Error when running bldit_cctm.csh for new MECH ebi, and CSQY

Hi CMAQ users:
I created new MECH, ebi, and CSQY by running chemmech, create_ebi, and jtable_proc. While, when I am trying to use them to run bldit_cctm.csh, it shows the error messages below. How could I deal with this issue? Could anyone have a look at it? I am also attaching the running log here.
Best
Huan

build_cctm.txt (112.4 KB)
hrdriver.F(80): error #5082: Syntax error, found IDENTIFIER ‘SUBST_PACTL_ID’ when expecting one of: <CHAR_CON_KIND_PARAM> <CHAR_NAM_KIND_PARAM> <CHARACTER_CONSTANT>
INCLUDE SUBST_PACTL_ID ! Process analysis control parameters
--------------^
hrdriver.F(80): error #5102: Cannot open include file ‘NULL_STRING>’
INCLUDE SUBST_PACTL_ID ! Process analysis control parameters
--------------^
compilation aborted for hrdriver.F (code 1)
make: *** [hrdriver.o] Error 1
ERROR while running make command

After CMAQ version 5.1, hrdriver.F stopped using the SUBST_PACTL_ID include file but the build log references version 5.2.1. Perhaps, you are using the wrong version of utilities’ for developing mechanisms, i.e., under the UTIL directory in the CMAQ repository in the version 5.2.1 branch.

1 Like

Exactly, I tried the chemmech of version 5.2.1, while it fails. I post the question previously (Comiling CHEMMECH), while I did not get the solution yet, so I used the one in version 5.1 instead. Could you have a look at it?

Best
Huan

Thank you for help~
I tried the UTIL of version 5.2.1 to generate MECH and ebi. Now, it shows the below error messages when running bldit_cctm.csh. I also attach the running log here.

hrprodloss.F(1752): error #6404: This name does not have a type, and must have an explicit type. [PAR]
PNEG( PAR ) = 0.0D0
------------^
compilation aborted for hrprodloss.F (code 1)
make: *** [hrprodloss.o] Error 1
ERROR while running make command
run_cctm.txt (267.9 KB)

My last reply was cut short. Did you run create_ebi using the below settings for a racm2 mechanism?

  setenv GC_NAME       RACM2    
  setenv AE_NAME       AE6
  setenv AQ_NAME       AQ
  
  setenv PAR_NEG_FLAG    F    # True for CB05 and cb6 but false for SAPRC07t and RACM2 
  setenv DEGRADE_SUBS    F    # include calls for HAPs degrade routines (true cb05tump and cb05mp51)
  setenv NO2EX_CYCLE     F    # modify group one solution to include excited NO2
  
  #Set the below compound names within the mechanism
   setenv MECH_NO    NO     #  Mechanism name for nitric oxide
   setenv MECH_NO2   NO2    #  Mechanism name for nitrogen dioxide
   setenv MECH_NO2EX NO2EX  #  SAPRC, RACM Mechanism name for excited nitrogen dioxide;       not in Carbon Bond
   setenv MECH_O3    O3     #  Mechanism name for ozone
   setenv MECH_O3P   O3P    #  SAPRC, RACM Mechanism name for ground state oxygen atom
   setenv MECH_O1D   O1D    #  Mechanism name for excited state oxygen atom; O1D for SAPRC,       RACM2
   setenv MECH_OH    HO     #  Mechanism name for hydroxyl radical
   setenv MECH_HO2   HO2    #  Mechanism name for hydroperoxy radical
   setenv MECH_HONO  HONO   #  Mechanism name for nitrous acid
   setenv MECH_HNO4  HNO4   #  SAPRC, RACM Mechanism name for peroxynitric acid
   setenv MECH_PAN   PAN    #  Mechanism name for peroxy acetyl nitrate
   setenv MECH_C2O3   ACO3  #  RACM, SAPRC Mechanism name for peroxy acetyl radical; ACO3       or MECO3
   setenv MECH_NO3   NO3    #  Mechanism name for nitrate radical
   setenv MECH_N2O5  N2O5   #  Mechanism name for dinitrogen pentoxide

Your log file indicates that PAR_NEG_FLAG and DEGRADE_SUBS were set to T.

I missed PAR_NEG_FLAG and DEGRADE_SUBS.
I just re-run create_ebi, and run bldit_cctm.csh again. Near the end, it shows the error messages below. I think it is due to the mechanism itself, is my understanding correct?

Thank you for your time
Best
Huan

RXNS_DATA_MODULE.o: In function rxns_data._': RXNS_DATA_MODULE.F90:(.text+0x0): multiple definition ofrxns_data.
RXNS_DATA_MODULE.o:RXNS_DATA_MODULE.F90:(.text+0x0): first defined here
RXNS_DATA_MODULE.o:(.bss+0x0): multiple definition of rxns_data_mp_krx7_' RXNS_DATA_MODULE.o:(.bss+0x0): first defined here RXNS_DATA_MODULE.o:(.bss+0x8): multiple definition ofrxns_data_mp_krx6

RXNS_DATA_MODULE.o:(.bss+0x8): first defined here
RXNS_DATA_MODULE.o:(.bss+0x10): multiple definition of rxns_data_mp_mapped_to_cgrid_' RXNS_DATA_MODULE.o:(.bss+0x10): first defined here RXNS_DATA_MODULE.o:(.data+0x0): multiple definition ofrxns_data_mp_rxlabel_’
RXNS_DATA_MODULE.o:(.data+0x0): first defined here
RXNS_DATA_MODULE.o:(.data+0x1c60): multiple definition of rxns_data_mp_hetero_' RXNS_DATA_MODULE.o:(.data+0x1c60): first defined here RXNS_DATA_MODULE.o:(.data+0x1cc0): multiple definition ofrxns_data_mp_photab_’
RXNS_DATA_MODULE.o:(.data+0x1cc0): first defined here
RXNS_DATA_MODULE.o:(.data+0x1eb0): multiple definition of rxns_data_mp_ihetero_' RXNS_DATA_MODULE.o:(.data+0x1eb0): first defined here RXNS_DATA_MODULE.o:(.data+0x1ee0): multiple definition ofrxns_data_mp_iph_’
RXNS_DATA_MODULE.o:(.data+0x1ee0): first defined here
RXNS_DATA_MODULE.o:(.data+0x20c0): multiple definition of rxns_data_mp_nprdct_' RXNS_DATA_MODULE.o:(.data+0x20c0): first defined here RXNS_DATA_MODULE.o:(.data+0x27e0): multiple definition ofrxns_data_mp_nreact_’
RXNS_DATA_MODULE.o:(.data+0x27e0): first defined here
RXNS_DATA_MODULE.o:(.data+0x2f00): multiple definition of rxns_data_mp_sc_' RXNS_DATA_MODULE.o:(.data+0x2f00): first defined here RXNS_DATA_MODULE.o:(.data+0xc400): multiple definition ofrxns_data_mp_irrfall_’
RXNS_DATA_MODULE.o:(.data+0xc400): first defined here
RXNS_DATA_MODULE.o:(.data+0xc480): multiple definition of rxns_data_mp_irr_' RXNS_DATA_MODULE.o:(.data+0xc480): first defined here RXNS_DATA_MODULE.o:(.data+0x16ec0): multiple definition ofrxns_data_mp_nrxwh2_’
RXNS_DATA_MODULE.o:(.data+0x16ec0): first defined here
RXNS_DATA_MODULE.o:(.data+0x16ec8): multiple definition of rxns_data_mp_nrxwch4_' RXNS_DATA_MODULE.o:(.data+0x16ec8): first defined here RXNS_DATA_MODULE.o:(.data+0x16ed0): multiple definition ofrxns_data_mp_nrxwn2_’
RXNS_DATA_MODULE.o:(.data+0x16ed0): first defined here
RXNS_DATA_MODULE.o:(.data+0x16ed8): multiple definition of rxns_data_mp_nrxwo2_' RXNS_DATA_MODULE.o:(.data+0x16ed8): first defined here RXNS_DATA_MODULE.o:(.data+0x16ef0): multiple definition ofrxns_data_mp_nrxww_’
RXNS_DATA_MODULE.o:(.data+0x16ef0): first defined here
RXNS_DATA_MODULE.o:(.data+0x16f00): multiple definition of rxns_data_mp_nrxwm_' RXNS_DATA_MODULE.o:(.data+0x16f00): first defined here RXNS_DATA_MODULE.o:(.data+0x16f08): multiple definition ofrxns_data_mp_krx5_’
RXNS_DATA_MODULE.o:(.data+0x16f08): first defined here
RXNS_DATA_MODULE.o:(.data+0x16f28): multiple definition of rxns_data_mp_krx4_' RXNS_DATA_MODULE.o:(.data+0x16f28): first defined here RXNS_DATA_MODULE.o:(.data+0x16f40): multiple definition ofrxns_data_mp_krx3_’
RXNS_DATA_MODULE.o:(.data+0x16f40): first defined here
RXNS_DATA_MODULE.o:(.data+0x17310): multiple definition of rxns_data_mp_krx2_' RXNS_DATA_MODULE.o:(.data+0x17310): first defined here RXNS_DATA_MODULE.o:(.data+0x17320): multiple definition ofrxns_data_mp_krx1_’
RXNS_DATA_MODULE.o:(.data+0x17320): first defined here
RXNS_DATA_MODULE.o:(.data+0x17520): multiple definition of rxns_data_mp_iorder_' RXNS_DATA_MODULE.o:(.data+0x17520): first defined here RXNS_DATA_MODULE.o:(.data+0x17c40): multiple definition ofrxns_data_mp_irxbits_’
RXNS_DATA_MODULE.o:(.data+0x17c40): first defined here
RXNS_DATA_MODULE.o:(.data+0x18360): multiple definition of rxns_data_mp_ktype_' RXNS_DATA_MODULE.o:(.data+0x18360): first defined here RXNS_DATA_MODULE.o:(.data+0x18a80): multiple definition ofrxns_data_mp_rfdat_’
RXNS_DATA_MODULE.o:(.data+0x18a80): first defined here
RXNS_DATA_MODULE.o:(.data+0x18ea0): multiple definition of rxns_data_mp_rtdat_' RXNS_DATA_MODULE.o:(.data+0x18ea0): first defined here RXNS_DATA_MODULE.o:(.data+0x1b930): multiple definition ofrxns_data_mp_kunits_’
RXNS_DATA_MODULE.o:(.data+0x1b930): first defined here
RXNS_DATA_MODULE.o:(.data+0x1b938): multiple definition of rxns_data_mp_halogen_parameter_' RXNS_DATA_MODULE.o:(.data+0x1b938): first defined here RXNS_DATA_MODULE.o:(.data+0x1b940): multiple definition ofrxns_data_mp_species_molwt_’
RXNS_DATA_MODULE.o:(.data+0x1b940): first defined here
RXNS_DATA_MODULE.o:(.data+0x1bc00): multiple definition of rxns_data_mp_convert_conc_' RXNS_DATA_MODULE.o:(.data+0x1bc00): first defined here RXNS_DATA_MODULE.o:(.data+0x1bec0): multiple definition ofrxns_data_mp_cgrid_index_’
RXNS_DATA_MODULE.o:(.data+0x1bec0): first defined here
RXNS_DATA_MODULE.o:(.data+0x1c180): multiple definition of rxns_data_mp_species_type_' RXNS_DATA_MODULE.o:(.data+0x1c180): first defined here RXNS_DATA_MODULE.o:(.data+0x1cc20): multiple definition ofrxns_data_mp_chemistry_spc_’
RXNS_DATA_MODULE.o:(.data+0x1cc20): first defined here
RXNS_DATA_MODULE.o:(.data+0x1d6c0): multiple definition of rxns_data_mp_gas_chem_spc_' RXNS_DATA_MODULE.o:(.data+0x1d6c0): first defined here /usr/bin/ld: link errors found, deleting executableCCTM_v521_racm_iso.exe’
/usr/bin/sha1sum: CCTM_v521_racm_iso.exe: No such file or directory
make: *** [CCTM_v521_racm_iso.exe] Error 1
ERROR while running make command

endif
else if ( 0 ) then
endif
mv Makefile Makefile.intel
if ( -e Makefile.intel && -e Makefile ) rm Makefile
ln -s Makefile.intel Makefile
if ( 0 != 0 ) then
if ( -e /scratch/brown/fang63/cmaq/CMAQ-5.2.1/CCTM/scripts/BLD_CCTM_v521_racm_iso_intel/CCTM_v521_racm_iso.cfg ) then
mv CCTM_v521_racm_iso.cfg.bld /scratch/brown/fang63/cmaq/CMAQ-5.2.1/CCTM/scripts/BLD_CCTM_v521_racm_iso_intel/CCTM_v521_racm_iso.cfg
exit

The problem could be that the Makefile lists RXNS_DATA_MODULE.o twice in the variables used to define the object files. In general,
duplicates are bad in the list of object files for assembling an executable. I
do not know why the duplication happened. Check your build script for CCTM.

Cannot make firm conclusions but check the path to initial conditions file and whether the file has the needed time step and data.