WRFv3.9.1.1 Nesting I/O Problem

Any issues with the actual running of the WRF.

WRFv3.9.1.1 Nesting I/O Problem

Postby twglotfe » Mon May 04, 2020 3:07 pm

Hello,

I'm trying to run a triple nested domain simulation using WRFv3.9.1.1 (i.e., 36km, 12km, 4km). The model initializes and runs successfully up until the first output period. Then the model will crash with a segmentation fault trying to write out the wrfout_d03 file. This file is created but contains no data.

My code is compiled with intel (dmpar) option 15 and I have added the optimization flags for knights landing and skylake nodes to run it on the stampede2 cluster. The code is compiled with large netCDF support on by default. And I am using the "limit stacksize unlimited" line in my run script.

If I deactivate the third nest. The simulation will run successfully. I have tried to change the d03 domain's size and position several times but the error is always the same. Any help with this issue would be greatly appreciated.

My namelist is:
&time_control
run_days = 10,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2009, 2009, 2009,
start_month = 10, 10, 10,
start_day = 01, 01, 01,
start_hour = 00, 00, 00,
start_minute = 00, 00, 00,
start_second = 00, 00, 00,
end_year = 2009, 2009, 2009,
end_month = 10, 10, 10,
end_day = 11, 11, 11,
end_hour = 00, 00, 00,
end_minute = 00, 00, 00,
end_second = 00, 00, 00,
interval_seconds = 21600
input_from_file = .true.,.true.,.true.,
history_interval = 60, 60, 60,
frames_per_outfile = 1, 1, 1,
restart = .false.,
restart_interval = 720,
io_form_history = 2
io_form_restart = 2
io_form_input = 2
io_form_boundary = 2
debug_level = 0
diag_print = 2,
io_form_auxinput2 = 2,
io_form_auxinput4 = 2,
auxinput4_inname = "wrflowinp_d<domain>"
auxinput4_interval = 360, 360, 360,
output_diagnostics = 1,
auxhist3_outname = "wrfxtrm_d<domain>_<date>"
io_form_auxhist3 = 2,
auxhist3_interval = 1440, 1440, 1440,
frames_per_auxhist3 = 1, 1, 1,
write_hist_at_0h_rst = .true.,
/

&domains
time_step = 120,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 3,
s_we = 1,1,1,
e_we = 271,265,301,
s_sn = 1,1,1,
e_sn = 257,220,310,
s_vert = 1, 1, 1,
e_vert = 30, 30, 30,
p_top_requested = 5000,
num_metgrid_levels = 38
dx = 36000,12000,4000,
dy = 36000,12000,4000,
grid_id = 1,2,3,
parent_id = 1,1,2,
i_parent_start = 1,147,62,
j_parent_start = 1,42,70,
parent_grid_ratio = 1,3,3,
parent_time_step_ratio = 1,3,3,
feedback = 1,
smooth_option = 0
wif_input_opt = 1,
num_wif_levels = 30,
/

&physics
mp_physics = 28, 28, 28,
ra_lw_physics = 4, 4, 4,
ra_sw_physics = 4, 4, 4,
radt = 30, 30, 30,
sf_sfclay_physics = 5, 5, 5,
sf_surface_physics = 5, 5, 5,
bl_pbl_physics = 5, 5, 5,
bldt = 0, 0, 0,
cu_physics = 16, 16, 0,
cudt = 5, 5, 5,
icloud = 1,
aer_opt = 3,
cu_rad_feedback = .true.,.true.,.true.,
num_soil_layers = 4,
num_land_cat = 21,
sf_urban_physics = 0, 0, 0,
sst_update = 1,
tmn_update = 1,
sst_skin = 1,
bucket_mm = 1000.0,
bucket_J = 1.e9
use_aero_icbc = .true.
/

&fdda
/

&dynamics
rk_ord = 3,
diff_opt = 1,
km_opt = 4, 4, 4,
diff_6th_opt = 2, 2, 2,
diff_6th_factor = 0.12, 0.12, 0.12,
damp_opt = 3,
base_temp = 290.,
zdamp = 5000., 5000., 5000.,
dampcoef = 0.05, 0.05, 0.05,
khdif = 0, 0, 0,
kvdif = 0, 0, 0,
smdiv = 0.1, 0.1, 0.1,
emdiv = 0.01, 0.01, 0.01,
epssm = 0.1, 0.1, 0.1,
non_hydrostatic = .true., .true., .true.,
top_lid = .false., .false., .false.,
mix_full_fields = .true.,
mix_isotropic = 0, 0, 0,
mix_upper_bound = 0.1, 0.1, 0.1,
tke_drag_coefficient = 0.0, 0.0, 0.0,
tke_heat_flux = 0.0, 0.0, 0.0,
h_mom_adv_order = 5, 5, 5,
v_mom_adv_order = 3, 3, 3,
h_sca_adv_order = 5, 5, 5,
v_sca_adv_order = 3, 3, 3,
moist_adv_opt = 2, 2, 2,
scalar_adv_opt = 2, 2, 2,
chem_adv_opt = 1, 1, 1,
tke_adv_opt = 2, 2, 2,
time_step_sound = 4, 4, 4,
gwd_opt = 0,
/

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


&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

My configure.wrf file has the following flags:

DESCRIPTION = INTEL ($SFC/$SCC)
DMPARALLEL = 1
OMPCPP = # -D_OPENMP
OMP = # -openmp -fpp -auto
OMPCC = # -openmp -fpp -auto
SFC = ifort
SCC = icc
CCOMP = icc
DM_FC = mpif90 -f90=$(SFC)
DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT
FC = time $(DM_FC)
CC = $(DM_CC) -DFSEEKO64_OK
LD = $(FC)
RWORDSIZE = $(NATIVE_RWORDSIZE)
PROMOTION = -real-size `expr 8 \* $(RWORDSIZE)` -i4
ARCH_LOCAL = -DNONSTANDARD_SYSTEM_FUNC -DWRF_USE_CLM
CFLAGS_LOCAL = -w -O3 -ip -xCORE-AVX2 -axCORE-AVX512,MIC-AVX512 #-xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -no-multibyte-chars
LDFLAGS_LOCAL = -ip -xCORE-AVX2 -axCORE-AVX512,MIC-AVX512 #-xHost -fp-model fast=2 -no-prec-div -no-prec-sqrt -ftz -align all -fno-alias -fno-common
CPLUSPLUSLIB =
ESMF_LDFLAG = $(CPLUSPLUSLIB)
FCOPTIM = -O3
FCREDUCEDOPT = $(FCOPTIM)
FCNOOPT = -O0 -fno-inline -no-ip
FCDEBUG = # -g $(FCNOOPT) -traceback # -fpe0 -check noarg_temp_created,bounds,format,output_conversion,pointers,uninit -ftrapuv -unroll0 -u
FORMAT_FIXED = -FI
FORMAT_FREE = -FR
FCSUFFIX =
BYTESWAPIO = -convert big_endian
RECORDLENGTH = -assume byterecl
FCBASEOPTS_NO_G = -ip -traceback -fp-model precise -w -ftz -align all -fno-alias $(FORMAT_FREE) $(BYTESWAPIO) -xCORE-AVX2 -axCORE-AVX512,MIC-AVX512 #-xHost -fp-model fast=2 -no-heap-arrays -no-prec-div -no-prec-sqrt -fno-common
FCBASEOPTS = $(FCBASEOPTS_NO_G) $(FCDEBUG)
MODULE_SRCH_FLAG =
TRADFLAG = -traditional-cpp
CPP = /lib/cpp -P -nostdinc
AR = ar
ARFLAGS = ru
M4 = m4
RANLIB = ranlib
RLFLAGS =
CC_TOOLS = $(SCC)


The segmentation fault message in the rsl.error files is as below:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
wrf.exe 0000000005DA0B2D Unknown Unknown Unknown
libpthread-2.17.s 00002AC4DD4BB5D0 Unknown Unknown Unknown
wrf.exe 0000000005E7DA10 Unknown Unknown Unknown
wrf.exe 000000000078E97E wrf_patch_to_glob 6703 module_dm.f90
wrf.exe 0000000001ABBBB1 collect_generic_a 21853 module_io.f90
wrf.exe 0000000001AB99A1 collect_real_and_ 21550 module_io.f90
wrf.exe 0000000001AB82DE collect_fld_and_c 21472 module_io.f90
wrf.exe 0000000001AB789D wrf_write_field1_ 21262 module_io.f90
wrf.exe 0000000001AB7475 wrf_write_field_ 21059 module_io.f90
wrf.exe 0000000001F49ADF wrf_ext_write_fie 159 wrf_ext_write_field.f90
wrf.exe 0000000001781B47 output_wrf_ 1241 output_wrf.f90
wrf.exe 000000000163A018 module_io_domain_ 53 module_io_domain.f90
wrf.exe 00000000018ECA1C open_hist_w_ 2081 mediation_integrate.f90
wrf.exe 00000000018EBD91 med_hist_out_ 892 mediation_integrate.f90
wrf.exe 00000000018E4E16 med_before_solve_ 67 mediation_integrate.f90
wrf.exe 000000000054AF0B module_integrate_ 317 module_integrate.f90
wrf.exe 000000000054B5B6 module_integrate_ 363 module_integrate.f90
wrf.exe 000000000054B5B6 module_integrate_ 363 module_integrate.f90
wrf.exe 000000000040DE34 module_wrf_top_mp 322 module_wrf_top.f90
wrf.exe 000000000040DDE4 MAIN__ 28 wrf.f90
wrf.exe 000000000040DD7E Unknown Unknown Unknown
libc-2.17.so 00002AC4DD9EC3D5 __libc_start_main Unknown Unknown
wrf.exe 000000000040DC69 Unknown Unknown Unknown
twglotfe
 
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