Problem running benchmark tutorial

CMAQ Run Time Errors and Issues
1

Hi
I was running cctm in domain 1 and I got this error.
I don’t know why I got the error.

WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 9, 10, 1) and species HNO3 Back-up number 1
WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 9, 10, 1) and species MEK Back-up number 2
WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 9, 10, 1) and species HNO3 Back-up number 3
WARNING: EBI Euler convergence failure
Reducing EBI time step because of convergence failure for
Cell ( 9, 10, 1) Back-up number 4
WARNING: EBI Euler convergence failure
Reducing EBI time step because of convergence failure for
Cell ( 9, 10, 1) Back-up number 5
ERROR: Max number of EBI time step reductions exceeded
Convergence failure for cell ( 9, 10, 1)
Convergence failure for the following species:
NO2

 *** ERROR ABORT in subroutine HRSOLVER on PE 017
 ERROR: Stopping because of EBI convergence failures

PM3EXIT: DTBUF 0:00:00 July 1, 2014
Date and time 0:00:00 July 1, 2014 (2014182:000000)

Someone could help me how can I do? Thanks in advance.

2

Please review the posting guidelines.

  • What version of the model are you using?
  • What is this modeling case? Is it the benchmark tutorial, or something of your own?
  • Does this error occur immediately, or after running for several hours or days?

Convergence problems in the chemistry solver are almost always due to something other than the chemistry. Most often, it’s the emissions. Check the log file. Are there earlier indications that something has gone wrong, such as NaNs or Infinity values after any of the science processes?

3

I am using CMAQv5.0.2. Modeling case is the benchmark tutorial.
And this error occur immediately…

I already ran this script once before. Same emission file, same model version, same year etc…
Just a different day.

Check the BCON, Completed, but only 4.1% run.
And I checked the CCTM log file that run once, there is no

after CHEM G 1.2139966E-01 A 7.7209222E+08 N 6.6850305E-05
Value for CTM_AERDIAG: N returning FALSE
after AERO G 1.2139888E-01 A 2.3707535E+09 N 3.8464957E-05

in this log file.

4

I do not understand what you mean when you say that BCON completed, but only 4.1% was run.

Since you are running the benchmark case, please follow the steps in the tutorial.
If you run into a problem, please post your run script and the entire log file. (Since the model aborts very quickly, the log file is not large.)

5
  • run script

#! /bin/csh -f

====================== CCTMv5.0.2 Run Script ======================

Usage: run.cctm >&! cctm_D502a.log &

The following environment variables must be set for this script to

execute properly:

setenv M3DATA = input/output data directory

To report problems or request help with this script/program:

http://www.cmascenter.org/html/help.html

===================================================================

#> Source the config.cmaq file to set the run environment
source …/config.cmaq

#> Check that M3DATA is set:
if ( ! -e $M3DATA ) then
echo " $M3DATA path does not exist"
exit 1
endif
echo " “; echo " Input data path, M3DATA set to $M3DATA”; echo " "

set Project = org
set do = d01
set YY = 2014
set Target_MM = 05
set MM_S = 04
set DD_S = 21
set J_SDATE = 111
set RUNLEN = 40

set PROC = mpi #> serial or mpi
set APPL = {Project}_{do}{YY}-{Target_MM}
set CFG = lea
set MECH = saprc99_ae5_aq
set EXEC = CCTM${CFG}_$EXEC_ID

#> horizontal domain decompositio
#if ( $PROC == serial ) then

setenv NPCOL_NPROW “1 1”; set NPROCS = 1 # single processor setting

#else
setenv NPCOL_NPROW “3 4”; set NPROCS = 12
#endif
#> Set the working directory:
set BASE = M3HOME/scripts/cctm set BLD = {BASE}/BLD_${CFG}

cd $BASE; date; cat $BASE/cfg.$CFG; echo " "; set echo

#> timestep run parameters

set STDATE = {YY}{J_SDATE} # beginning date
set STTIME = 000000 # beginning GMT time (HHMMSS)
set NSTEPS = 9600000 # time duration (HHMMSS) for this run
set TSTEP = 010000 # output time step interval (HHMMSS)
set YEAR = {YY} set YR = 14 set MONTH = {MM_S}
set DAY = {DD_S} set YMD = {YY}{MM_S}{DD_S}

=====================================================================

CCTM Configuration Options

=====================================================================

#setenv LOGFILE $BASE/$APPL.log #> log file name; uncomment to write standard output to a log, otherwise write to screen

setenv GRIDDESC /home/lea/mcip/{do}_{YY}${J_SDATE}/GRIDDESC #> horizontal grid defn
setenv GRID_NAME 01 #> check GRIDDESC file for GRID_NAME options

#setenv CONC_SPCS “O3” #> CONC file species; comment or set to “ALL” to write all species to CONC
#setenv CONC_BLEV_ELEV " 1 1" #> CONC file layer range; comment to write all layers to CONC

setenv AVG_CONC_SPCS “ALL” #> ACONC file species; comment or set to “ALL” to write all species to ACONC
setenv ACONC_BLEV_ELEV " 1 15" #> ACONC file layer range; comment to write all layers to ACONC
#setenv ACONC_END_TIME Y #> override default beginning ACON timestamp [ default: N ]

setenv CTM_MAXSYNC 300 #> max sync time step (sec) [default: 720]
setenv CTM_MINSYNC 60 #> min sync time step (sec) [default: 60]
setenv CTM_CKSUM Y #> write cksum report [ default: Y ]
setenv CLD_DIAG N #> write cloud diagnostic file [ default: N ]
setenv CTM_AERDIAG N #> aerosol diagnostic file [ default: N ]
setenv CTM_PHOTDIAG N #> photolysis diagnostic file [ default: N ]
setenv CTM_SSEMDIAG N #> sea-salt emissions diagnostic file [ default: N ]
setenv CTM_PHOTDIAG N #> photolysis diagnostic file [ default: N ]
setenv CTM_SSEMDIAG N #> sea-salt emissions diagnostic file [ default: N ]
setenv CTM_WB_DUST N #> use inline windblown dust emissions [ default: Y ]
setenv CTM_ERODE_AGLAND N #> use agricultural activity for windblown dust [ default: N ]; ignore if CTM_WB_DUST = N
setenv CTM_DUSTEM_DIAG N #> windblown dust emissions diagnostic file [ default: N ]; ignore if CTM_WB_DUST = N
setenv CTM_LTNG_NO N #> turn on lightning NOx [ default: N ]
setenv CTM_WVEL N #> save derived vertical velocity component to conc file [ default: N ]
setenv KZMIN Y #> use Min Kz option in edyintb [ default: Y ], otherwise revert to Kz0UT
setenv CTM_ILDEPV Y #> calculate in-line deposition velocities [ default: Y ]
setenv CTM_MOSAIC N #> landuse specific deposition velocities [ default: N ]
setenv CTM_ABFLUX N #> Ammonia bi-directional flux for in-line deposition velocities [ default: N ]; ignore if CTM_ILDEPV = N
setenv CTM_HGBIDI N #> Mercury bi-directional flux for in-line deposition velocities [ default: N ]; ignore if CTM_ILDEPV = N
setenv CTM_SFC_HONO N #> Surface HONO interaction [ default: Y ]; ignore if CTM_ILDEPV = N
setenv CTM_DEPV_FILE Y #> write diagnostic file for deposition velocities [ default: N ]
setenv CTM_BIOGEMIS N #> calculate in-line biogenic emissions [ default: N ]
setenv B3GTS_DIAG N #> write biogenic mass emissions diagnostic file [ default: N ]; ignore if CTM_BIOGEMIS = N
setenv CTM_PT3DEMIS N #> calculate in-line plume rise for elevated point emissions [ default: N ]
setenv PT3DDIAG N #> optional 3d point source emissions diagnostic file [ default: N]; ignore if CTM_PT3DEMIS = N
setenv PT3DFRAC N #> optional layer fractions diagnostic (play) file(s) [ default: N]; ignore if CTM_PT3DEMIS = N
setenv IOAPI_LOG_WRITE F #> turn on excess WRITE3 logging [ options: T | F ]
setenv FL_ERR_STOP N #> stop on inconsistent input files
setenv PROMPTFLAG F #> turn on I/O-API PROMPT*FILE interactive mode [ options: T | F ]
setenv IOAPI_OFFSET_64 NO #> support large timestep records (>2GB/timestep record) [ options: YES | NO ]
setenv EXECUTION_ID $EXEC #> define the model execution id

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

=====================================================================

#> Input/Output Directories

=====================================================================

set ICpath = M3DATA/icon/{APPL} #> initial conditions input directory
set BCpath = M3DATA/bcon/{APPL} #> boundary conditions input directory
set EMISpath = /home/lea/SMOKEv3.5/data/run_saprc99_{Project}_{do}{YY}-{Target_MM}/output/merge #> surface emissions input directory
set IN_PTpath = $M3DATA/emis #> elevated emissions input directory (in-line point only)
set IN_LTpath = M3DATA/lightning #> lightning NOx input directory set METpath = /home/lea/mcip/{do}{YY}{J_SDATE} #> meteorology input directory
set JVALpath = $M3DATA/jproc #> offline photolysis rate table directory
set OMIpath = $M3DATA/raw/phot #> ozone columne data for the photolysis model
set LUpath = $M3DATA/dust #> BELD landuse data for windblown dust model
set SZpath = $M3DATA/ocean #> Surf zone file for in-line seasalt emissions

set OUTDIR = M3DATA/cctm/{APPL} #> output file directory

=====================================================================

#> Input Files

=====================================================================

#> Initial conditions
set ICFILE = ICON_{Project}_{do}_{YY}-{Target_MM}lea
#set ICFILE = ICON_auto2015_27${MONTH}_prof_saprc99_ae5_profile

#> Boundary conditions
set BCFILE = BCON_{Project}_{do}_{YY}-{Target_MM}_lea

#> Off-line photolysis rates
set JVALfile = JTABLE_${STDATE}

#> Ozone column data
set OMIfile = OMI.dat

#> MCIP meteorology files
set EXTN = {do}_{STDATE}
setenv GRID_DOT_2D METpath/GRIDDOT2D_{EXTN}
setenv GRID_CRO_2D METpath/GRIDCRO2D_{EXTN}
setenv MET_CRO_2D METpath/METCRO2D_{EXTN}
setenv MET_CRO_3D METpath/METCRO3D_{EXTN}
setenv MET_DOT_3D METpath/METDOT3D_{EXTN}
setenv MET_BDY_3D METpath/METBDY3D_{EXTN}

#> Emissions files
setenv EMISDATE ${YMD}

if ( CTM_PT3DEMIS == 'N' ) then set EMISfile = egts_l.{STDATE}.{RUNLEN}.SMK.saprc99_{Project}{do}_{YY}-{Target_MM}.ncf #> Offline 3d emissions file name else #> In-line emissions configuration set CASE1 = 12US1_C25_2006am set CASE2 = 12US1_cmaq_cb05_tx_C25_2006am setenv CASE {EMISDATE}CASE2 set EMISfile = egts_l.{STDATE}.10.asia27.auto_${MONTH}21_saprc99_d01.ncf #> Surface emissions
setenv NPTGRPS 5 #> Number of elevated source groups
setenv STK_GRPS_01 IN_PTpath/stack_groups_ptnonipm_{CASE1}.ncf
setenv STK_GRPS_02 IN_PTpath/stack_groups_ptipm_{CASE1}.ncf
setenv STK_GRPS_03 IN_PTpath/stack_groups_othpt_{CASE1}.ncf
setenv STK_GRPS_04 IN_PTpath/stack_groups_seca_c3_{CASE1}.ncf
setenv STK_GRPS_05 IN_PTpath/stack_groups_ptfire_{EMISDATE}_${CASE1}.ncf
setenv LAYP_STTIME $STTIME
setenv LAYP_NSTEPS $NSTEPS
setenv STK_EMIS_01 IN_PTpath/inln_mole_ptnonipm_{CASE}.ncf
setenv STK_EMIS_02 IN_PTpath/inln_mole_ptipm_{CASE}.ncf
setenv STK_EMIS_03 IN_PTpath/inln_mole_othpt_{CASE}.ncf
setenv STK_EMIS_04 IN_PTpath/inln_mole_seca_c3_{CASE}.ncf
setenv STK_EMIS_05 IN_PTpath/inln_mole_ptfire_{CASE}.ncf
setenv LAYP_STDATE $STDATE
endif

#> Lightning NOx configuration
if ( $CTM_LTNG_NO == ‘Y’ ) then
setenv LTNGNO $IN_LTpath/nox_CMAQ-BENCHMARK.35L.$EMISDATE #> offline calculated lightning NOx

setenv LTNGNO “InLine” #> set LTNGNO to “Inline” to activate in-line calculation

#> In-line lightning NOx options
setenv LTNGPARAM N #> use lightning parameter file? [ default: Y ]
setenv LTNGPARM_FILE $M3DATA/params/LTNG_RATIO.2004.$MONTH.ioapi #> lightning parameter file; ignore if LTNGPARAM = N
setenv LTNGDIAG N #> write lightning diagnostic file [ default: N ]
setenv LTNGOUT $OUTDIR/EXEC.LTNGDIAG.{CFG}_${EMISDATE} #> lightning diagnostic file; ignore if LTNGDIAG = N
endif

#> In-line biogenic emissions configuration
if ( CTM_BIOGEMIS == 'Y' ) then set GSPROpath = {M3DATA}/emis
setenv GSPRO GSPROpath/gspro_cb05soa_notoxics_cmaq_poc_09nov2007.txt set IN_BEISpath = {M3DATA}/emis
setenv B3GRD $IN_BEISpath/b3grd_CMAQ-BENCHMARK_C70_2006am_Fulltox.ncf
setenv BIOG_SPRO B10C5 # speciation profile to use for biogenics
setenv BIOSW_YN N # use frost date switch [ default: Y ]
setenv BIOSEASON $IN_BEISpath/bioseason.cmaq.2002_02b_CMAQ-BENCHMARK_v31.ncf #> ignore season switch file if BIOSW_YN = N
setenv SUMMER_YN Y # Use summer normalized emissions? [ default: Y ]
setenv PX_VERSION N # MCIP is PX version? [ default: N ]
setenv B3GTS_DIAG Y #> beis mass emissions diagnostic file [ default: N ]
setenv INITIAL_RUN Y # non-existent or not using SOILINP [ default: N ]; default uses SOILINP
setenv SOILINP $OUTDIR/EXEC.SOILINP.{CFG}_${EMISDATE} # Biogenic NO soil input file; ignore if INITIAL_RUN = Y
endif
#> Windblown dust emissions configuration
if ( $CTM_WB_DUST == ‘Y’ ) then
setenv DUST_LU_1 $LUpath/beld3_CMAQ-BENCHMARK_output_a.ncf
setenv DUST_LU_2 $LUpath/beld3_CMAQ-BENCHMARK_output_tot.ncf
if ( CTM_ERODE_AGLAND == 'Y' ) then setenv CROPMAP01 {M3DATA}/crop/BeginPlanting_12km_CMAQ-BENCHMARK
setenv CROPMAP04 {M3DATA}/crop/EndPlanting_12km_CMAQ-BENCHMARK setenv CROPMAP08 {M3DATA}/crop/EndHarvesting_12km_CMAQ-BENCHMARK
endif
endif

#> In-line sea salt emisisions configuration
setenv OCEAN_1 $SZpath/FIP_LAND.EI_27_01.ncf #> horizontal grid-dependent surf zone file

=====================================================================

#> Output Files

=====================================================================

#> set output file name extensions
setenv CTM_APPL {CFG}_{YMD}
#> set output file names
set CONCfile = EXEC.CONC.{CTM_APPL} # CTM_CONC_1
set ACONCfile = EXEC.ACONC.{CTM_APPL} # CTM_ACONC_1
set CGRIDfile = EXEC.CGRID.{CTM_APPL} # CTM_CGRID_1
set DD1file = EXEC.DRYDEP.{CTM_APPL} # CTM_DRY_DEP_1
set DV1file = EXEC.DEPV.{CTM_APPL} # CTM_DEPV_DIAG
set PT1file = EXEC.PT3D.{CTM_APPL} # CTM_PT3D_DIAG
set BIO1file = EXEC.B3GTS_S.{CTM_APPL} # B3GTS_S
set SOIL1file = EXEC.SOILOUT.{CTM_APPL} # SOILOUT
set WD1file = EXEC.WETDEP1.{CTM_APPL} # CTM_WET_DEP_1
set WD2file = EXEC.WETDEP2.{CTM_APPL} # CTM_WET_DEP_2
set AV1file = EXEC.AEROVIS.{CTM_APPL} # CTM_VIS_1
set AD1file = EXEC.AERODIAM.{CTM_APPL} # CTM_DIAM_1
set RJ1file = EXEC.PHOTDIAG1.{CTM_APPL} # CTM_RJ_2
set RJ2file = EXEC.PHOTDIAG2.{CTM_APPL} # CTM_RJ_2
set SSEfile = $EXEC.SSEMIS.$CTM_APPL # CTM_SSEMIS_1
set DSEfile = $EXEC.DUSTEMIS.$CTM_APPL # CTM_DUST_EMIS_1
set PA1file = EXEC.PA_1.{CTM_APPL} # CTM_IPR_1
set PA2file = EXEC.PA_2.{CTM_APPL} # CTM_IPR_2
set PA3file = EXEC.PA_3.{CTM_APPL} # CTM_IPR_3
set IRR1file = EXEC.IRR_1.{CTM_APPL} # CTM_IRR_1
set IRR2file = EXEC.IRR_2.{CTM_APPL} # CTM_IRR_2
set IRR3file = EXEC.IRR_3.{CTM_APPL} # CTM_IRR_3
set DEPVFSTfile = EXEC.DEPVFST.{CTM_APPL} # CTM_DEPV_FST
set DEPVMOSfile = EXEC.DEPVMOS.{CTM_APPL} # CTM_DEPV_MOS
set DDFSTfile = EXEC.DDFST.{CTM_APPL} # CTM_DRY_DEP_FST
set DDMOSfile = EXEC.DDMOS.{CTM_APPL} # CTM_DRY_DEP_MOS
#> In-line biogenic emissions output files
if ( $CTM_BIOGEMIS == ‘Y’ ) then
setenv B3GTS_S $OUTDIR/EXEC".B3GTS_S".{CTM_APPL}
setenv SOILOUT $OUTDIR/EXEC".SOILOUT".{CTM_APPL} # Biogenic NO soil output file
endif

#> set floor file (neg concs)
setenv FLOOR_FILE BASE/FLOOR_{CTM_APPL}

#> create output directory
if ( ! -d “$OUTDIR” ) mkdir -p $OUTDIR

#> look for existing log files

set test = ls CTM_LOG_???.${CTM_APPL}
if ( “$test” != “” ) then
if ( $DISP == ‘delete’ ) then
echo " ancillary log files being deleted"
foreach file ( $test )
echo " deleting $file"
rm $file
end
else
echo “*** Logs exist - run ABORTED ***”
exit 1
endif
endif

#> for the run control …

setenv CTM_STDATE $STDATE
setenv CTM_STTIME $STTIME
setenv CTM_RUNLEN $NSTEPS
setenv CTM_TSTEP $TSTEP
setenv EMIS_1 $EMISpath/$EMISfile
setenv INIT_GASC_1 $ICpath/$ICFILE
setenv INIT_AERO_1 $INIT_GASC_1
setenv INIT_NONR_1 $INIT_GASC_1
setenv INIT_TRAC_1 $INIT_GASC_1
setenv BNDY_GASC_1 $BCpath/$BCFILE
setenv BNDY_AERO_1 $BNDY_GASC_1
setenv BNDY_NONR_1 $BNDY_GASC_1
setenv BNDY_TRAC_1 $BNDY_GASC_1
setenv OMI $OMIpath/$OMIfile
setenv XJ_DATA $JVALpath/$JVALfile
set TR_DVpath = $METpath
set TR_DVfile = $MET_CRO_2D

#> species defn & photolysis
setenv gc_matrix_nml ${BLD}/GC_MECH.nml setenv ae_matrix_nml {BLD}/AE_MECH.nml setenv nr_matrix_nml {BLD}/NR_MECH.nml setenv tr_matrix_nml {BLD}/Species_Table_TR_0.nml

#> check for photolysis input data
setenv CSQY_DATA ${BLD}/CSQY_DATA_$MECH
if (! (-e $CSQY_DATA ) ) then
echo " $CSQY_DATA not found "
exit 1
endif

#>- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

source $BASE/outck.q

ls -l $BLD/$EXEC; size $BLD/$EXEC
unlimit
limit

#> Executable call for single PE, uncomment to invoke

/usr/bin/time $BLD/$EXEC

#> Executable call for multi PE, configure for your system
set MPI = /usr/local/mpi/pgi/mpich-3.1.2/bin
set MPIRUN = $MPI/mpirun

time $MPIRUN -r ssh -np $NPROCS $BLD/$EXEC

time $MPIRUN -np $NPROCS $BLD/$EXEC

date
exit

6
  • LOG file

This program uses the EPA-AREAL/MCNC-EnvPgms/BAMS Models-3
I/O Applications Programming Interface, [I/O API] which is
built on top of the netCDF I/O library (Copyright 1993, 1996
University Corporation for Atmospheric Research/Unidata
Program) and the PVM parallel-programming library (from
Oak Ridge National Laboratory). Copyright (C) 1992-2002 MCNC
and Carlie J. Coats, Jr., and 2003-2006 Baron Advanced
Meteorological Systems, LLC and released under the GNU LGPL
License, version 2.1. See URL

     http://www.baronams.com/products/ioapi/LGPL.txt

 for conditions of use.

 Library release tag: $JDate: 2010068 $

 $Id: @(#) ioapi library version 3.1 $
 Version with PARMS3.EXT/PARAMETER::MXVARS3= 2048
 netCDF version 4.1.3 of Mar 30 2015 17:28:43 $


 EXECUTION_ID: CCTM_lea_Linux2_x86_64pgi
 Value for GRID_NAME:  '01'

 File "GRIDDESC" opened for input on unit:  98
 /home/lea/mcip/d01_2014111/GRIDDESC

 Value for NPCOL_NPROW:  '3 4'
 Value for IOAPI_CHECK_HEADERS not defined;returning default:   FALSE

 "MET_CRO_3D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/METCRO3D_d01_2014111"
 File type GRDDED3
 Execution ID "mcip"
 Grid name "METCRO_01_CROSS"
 Dimensions: 125 rows, 118 cols, 30 lays, 14 vbles
 NetCDF ID:     65536  opened as READONLY
 Starting date and time  2014111:000000 (0:00:00   April 21, 2014)
 Timestep                          010000 (1:00:00 hh:mm:ss)
 Maximum current record number       937

 GC Species Namelist:

/home/lea/CMAQv5.0.2/scripts/cctm/BLD_lea/GC_saprc99_ae5_aq.nml

 AE Species Namelist:

/home/lea/CMAQv5.0.2/scripts/cctm/BLD_lea/AE_saprc99_ae5_aq.nml

 NR Species Namelist:

/home/lea/CMAQv5.0.2/scripts/cctm/BLD_lea/NR_saprc99_ae5_aq.nml

 TR Species Namelist:

/home/lea/CMAQv5.0.2/scripts/cctm/BLD_lea/Species_Table_TR_0.nml
Value for CONC_SPCS not defined; returning defaultval ': ‘VARLIST’

 >>--->> WARNING in subroutine GET_ENVLIST
 Environment variable CONC_SPCS                        not set

 Value for CONC_BLEV_ELEV not defined; returning defaultval ':  'VARLIST'

 >>--->> WARNING in subroutine GET_ENVLIST
 Environment variable CONC_BLEV_ELEV                   not set

 Value for AVG_CONC_SPCS:  'ALL'
 Value for ACONC_BLEV_ELEV:  ' 1 15'
 Value for CTM_WVEL:  N returning FALSE
 Value for CTM_TSTEP:  10000
 Value for CTM_PROGNAME not defined; returning defaultval ':  'DRIVER'
 Main Program Name
 Environment variable not set ... Using default:                                                        62
 Value for CTM_STDATE:  2014111
 Value for CTM_STTIME:  0
 Value for CTM_RUNLEN:  9600000

 "GRID_CRO_2D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/GRIDCRO2D_d01_2014111"
 File type GRDDED3
 Execution ID "mcip"
 Grid name "GRIDOUT_01_CROSS"
 Dimensions: 125 rows, 118 cols, 1 lays, 31 vbles
 NetCDF ID:    131072  opened as READONLY
 Time-independent data.

 "INIT_GASC_1" opened as OLD:READ-ONLY

File name “/home/lea/CMAQv5.0.2/data/icon/org_d01_2014-05/ICON_org_d01_2014-05_lea”
File type GRDDED3
Execution ID “ICON_lea_Linux2_x86_64pgi”
Grid name “01”
Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles
NetCDF ID: 196608 opened as READONLY
Time-independent data.

 IC/BC Factors used for transported gas-phase species
   1  NO2                1.0000
   2  NO                 1.0000
 No IC found for species O3P in INIT_GASC_1; set to 1.00E-30
   3  O3                 1.0000
   4  NO3                1.0000
   5  N2O5               1.0000
   6  HNO3               1.0000
 No IC found for species O1D2 in INIT_GASC_1; set to 1.00E-30
   7  HO                 1.0000
   8  HONO               1.0000
   9  HO2                1.0000
  10  CO                 1.0000
  11  HNO4               1.0000
  12  HO2H               1.0000
  13  SO2                1.0000
  14  SULF               1.0000
 No IC found for species SULRXN in INIT_GASC_1; set to 1.00E-30
 No IC found for species C_O2 in INIT_GASC_1; set to 1.00E-30
  15  HCHO               1.0000
  16  COOH               1.0000
 No IC found for species MEOH in INIT_GASC_1; set to 1.00E-30
 No IC found for species RO2_R in INIT_GASC_1; set to 1.00E-30
  17  ROOH               1.0000
 No IC found for species R2O2 in INIT_GASC_1; set to 1.00E-30
 No IC found for species RO2_N in INIT_GASC_1; set to 1.00E-30
  18  RNO3               1.0000
  19  MEK                1.0000
 No IC found for species PROD2 in INIT_GASC_1; set to 1.00E-30
  20  CCO_O2             1.0000
  21  PAN                1.0000
  22  CCO_OOH            1.0000
  23  CCO_OH             1.0000

No IC found for species RCO_O2 in INIT_GASC_1; set to 1.00E-30
24 PAN2 1.0000
25 CCHO 1.0000
No IC found for species RCO_OOH in INIT_GASC_1; set to 1.00E-30
No IC found for species RCO_OH in INIT_GASC_1; set to 1.00E-30
No IC found for species BZCO_O2 in INIT_GASC_1; set to 1.00E-30
No IC found for species PBZN in INIT_GASC_1; set to 1.00E-30
No IC found for species BZ_O in INIT_GASC_1; set to 1.00E-30
No IC found for species MA_RCO3 in INIT_GASC_1; set to 1.00E-30
No IC found for species MA_PAN in INIT_GASC_1; set to 1.00E-30
No IC found for species TBU_O in INIT_GASC_1; set to 1.00E-30
No IC found for species ACET in INIT_GASC_1; set to 1.00E-30
No IC found for species NPHE in INIT_GASC_1; set to 1.00E-30
No IC found for species PHEN in INIT_GASC_1; set to 1.00E-30
No IC found for species BZNO2_O in INIT_GASC_1; set to 1.00E-30
No IC found for species HOCOO in INIT_GASC_1; set to 1.00E-30
26 HCOOH 1.0000
No IC found for species RCHO in INIT_GASC_1; set to 1.00E-30
27 GLY 1.0000
28 MGLY 1.0000
No IC found for species BACL in INIT_GASC_1; set to 1.00E-30
29 CRES 1.0000
No IC found for species BALD in INIT_GASC_1; set to 1.00E-30
30 METHACRO 1.0000
31 MVK 1.0000
No IC found for species ISOPROD in INIT_GASC_1; set to 1.00E-30
No IC found for species DCB1 in INIT_GASC_1; set to 1.00E-30
32 DCB2 1.0000
No IC found for species DCB3 in INIT_GASC_1; set to 1.00E-30
33 ETHENE 1.0000
34 ISOPRENE 1.0000
No IC found for species ISOPRXN in INIT_GASC_1; set to 1.00E-30
No IC found for species TRP1 in INIT_GASC_1; set to 1.00E-30
No IC found for species TRPRXN in INIT_GASC_1; set to 1.00E-30
35 ALK1 1.0000
36 ALK2 1.0000
37 ALK3 1.0000
38 ALK4 1.0000
39 ALK5 1.0000
No IC found for species ALK5RXN in INIT_GASC_1; set to 1.00E-30
40 ARO1 1.0000
No IC found for species ARO1RO2 in INIT_GASC_1; set to 1.00E-30
No IC found for species TOLNRXN in INIT_GASC_1; set to 1.00E-30
No IC found for species TOLHRXN in INIT_GASC_1; set to 1.00E-30
41 ARO2 1.0000
No IC found for species ARO2RO2 in INIT_GASC_1; set to 1.00E-30
No IC found for species XYLNRXN in INIT_GASC_1; set to 1.00E-30
No IC found for species XYLHRXN in INIT_GASC_1; set to 1.00E-30
42 BENZENE 1.0000
No IC found for species BENZRO2 in INIT_GASC_1; set to 1.00E-30
No IC found for species BNZNRXN in INIT_GASC_1; set to 1.00E-30
No IC found for species BNZHRXN in INIT_GASC_1; set to 1.00E-30
43 OLE1 1.0000
44 OLE2 1.0000
No IC found for species SESQ in INIT_GASC_1; set to 1.00E-30
No IC found for species SESQRXN in INIT_GASC_1; set to 1.00E-30

 GC loaded into CGRID

 Density*Jacobian loaded into CGRID

 "INIT_AERO_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/icon/org_d01_2014-05/ICON_org_d01_2014-05_lea"
 File type GRDDED3
 Execution ID "ICON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles
 NetCDF ID:    262144  opened as READONLY
 Time-independent data.

 IC/BC Factors used for transported aerosol species
  45  ASO4J              1.0000
  46  ASO4I              1.0000
 No IC found for species ANH4J in INIT_AERO_1; set to 1.00E-30
 No IC found for species ANH4I in INIT_AERO_1; set to 1.00E-30
 No IC found for species ANO3J in INIT_AERO_1; set to 1.00E-30
 No IC found for species ANO3I in INIT_AERO_1; set to 1.00E-30
  47  AALKJ              1.0000
  48  AXYL1J             1.0000
  49  AXYL2J             1.0000
  50  AXYL3J             1.0000
  51  ATOL1J             1.0000

52 ATOL2J 1.0000
53 ATOL3J 1.0000
54 ABNZ1J 1.0000
55 ABNZ2J 1.0000
56 ABNZ3J 1.0000
57 ATRP1J 1.0000
58 ATRP2J 1.0000
59 AISO1J 1.0000
60 AISO2J 1.0000
61 ASQTJ 1.0000
No IC found for species AORGCJ in INIT_AERO_1; set to 1.00E-30
62 AORGPAJ 1.0000
63 AORGPAI 1.0000
No IC found for species AECJ in INIT_AERO_1; set to 1.00E-30
No IC found for species AECI in INIT_AERO_1; set to 1.00E-30
No IC found for species A25J in INIT_AERO_1; set to 1.00E-30
No IC found for species A25I in INIT_AERO_1; set to 1.00E-30
64 ACORS 1.0000
65 ASOIL 1.0000
66 NUMATKN 1.0000
67 NUMACC 1.0000
68 NUMCOR 1.0000
69 SRFATKN 1.0000
70 SRFACC 1.0000
71 SRFCOR 1.0000
No IC found for species AH2OJ in INIT_AERO_1; set to 1.00E-30
No IC found for species AH2OI in INIT_AERO_1; set to 1.00E-30
No IC found for species ANAJ in INIT_AERO_1; set to 1.00E-30
No IC found for species ANAI in INIT_AERO_1; set to 1.00E-30
No IC found for species ACLJ in INIT_AERO_1; set to 1.00E-30
No IC found for species ACLI in INIT_AERO_1; set to 1.00E-30
No IC found for species ANAK in INIT_AERO_1; set to 1.00E-30
No IC found for species ACLK in INIT_AERO_1; set to 1.00E-30
No IC found for species ASO4K in INIT_AERO_1; set to 1.00E-30
No IC found for species ANH4K in INIT_AERO_1; set to 1.00E-30
No IC found for species ANO3K in INIT_AERO_1; set to 1.00E-30
No IC found for species AH2OK in INIT_AERO_1; set to 1.00E-30
72 AISO3J 1.0000
73 AOLGAJ 1.0000
74 AOLGBJ 1.0000
AE loaded into CGRID

 "INIT_NONR_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/icon/org_d01_2014-05/ICON_org_d01_2014-05_lea"
 File type GRDDED3
 Execution ID "ICON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles
 NetCDF ID:    327680  opened as READONLY
 Time-independent data.

 IC/BC Factors used for transported non-reactive gas species
  75  NH3                1.0000
 No IC found for species HCL in INIT_NONR_1; set to 1.00E-30
  76  SV_ALK             1.0000
  77  SV_XYL1            1.0000
  78  SV_XYL2            1.0000
  79  SV_TOL1            1.0000
  80  SV_TOL2            1.0000
  81  SV_BNZ1            1.0000
  82  SV_BNZ2            1.0000
  83  SV_TRP1            1.0000
  84  SV_TRP2            1.0000
  85  SV_ISO1            1.0000
  86  SV_ISO2            1.0000
  87  SV_SQT             1.0000

 NR loaded into CGRID
 CTM_CONC_1      :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.CONC.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 Could not open CTM_CONC_1 for update - try to open new

   Conc File Header Description:
 => Concentration file output
 => From CMAQ model dyn alloc version CTM
 => Set of variables (possibly) reduced from CGRID
 => For next scenario continuation runs,
 => use the "one-step" CGRID file

=> Layer 1 to 1
=> Layer 2 to 2
=> Layer 3 to 3
=> Layer 4 to 4
=> Layer 5 to 5
=> Layer 6 to 6
=> Layer 7 to 7
=> Layer 8 to 8
=> Layer 9 to 9
=> Layer 10 to 10
=> Layer 11 to 11
=> Layer 12 to 12
=> Layer 13 to 13
=> Layer 14 to 14
=> Layer 15 to 15
=> Layer 16 to 16
=> Layer 17 to 17
=> Layer 18 to 18
=> Layer 19 to 19
=> Layer 20 to 20
=> Layer 21 to 21
=> Layer 22 to 22
=> Layer 23 to 23
=> Layer 24 to 24
=> Layer 25 to 25
=> Layer 26 to 26
=> Layer 27 to 27
=> Layer 28 to 28
=> Layer 29 to 29
=> Layer 30 to 30

 Gas Chem species saved to CONC file:
 Value for IOAPI_LOG_WRITE:  F returning FALSE
    1 (  1) NO2
    2 (  2) NO
    3 (  3) O3P
    4 (  4) O3
    5 (  5) NO3
    6 (  6) N2O5
    7 (  7) HNO3

8 ( 8) O1D2
9 ( 9) HO
10 ( 10) HONO
11 ( 11) HO2
12 ( 12) CO
13 ( 13) HNO4
14 ( 14) HO2H
15 ( 15) SO2
16 ( 16) SULF
17 ( 17) C_O2
18 ( 18) HCHO
19 ( 19) COOH
20 ( 20) MEOH
21 ( 21) RO2_R
22 ( 22) ROOH
23 ( 23) R2O2
24 ( 24) RO2_N
25 ( 25) RNO3
26 ( 26) MEK
27 ( 27) PROD2
28 ( 28) CCO_O2
29 ( 29) PAN
30 ( 30) CCO_OOH
31 ( 31) CCO_OH
32 ( 32) RCO_O2
33 ( 33) PAN2
34 ( 34) CCHO
35 ( 35) RCO_OOH
36 ( 36) RCO_OH
37 ( 37) BZCO_O2
38 ( 38) PBZN
39 ( 39) BZ_O
40 ( 40) MA_RCO3
41 ( 41) MA_PAN
42 ( 42) TBU_O
43 ( 43) ACET
44 ( 44) NPHE
45 ( 45) PHEN
46 ( 46) BZNO2_O
47 ( 47) HOCOO
48 ( 48) HCOOH
49 ( 49) RCHO
50 ( 50) GLY
51 ( 51) MGLY
52 ( 52) BACL
53 ( 53) CRES
54 ( 54) BALD
55 ( 55) METHACRO
56 ( 56) MVK
57 ( 57) ISOPROD
58 ( 58) DCB1
59 ( 59) DCB2
60 ( 60) DCB3
61 ( 61) ETHENE
62 ( 62) ISOPRENE
63 ( 63) TRP1
64 ( 64) ALK1
65 ( 65) ALK2
66 ( 66) ALK3
67 ( 67) ALK4
68 ( 68) ALK5
69 ( 69) ARO1
70 ( 70) ARO1RO2
71 ( 71) ARO2
72 ( 72) ARO2RO2
73 ( 73) BENZENE
74 ( 74) BENZRO2
75 ( 75) OLE1
76 ( 76) OLE2
77 ( 77) SESQ

 Aerosol species saved to CONC file:
    1 ( 78) ASO4J
    2 ( 79) ASO4I
    3 ( 80) ANH4J
    4 ( 81) ANH4I
    5 ( 82) ANO3J
    6 ( 83) ANO3I
    7 ( 84) AALKJ
    8 ( 85) AXYL1J
    9 ( 86) AXYL2J
   10 ( 87) AXYL3J

11 ( 88) ATOL1J
12 ( 89) ATOL2J
13 ( 90) ATOL3J
14 ( 91) ABNZ1J
15 ( 92) ABNZ2J
16 ( 93) ABNZ3J
17 ( 94) ATRP1J
18 ( 95) ATRP2J
19 ( 96) AISO1J
20 ( 97) AISO2J
21 ( 98) ASQTJ
22 ( 99) AORGCJ
23 (100) AORGPAJ
24 (101) AORGPAI
25 (102) AECJ
26 (103) AECI
27 (104) A25J
28 (105) ACORS
29 (106) ASOIL
30 (107) NUMATKN
31 (108) NUMACC
32 (109) NUMCOR
33 (110) SRFATKN
34 (111) SRFACC
35 (112) SRFCOR
36 (113) AH2OJ
37 (114) AH2OI
38 (115) ANAJ
39 (116) ACLJ
40 (117) ACLI
41 (118) ANAK
42 (119) ACLK
43 (120) ASO4K
44 (121) ANH4K
45 (122) ANO3K
46 (123) AH2OK
47 (124) AISO3J
48 (125) AOLGAJ
49 (126) AOLGBJ

 Non-reactive species saved to CONC file:

1 (127) NH3
2 (128) HCL
3 (129) SV_ALK
4 (130) SV_XYL1
5 (131) SV_XYL2
6 (132) SV_TOL1
7 (133) SV_TOL2
8 (134) SV_BNZ1
9 (135) SV_BNZ2
10 (136) SV_TRP1
11 (137) SV_TRP2
12 (138) SV_ISO1
13 (139) SV_ISO2
14 (140) SV_SQT

 Timestep written to CTM_CONC_1       for date and time  2014111:000000
 from timestep on initial data files for date and time  2014111:000000

after INITSCEN G 1.2127510E-01 A 7.7093043E+08 N 6.5386215E-05

 = = = = = = = = = = = = = = Start FLCHECK = = = = = = = = = = = = = =

 Value for FL_ERR_STOP:  N returning FALSE
 Value for CTM_RUNLEN:  9600000

 "GRID_DOT_2D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/GRIDDOT2D_d01_2014111"
 File type GRDDED3
 Execution ID "mcip"
 Grid name "GRIDOUT_01_DOT"
 Dimensions: 126 rows, 119 cols, 1 lays, 9 vbles
 NetCDF ID:    393216  opened as READONLY
 Time-independent data.
 Checking header data for file: GRID_DOT_2D
 Checking header data for file: GRID_CRO_2D
 GRID_CRO_3D     :GRID_CRO_3D

 >>--->> WARNING in subroutine OPEN3
 File not available.

 GRID_BDY_2D     :GRID_BDY_2D

>>--->> WARNING in subroutine OPEN3
 File not available.


 "EMIS_1" opened as OLD:READ-ONLY
 File name "/home/lea/SMOKEv3.5/data/run_saprc99_org_d01_2014-05/output/merge/egts_l.2014111.40.SMK.saprc99_org_d01_2014-05.ncf"
 File type GRDDED3
 Execution ID "????????????????"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 23 lays, 54 vbles
 NetCDF ID:    458752  opened as READONLY
 Starting date and time  2014111:000000 (0:00:00   April 21, 2014)
 Timestep                          010000 (1:00:00 hh:mm:ss)
 Maximum current record number       937
 Checking header data for file: EMIS_1
 netCDF error number  -40
 Ending time not on file

 "OCEAN_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/ocean/FIP_LAND.EI_27_01.ncf"
 File type GRDDED3
 Execution ID "????????????????"
 Grid name "LAM_38N126"
 Dimensions: 128 rows, 121 cols, 1 lays, 5 vbles
 NetCDF ID:    524288  opened as READONLY
 Time-independent data.
 Checking header data for file: OCEAN_1
     Inconsistent values for GL_NCOLS: 121 versus 118
     Inconsistent values for GL_NROWS: 128 versus 125
     Inconsistent values for XORIG: -1.6335E+06 versus -1.5795E+06
     Inconsistent values for YORIG: -1.7280E+06 versus -1.6740E+06
 MET_BDY_2D      :MET_BDY_2D

 >>--->> WARNING in subroutine OPEN3
 File not available.


 "MET_BDY_3D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/METBDY3D_d01_2014111"
 File type BNDARY3
 Execution ID "mcip"

Grid name “METCRO_01_CROSS”
Dimensions: 125 rows, 118 cols, 30 lays, 14 vbles, 1 cells thick
NetCDF ID: 589824 opened as READONLY
Starting date and time 2014111:000000 (0:00:00 April 21, 2014)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 937
Checking header data for file: MET_BDY_3D
netCDF error number -40
Ending time not on file

 "MET_DOT_3D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/METDOT3D_d01_2014111"
 File type GRDDED3
 Execution ID "mcip"
 Grid name "METDOT_01_DOT"
 Dimensions: 126 rows, 119 cols, 30 lays, 6 vbles
 NetCDF ID:    655360  opened as READONLY
 Starting date and time  2014111:000000 (0:00:00   April 21, 2014)
 Timestep                          010000 (1:00:00 hh:mm:ss)
 Maximum current record number       937
 Checking header data for file: MET_DOT_3D
 netCDF error number  -40
 Ending time not on file

 "MET_CRO_2D" opened as OLD:READ-ONLY
 File name "/home/lea/mcip/d01_2014111/METCRO2D_d01_2014111"
 File type GRDDED3
 Execution ID "mcip"
 Grid name "METCRO_01_CROSS"
 Dimensions: 125 rows, 118 cols, 1 lays, 34 vbles
 NetCDF ID:    720896  opened as READONLY
 Starting date and time  2014111:000000 (0:00:00   April 21, 2014)
 Timestep                          010000 (1:00:00 hh:mm:ss)
 Maximum current record number       937
 Checking header data for file: MET_CRO_2D
 netCDF error number  -40
 Ending time not on file
 Checking header data for file: MET_CRO_3D
 netCDF error number  -40
 Ending time not on file

“CTM_CONC_1” opened as OLD:READ-ONLY
File name “/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.CONC.lea_20140421”
File type GRDDED3
Execution ID “CCTM_lea_Linux2_x86_64pgi”
Grid name “01”
Dimensions: 125 rows, 118 cols, 30 lays, 140 vbles
NetCDF ID: 786432 opened as VOLATILE READONLY
Starting date and time 2014111:000000 (0:00:00 April 21, 2014)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 1
Checking header data for file: CTM_CONC_1
CTM_DRY_DEP_1 :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DRYDEP.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_WET_DEP_1   :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.WETDEP1.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_WET_DEP_2   :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.WETDEP2.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_SSEMIS_1    :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.SSEMIS.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_DUST_EMIS_1 :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DUSTEMIS.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_VIS_1       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.AEROVIS.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

CTM_DIAM_1 :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.AERODIAM.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IPR_1       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PA_1.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IPR_2       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PA_2.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IPR_3       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PA_3.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IRR_1       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.IRR_1.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IRR_2       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.IRR_2.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_IRR_3       :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.IRR_3.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 A_CONC_1        :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.ACONC.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 S_CGRID         :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.CGRID.lea_20140421

—>> WARNING in subroutine OPEN3
File not available.

 Checking header data for file: INIT_GASC_1

 "BNDY_GASC_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/bcon/org_d01_2014-05/BCON_org_d01_2014-05_lea"
 File type BNDARY3
 Execution ID "BCON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles, 1 cells thick
 NetCDF ID:    851968  opened as READONLY
 Time-independent data.
 Checking header data for file: BNDY_GASC_1
 Checking header data for file: INIT_AERO_1

 "BNDY_AERO_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/bcon/org_d01_2014-05/BCON_org_d01_2014-05_lea"
 File type BNDARY3
 Execution ID "BCON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles, 1 cells thick
 NetCDF ID:    917504  opened as READONLY
 Time-independent data.
 Checking header data for file: BNDY_AERO_1
 Checking header data for file: INIT_NONR_1

 "BNDY_NONR_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/bcon/org_d01_2014-05/BCON_org_d01_2014-05_lea"
 File type BNDARY3
 Execution ID "BCON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles, 1 cells thick
 NetCDF ID:    983040  opened as READONLY
 Time-independent data.
 Checking header data for file: BNDY_NONR_1

 "INIT_TRAC_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/icon/org_d01_2014-05/ICON_org_d01_2014-05_lea"
 File type GRDDED3

Execution ID “ICON_lea_Linux2_x86_64pgi”
Grid name “01”
Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles
NetCDF ID: 1048576 opened as READONLY
Time-independent data.
Checking header data for file: INIT_TRAC_1

 "BNDY_TRAC_1" opened as OLD:READ-ONLY
 File name "/home/lea/CMAQv5.0.2/data/bcon/org_d01_2014-05/BCON_org_d01_2014-05_lea"
 File type BNDARY3
 Execution ID "BCON_lea_Linux2_x86_64pgi"
 Grid name "01"
 Dimensions: 125 rows, 118 cols, 30 lays, 87 vbles, 1 cells thick
 NetCDF ID:   1114112  opened as READONLY
 Time-independent data.
 Checking header data for file: BNDY_TRAC_1
 DEPV_TRAC_1     :DEPV_TRAC_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 EMIS_TRAC_1     :EMIS_TRAC_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_DEPV_DIAG   :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DEPV.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.
7 
 CTM_PT3D_DIAG   :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PT3D.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_RJ_1        :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PHOTDIAG1.lea_20140421

—>> WARNING in subroutine OPEN3
File not available.

 CTM_RJ_2        :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.PHOTDIAG2.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 INIT_MEDC_1     :INIT_MEDC_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 MEDIA_CONC      :MEDIA_CONC

 >>--->> WARNING in subroutine OPEN3
 File not available.

 REGIONS_1       :REGIONS_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 EMIS_A          :EMIS_A

 >>--->> WARNING in subroutine OPEN3
 File not available.

 EMIS_B          :EMIS_B

 >>--->> WARNING in subroutine OPEN3
 File not available.

 EMIS_M          :EMIS_M

 >>--->> WARNING in subroutine OPEN3
 File not available.

 EMIS_P          :EMIS_P

—>> WARNING in subroutine OPEN3
File not available.

 EMIS_N          :EMIS_N

 >>--->> WARNING in subroutine OPEN3
 File not available.

 INIT_GASC_S     :INIT_GASC_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 INIT_AERO_S     :INIT_AERO_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 INIT_NONR_S     :INIT_NONR_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 BNDY_GASC_S     :BNDY_GASC_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 BNDY_AERO_S     :BNDY_AERO_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 BNDY_NONR_S     :BNDY_NONR_S

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_SENS_1      :CTM_SENS_1

 >>--->> WARNING in subroutine OPEN3

A_SENS_1 :A_SENS_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_SWETDEP_1   :CTM_SWETDEP_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_SDRYDEP_1   :CTM_SDRYDEP_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 DUST_LU_1       :DUST_LU_1

 >>--->> WARNING in subroutine OPEN3
 File not available.

 DUST_LU_2       :DUST_LU_2

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_DEPV_MOS    :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DEPVMOS.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_DRY_DEP_MOS :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DDMOS.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_DRY_DEP_FST :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DDFST.lea_20140421

 >>--->> WARNING in subroutine OPEN3

File not available.

 CTM_DEPV_FST    :/home/lea/CMAQv5.0.2/data/cctm/org_d01_2014-05/CCTM_lea_Linux2_x86_64pgi.DEPVFST.lea_20140421

 >>--->> WARNING in subroutine OPEN3
 File not available.

 E2C_FERT        :E2C_FERT

 >>--->> WARNING in subroutine OPEN3
 File not available.

 E2C_SOIL        :E2C_SOIL

 >>--->> WARNING in subroutine OPEN3
 File not available.

 BELD4_LU        :BELD4_LU

 >>--->> WARNING in subroutine OPEN3
 File not available.

 CTM_SD_TS       :CTM_SD_TS

 >>--->> WARNING in subroutine OPEN3
 File not available.


 >>--->> WARNING in subroutine FLCHECK on PE 006
 Inconsistent header data on input files
 M3WARN:  DTBUF 0:00:00   April 21, 2014

 = = = = = = = = = = = = = =  End  FLCHECK = = = = = = = = = = = = = =

 Value for CTM_MAXSYNC:  300
 Value for CTM_MINSYNC:  60
 Value for CTM_ADV_CFL not defined; returning default :  0.75
 Maximum CFL number allowed

Value for SIGMA_SYNC_TOP not defined; returning default : 0.7
Minimum layer limit for which adv = sync
Value for ADV_HDIV_LIM not defined; returning default : 0.9
Maximum horiz. div. limit for adv step adjustment
Top layer thru which sync step determined: 12

 From ADVSTEP - date/time:  2014111/000000

 Computed synchronization step (HHMMSS): 000500
 Number of Synchronization steps:   12


 Layer   Advection   per Sync
       Step (HHMMSS)  Step
   30      000500       1
   29      000500       1
   28      000500       1
   27      000500       1
   26      000500       1
   25      000500       1
   24      000500       1
   23      000500       1
   22      000500       1
   21      000230       2
   20      000500       1
   19      000500       1
   18      000500       1
   17      000500       1
   16      000500       1
   15      000500       1
   14      000500       1
   13      000500       1
   12      000500       1
   11      000500       1
   10      000500       1
    9      000500       1
    8      000500       1
    7      000500       1
    6      000500       1
    5      000500       1

4 000500 1
3 000500 1
2 000500 1
1 000500 1
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_DEPV_FILE: Y returning TRUE
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 CTM_BIOGEMIS:  N returning FALSE

 >>--->> WARNING in subroutine OPEMIS on PE 006
 Emissions species HONO not found on EMIS_1
 M3WARN:  DTBUF 0:00:00   April 21, 2014

 >>--->> WARNING in subroutine OPEMIS on PE 006
 Emissions species ARO1NBZ not found on EMIS_1
 M3WARN:  DTBUF 0:00:00   April 21, 2014

 >>--->> WARNING in subroutine OPEMIS on PE 006
 Emissions species BENZENE not found on EMIS_1
 M3WARN:  DTBUF 0:00:00   April 21, 2014

 >>--->> WARNING in subroutine OPEMIS on PE 006
 Emissions species SESQ not found on EMIS_1
 M3WARN:  DTBUF 0:00:00   April 21, 2014

      Gas Chemistry Emissions Processing in Vertical diffusion ...

      Non-reactives Emissions Processing in Vertical diffusion ...

      Number of Emissions Layers:          23
      out of total Number of Model Layers: 30
 Value for CTM_STDATE:  2014111
 Value for CTM_STTIME:  0
 Value for CTM_RUNLEN:  9600000

Value for CTM_LTNG_NO: N returning FALSE

 Aerosol Emissions Processing in Vertical diffusion ...
  --- Precursor Species Mapped ---
 Value for CTM_SSEMDIAG:  N returning FALSE
 Value for CTM_PT3DEMIS:  N returning FALSE

======================================================================
— Subroutine: M3DRY
— Found canopy wetness (WR) in MET_CRO_2D

======================================================================
— Subroutine: M3DRY
— Found 2-m water vapor mixing ratio (Q2) in MET_CRO_2D

 >>--->> WARNING in subroutine GET_EMIS:INTERPX
 Variable "HONO" not in file EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS on PE 006
 Could not read HONO from EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS:INTERPX
 Variable "ARO1NBZ" not in file EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS on PE 006
 Could not read ARO1NBZ from EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS:INTERPX
 Variable "BENZENE" not in file EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS on PE 006
 Could not read BENZENE from EMIS_1
 >>--->> WARNING in subroutine GET_EMIS:INTERPX
 Variable "SESQ" not in file EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014

 >>--->> WARNING in subroutine GET_EMIS on PE 006
 Could not read SESQ from EMIS_1
 M3WARN:  DTBUF 0:02:30   April 21, 2014
 Value for KZMIN:  Y returning TRUE


 Maximum eddy diffusivity of:   1000.0     (m**2/sec)
 at col, row, layer:  13,   2,   1
 corresponding to a free tropospheric wind shear of:  7.64031E-03 (/sec),
                        a bulk Richardson Number of: -0.55021    ,
 and pot. temps. in layer and layer+1:   296.81       296.78

after VDIFF G 1.2145977E-01 A 7.7443283E+08 N 6.7672423E-05
after COUPLE_WR G 1.1215237E+03 A 8.9221696E+12 N 6.2642282E-01

 No BC's in file BNDY_GASC_1 for the following adv species: Set to 1.00E-30
      MEOH
      PROD2
      RCO_OOH
      RCO_OH
      PBZN
      MA_PAN
      ACET
      NPHE
      PHEN
      RCHO
      BACL
      BALD
      ISOPROD
      DCB1
      DCB3
      TRP1
      SESQ

 No BC's in file BNDY_AERO_1 for the following adv species: Set to 1.00E-30

ANH4J
ANH4I
ANO3J
ANO3I
AORGCJ
AECJ
AECI
A25J
A25I
AH2OJ
AH2OI
ANAJ
ANAI
ACLJ
ACLI
ANAK
ACLK
ASO4K
ANH4K
ANO3K
AH2OK

 No BC's in file BNDY_NONR_1 for the following adv species: Set to 1.00E-30
      HCL

 Reading U-windfield from MET_DOT_3D for variable: UWINDC

 Reading V-windfield from MET_DOT_3D for variable: VWINDC

 layer    S (X3FACE_GD) Delta S
   1     0.0040000     0.0040000     1.0000000
   2     0.0100000     0.0060000     1.0000000
   3     0.0200000     0.0100000     1.0000000
   4     0.0220000     0.0020000     1.0000000
   5     0.0360000     0.0140000     1.0000000
   6     0.0540000     0.0180000     1.0000000
   7     0.0780000     0.0240000     1.0000000
   8     0.1060000     0.0280000     1.0000000
   9     0.1400000     0.0340000     1.0000000
  10     0.1830000     0.0430000     1.0000000
  11     0.2340000     0.0510000     1.0000000
  12     0.2930000     0.0590000     1.0000000
  13     0.3560000     0.0630000     1.0000000
  14     0.4240000     0.0680000     1.0000000
  15     0.4930000     0.0689999     1.0000000
  16     0.5560000     0.0630000     1.0000000
  17     0.6200000     0.0640000     1.0000000
  18     0.6760000     0.0560000     1.0000000
  19     0.7270000     0.0510000     1.0000000
  20     0.7720000     0.0450000     1.0000000
  21     0.8120000     0.0400000     1.0000000
  22     0.8480000     0.0360000     1.0000000
  23     0.8550000     0.0070000     1.0000000
  24     0.8790000     0.0240000     1.0000000
  25     0.9070000     0.0280000     1.0000000
  26     0.9310000     0.0240000     1.0000000
  27     0.9520000     0.0210000     1.0000000
  28     0.9710000     0.0190000     1.0000000
  29     0.9860000     0.0150000     1.0000000
  30     1.0000000     0.0140000     1.0000000

after ADV G 1.1215513E+03 A 8.9243360E+12 N 6.2871039E-01

 H-eddy DT & integration steps:   3.0000000E+02       1

after HDIFF G 1.1215513E+03 A 8.9243360E+12 N 6.2871039E-01
after DECOUPLE_ G 1.2146239E-01 A 7.7453261E+08 N 6.7930945E-05
Value for CLD_DIAG: N returning FALSE

 >>--->> WARNING in subroutine RESCLD on PE 006
 Parameter QI (cloud ice) was not found on file MET_CRO_3D
 M3WARN:  DTBUF 0:00:00   April 21, 2014

      YOU SHOULD VERIFY that the cloud microphysics scheme used
      in the Meteorological Model did not include ice/snow.  If
      it did, then you need to reprocess the meteorological data
      through MCIP and pass QI to file  MET_CRO_3D  to avoid
      errors in the wet deposition.

 Processing will continue with QI set to ZERO.  <<---<<


 >>--->> WARNING in subroutine RESCLD on PE 006
 Parameter QS (snow) was not found on file MET_CRO_3D
 M3WARN:  DTBUF 0:00:00   April 21, 2014

      YOU SHOULD VERIFY that the cloud microphysics scheme used
      in the Meteorological Model did not include ice/snow.  If
      it did, then you need to reprocess the meteorological data
      through MCIP and pass QS to file  MET_CRO_3D  to avoid
      errors in the wet deposition.

 Processing will continue with QS set to ZERO.  <<--<<

 no surrogates for aqueous species CO2...using background value of 340.0000
 no surrogates for aqueous species CACO3...using background value of   0.0000
 no surrogates for aqueous species MGCO3...using background value of   0.0000
 no surrogates for aqueous species A3FE...using background value of   0.0100
 no surrogates for aqueous species B2MN...using background value of   0.0050
 no surrogates for aqueous species K...using background value of   0.0000

after CLDPROC G 1.2146232E-01 A 7.7448230E+08 N 6.7923756E-05

      Euler Backward Iterative Parameters -
      Chemistry Integration Time Interval (min):      5.0000
      EBI maximum time step (min):                    2.5000


      Species convergence tolerances:
      NO2                   1.00E-03
      NO                    1.00E-03
      O3P                   1.00E+00
      O3                    1.00E-03
      NO3                   1.00E-03
      N2O5                  1.00E-03
      HNO3                  1.00E-03
      O1D2                  1.00E+00
      HO                    1.00E-03
      HONO                  1.00E-03
      HO2                   1.00E-03
      CO                    1.00E-03
      HNO4                  1.00E-03
      HO2H                  1.00E-03
      SO2                   1.00E-03
      SULF                  1.00E+00
      SULRXN                1.00E+00
      C_O2                  1.00E-03
      HCHO                  1.00E-03
      COOH                  1.00E-03
      MEOH                  1.00E-03
      RO2_R                 1.00E-03
      ROOH                  1.00E-03
      R2O2                  1.00E-03
      RO2_N                 1.00E-03
      RNO3                  1.00E-03
      MEK                   1.00E-03
      PROD2                 1.00E-03
      CCO_O2                1.00E-03
      PAN                   1.00E-03
      CCO_OOH               1.00E-03
      CCO_OH                1.00E-03
      RCO_O2                1.00E-03
      PAN2                  1.00E-03
      CCHO                  1.00E-03
      RCO_OOH               1.00E-03
      RCO_OH                1.00E-03
      BZCO_O2               1.00E-03
      PBZN                  1.00E-03
      BZ_O                  1.00E+00
      MA_RCO3               1.00E-03
      MA_PAN                1.00E-03
      TBU_O                 1.00E+00
      ACET                  1.00E-03
      NPHE                  1.00E-03
      PHEN                  1.00E-03
      BZNO2_O               1.00E+00
      HOCOO                 1.00E+00
      HCOOH                 1.00E-03
      RCHO                  1.00E-03
      GLY                   1.00E-03
      MGLY                  1.00E-03
      BACL                  1.00E-03
      CRES                  1.00E-03
      BALD                  1.00E-03
      METHACRO              1.00E-03
      MVK                   1.00E-03
      ISOPROD               1.00E-03
      DCB1                  1.00E-03
      DCB2                  1.00E-03
      DCB3                  1.00E-03
      ETHENE                1.00E-03
      ISOPRENE              1.00E-03
      ISOPRXN               1.00E+00
      TRP1                  1.00E-03
      TRPRXN                1.00E+00
      ALK1                  1.00E-03
      ALK2                  1.00E-03
      ALK3                  1.00E-03
      ALK4                  1.00E-03
      ALK5                  1.00E-03
      ALK5RXN               1.00E+00
      ARO1                  1.00E-03
      ARO1RO2               1.00E-03
      TOLNRXN               1.00E+00
      TOLHRXN               1.00E+00
      ARO2                  1.00E-03
      ARO2RO2               1.00E-03
      XYLNRXN               1.00E+00
      XYLHRXN               1.00E+00
      BENZENE               1.00E-03
      BENZRO2               1.00E-03
      BNZNRXN               1.00E+00
      BNZHRXN               1.00E+00
      OLE1                  1.00E-03
      OLE2                  1.00E-03
      SESQ                  1.00E-03
      SESQRXN               1.00E+00
 Value for CTM_PHOTDIAG:  N returning FALSE

 File "CSQY_DATA" opened for input on unit:  94
 /home/lea/CMAQv5.0.2/scripts/cctm/BLD_lea/CSQY_DATA_saprc99_ae5_aq

Sucessfully Loaded JTABLE
PHOT: Identified USGS24 land use scheme for surface albedo used by inline photolysis calculation.

 File "OMI" opened for input on unit:  93
 /home/lea/CMAQv5.0.2/data/raw/phot/OMI.dat
 >>--->> WARNING in subroutine O3TOTCOL on PE 006
 Requested date is beyond available data on OMI file:  <0:00:00   July 28, 2013
 M3WARN:  DTBUF 0:00:00   April 21, 2014
 Total column ozone will be estimated from the corresponding Julian Day
 of the last available year on the OMI input file:0:00:00   April 21, 2013<<---<<

WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 11, 14, 2) and species HNO3 Back-up number 1
WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 11, 14, 2) and species NPHE Back-up number 2
WARNING: EBI Euler convergence failure
Reducing EBI time step because of MAXPRED convergence failure for
Cell ( 11, 14, 2) and species HCHO Back-up number 3
WARNING: EBI Euler convergence failure
Reducing EBI time step because of convergence failure for
Cell ( 11, 14, 2) Back-up number 4
WARNING: EBI Euler convergence failure
Reducing EBI time step because of convergence failure for
Cell ( 11, 14, 2) Back-up number 5
ERROR: Max number of EBI time step reductions exceeded
Convergence failure for cell ( 11, 14, 2)
Convergence failure for the following species:
NO2

 *** ERROR ABORT in subroutine HRSOLVER on PE 006
 ERROR: Stopping because of EBI convergence failures

PM3EXIT: DTBUF 0:00:00 April 21, 2014
Date and time 0:00:00 April 21, 2014 (2014111:000000)

I deleted the log file I had run. Post the new log file.

8

Hi,
It would be helpful if you would save your log file as a txt file and then upload the file as an attachment to this issue for us to review. Reading the log files that are copied and pasted into the forum directory is difficult due to the automatic formatting.
Please also attach your run script, so we can review the settings.
I did notice the following setting
set NSTEPS = 9600000 # time duration (HHMMSS) for this run

Typically NSTEPS is set to 240000

error message:

Grid name “METCRO_01_CROSS”
Dimensions: 125 rows, 118 cols, 30 lays, 14 vbles, 1 cells thick
NetCDF ID: 589824 opened as READONLY
Starting date and time 2014111:000000 (0:00:00 April 21, 2014)
Timestep 010000 (1:00:00 hh:mm:ss)
Maximum current record number 937
Checking header data for file: MET_BDY_3D
netCDF error number -40
Ending time not on file
9

And see the I/O API’s trouble-shooting page, on the topic of netCDF error-numbers:
https://cjcoats.github.io/ioapi/ERRORS.html#ncf331

where we see:

ncecoord = nf_einvalcoords = -40: coordinates out of range – probably, attempt to read past the last date-and-time on the file.