Segmentation fault, receiving exit code:139 when running WRF

Any issues with the actual running of the WRF.

Segmentation fault, receiving exit code:139 when running WRF

Postby samputland » Wed Oct 16, 2019 1:23 am

Using the following to start the run-
mpirun -np 18 ./wrf.exe

The run is crashing about 24hrs into the run with the following error-

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 4748 RUNNING AT samputland-Precision-5820-Tower
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

namelist is below-

&time_control
run_days = 11,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2016, 2016, 2016,
start_month = 12, 12, 12,
start_day = 29, 29, 29,
start_hour = 12, 12, 12,
end_year = 2017, 2017, 2017,
end_month = 01, 01, 01,
end_day = 09, 09, 09,
end_hour = 12, 12, 12,
interval_seconds = 10800
input_from_file = .true.,.true.,.true.,
history_interval = 180, 180, 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
/

&domains
time_step = 180,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 3,
e_we = 338, 268, 124,
e_sn = 230, 322, 148,
e_vert = 35, 35, 35,
p_top_requested = 5000,
num_metgrid_levels = 32,
num_metgrid_soil_levels = 4,
dx = 36000, 12000, 4000,
dy = 36000, 12000, 4000,
grid_id = 1, 2, 3,
parent_id = 0, 1, 2,
i_parent_start = 1, 136, 164,
j_parent_start = 1, 38, 142,
parent_grid_ratio = 1, 3, 3,
parent_time_step_ratio = 1, 3, 3,
feedback = 0,
smooth_option = 0
/

&physics
physics_suite = 'CONUS'
mp_physics = -1, -1, -1,
cu_physics = -1, -1, 0,
ra_lw_physics = -1, -1, -1,
ra_sw_physics = -1, -1, -1,
bl_pbl_physics = -1, -1, -1,
sf_sfclay_physics = -1, -1, -1,
sf_surface_physics = -1, -1, -1,
radt = 30, 30, 30,
bldt = 0, 0, 0,
cudt = 5, 5, 5,
icloud = 1,
num_land_cat = 21,
sf_urban_physics = 0, 0, 0,
/

&fdda
/

&dynamics
hybrid_opt = 2,
w_damping = 0,
diff_opt = 1, 1, 1,
km_opt = 4, 4, 4,
diff_6th_opt = 0, 0, 0,
diff_6th_factor = 0.12, 0.12, 0.12,
base_temp = 290.
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.,
moist_adv_opt = 1, 1, 1,
scalar_adv_opt = 1, 1, 1,
gwd_opt = 1,
/

&bdy_control
spec_bdy_width = 5,
specified = .true.
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

... and information from the error file.

d01 2016-12-30_09:00:00 Input data is acceptable to use:
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 2 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 3 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 3 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 3 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 1 grid%oid 2
d01 2016-12-30_12:00:00 Input data is acceptable to use:
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 2 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 3 grid%oid 2
mediation_integrate.G 1943 DATASET=HISTORY
mediation_integrate.G 1944 grid%id 3 grid%oid 2

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

Backtrace for this error:
#0 0x14712044b31a
#1 0x14712044a503
#2 0x14711fac7f1f
#3 0x563ef2c07ee5
#4 0x563ef2c26c57
#5 0x563ef2c49961
#6 0x563ef2c591a5
#7 0x563ef27ce075
#8 0x563ef288c92e
#9 0x563ef23d0168
#10 0x563ef22cbf56
#11 0x563ef166c68c
#12 0x563ef1601f59
#13 0x563ef16018ae
#14 0x14711faaab96
#15 0x563ef16018e9
#16 0xffffffffffffffff

I did try setting ulimit -s unlimited
But that didnt work. Any help would be appreciated.
Thanks,
Sam
samputland
 
Posts: 1
Joined: Wed Oct 16, 2019 1:12 am

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