wrf.exe....segmentation fault (core dumped)

Any issues with the actual running of the WRF.

wrf.exe....segmentation fault (core dumped)

Postby Bhavana Medisetti » Tue Sep 26, 2017 1:27 am

Hello all, while running wrf.exe I am getting error help me.
error:
code: calling inc/PERIOD_BDY_EM_INIT_inline.inc
calling inc/PERIOD_BDY_EM_MOIST_inline.inc
calling inc/PERIOD_BDY_EM_TKE_inline.inc
calling inc/PERIOD_BDY_EM_SCALAR_inline.inc
calling inc/PERIOD_BDY_EM_CHEM_inline.inc
calling inc/HALO_EM_INIT_1_inline.inc
calling inc/HALO_EM_INIT_2_inline.inc
calling inc/HALO_EM_INIT_3_inline.inc
calling inc/HALO_EM_INIT_4_inline.inc
calling inc/HALO_EM_INIT_5_inline.inc
calling inc/PERIOD_BDY_EM_INIT_inline.inc
calling inc/PERIOD_BDY_EM_MOIST_inline.inc
calling inc/PERIOD_BDY_EM_TKE_inline.inc
calling inc/PERIOD_BDY_EM_SCALAR_inline.inc
calling inc/PERIOD_BDY_EM_CHEM_inline.inc
start_domain_em: Returning
open_hist_w : opening wrfout_d01_2017-08-19_00:00:00 for writing.
calling wrf_open_for_write_begin in open_w_dataset
module_io.F: in wrf_open_for_write_begin, FileName = wrfout_d01_2017-08-19_00:00:00
calling outsub in open_w_dataset
back from outsub in open_w_dataset
calling wrf_open_for_write_commit in open_w_dataset
Information: NOFILL being set for writing to wrfout_d01_2017-08-19_00:00:00
back from wrf_open_for_write_commit in open_w_dataset
med_hist_out: opened wrfout_d01_2017-08-19_00:00:00 as DATASET=HISTORY
mediation_integrate.b 1724 DATASET=HISTORY
mediation_integrate.b 1725 grid%id 1 grid%oid 1
Timing for Writing wrfout_d01_2017-08-19_00:00:00 for domain 1: 0.98959 elapsed seconds
in med_latbound_in preparing to read
Opening: wrfbdy_d01
med_latbound_in: calling input_boundary
mminlu = 'USGS'
Timing for processing lateral boundary for domain 1: 0.25734 elapsed seconds
module_integrate: calling solve interface
WRF NUMBER OF TILES FROM OMP_GET_MAX_THREADS = 1
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 227 JS 1 JE 114
WRF NUMBER OF TILES = 1
grid spacing, dt, time_step_sound= 3000.00000 12.0000000 4
calling inc/HALO_EM_A_inline.inc
calling inc/PERIOD_BDY_EM_A_inline.inc
calling inc/HALO_EM_PHYS_A_inline.inc
Top of Radiation Driver
CALL cldfra1
Have o3rad
CALL rrtmg_lw
CALL swrad
calling inc/HALO_PWP_inline.inc
in MYJSFC
in NOAH DRV

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x2AAAAB10EBF7
#1 0x2AAAAB10DDF0
#2 0x2AAAABDC266F
#3 0x22A69AE in __module_sf_noahdrv_MOD_lsm
#4 0x1A9D6FB in __module_surface_driver_MOD_surface_driver._omp_fn.8 at module_surface_driver.f90:?
#5 0x2AAAAB7209EE
#6 0x1AEE794 in __module_surface_driver_MOD_surface_driver
#7 0x1459FA5 in __module_first_rk_step_part1_MOD_first_rk_step_part1
#8 0x100695A in solve_em_
#9 0xF1B8BB in solve_interface_
#10 0x4646FE in __module_integrate_MOD_integrate
#11 0x406A63 in __module_wrf_top_MOD_wrf_run

namelist.wps

code: &share
wrf_core = 'ARW',
max_dom = 2,
start_date = '2017-08-19_00:00:00', '2017-08-19_00:00:00',
end_date = '2017-08-23_00:00:00', '2017-08-23_00:00:00',
interval_seconds = 21600,
io_form_geogrid = 2,
opt_output_from_geogrid_path = '/home/mbhavana/GFS_data/BEP+LULC+LSP/',
debug_level = 1000,
/

&geogrid
parent_id = 1,1,
parent_grid_ratio = 1,3,
i_parent_start = 1,78,
j_parent_start = 1,79,
e_we = 227,217,
e_sn = 228,214,
geog_data_res = 'CHA+default+31s','CHA+30s',
dx = 3000,
dy = 3000,
map_proj = 'mercator',
ref_lat = 30.718,
ref_lon = 76.759,
truelat1 = 30.718,
truelat2 = 0,
stand_lon = 78.748,


namelist.input

code: &time_control
run_days = 4,
run_hours = 00,
run_minutes = 0,
run_seconds = 0,
start_year = 2017, 2017,
start_month = 08, 08,
start_day = 19, 19,
start_hour = 00, 00,
start_minute = 00, 00,
start_second = 00, 00,
end_year = 2017, 2017,
end_month = 08, 08,
end_day = 23, 23,
end_hour = 00, 00,
end_minute = 00, 00,
end_second = 00, 00,
interval_seconds = 21600,
input_from_file = .true., .false.,
history_interval = 60, 60,
frames_per_outfile = 1, 1,
restart = .false.,
restart_interval = 5000,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 100,
/

&domains
eta_levels = 1.0, 0.9937, 0.9874, 0.9811, 0.9748, 0.9686, 0.9617, 0.9539, 0.9449, 0.9343, 0.9217, 0.9063, 0.8875, 0.8647, 0.8369, 0.8037, 0.7647, 0.7199, 0.6699, 0.6155, 0.558, 0.4988, 0.439, 0.38, 0.3225, 0.2674, 0.2149, 0.1656, 0.1194, 0.0764, 0.0366, 0.0,
time_step = 12,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 2,
e_we = 227, 217,
e_sn = 228, 214,
e_vert = 32, 32,
p_top_requested = 5000,
num_metgrid_levels = 32,
num_metgrid_soil_levels = 4,
dx = 3000, 1000,
dy = 3000, 1000,
grid_id = 1, 2,
parent_id = 1, 1,
i_parent_start = 1, 78,
j_parent_start = 1, 79,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0,
/

&physics
mp_physics = 21, 21,
ra_lw_physics = 4, 4,
ra_sw_physics = 1, 1,
radt = 3, 1,
sf_sfclay_physics = 2, 2,
sf_surface_physics = 2, 2,
bl_pbl_physics = 2, 2,
bldt = 0, 0,
cu_physics = 14, 14,
cudt = 0, 0,
[isfflx = 1,
ifsnow = 0,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 2, 2,
num_urban_layers = 5400,
num_land_cat = 24,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
/

&fdda
/

&dynamics
w_damping = 0,
diff_opt = 1,
km_opt = 4,
diff_6th_opt = 0, 0,
diff_6th_factor = 0.12, 0.12,
base_temp = 290.,
damp_opt = 0,
zdamp = 5000., 5000.,
dampcoef = 0.2, 0.2,
khdif = 0, 0,
kvdif = 0, 0,
non_hydrostatic = .true., .true.,
moist_adv_opt = 1, 1,
scalar_adv_opt = 1, 1,
/

&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true., .false.,
nested = .false., .true.,
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/
Bhavana Medisetti
 
Posts: 7
Joined: Fri Sep 01, 2017 7:33 am

Re: wrf.exe....segmentation fault (core dumped)

Postby kwthomas » Thu Sep 28, 2017 4:33 pm

Hi...

Any chance you are using Intel compiler version 17.0.4.196 Build 20170411 (ifort -V)?

It builds bad binaries for me on STAMPEDE2. All seg fault or hang early. I had opt=2 and opt=3 do this. I had to use opt=0 to get it to run in an operational experiment. I didn't try opt=1.

For the compiler, WRF was built at opt=2, as one of the microphysics schemes we use would always crash at startup with opt=3.
Kevin W. Thomas
Center for Analysis and Prediction of Storms
University of Oklahoma
kwthomas
 
Posts: 208
Joined: Thu Aug 07, 2008 6:53 pm

Re: wrf.exe....segmentation fault (core dumped)

Postby Bhavana Medisetti » Thu Oct 12, 2017 5:58 am

kwthomas wrote:Hi...

Any chance you are using Intel compiler version 17.0.4.196 Build 20170411 (ifort -V)?

It builds bad binaries for me on STAMPEDE2. All seg fault or hang early. I had opt=2 and opt=3 do this. I had to use opt=0 to get it to run in an operational experiment. I didn't try opt=1.

For the compiler, WRF was built at opt=2, as one of the microphysics schemes we use would always crash at startup with opt=3.



Sir,
I made changes what you said but again I got same issue ,while running wrf.exe it's showing segmentation fault(core dumped).
Bhavana Medisetti
 
Posts: 7
Joined: Fri Sep 01, 2017 7:33 am

Re: wrf.exe....segmentation fault (core dumped)

Postby kwthomas » Thu Oct 12, 2017 5:52 pm

Hi...

It is always possible you are using in incompatible set of physics schemes. We've run into
that from time to time. You might try some alternate values to see what happens. Since
we've never run the NSSL 1-moment schemes (even though we work with NSSL), I don't
know what might not work.

Since you are aborting quickly, maybe there is a problem with your initial conditions.

You can always do the standard of reducing your timestep and see if that fixes it. 12 secs is
already a bit low for a 3km run, however, we've had some not work with older versions of
WRF, those these are initialize with real data include NEXRAD data. It will be slow, but
you can try 9 secs.

You might also try a "configure -d", which will set you up for a debug run. Maybe more
useful info will come out here.
Kevin W. Thomas
Center for Analysis and Prediction of Storms
University of Oklahoma
kwthomas
 
Posts: 208
Joined: Thu Aug 07, 2008 6:53 pm


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