# Problem running benchmark tutorial

**URL:** <https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705>\
**Category:** Run Time Errors and Issues\
**Created:** [August 7, 2020, 9:38am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705 "2020-08-07T09:38:36Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![ddmmssddoo](https://avatars.discourse-cdn.com/v4/letter/d/59ef9b/32.png) [@ddmmssddoo](https://forum.cmascenter.org/u/ddmmssddoo)\
**Post date:** [August 7, 2020, 9:38am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/1 "2020-08-07T09:38:36Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![cgnolte](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/cgnolte/32/53_2.png) [@cgnolte](https://forum.cmascenter.org/u/cgnolte)\
**Post date:** [August 10, 2020, 3:40pm UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/2 "2020-08-10T15:40:22Z")

</div>

Please review the posting [guidelines](https://forum.cmascenter.org/t/please-read-before-posting/1321).

- 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?

---

<div class="post-metadata">

**Author:** ![ddmmssddoo](https://avatars.discourse-cdn.com/v4/letter/d/59ef9b/32.png) [@ddmmssddoo](https://forum.cmascenter.org/u/ddmmssddoo)\
**Post date:** [August 11, 2020, 8:59am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/3 "2020-08-11T08:59:48Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![cgnolte](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/cgnolte/32/53_2.png) [@cgnolte](https://forum.cmascenter.org/u/cgnolte)\
**Post date:** [August 11, 2020, 12:19pm UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/4 "2020-08-11T12:19:08Z")

</div>

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](https://github.com/USEPA/CMAQ/blob/master/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_benchmark.md).  
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.)

---

<div class="post-metadata">

**Author:** ![ddmmssddoo](https://avatars.discourse-cdn.com/v4/letter/d/59ef9b/32.png) [@ddmmssddoo](https://forum.cmascenter.org/u/ddmmssddoo)\
**Post date:** [September 21, 2020, 8:32am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/5 "2020-09-21T08:32:17Z")

</div>

- 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](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

---

<div class="post-metadata">

**Author:** ![ddmmssddoo](https://avatars.discourse-cdn.com/v4/letter/d/59ef9b/32.png) [@ddmmssddoo](https://forum.cmascenter.org/u/ddmmssddoo)\
**Post date:** [September 21, 2020, 8:43am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/6 "2020-09-21T08:43:10Z")

</div>

- 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.

```

---

<div class="post-metadata">

**Author:** ![ddmmssddoo](https://avatars.discourse-cdn.com/v4/letter/d/59ef9b/32.png) [@ddmmssddoo](https://forum.cmascenter.org/u/ddmmssddoo)\
**Post date:** [September 21, 2020, 8:43am UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/7 "2020-09-21T08:43:23Z")

</div>

```
 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.

---

<div class="post-metadata">

**Author:** ![lizadams](https://avatars.discourse-cdn.com/v4/letter/l/49beb7/32.png) [@lizadams](https://forum.cmascenter.org/u/lizadams)\
**Post date:** [October 2, 2020, 5:50pm UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/8 "2020-10-02T17:50:06Z")

</div>

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:

```auto
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

```

---

<div class="post-metadata">

**Author:** ![cjcoats](https://avatars.discourse-cdn.com/v4/letter/c/ac8455/32.png) [@cjcoats](https://forum.cmascenter.org/u/cjcoats)\
**Post date:** [October 2, 2020, 6:14pm UTC](https://forum.cmascenter.org/t/problem-running-benchmark-tutorial/1705/9 "2020-10-02T18:14:41Z")

</div>

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](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._