Two-way coupled WRF-CMAQ process?

Hi ESM,

If you are using ksh, try looking for the .profile file, and edit it to add the path to your mpirun command.

Liz

Hi ESM,

Please change this command from

mpirun -r ssh -np 8 wrf.exe

to

mpirun -np 8 wrf.exe

Hi Liz,

Thank you. It solved that problem, but I have another problem:

set NPROCS = 8
set start_year = 2013
set end_year = 2013
set start_month = 8
set end_month = 8
set start_day = 1
set end_day = 1
set cycle = 0
set firstday = 20130728
set STTIME = 0
set NSTEPS = 240000
set TSTEP = 010000
set version = 3852
set MECH = cb6r3_ae6_aq
set resolution = 12km
setenv NZ 35
set ROOT_DIR = /home/ensiyeh/online
set WRF_DIR = /home/ensiyeh/online/WRFV38
set INPDIR = /home/ensiyeh/online/wrf_38_cmaq_52_input
set OMIpath = /home/ensiyeh/online/WRFV38/cmaq
set OUTPUT_ROOT = /home/ensiyeh/online
set NMLpath = /home/ensiyeh/online/WRFV38/cmaq
set NMLpath2 = /home/ensiyeh/online/WRFV38/cmaq
set NUM_LAND_USE_TYPE = 40
set cont_from_spinup_run = T
set radt = 20
setenv RUN_CMAQ_DRIVER T
setenv DO_SW_CAL T
setenv DO_LW_CAL F
setenv WRF_CMAQ_FREQ 5
setenv CREATE_PHYSICAL_FILE F
setenv FILE_TIME_STEP 10000
setenv WRF_COL_DIM 251
setenv WRF_ROW_DIM 185
setenv WRF_LAY_DIM 36
setenv CMAQ_COL_DIM 236
setenv CMAQ_ROW_DIM 170
setenv TWOWAY_DELTA_X 7
setenv TWOWAY_DELTA_Y 7
setenv WRF_LC_REF_LAT 40.0
setenv CTM_TURN_ON_PV N
setenv SD_TIME_SERIES F
setenv SD_SCOL 241
setenv SD_ECOL 248
setenv SD_SROW 160
setenv SD_EROW 169
setenv SD_CONC_SPCS NO2 NO O3 NO3 CO ASO4J ASO4I ANH4J ANH4I ANO3J ANO3I AORGAJ AORGAI AORGPAJ AORGPAI AORGBJ AORGBI AECJ AECI A25J A25I ACORS ASEAS ASOIL
setenv AVG_CONC_SPCS ALL
setenv CONC_SPCS
setenv CONC_BLEV_ELEV 1 35
setenv ACONC_BLEV_ELEV 1 1
setenv CTM_PROCAN N
setenv PA_BCOL_ECOL 30 100
setenv PA_BROW_EROW 10 50
setenv PA_BLEV_ELEV 1 5
setenv CTM_MAXSYNC 300
setenv CTM_MINSYNC 90
setenv SIGMA_SYNC_TOP 0.7
setenv CTM_ADV_CFL 0.95
setenv AVG_FILE_ENDTIME Y
setenv CTM_CKSUM Y
setenv CTM_WB_DUST N
setenv CTM_ERODE_AGLAND N
setenv CTM_WBDUST_BELD BELD3
setenv CTM_LTNG_NO N
setenv CTM_WVEL N
setenv KZMIN Y
setenv CTM_ILDEPV Y
setenv CTM_MOSAIC N
setenv CTM_ABFLUX N
setenv CTM_HGBIDI N
setenv CTM_SFC_HONO N
setenv CTM_PING N
setenv CTM_PT3DEMIS Y
setenv CTM_FST N
setenv CTM_BIOGEMIS N
setenv PX_VERSION Y
setenv BIOSW_YN N
setenv SUMMER_YN N
setenv AVG_FILE_ENDTIME N
setenv CTM_GRAV_SETL Y
setenv CORESHELL_OPTICS N
setenv MIE_OPTICS N
setenv LTNGPARAM N
setenv LTNG_ASSIM_FLAG N
setenv CTM_ZERO_PCSOA N
setenv IOAPI_LOG_WRITE F
setenv FL_ERR_STOP F
setenv IOAPI_OFFSET_64 Y
setenv CTM_EMISCHK N
setenv PROMPTFLAG F
setenv CLD_DIAG N
setenv CTM_PMDIAG Y
setenv CTM_APMDIAG Y
setenv CTM_AVISDIAG Y
setenv CTM_PHOTDIAG N
setenv CTM_SSEMDIAG N
setenv CTM_DUSTEM_DIAG N
setenv CTM_DEPV_FILE N
setenv B3GTS_DIAG N
setenv APT_DIAG N
setenv PT3DDIAG N
setenv PT3DFRAC N
setenv LTNGDIAG N
setenv VDIFF_DIAG_FILE N
setenv CTM_AOD N
setenv CTM_MGEMDIAG N
setenv REP_LAYER_MIN -1
setenv MPI_SM_POOL 16000
setenv MP_EAGER_LIMIT 65536
setenv MP_SINGLE_THREAD yes
setenv MP_STDOUTMODE ordered
setenv MP_LABELIO yes
setenv MP_SHARED_MEMORY yes
setenv MP_ADAPTER_USE shared
setenv MP_CPU_USE multiple
setenv MP_CSS_INTERRUPT yes
set OCEANfile = ssmask.4BEARPEX2.ncf
set OMIfile = OMI_1979_to_2015.dat
set OPTICSfile = PHOT_OPTICS.dat
set CSQYfile = CSQY_DATA_cb6r3_ae6_aq
set ICFILE = ICON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
set BCFILE = BCON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv RUNID v3852
set ICpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc
set BCpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc
set EMISpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/emis
set IN_PTpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point
set IN_LTpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/lightning
set METpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf
set LUpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/land
set SZpath = /home/ensiyeh/online/wrf_38_cmaq_52_input/land
if ( ( T == T ) || ( F == T ) ) then
setenv CMAQ_WRF_FEEDBACK T
else
set rad_scheme = _rrtmg_20
if ( T == T ) then
if ( F == T ) then
set feedback = sf
endif
else
set call_ratio = 5_1
set output_direct_name = output_12km_sf_rrtmg_20_5_1_v3852_2013
set EXEC = CCTM
set year = 2013
@ pre_year = 2013 - 1
@ cur_year = 2013
@ yr = 2013
@ start_hour = 0 / 10000
@ end_hour = ( 0 + 23 ) % 24
@ cur_year = 2013 - 1
while ( 2012 < 2013 )
@ cur_year++
if ( ( 2013 % 4 ) != 0 ) then
set leap_year_cur_year = 0
else if ( ( 2013 % 400 ) == 0 ) then
if ( 0 ) then
set numday_cur_year = ( 31 28 31 30 31 30 31 31 30 31 30 31 )
if ( ( 2012 % 4 ) != 0 ) then
if ( ( 2012 % 400 ) == 0 ) then
if ( ( 2012 % 100 ) == 0 ) then
set leap_year_pre_year = 1
endif
endif
if ( 2013 == 2013 ) then
@ cur_day_j = 0
@ temp_month = 1
while ( 1 < 8 )
@ cur_day_j = 0 + 31
@ temp_month++
end
while ( 2 < 8 )
@ cur_day_j = 31 + 28
@ temp_month++
end
while ( 3 < 8 )
@ cur_day_j = 59 + 31
@ temp_month++
end
while ( 4 < 8 )
@ cur_day_j = 90 + 30
@ temp_month++
end
while ( 5 < 8 )
@ cur_day_j = 120 + 31
@ temp_month++
end
while ( 6 < 8 )
@ cur_day_j = 151 + 30
@ temp_month++
end
while ( 7 < 8 )
@ cur_day_j = 181 + 31
@ temp_month++
end
while ( 8 < 8 )
@ cur_day_j = 212 + 1
@ pre_day_j = 213 - 1
else
if ( 213 == 1 ) then
if ( 2013 == 2013 ) then
@ cur_month = 8
else
if ( 2013 == 2013 ) then
@ cur_end_month = 8
else
@ cur_month = 8 - 1
while ( 7 < 8 )
@ cur_month++
@ cur_day = 0
@ cur_month_end_day = 31
if ( ( 2013 == 2013 ) && ( 8 == 8 ) ) then
@ cur_day = 1 - 1
endif
if ( ( 2013 == 2013 ) && ( 8 == 8 ) ) then
@ cur_month_end_day = 1
endif
while ( 0 < 1 )
@ cur_day++
set loc_pre_year = 2013
if ( 1 == 1 ) then
@ pre_month = 8 - 1
if ( 7 == 0 ) then
set yest = 31
set yesterday = printf "%d%2.2d%2.2d\n" $loc_pre_year $pre_month $yest
printf %d%2.2d%2.2d\n 2013 7 31
else
set today = printf "%d%2.2d%2.2d\n" $cur_year $cur_month $cur_day
printf %d%2.2d%2.2d\n 2013 8 1
set YYYYMMDD = 20130801
set G_DAY = 20130801
set today_j = printf "%d%3.3d\n" $cur_year $cur_day_j
printf %d%3.3d\n 2013 213
set yesterday_j = printf "%d%3.3d\n" $loc_pre_year $pre_day_j
printf %d%3.3d\n 2013 212
set wrf_tstep = 20
setenv CTM_APPL v3852_20130801
setenv CTM_APPL_yesterday v3852_20130731
if ( ! -d /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013 ) then
set use_profile_init = 0
if ( 20130801 == 20130728 ) then
if ( T == T ) then
setenv FEEDBACK_RSTFLAG .false.
set cont_from_spinup_run = F
set use_profile_init = 1
else
setenv WRF_RSTFLAG .true.
setenv pxlsm_smois_init 0
endif
mkdir /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/20130801
mkdir: cannot create directory ‘/home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/20130801’: File exists
set STDATE = 2013213
set APPL = 20130801
setenv GRIDDESC /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/GRIDDESC
setenv GRID_NAME WRF_CMAQ_2WAY
set DISP = delete
set OUTDIR = /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013
set YEAR = 2013
set MONTH = printf "%2.2d\n" $cur_month
printf %2.2d\n 8
set day = 1
set EMISDATE = printf "%4d%2.2d%2.2d\n" ${YEAR} $cur_month $cur_day
printf %4d%2.2d%2.2d\n 2013 8 1
if ( 1 ) then
setenv INITIAL_RUN Y
else
set test = ls CTM_LOG_???.${APPL}
ls: No match.
if ( != ) then
if ( N == Y ) then
if ( N == Y ) then
if ( N == Y ) then
if ( N == Y ) then
setenv CSQY_DATA /home/ensiyeh/online/WRFV38/cmaq/CSQY_DATA_cb6r3_ae6_aq
if ( ! ( -e /home/ensiyeh/online/WRFV38/cmaq/CSQY_DATA_cb6r3_ae6_aq ) ) then
setenv OCEAN_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/land/ssmask.4BEARPEX2.ncf
setenv EMISfile emis_mole_all_20130801_4BEARPEX2_cmaq_cb05e51_2013ej_v6_13i.ncf
setenv EMIS_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/emis_mole_all_20130801_4BEARPEX2_cmaq_cb05e51_2013ej_v6_13i.ncf
if ( Y == Y || Y == T ) then
setenv NPTGRPS 5
set iday = grep ^$STDATE $INPDIR/mergedates.2013.txt
grep ^2013213 /home/ensiyeh/online/wrf_38_cmaq_52_input/mergedates.2013.txt
setenv STK_GRPS_01 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/stack_groups_ptnonipm_12US1_2013ej_v6_13i.ncf
setenv STK_EMIS_01 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/inln_mole_ptnonipm_20130806_12US1_cmaq_cb05e51_2013ej_v6_13i.ncf
setenv STK_GRPS_02 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/stack_groups_othpt_12US1_2013ej_v6_13i.ncf
setenv STK_EMIS_02 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/inln_mole_othpt_20130806_12US1_cmaq_cb05e51_2013ej_v6_13i.ncf
setenv STK_GRPS_03 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/stack_groups_ptegu_12US1_2013ej_v6_13i.ncf
setenv STK_EMIS_03 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/inln_mole_ptegu_20130801_12US1_cmaq_cb05e51_2013ej_v6_13i.ncf
setenv STK_GRPS_04 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/stack_groups_pt_oilgas_12US1_2013ej_v6_13i.ncf
setenv STK_EMIS_04 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/inln_mole_pt_oilgas_20130806_12US1_cmaq_cb05e51_2013ej_v6_13i.ncf
setenv STK_GRPS_05 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/stack_groups_ptfire_20130801_12US1_2013ej_v6_13i.ncf
setenv STK_EMIS_05 /home/ensiyeh/online/wrf_38_cmaq_52_input/emis/inln_point/inln_mole_ptfire_20130801_12US1_cmaq_cb05e51_2013ej_v6_13i.ncf
unset echo
setenv LAYP_STDATE 2013213
setenv LAYP_STTIME 0
setenv LAYP_NSTEPS 240000
endif
setenv S_CGRID /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_CGRID_v3852_20130801.nc
setenv CTM_CONC_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_CONC_v3852_20130801.nc -v
setenv A_CONC_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_ACONC_v3852_20130801.nc -v
setenv MEDIA_CONC /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_MEDIA_CONC_v3852_20130801.nc -v
setenv CTM_DRY_DEP_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DRYDEP_v3852_20130801.nc -v
setenv CTM_DEPV_DIAG /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DEPV_v3852_20130801.nc -v
setenv CTM_PT3D_DIAG /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PT3D_v3852_20130801.nc -v
setenv B3GTS_S /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_B3GTS_S_v3852_20130801.nc -v
setenv SOILOUT /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_SOILOUT_v3852_20130801.nc
setenv CTM_WET_DEP_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_WETDEP1_v3852_20130801.nc -v
setenv CTM_WET_DEP_2 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_WETDEP2_v3852_20130801.nc -v
setenv CTM_VIS_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PMVIS_v3852_20130801.nc -v
setenv CTM_AVIS_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_APMVIS_v3852_20130801.nc -v
setenv CTM_PMDIAG_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PMDIAG_v3852_20130801.nc -v
setenv CTM_APMDIAG_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_APMDIAG_v3852_20130801.nc -v
setenv CTM_RJ_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PHOTDIAG1_v3852_20130801.nc -v
setenv CTM_RJ_2 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PHOTDIAG2_v3852_20130801.nc -v
setenv CTM_SSEMIS_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_SSEMIS.v3852_20130801.nc -v
setenv CTM_DUST_EMIS_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DUSTEMIS.v3852_20130801.nc -v
setenv CTM_IPR_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PA_1_v3852_20130801.nc -v
setenv CTM_IPR_2 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PA_2_v3852_20130801.nc -v
setenv CTM_IPR_3 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_PA_3_v3852_20130801.nc -v
setenv CTM_IRR_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_IRR_1_v3852_20130801.nc -v
setenv CTM_IRR_2 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_IRR_2_v3852_20130801.nc -v
setenv CTM_IRR_3 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_IRR_3_v3852_20130801.nc -v
setenv CTM_DRY_DEP_MOS /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DDMOS_v3852_20130801.nc -v
setenv CTM_DRY_DEP_FST /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DDFST_v3852_20130801.nc -v
setenv CTM_DEPV_MOS /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DEPVFST_v3852_20130801.nc -v
setenv CTM_DEPV_FST /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DEPVMOS_v3852_20130801.nc -v
setenv CTM_VDIFF_DIAG /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_VDIFF_DIAG_v3852_20130801.nc -v
setenv CTM_VSED_DIAG /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_VSED_DIAG_v3852_20130801.nc -v
setenv CTM_AOD_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_AOD_DIAG_v3852_20130801.nc -v
setenv CTM_LTNGDIAG_1 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_LTNGHRLY_v3852_20130801.nc -v
setenv CTM_LTNGDIAG_2 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_LTNGCOL_v3852_20130801.nc -v
setenv FLOOR_FILE /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/FLOOR_v3852_20130801.txt
setenv LAYER_FILE MET_CRO_3D
setenv GRID_DOT_2D BUFFERED
setenv GRID_CRO_2D BUFFERED
setenv MET_CRO_2D BUFFERED
setenv MET_DOT_3D BUFFERED
setenv MET_CRO_3D BUFFERED
@ n = 0
while ( 0 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 0
setenv feed_back_000 BUFFERED
@ n++
end
while ( 1 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 1
setenv feed_back_001 BUFFERED
@ n++
end
while ( 2 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 2
setenv feed_back_002 BUFFERED
@ n++
end
while ( 3 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 3
setenv feed_back_003 BUFFERED
@ n++
end
while ( 4 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 4
setenv feed_back_004 BUFFERED
@ n++
end
while ( 5 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 5
setenv feed_back_005 BUFFERED
@ n++
end
while ( 6 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 6
setenv feed_back_006 BUFFERED
@ n++
end
while ( 7 < 8 )
set name = printf "_%3.3d\n" $n
printf _%3.3d\n 7
setenv feed_back_007 BUFFERED
@ n++
end
while ( 8 < 8 )
setenv PGRID_DOT_2D /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/GRID_DOT_2D20130801 -v
setenv PGRID_CRO_2D /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/GRID_CRO_2D20130801 -v
setenv PMET_CRO_2D /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/MET_CRO_2D20130801 -v
setenv PMET_DOT_3D /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/MET_DOT_2D20130801 -v
setenv PMET_CRO_3D /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/MET_CRO_3D20130801 -v
if ( F == T ) then
setenv CTM_STDATE 2013213
setenv CTM_STTIME 0
setenv CTM_RUNLEN 240000
setenv CTM_TSTEP 010000
setenv CTM_PROGNAME CCTM
setenv INIT_GASC_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/ICON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv INIT_AERO_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/ICON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv INIT_NONR_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/ICON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv INIT_TRAC_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/ICON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv BNDY_GASC_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/BCON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv BNDY_AERO_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/BCON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv BNDY_NONR_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/BCON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv BNDY_TRAC_1 /home/ensiyeh/online/wrf_38_cmaq_52_input/icbc/BCON.2013213.4BEARPEX2.2013ej_v6_13i.ncf
setenv OMI /home/ensiyeh/online/WRFV38/cmaq/OMI_1979_to_2015.dat
setenv OPTICS_DATA /home/ensiyeh/online/WRFV38/cmaq/PHOT_OPTICS.dat
cd /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013
ln -s /home/ensiyeh/online/WRFV38/cmaq/GC_cb6r3_ae6_aq.nml gc_matrix_nml
ln: failed to create symbolic link ‘gc_matrix_nml’: File exists
ln -s /home/ensiyeh/online/WRFV38/cmaq/AE_cb6r3_ae6_aq.nml ae_matrix_nml
ln: failed to create symbolic link ‘ae_matrix_nml’: File exists
ln -s /home/ensiyeh/online/WRFV38/cmaq/NR_cb6r3_ae6_aq.nml nr_matrix_nml
ln: failed to create symbolic link ‘nr_matrix_nml’: File exists
ln -s /home/ensiyeh/online/WRFV38/cmaq/Species_Table_TR_0.nml tr_matrix_nml
ln: failed to create symbolic link ‘tr_matrix_nml’: File exists
if ( -f namelist.input ) rm -f namelist.input
rm -f namelist.input
cat
rm -f wrfbdy_d01 wrffdda_d01 wrfsfdda_d01 wrfinput_d01 wrflowinp_d01
ln -s /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf/wrfbdy_d01 wrfbdy_d01
ln -s /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf/wrffdda_d01 wrffdda_d01
ln -s /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf/wrfsfdda_d01 wrfsfdda_d01
if ( .true. == .false. ) then
ln -s /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf/wrfrst_d01_2013-08-01_00:00:00 wrfrst_d01_2013-08-01_00:00:00
ln: failed to create symbolic link ‘wrfrst_d01_2013-08-01_00:00:00’: File exists
endif
ln -s /home/ensiyeh/online/wrf_38_cmaq_52_input/met_wrf/wrflowinp_d01 wrflowinp_d01
if ( -f wrf.exe ) rm -f wrf.exe
rm -f wrf.exe
if ( -f ETAMPNEW_DATA ) rm -f ETAMPNEW_DATA
rm -f ETAMPNEW_DATA
if ( -f GENPARM.TBL ) rm -f GENPARM.TBL
rm -f GENPARM.TBL
if ( -f landFilenames ) rm -f landFilenames
rm -f landFilenames
if ( -f LANDUSE.TBL ) rm -f LANDUSE.TBL
rm -f LANDUSE.TBL
if ( -f RRTM_DATA ) rm -f RRTM_DATA
rm -f RRTM_DATA
if ( -f SOILPARM.TBL ) rm -f SOILPARM.TBL
rm -f SOILPARM.TBL
if ( -f tr49t67 ) rm -f tr49t67
rm -f tr49t67
if ( -f tr49t85 ) rm -f tr49t85
rm -f tr49t85
if ( -f tr67t85 ) rm -f tr67t85
rm -f tr67t85
if ( -f VEGPARM.TBL ) rm -f VEGPARM.TBL
rm -f VEGPARM.TBL
ln -s /home/ensiyeh/online/WRFV38/main/wrf.exe wrf.exe
ln -s /home/ensiyeh/online/WRFV38/test/em_real/ETAMPNEW_DATA ETAMPNEW_DATA
ln -s /home/ensiyeh/online/WRFV38/test/em_real/GENPARM.TBL GENPARM.TBL
ln -s /home/ensiyeh/online/WRFV38/test/em_real/landFilenames landFilenames
ln -s /home/ensiyeh/online/WRFV38/test/em_real/LANDUSE.TBL LANDUSE.TBL
ln -s /home/ensiyeh/online/WRFV38/test/em_real/RRTM_DATA RRTM_DATA
ln -s /home/ensiyeh/online/WRFV38/test/em_real/RRTMG_SW_DATA RRTMG_SW_DATA
ln: failed to create symbolic link ‘RRTMG_SW_DATA’: File exists
ln -s /home/ensiyeh/online/WRFV38/test/em_real/RRTMG_LW_DATA RRTMG_LW_DATA
ln: failed to create symbolic link ‘RRTMG_LW_DATA’: File exists
ln -s /home/ensiyeh/online/WRFV38/test/em_real/SOILPARM.TBL SOILPARM.TBL
ln -s /home/ensiyeh/online/WRFV38/test/em_real/tr49t67 tr49t67
ln -s /home/ensiyeh/online/WRFV38/test/em_real/tr49t85 tr49t85
ln -s /home/ensiyeh/online/WRFV38/test/em_real/tr67t85 tr67t85
ln -s /home/ensiyeh/online/WRFV38/test/em_real/VEGPARM.TBL VEGPARM.TBL
ln -s /home/ensiyeh/online/WRFV38/test/em_real/ozone_plev.formatted ozone_plev.formatted
ln: failed to create symbolic link ‘ozone_plev.formatted’: File exists
ln -s /home/ensiyeh/online/WRFV38/test/em_real/ozone_lat.formatted ozone_lat.formatted
ln: failed to create symbolic link ‘ozone_lat.formatted’: File exists
ln -s /home/ensiyeh/online/WRFV38/test/em_real/ozone.formatted ozone.formatted
ln: failed to create symbolic link ‘ozone.formatted’: File exists
date +Started wrf.exe at %m/%d/%y %H:%M:%S
Started wrf.exe at 09/06/19 00:13:13
mpirun -np 8 /home/ensiyeh/online/WRFV38/main/wrf.exe
starting wrf task 0 of 8
starting wrf task 1 of 8
starting wrf task 2 of 8
starting wrf task 3 of 8
starting wrf task 4 of 8
starting wrf task 5 of 8
starting wrf task 6 of 8
starting wrf task 7 of 8

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= 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
177.9u 4.9s 0:25.12 727.9% 0+0k 2290496+588504io 357pf+0w
date +Completed WRF at %m/%d/%y %H:%M:%S%n
Completed WRF at 09/06/19 00:13:38

mv rsl.error.0000 rsl.error.0001 rsl.error.0002 rsl.error.0003 rsl.error.0004 rsl.error.0005 rsl.error.0006 rsl.error.0007 rsl.out.0000 rsl.out.0001 rsl.out.0002 rsl.out.0003 rsl.out.0004 rsl.out.0005 rsl.out.0006 rsl.out.0007 /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/20130801
if ( F == T ) then
if ( N == M-bM^@M^XYM-bM^@M^Y ) then
@ cur_day_j++
@ pre_day_j++
if ( 213 > 214 ) then
end
while ( 1 < 1 )
end
while ( 8 < 8 )
@ pre_year++
end
while ( 2013 < 2013 )

Hi ESM,

If you are using csh or tcsh, try this:

limit stacksize unlimited

If you are using sh or bash, use this command:

ulimit -s unlimited

This may not solve your problem but the default stack size is often quite small and may result in segmentation faults due to insufficient stack memory.

Liz

Hi Liz,

Thank you. That didn’t solve the problem. I searched on GOOGLE and find that it related to timestep, but how can I solve it? Could you guide me, please?
Thank you

In the run script there is a command to mv the rsl.error* files to the following directory.

/home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/20130801

Please examine these files for any additional error messages.

This is the first file:

taskid: 0 hostname: ensiyeh
module_io_quilt_old.F 2931 F
Quilting with 1 groups of 0 I/O tasks.
Ntasks in X 2, ntasks in Y 4
— WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero.
— 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 in use, setting: levsiz=59, alevsiz=12, no_src_types=6
— NOTE: num_soil_layers has been set to 2
WRF V3.8 MODEL


Parent domain
ids,ide,jds,jde 1 251 1 185
ims,ime,jms,jme -4 132 -4 53
ips,ipe,jps,jpe 1 125 1 46


DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1, 272131872 bytes allocated
RESTART run: opening wrfrst_d01_2013-08-01_00:00:00 for reading
Timing for processing restart file for domain 1: 7.44452 elapsed seconds
INITIALIZE THREE Noah LSM RELATED TABLES
Skipping over LUTYPE = USGS
Skipping over LUTYPE = MODIFIED_IGBP_MODIS_NOAH
LANDUSE TYPE = NLCD40 FOUND 40 CATEGORIES
INPUT SOIL TEXTURE CLASSIFICATION = STAS
SOIL TEXTURE CLASSIFICATION = STAS FOUND 19 CATEGORIES
D01 3-D analysis nudging for wind is applied and Guv= 0.5000E-04
D01 3-D analysis nudging for temperature is applied and Gt= 0.5000E-04
D01 3-D analysis nudging for water vapor mixing ratio is applied and Gq= 0.1000E-04
D01 3-D analysis nudging for wind is turned off within the PBL.
D01 3-D analysis nudging for temperature is turned off within the PBL.
D01 3-D analysis nudging for water vapor mixing ratio is turned off within the PBL.
D01 surface analysis nudging for wind is not applied and Guv_sfc= 0.0000E+00
D01 surafce analysis nudging for temperature is not applied and Gt_sfc= 0.0000E+00
D01 surface analysis nudging for water vapor mixing ratio is not applied and Gq_sfc= 0.0000E+00
Timing for Writing wrfout_d01_2013-08-01_00:00:00 for domain 1: 6.34706 elapsed seconds
Time in file: 2013-07-31_21:00:00
Time on domain: 2013-08-01_00:00:00
WARNING Time in input file not equal to time on domain WARNING
WARNING Trying next time in file wrflowinp_d01 …
d01 2013-08-01_00:00:00 Input data processed for aux input 4 for domain 1
Time in file: 2013-07-31_21:00:00
Time on domain: 2013-08-01_00:00:00
WARNING Time in input file not equal to time on domain WARNING
WARNING Trying next time in file wrfsfdda_d01 …
d01 2013-08-01_00:00:00 Input data processed for aux input 9 for domain 1
Time in file: 2013-07-31_21:00:00
Time on domain: 2013-08-01_00:00:00
WARNING Time in input file not equal to time on domain WARNING
WARNING Trying next time in file wrffdda_d01 …
d01 2013-08-01_00:00:00 Input data processed for aux input 10 for domain 1
d01 2013-08-01_00:00:00 WRF restart, LBC starts at 2013-07-31_21:00:00 and restart starts at 2013-08-01_00:00:00
LBC for restart: Starting valid date = 2013-07-31_21:00:00, Ending valid date = 2013-07-32_00:00:00
LBC for restart: Restart time = 2013-08-01_00:00:00
LBC for restart: Looking for a bounding time
LBC for restart: Starting valid date = 2013-08-01_00:00:00, Ending valid date = 2013-08-01_03:00:00
LBC for restart: Found the correct bounding LBC time periods for restart time = 2013-08-01_00:00:00
Timing for processing lateral boundary for domain 1: 0.08487 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 125 JS 1 JE 46
WRF NUMBER OF TILES = 1
D01 3-D analysis nudging reads new data at time = 4320.000 min.
D01 3-D analysis nudging bracketing times = 4320.00 4500.00 min.
D01 surface analysis nudging reads new data at time = 4320.000 min.
D01 surface analysis nudging bracketing times = 4320.00 4500.00 min.
Timing for main: time 2013-08-01_00:00:20 on domain 1: 21.26612 elapsed seconds
Timing for main: time 2013-08-01_00:00:40 on domain 1: 2.56015 elapsed seconds
Timing for main: time 2013-08-01_00:01:00 on domain 1: 2.55300 elapsed seconds
Timing for main: time 2013-08-01_00:01:20 on domain 1: 2.51556 elapsed seconds
Timing for main: time 2013-08-01_00:01:40 on domain 1: 2.48356 elapsed seconds
application called MPI_Abort(MPI_COMM_WORLD, 74006504) - process 0

Try the following commands to search for an error message in either the rsl.error* files or the rsl.out* files

cd /home/ensiyeh/online/output_12km_sf_rrtmg_20_5_1_v3852_2013/20130801
grep -i error rsl.error*
grep -i error rsl.out*

above file was rsl.error.0000
belove file is rsl.out.0000

rsl.out (copy).0000.txt (60.7 KB)

Hi ESM,

This message was at the end of your rsl.out* file
>>—>> WARNING in subroutine OPEN3
File CTM_DRY_DEP_1 already opened READONLY; cannot subsequently open it for READ/WRITE.

 Could not open CTM_DRY_DEP_1    file for update - try to open new
 
 >>--->> WARNING in subroutine OPEN3
 File CTM_DRY_DEP_1    already opened; cannot subsequently create it "NEW".
 


 *** ERROR ABORT in subroutine OPDDEP on PE 000          
 Could not create CTM_DRY_DEP_1    file
 Date and time 1:00:00   Aug. 1, 2013   (2013213:010000)

It may be occurring because you ran the model once, and generated output that it is then trying to overwrite the second time that you run the model.
Be sure to change the run script to allow it to overwrite the output data, if the following type of environment variable is available in your script.

#> Keep or Delete Existing Output Files
set CLOBBER_DATA = TRUE

If it is not available, then just be sure to remove or move the output prior to re-running the model.

Hi Liz,
Thank you. I did it and run.log is the same. The rsl.out.0000 file is:
New Text Document (2).txt (145.1 KB)

Hi ESM,

This time, the end of your rsl.out.000 file contains a different error message.

 >>> WARNING in subroutine WRITE3 <<<
 Time step error writing file:  S_CGRID         
 Requested date & time:      2013213:000320
 File starting date & time:  2013213:000140
 File time step:                     ******

 *** ERROR ABORT in subroutine WR_CGRID on PE 000        
 Could not write S_CGRID
 Date and time 0:03:20   Aug. 1, 2013   (2013213:000320)

I am not familiar with this error.

@wong.david-c David - do you have any suggestions for how to diagnose this error?

Hi,

Which version of the two-way model are you using?

Hi David,

According to the log file, the WRF version was 3.8.

ESM - can you try using the latest release of the two-way version that is available from the CMAS Center Download site under the CMAQ v5.3 page. CMAQ version 5.3 Release (August 2019)
Please download and try the WRFv4.1.1-CMAQv5.3 Tarball

Thank you,
Liz

Hi ESM,

Please try the latest version of the WRF-CMAQ two-way coupled model as Liz has suggested. If you insist to use an older version, I can work with you directly to resolve your issue.

Hi David,

Thank you for your answer. I use WRF-3.8 and CMAQ-5.2.

Hi

I installed WRFV3.8-CMAQV5.2 TWO-WAY. But I couldn’t run it. The error is:

 Value for CTM_CKSUM:  Y returning TRUE
 Value for CTM_ILDEPV:  Y returning TRUE
 Value for CTM_ABFLUX:  N returning FALSE
 Value for CTM_SFC_HONO:  N returning FALSE
 Value for CTM_MOSAIC:  N returning FALSE
 Value for CTM_HGBIDI:  N returning FALSE
 Value for CTM_DEPV_FILE:  N returning FALSE
 Flag for writing the DEPV diagnostic file                                       
 DEPV_INIT: writes GAS DEPV values to CTM_DEPV_FILE                                                                      
 DEPV_INIT: completed INIT_GAS_DV block 

 Value for KZMIN:  Y returning TRUE
 Value for CTM_GRAV_SETL:  Y returning TRUE
 Using J-,K-mode aerosols gravitational settling                                 
 Value for VDIFF_DIAG_FILE:  N returning FALSE
 Writing the VDIFF diagnostic files                                              
 
 >>--->> WARNING in subroutine OPEN3
 File CTM_DRY_DEP_1    already opened READONLY; cannot subsequently open it for READ/WRITE.
 
 Could not open CTM_DRY_DEP_1    file for update - try to open new
 
 >>--->> WARNING in subroutine OPEN3
 File CTM_DRY_DEP_1    already opened; cannot subsequently create it "NEW".
 


 *** ERROR ABORT in subroutine OPDDEP on PE 000          
 Could not create CTM_DRY_DEP_1    file
 Date and time 1:00:00   Aug. 1, 2013   (2013213:010000)

Could you help me, please?
Thank you

New Text Document (8).txt (62.2 KB)

Please either move or remove the existing file
/home/fce/TEST/output_12km_sf_rrtmg_20_5_1_v3852_2013/CCTM_DRYDEP_v3852_20130801.nc"

Or, if you are running CMAQv5.3, you can use this setting in your run script to automatically delete existing output files.

#> Keep or Delete Existing Output Files
set CLOBBER_DATA = TRUE

For CMAQv5.2 use the following setting:

set DISP = delete            #> [ delete | update | keep ] existing output files

Hi Wong,
I am using WRF 4.1.1 and latest version of CMAQ now ( WRF-CMAQ two-way). But my question is how to run the model? I have done the benchmark successfully, but how can I do my own simulation?
Is there any user guide?
Please kindly help me in this regard,
Best wishes

Hi Setareh,

If you have run the coupled successfully with the EPA provided test dataset, you can replace the data path in the script with the path of your own data. If you have additional question, please contact me directly.