m Thickness = 81.4 m
Full level index = 4 Height = 244.7 m Thickness = 106.8 m
Full level index = 5 Height = 377.6 m Thickness = 132.9 m
Full level index = 6 Height = 546.3 m Thickness = 168.7 m
Full level index = 7 Height = 761.1 m Thickness = 214.8 m
Full level index = 8 Height = 1016.2 m Thickness = 255.0 m
Full level index = 9 Height = 1336.5 m Thickness = 320.3 m
Full level index = 10 Height = 1667.4 m Thickness = 330.9 m
Full level index = 11 Height = 2009.7 m Thickness = 342.3 m
Full level index = 12 Height = 2364.2 m Thickness = 354.5 m
Full level index = 13 Height = 3038.0 m Thickness = 673.8 m
Full level index = 14 Height = 3711.9 m Thickness = 673.8 m
Full level index = 15 Height = 4385.7 m Thickness = 673.8 m
Full level index = 16 Height = 5059.5 m Thickness = 673.8 m
Full level index = 17 Height = 5733.3 m Thickness = 673.8 m
Full level index = 18 Height = 6407.1 m Thickness = 673.8 m
Full level index = 19 Height = 7080.9 m Thickness = 673.8 m
Full level index = 20 Height = 7754.8 m Thickness = 673.8 m
Full level index = 21 Height = 8428.6 m Thickness = 673.8 m
Full level index = 22 Height = 9102.4 m Thickness = 673.8 m
Full level index = 23 Height = 9776.2 m Thickness = 673.8 m
Full level index = 24 Height = 10450.0 m Thickness = 673.8 m
Full level index = 25 Height = 11123.8 m Thickness = 673.8 m
Full level index = 26 Height = 11797.7 m Thickness = 673.8 m
Full level index = 27 Height = 12471.5 m Thickness = 673.8 m
Full level index = 28 Height = 13145.3 m Thickness = 673.8 m
Full level index = 29 Height = 13819.1 m Thickness = 673.8 m
Full level index = 30 Height = 14492.9 m Thickness = 673.8 m
Full level index = 31 Height = 15166.8 m Thickness = 673.8 m
Full level index = 32 Height = 15840.6 m Thickness = 673.8 m
Full level index = 33 Height = 16514.4 m Thickness = 673.8 m
Full level index = 34 Height = 17188.2 m Thickness = 673.8 m
Full level index = 35 Height = 17862.0 m Thickness = 673.8 m
Full level index = 36 Height = 18535.8 m Thickness = 673.8 m
Full level index = 37 Height = 19209.7 m Thickness = 673.8 m
Full level index = 38 Height = 19883.5 m Thickness = 673.8 m
flag value of flag_qnwfa is 0
Old data, no inland lake information
Assume Noah LSM input
127 51 water and category 7 both at 50%, landmask is 0.00000000
110 74 water and category 7 both at 50%, landmask is 0.00000000
98 150 water and category 19 both at 50%, landmask is 0.00000000
54 190 water and category 15 both at 50%, landmask is 0.00000000
70 201 water and category 15 both at 50%, landmask is 0.00000000
68 222 water and category 15 both at 50%, landmask is 0.00000000
76 222 water and category 15 both at 50%, landmask is 0.00000000
63 223 water and category 15 both at 50%, landmask is 0.00000000
61 254 water and category 15 both at 50%, landmask is 0.00000000
78 275 water and category 15 both at 50%, landmask is 0.00000000
forcing artificial silty clay loam at 89 points, out of 72051
LAND CHANGE = 0
WATER CHANGE = 0
Timing for processing 6 s.
Timing for output 2 s.
Timing for loop # 1 = 10 s.

-----------------------------------------------------------------------------

Domain 1: Current date being processed: 2017-07-20_15:00:00.0000, which is loop # 2 out of 2
configflags%julyr, %julday, %gmt: 2017 201 15.0000000
metgrid input_wrf.F first_date_input = 2017-07-20_15:00:00
metgrid input_wrf.F first_date_nml = 2017-07-20_12:00:00
Timing for input 1 s.
flag_soil_layers read from met_em file is 1
Using sfcprs3 to compute psfc
flag value of flag_qnwfa is 0
Old data, no inland lake information
Assume Noah LSM input
forcing artificial silty clay loam at 1 points, out of 72051
LAND CHANGE = 0
WATER CHANGE = 0
Timing for processing 1 s.
LBC valid between these times 2017-07-20_12:00:00.0000 2017-07-20_15:00:00
Timing for output 1 s.
Timing for loop # 2 = 3 s.
real_em: SUCCESS COMPLETE REAL_EM INIT


WRF.log
--- WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero.
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: grid_fdda is 0 for domain 1, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 1, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: bl_pbl_physics /= 4, implies mfshconv must be 0, resetting
Need MYNN PBL for icloud_bl = 1, resetting to 0
--- NOTE: RRTMG radiation is not used, setting: o3input=0 to avoid data pre-processing
*************************************
No physics suite selected.
Physics options will be used directly from the namelist.
*************************************
--- NOTE: num_soil_layers has been set to 4
WRF V3.9.1 MODEL
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 1640922180 bytes allocated
med_initialdata_input: calling input_input
Timing for processing wrfinput file (stream 0) for domain 1: 0.60460 elapsed seconds
Max map factor in domain 1 = 1.02. Scale the dt in the model accordingly.
INPUT LandUse = "USGS"
LANDUSE TYPE = "USGS" FOUND 33 CATEGORIES 2 SEASONS WATER CATEGORY = 16 SNOW CATEGORY = 24
INITIALIZE THREE Noah LSM RELATED TABLES
LANDUSE TYPE = USGS FOUND 27 CATEGORIES
INPUT SOIL TEXTURE CLASSIFICATION = STAS
SOIL TEXTURE CLASSIFICATION = STAS FOUND 19 CATEGORIES
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Timing for Writing wrfout_d01_2017-07-20_12:00:00 for domain 1: 0.93697 elapsed seconds
Timing for processing lateral boundary for domain 1: 0.05802 elapsed seconds
WRF NUMBER OF TILES FROM OMP_GET_MAX_THREADS = 8
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 220 JS 1 JE 42
WRF TILE 2 IS 1 IE 220 JS 43 JE 83
WRF TILE 3 IS 1 IE 220 JS 84 JE 124
WRF TILE 4 IS 1 IE 220 JS 125 JE 165
WRF TILE 5 IS 1 IE 220 JS 166 JE 206
WRF TILE 6 IS 1 IE 220 JS 207 JE 247
WRF TILE 7 IS 1 IE 220 JS 248 JE 288
WRF TILE 8 IS 1 IE 220 JS 289 JE 330
WRF NUMBER OF TILES = 8
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Timing for main (dt= 28.00): time 2017-07-20_12:00:28 on domain 1: 8.42377 elapsed seconds
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ngallia
 
Posts: 6
Joined: Thu Jun 23, 2016 1:20 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby ngallia » Mon Feb 26, 2018 7:48 am

No one? Where else can I go for help?
ngallia
 
Posts: 6
Joined: Thu Jun 23, 2016 1:20 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby MeteoAdriatic » Tue Feb 27, 2018 1:51 pm

Did you updated Vtable.GFS?
MeteoAdriatic
 
Posts: 18
Joined: Wed Apr 30, 2008 6:07 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby ngallia » Wed Feb 28, 2018 8:01 am

MeteoAdriatic wrote:Did you updated Vtable.GFS?


Hi MeteoAdriatic
I did, updated both Vtable.GFS, and METGRID.TBL.ARW from the WPSV3.9.1.TAR file.
ngallia
 
Posts: 6
Joined: Thu Jun 23, 2016 1:20 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby MeteoAdriatic » Wed Feb 28, 2018 4:26 pm

OK. What is your input data. Is it whole GFS grib or partial output cut by gribfilter or something similar?
MeteoAdriatic
 
Posts: 18
Joined: Wed Apr 30, 2008 6:07 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby ngallia » Thu Mar 01, 2018 12:16 pm

MeteoAdriatic wrote:OK. What is your input data. Is it whole GFS grib or partial output cut by gribfilter or something similar?


Indeed, It's a partial output obtained from gribfilter every day... makes me think, I havent tried generating a new "magic URL", yet.
ngallia
 
Posts: 6
Joined: Thu Jun 23, 2016 1:20 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby MeteoAdriatic » Sat Mar 03, 2018 6:28 am

Oh, did you included new variable named LANDN in your gribfilter fetch?
MeteoAdriatic
 
Posts: 18
Joined: Wed Apr 30, 2008 6:07 pm

Re: Cant run WRF after Dataset Upgrade on 7/19/2017

Postby ngallia » Tue Mar 20, 2018 12:36 pm

Sorry for the radio silence. You've hit the nail, I added LANDN to gribfilter and I was able to execute WRF again. Very much appreciated.
ngallia
 
Posts: 6
Joined: Thu Jun 23, 2016 1:20 pm


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