allen6510w
New member
I am getting a segmentation fault almost immediately when I run v4.3 of WRF-Chem with KPP using cu_physics = 3 and chem_opt = 112. For debug_level = 3000, the last output I see is
d01 2012-05-19_18:00:00 call cumulus_driver
d01 2012-05-19_18:00:00 calling inc/HALO_CUP_G3_IN_inline.inc
d01 2012-05-19_18:00:00 in grelldrv
[borgu024:17293:0:17293] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8)
The code runs for cu_physics = 5 or 0 and it also runs for cu_physics = 3 when chem_opt = 0.
Can you see any issues with my namelist or job script that might be responsible for the error? Do you have any suggestions for debugging etc.
Thanks, Dale
&time_control
run_days = 0,
run_hours = 6,
run_minutes = 0,
run_seconds = 0,
start_year = 2012, 2012,
start_month = 05, 05,
start_day = 19, 19,
start_hour = 18, 18,
start_minute = 00, 00,
start_second = 00, 00,
end_year = 2012, 2012,
end_month = 05, 05,
end_day = 20, 20,
end_hour = 00, 00,
end_minute = 00, 00,
end_second = 00, 00,
interval_seconds = 21600
input_from_file = .true.,.true.,
history_interval = 10, 10,
frames_per_outfile = 1000, 1000,
restart = .false.,
restart_interval = 720,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 3000,
io_form_auxinput5 = 2,
frames_per_auxinput5 = 1, 1,
auxinput5_inname = 'wrfchemi_d<domain>_<date>',
auxinput5_interval_m = 60, 60,
io_form_auxinput6 = 2,
frames_per_auxinput6 = 1, 1,
auxinput6_inname = 'wrfbiochemi_d<domain>',
auxinput6_interval_m = 2160, 720, 43200,
io_form_auxinput7 = 2,
frames_per_auxinput7 = 1, 1,
auxinput7_inname = 'wrffirechemi_d<domain>_<date>',
auxinput7_interval_m = 60, 60,
io_form_auxinput14 = 2,
frames_per_auxinput14 = 1, 1,
auxinput14_inname = 'wrfaircraftchemi_d<domain>_<date>',
auxinput14_interval_m = 60, 60,
ignore_iofields_warning = .true.,
force_use_old_data = .true.,
!io_form_auxinput? = 2,
!frames_per_auxinput? = 1, 1, 1,
!auxinput?_inname = 'wrflda_d<domain>_<date>',
!auxinput?_interval_m = 10, 10, 60,
!auxinput?_begin_h = 4,4,
!auxinput?_end_h = 8,8,
nocolons = .true.,
/
&domains
time_step = 30,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
e_we = 200, 331,
e_sn = 160, 256,
e_vert = 90, 90,
p_top_requested = 5000,
num_metgrid_levels = 40,
num_metgrid_soil_levels = 4,
dx = 6000, 2000,
dy = 6000, 2000,
grid_id = 1, 2,
parent_id = 0, 1,
i_parent_start = 1, 43,
j_parent_start = 1, 44,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0,
track_loc_in = 4,
eta_levels = 1.000000, 0.995800, 0.991700, 0.983400, 0.975000, 0.956500, 0.937100, 0.917600, 0.897900, 0.878000, 0.857700, 0.837500, 0.816800,
0.796200, 0.775400, 0.754500, 0.733500, 0.712500, 0.691500, 0.670600, 0.649800, 0.629300, 0.608900, 0.588800, 0.569100, 0.549800, 0.530900,
0.512700, 0.494900, 0.477500, 0.460600, 0.444000, 0.427900, 0.412100, 0.396700, 0.381700, 0.367100, 0.353000, 0.339300, 0.325800, 0.312800,
0.300100, 0.287800, 0.275800, 0.264200, 0.252900, 0.242000, 0.231400, 0.221100, 0.211100, 0.201400, 0.192100, 0.183000, 0.174300, 0.165800,
0.157600, 0.149700, 0.142100, 0.134700, 0.127500, 0.120700, 0.113900, 0.107500, 0.101200, 0.095200, 0.089400, 0.083900, 0.078500, 0.073400,
0.068400, 0.063500, 0.058900, 0.054300, 0.049800, 0.045600, 0.041500, 0.037600, 0.033900, 0.030400, 0.026900, 0.023700, 0.020500, 0.017500,
0.014600, 0.011900, 0.009300, 0.006800, 0.004400, 0.002200, 0.000000
/
&physics
mp_physics = 17, 17,
ra_lw_physics = 4, 4,
ra_sw_physics = 4, 4,
radt = 10, 10,
do_radar_ref = 1,
sf_sfclay_physics = 1, 1,
sf_surface_physics = 2, 2,
num_soil_layers = 4,
bl_pbl_physics = 1, 1,
bldt = 0, 0,
cudt = 0, 0,
cu_rad_feedback = .true.,.true.,
cu_diag = 1, 1,
cu_physics = 3, 0,
cugd_avedx = 1,
isfflx = 1,
ifsnow = 0,
icloud = 1,
ishallow = 1,
surface_input_source = 1,
num_land_cat = 24,
sf_urban_physics = 0, 0,
sf_ocean_physics = 0,
topo_wind = 0, 0,
mp_zero_out = 2,
hail_opt = 1,
lightning_option = 1, 1,
lightning_dt = 30, 10,
lightning_start_seconds = 600,600,
flashrate_factor = 17,2.496,
cldtop_adjustment = 0, 2,
iccg_method = 2, 2,
!ltng_temp_upper = -45., -45.,
!ltng_temp_lower = -40., -40.,
!lda_opt = 1,
!lda_start_h = 4,
!lda_start_min = 0,
!lda_end_h = 8,
!lda_end_min = 0,
!ldaa = 0.30,
!ldab = 0.2,
!ldac = 0.02,
!ldad = 0.25,
!ldarhmax = 1.00,
!ldatmin = 263.15,
!ldatmax = 285.15,
!ldarhtd = 0.95,
!ldarhtd_damp = 0.75,
!lda_flash_min = 800,
/
&fdda
/
&dynamics
tracer_opt = 0, 0, 2, 2,
w_damping = 1,
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 = 1,
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 = 2, 2, 2, 2,
scalar_adv_opt = 2, 2, 2, 2,
tracer_adv_opt = 2, 2, 2, 2,
chem_adv_opt = 2, 2, 2, 2,
tke_adv_opt = 2, 2, 2, 2,
moist_adv_opt = 2, 2, 1,
scalar_adv_opt = 2, 2, 1,
gwd_opt = 1,
use_baseparam_fr_nml = .true.,
emdiv = 0.01
smdiv = 0.1
epssm = 0.1
iso_temp = 0,
/
&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true., .false.,.false.,
nested = .false., .true., .true.,
/
&grib2
/
&chem
kemit = 11,
kemit_aircraft = 90,
chem_opt = 112, 112,
!chem_opt = 0, 0,
track_chem_num = 4,
track_chem_name = 'o3','co','no','no2',
bioemdt = 60, 60,
photdt = 60, 60,
chemdt = 2., 2.,
io_style_emissions = 2,
emiss_inpt_opt = 111, 111,
emiss_opt = 8, 8,
emiss_opt_vol = 0,
aircraft_emiss_opt = 1, 1,
chem_in_opt = 1, 1,
phot_opt = 3, 3,
gas_drydep_opt = 1, 1,
aer_drydep_opt = 1, 1,
bio_emiss_opt = 3, 3,
ne_area = 118,
gas_bc_opt = 112, 112,
gas_ic_opt = 112, 112,
aer_bc_opt = 112, 112,
aer_ic_opt = 112, 112,
gaschem_onoff = 1, 1,
aerchem_onoff = 0, 0,
wetscav_onoff = 1, 1,
!wetscav_onoff = 0, 0,
cldchem_onoff = 0, 0,
vertmix_onoff = 1, 1,
!chem_conv_tr = 0, 0,
chem_conv_tr = 1, 1,
conv_tr_wetscav = 1, 1,
conv_tr_aqchem = 1, 1,
seas_opt = 1,
dust_opt = 1,
dmsemis_opt = 1,
biomass_burn_opt = 1, 1,
plumerisefire_frq = 60, 30,
have_bcs_chem = .true., .true.,
aer_ra_feedback = 0, 0,
opt_pars_out = 0,
chemdiag = 1, 1,
! lnox_opt = 0, 0,
! N_IC = 82, 300,82,
! N_CG = 82, 300,82,
! lnox_passive = .false.,.false.,
! ltg_temp_upper = -45., -45.,
! ltg_temp_lower = -40., -40.,
/
&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/
Job Script:
#!/usr/bin/csh
#SBATCH -J e0519_a0
#SBATCH --nodes=4 --ntasks=24 --cpus-per-task=2 --ntasks-per-node=6
#SBATCH --constraint=hasw
#SBATCH --time=1:00:00
#SBATCH -o output.%j
#SBATCH --account=????
source /usr/share/modules/init/csh
module purge
module load comp/gcc/9.2.0 mpi/impi/2021.4.0
setenv HOME /discover/nobackup/USRID/wrfchem
setenv DIR $HOME/WRFCHEM/Libs
setenv LDFLAGS -L$DIR/grib2/lib
setenv CPPFLAGS -I$DIR/grib2/include
setenv LD_LIBRARY_PATH $DIR/grib2/lib:$LD_LIBRARY_PATH
setenv JASPERLIB $DIR/grib2/lib
setenv JASPERINC $DIR/grib2/include
setenv HDF5 $DIR/grib2
setenv CPPFLAGS -I$DIR/grib2/include
setenv LDFLAGS -L$DIR/grib2/lib
setenv PATH $DIR/NETCDF/bin:$PATH
setenv CPPFLAGS -I$DIR/NETCDF/include
setenv LDFLAGS -L$DIR/NETCDF/lib
setenv LD_LIBRARY_PATH $DIR/NETCDF/lib:$LD_LIBRARY_PATH
setenv JASPER_INC $DIR/grib2/include
setenv PNG_INC $DIR/grib2/include
setenv NCEPLIBS_DIR $DIR/nceplibs
setenv NETCDF $DIR/NETCDF
setenv PATH $HOME/WRFCHEM/GrADS/Contents:$PATH
setenv WRF_EM_CORE 1
setenv WRF_NMM_CORE 0
setenv WRF_CHEM 1
setenv WRF_KPP 1
setenv YACC '/usr/bin/yacc -d'
setenv KPP_HOME $HOME/WRFCHEM/WRF-4.3/chem/KPP/kpp/kpp-2.1
setenv WRF_SRC_ROOT_DIR $HOME/WRFCHEM/WRF-4.3
setenv PATH $KPP_HOME/bin:$PATH
setenv SED /usr/bin/sed
setenv WRFIO_NCD_LARGE_FILE_SUPPORT 1
setenv FLEX /usr/local/other/Flex/2.5.35/bin/flex
setenv FLEX_LIB_DIR /usr/local/other/Flex/2.5.35/lib
#setenv OMP_NUM_THREADS 2
#setenv OMP_STACKSIZE 1G
#setenv KMP_AFFINITY compact
#setenv I_MPI_PIN_DOMAIN auto
mpirun -perhost 6 -np 24 ./wrf.exe
echo "Hello World"
d01 2012-05-19_18:00:00 call cumulus_driver
d01 2012-05-19_18:00:00 calling inc/HALO_CUP_G3_IN_inline.inc
d01 2012-05-19_18:00:00 in grelldrv
[borgu024:17293:0:17293] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8)
The code runs for cu_physics = 5 or 0 and it also runs for cu_physics = 3 when chem_opt = 0.
Can you see any issues with my namelist or job script that might be responsible for the error? Do you have any suggestions for debugging etc.
Thanks, Dale
&time_control
run_days = 0,
run_hours = 6,
run_minutes = 0,
run_seconds = 0,
start_year = 2012, 2012,
start_month = 05, 05,
start_day = 19, 19,
start_hour = 18, 18,
start_minute = 00, 00,
start_second = 00, 00,
end_year = 2012, 2012,
end_month = 05, 05,
end_day = 20, 20,
end_hour = 00, 00,
end_minute = 00, 00,
end_second = 00, 00,
interval_seconds = 21600
input_from_file = .true.,.true.,
history_interval = 10, 10,
frames_per_outfile = 1000, 1000,
restart = .false.,
restart_interval = 720,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 3000,
io_form_auxinput5 = 2,
frames_per_auxinput5 = 1, 1,
auxinput5_inname = 'wrfchemi_d<domain>_<date>',
auxinput5_interval_m = 60, 60,
io_form_auxinput6 = 2,
frames_per_auxinput6 = 1, 1,
auxinput6_inname = 'wrfbiochemi_d<domain>',
auxinput6_interval_m = 2160, 720, 43200,
io_form_auxinput7 = 2,
frames_per_auxinput7 = 1, 1,
auxinput7_inname = 'wrffirechemi_d<domain>_<date>',
auxinput7_interval_m = 60, 60,
io_form_auxinput14 = 2,
frames_per_auxinput14 = 1, 1,
auxinput14_inname = 'wrfaircraftchemi_d<domain>_<date>',
auxinput14_interval_m = 60, 60,
ignore_iofields_warning = .true.,
force_use_old_data = .true.,
!io_form_auxinput? = 2,
!frames_per_auxinput? = 1, 1, 1,
!auxinput?_inname = 'wrflda_d<domain>_<date>',
!auxinput?_interval_m = 10, 10, 60,
!auxinput?_begin_h = 4,4,
!auxinput?_end_h = 8,8,
nocolons = .true.,
/
&domains
time_step = 30,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
e_we = 200, 331,
e_sn = 160, 256,
e_vert = 90, 90,
p_top_requested = 5000,
num_metgrid_levels = 40,
num_metgrid_soil_levels = 4,
dx = 6000, 2000,
dy = 6000, 2000,
grid_id = 1, 2,
parent_id = 0, 1,
i_parent_start = 1, 43,
j_parent_start = 1, 44,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0,
track_loc_in = 4,
eta_levels = 1.000000, 0.995800, 0.991700, 0.983400, 0.975000, 0.956500, 0.937100, 0.917600, 0.897900, 0.878000, 0.857700, 0.837500, 0.816800,
0.796200, 0.775400, 0.754500, 0.733500, 0.712500, 0.691500, 0.670600, 0.649800, 0.629300, 0.608900, 0.588800, 0.569100, 0.549800, 0.530900,
0.512700, 0.494900, 0.477500, 0.460600, 0.444000, 0.427900, 0.412100, 0.396700, 0.381700, 0.367100, 0.353000, 0.339300, 0.325800, 0.312800,
0.300100, 0.287800, 0.275800, 0.264200, 0.252900, 0.242000, 0.231400, 0.221100, 0.211100, 0.201400, 0.192100, 0.183000, 0.174300, 0.165800,
0.157600, 0.149700, 0.142100, 0.134700, 0.127500, 0.120700, 0.113900, 0.107500, 0.101200, 0.095200, 0.089400, 0.083900, 0.078500, 0.073400,
0.068400, 0.063500, 0.058900, 0.054300, 0.049800, 0.045600, 0.041500, 0.037600, 0.033900, 0.030400, 0.026900, 0.023700, 0.020500, 0.017500,
0.014600, 0.011900, 0.009300, 0.006800, 0.004400, 0.002200, 0.000000
/
&physics
mp_physics = 17, 17,
ra_lw_physics = 4, 4,
ra_sw_physics = 4, 4,
radt = 10, 10,
do_radar_ref = 1,
sf_sfclay_physics = 1, 1,
sf_surface_physics = 2, 2,
num_soil_layers = 4,
bl_pbl_physics = 1, 1,
bldt = 0, 0,
cudt = 0, 0,
cu_rad_feedback = .true.,.true.,
cu_diag = 1, 1,
cu_physics = 3, 0,
cugd_avedx = 1,
isfflx = 1,
ifsnow = 0,
icloud = 1,
ishallow = 1,
surface_input_source = 1,
num_land_cat = 24,
sf_urban_physics = 0, 0,
sf_ocean_physics = 0,
topo_wind = 0, 0,
mp_zero_out = 2,
hail_opt = 1,
lightning_option = 1, 1,
lightning_dt = 30, 10,
lightning_start_seconds = 600,600,
flashrate_factor = 17,2.496,
cldtop_adjustment = 0, 2,
iccg_method = 2, 2,
!ltng_temp_upper = -45., -45.,
!ltng_temp_lower = -40., -40.,
!lda_opt = 1,
!lda_start_h = 4,
!lda_start_min = 0,
!lda_end_h = 8,
!lda_end_min = 0,
!ldaa = 0.30,
!ldab = 0.2,
!ldac = 0.02,
!ldad = 0.25,
!ldarhmax = 1.00,
!ldatmin = 263.15,
!ldatmax = 285.15,
!ldarhtd = 0.95,
!ldarhtd_damp = 0.75,
!lda_flash_min = 800,
/
&fdda
/
&dynamics
tracer_opt = 0, 0, 2, 2,
w_damping = 1,
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 = 1,
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 = 2, 2, 2, 2,
scalar_adv_opt = 2, 2, 2, 2,
tracer_adv_opt = 2, 2, 2, 2,
chem_adv_opt = 2, 2, 2, 2,
tke_adv_opt = 2, 2, 2, 2,
moist_adv_opt = 2, 2, 1,
scalar_adv_opt = 2, 2, 1,
gwd_opt = 1,
use_baseparam_fr_nml = .true.,
emdiv = 0.01
smdiv = 0.1
epssm = 0.1
iso_temp = 0,
/
&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true., .false.,.false.,
nested = .false., .true., .true.,
/
&grib2
/
&chem
kemit = 11,
kemit_aircraft = 90,
chem_opt = 112, 112,
!chem_opt = 0, 0,
track_chem_num = 4,
track_chem_name = 'o3','co','no','no2',
bioemdt = 60, 60,
photdt = 60, 60,
chemdt = 2., 2.,
io_style_emissions = 2,
emiss_inpt_opt = 111, 111,
emiss_opt = 8, 8,
emiss_opt_vol = 0,
aircraft_emiss_opt = 1, 1,
chem_in_opt = 1, 1,
phot_opt = 3, 3,
gas_drydep_opt = 1, 1,
aer_drydep_opt = 1, 1,
bio_emiss_opt = 3, 3,
ne_area = 118,
gas_bc_opt = 112, 112,
gas_ic_opt = 112, 112,
aer_bc_opt = 112, 112,
aer_ic_opt = 112, 112,
gaschem_onoff = 1, 1,
aerchem_onoff = 0, 0,
wetscav_onoff = 1, 1,
!wetscav_onoff = 0, 0,
cldchem_onoff = 0, 0,
vertmix_onoff = 1, 1,
!chem_conv_tr = 0, 0,
chem_conv_tr = 1, 1,
conv_tr_wetscav = 1, 1,
conv_tr_aqchem = 1, 1,
seas_opt = 1,
dust_opt = 1,
dmsemis_opt = 1,
biomass_burn_opt = 1, 1,
plumerisefire_frq = 60, 30,
have_bcs_chem = .true., .true.,
aer_ra_feedback = 0, 0,
opt_pars_out = 0,
chemdiag = 1, 1,
! lnox_opt = 0, 0,
! N_IC = 82, 300,82,
! N_CG = 82, 300,82,
! lnox_passive = .false.,.false.,
! ltg_temp_upper = -45., -45.,
! ltg_temp_lower = -40., -40.,
/
&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/
Job Script:
#!/usr/bin/csh
#SBATCH -J e0519_a0
#SBATCH --nodes=4 --ntasks=24 --cpus-per-task=2 --ntasks-per-node=6
#SBATCH --constraint=hasw
#SBATCH --time=1:00:00
#SBATCH -o output.%j
#SBATCH --account=????
source /usr/share/modules/init/csh
module purge
module load comp/gcc/9.2.0 mpi/impi/2021.4.0
setenv HOME /discover/nobackup/USRID/wrfchem
setenv DIR $HOME/WRFCHEM/Libs
setenv LDFLAGS -L$DIR/grib2/lib
setenv CPPFLAGS -I$DIR/grib2/include
setenv LD_LIBRARY_PATH $DIR/grib2/lib:$LD_LIBRARY_PATH
setenv JASPERLIB $DIR/grib2/lib
setenv JASPERINC $DIR/grib2/include
setenv HDF5 $DIR/grib2
setenv CPPFLAGS -I$DIR/grib2/include
setenv LDFLAGS -L$DIR/grib2/lib
setenv PATH $DIR/NETCDF/bin:$PATH
setenv CPPFLAGS -I$DIR/NETCDF/include
setenv LDFLAGS -L$DIR/NETCDF/lib
setenv LD_LIBRARY_PATH $DIR/NETCDF/lib:$LD_LIBRARY_PATH
setenv JASPER_INC $DIR/grib2/include
setenv PNG_INC $DIR/grib2/include
setenv NCEPLIBS_DIR $DIR/nceplibs
setenv NETCDF $DIR/NETCDF
setenv PATH $HOME/WRFCHEM/GrADS/Contents:$PATH
setenv WRF_EM_CORE 1
setenv WRF_NMM_CORE 0
setenv WRF_CHEM 1
setenv WRF_KPP 1
setenv YACC '/usr/bin/yacc -d'
setenv KPP_HOME $HOME/WRFCHEM/WRF-4.3/chem/KPP/kpp/kpp-2.1
setenv WRF_SRC_ROOT_DIR $HOME/WRFCHEM/WRF-4.3
setenv PATH $KPP_HOME/bin:$PATH
setenv SED /usr/bin/sed
setenv WRFIO_NCD_LARGE_FILE_SUPPORT 1
setenv FLEX /usr/local/other/Flex/2.5.35/bin/flex
setenv FLEX_LIB_DIR /usr/local/other/Flex/2.5.35/lib
#setenv OMP_NUM_THREADS 2
#setenv OMP_STACKSIZE 1G
#setenv KMP_AFFINITY compact
#setenv I_MPI_PIN_DOMAIN auto
mpirun -perhost 6 -np 24 ./wrf.exe
echo "Hello World"