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Fail to compile emi_conv in WRFv4.0

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S

slam14

New member
Hi All,
I am new to WRF-Chem. I am trying to install WRF-Chem using g-fortran on Pawsey (HPC).
WRF is successfully compiled and created 4*exe but I fail to compile emi_conv in the next step.

I am following the online tutorial
https://ruc.noaa.gov/wrf/wrf-chem/wrf_tutorial_exercises_v35/compiling_code.html

My environment variables are:
module swap PrgEnv-cray PrgEnv-gnu
module load flex
module load cray-netcdf
export WRF_CHEM=1
export WRF_KPP=1
export FLEX_LIB_DIR=$FLEX_ROOT/lib
export YACC='/group/pawsey0210/slam1/byacc/bin/yacc -d'
export NETCDF=$NETCDF_DIR

WRF is built successful with some warnings and errors. Is it acceptable?

Code: 
code.c:129:5: warning: implicit declaration of function 'FatalError'; did you mean 'strerror'? [-Wimplicit-function-declaration]
     FatalError(3,"%s: Can't create file", bufname );
     ^~~~~~~~~~
     strerror
  cc -O -c code_c.c
code_c.c: In function 'C_Decl':
code_c.c:262:17: warning: implicit declaration of function 'Message' [-Wimplicit-function-declaration]
                 Message( "Can not declare type %d", var->type );
                 ^~~~~~~
  cc -O -c code_f77.c
  cc -O -c code_f90.c
  cc -O -c code_matlab.c
code_matlab.c: In function 'MATLAB_FunctionBegin':
code_matlab.c:606:5: warning: implicit declaration of function 'FatalError'; did you mean 'strerror'? [-Wimplicit-function-declaration]
     FatalError(3,"%s: Can't create file", buf );
     ^~~~~~~~~~
     strerror

......
# Tail end
==========================================================================
build started:   Wed Oct 31 14:57:36 AWST 2018
build completed: Wed Oct 31 15:52:08 AWST 2018
 
--->                  Executables successfully built                  <---
 
-rwxrwx--x+ 1 slam1 pawsey0210 81549656 Oct 31 15:51 main/ndown.exe
-rwxrwx--x+ 1 slam1 pawsey0210 81423368 Oct 31 15:52 main/real.exe
-rwxrwx--x+ 1 slam1 pawsey0210 80675848 Oct 31 15:52 main/tc.exe
-rwxrwx--x+ 1 slam1 pawsey0210 96026264 Oct 31 15:47 main/wrf.exe
 
==========================================================================

Then I type
Code: 
compile emi_conv >& emcompile.log
Log file is here:
Code: 
====================================================
starting compile_wkc
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  WKC - WRF-Chem/KPP coupler


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  KPP - symbolic chemistry Kinetics PreProcessor, Version 2.1
        (http://www.cs.vt.edu/~asandu/Software/KPP)
  KPP is distributed under GPL, the general public licence
        (http://www.gnu.org/copyleft/gpl.html)
    (C) 1995-1997, V. Damian & A. Sandu, CGRER, Univ. Iowa
    (C) 1997-2003, A. Sandu, Michigan Tech
    (C) 2003-2005, A. Sandu, Virginia Polytechnic Institute and State University
        with contributions from:
        R. Sander, Max-Planck Institute for Chemistry, Mainz, Germany


   The current version of KPP was modified for WRF-Chem.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
------------------------------------------
 configure_kpp, settings:
location of flex library: /pawsey/cle60up05/devel/gcc/4.8.5/flex/2.6.4/lib/libfl.a
OMPCC = # -fopenmp CCOMP = cc #gcc DM_CC = cc #mpicc CC = $(DM_CC) -DFSEEKO64_OK
DESCRIPTION = GNU ($SFC/$SCC) SCC = cc #gcc CC_TOOLS = $(SCC) CC="$(SCC)" CFLAGS="$(CFLAGS)" \
writing chem/KPP/configure.kpp
/group/pawsey0210/slam1/WRF
-----------------------------------------
compile kpp
make[1]: Entering directory '/group/pawsey0210/slam1/WRF/chem/KPP/kpp/kpp-2.1/src'
  cc -O y.tab.o lex.yy.o scanner.o scanutil.o kpp.o gen.o code.o code_c.o code_f77.o code_f90.o code_matlab.o debug.o -lm -L/pawsey/cle60up05/devel/gcc/4.8.5/flex/2.6.4/lib -lfl -o kpp
make[1]: Leaving directory '/group/pawsey0210/slam1/WRF/chem/KPP/kpp/kpp-2.1/src'
-----------------------------------------
compile the coupler
cc  -I../../../../inc  -c -g  gen_kpp.c
gen_kpp.c: In function 'gen_kpp':
gen_kpp.c:75:27: warning: implicit declaration of function 'write_list_to_screen' [-Wimplicit-function-declaration]
        if ( DEBUGR == 2 ) write_list_to_screen( WRFC_packs ) ;
                           ^~~~~~~~~~~~~~~~~~~~
gen_kpp.c:115:6: warning: implicit declaration of function 'screen_out' [-Wimplicit-function-declaration]
      screen_out( );
      ^~~~~~~~~~
gen_kpp.c:120:6: warning: implicit declaration of function 'check_all' [-Wimplicit-function-declaration]
      check_all ( kpp_dirname );
      ^~~~~~~~~
cc  -o registry_kpp -g   registry_kpp.o  my_strtok.o data.o type.o misc.o reg_parse.o gen_kpp.o get_wrf_chem_specs.o gen_kpp_mech_dr.o gen_kpp_interface.o get_kpp_chem_specs.o compare_kpp_to_species.o get_wrf_radicals.o get_wrf_jvals.o gen_kpp_utils.o change_chem_Makefile.o gen_kpp_interf_utils.o gen_kpp_args_to_Update_Rconst.o  kpp_data.o sym.o symtab_gen.o
compile the tuv_kpp
make: 'tuv_kpp' is up to date.
-----------------------------------------
check if Registry was touched
make: 'mod_registry.temp' is up to date.
-----------------------------------------
Run kpp for mechanisms in chem/KPP/mechanisms
=========================================================
mechanisms/cb05_sorg_aq
model cb05_sorg_aq
make: 'cb05_sorg_aq_Integrator.f90' is up to date.
=========================================================
mechanisms/cb05_sorg_vbs_aq
model cb05_sorg_vbs_aq
make: 'cb05_sorg_vbs_aq_Integrator.f90' is up to date.
=========================================================
mechanisms/cbm4
model cbm4
make: 'cbm4_Integrator.f90' is up to date.
=========================================================
mechanisms/cbmz_bb
model cbmz_bb
make: 'cbmz_bb_Integrator.f90' is up to date.
=========================================================
mechanisms/cbmz_mosaic
model cbmz_mosaic
make: 'cbmz_mosaic_Integrator.f90' is up to date.
=========================================================
mechanisms/cri_mosaic_4bin_aq
model cri_mosaic_4bin_aq
make: 'cri_mosaic_4bin_aq_Integrator.f90' is up to date.
=========================================================
mechanisms/cri_mosaic_8bin_aq
model cri_mosaic_8bin_aq
make: 'cri_mosaic_8bin_aq_Integrator.f90' is up to date.
=========================================================
mechanisms/crimech
model crimech
make: 'crimech_Integrator.f90' is up to date.
=========================================================
mechanisms/gocartracm
model gocartracm
make: 'gocartracm_Integrator.f90' is up to date.
=========================================================
mechanisms/mozart
model mozart
make: 'mozart_Integrator.f90' is up to date.
=========================================================
mechanisms/mozart_mosaic_4bin
model mozart_mosaic_4bin
make: 'mozart_mosaic_4bin_Integrator.f90' is up to date.
tuv_kpp: Argument = FIRST
tuv_kpp: Argument = mozart_mosaic_4bin
tuv_kpp: Mechanism = mozart_mosaic_4bin
=========================================================
mechanisms/mozart_mosaic_4bin_aq
model mozart_mosaic_4bin_aq
make: 'mozart_mosaic_4bin_aq_Integrator.f90' is up to date.
tuv_kpp: Argument = mozart_mosaic_4bin_aq
tuv_kpp: Mechanism = mozart_mosaic_4bin_aq
=========================================================
mechanisms/mozcart
model mozcart
make: 'mozcart_Integrator.f90' is up to date.
tuv_kpp: Argument = mozcart
tuv_kpp: Mechanism = mozcart
=========================================================
mechanisms/nmhc9
model nmhc9
make: 'nmhc9_Integrator.f90' is up to date.
=========================================================
mechanisms/racm
model racm
make: 'racm_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_esrlsorg
model racm_esrlsorg
make: 'racm_esrlsorg_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_esrlsorg_aqchem
model racm_esrlsorg_aqchem
make: 'racm_esrlsorg_aqchem_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_mim
model racm_mim
make: 'racm_mim_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_soa_vbs
model racm_soa_vbs
make: 'racm_soa_vbs_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_soa_vbs_aqchem
model racm_soa_vbs_aqchem
make: 'racm_soa_vbs_aqchem_Integrator.f90' is up to date.
=========================================================
mechanisms/racm_soa_vbs_het
model racm_soa_vbs_het
make: 'racm_soa_vbs_het_Integrator.f90' is up to date.
=========================================================
mechanisms/racmpm
model racmpm
make: 'racmpm_Integrator.f90' is up to date.
=========================================================
mechanisms/racmsorg
model racmsorg
make: 'racmsorg_Integrator.f90' is up to date.
=========================================================
mechanisms/racmsorg_aqchem
model racmsorg_aqchem
make: 'racmsorg_aqchem_Integrator.f90' is up to date.
=========================================================
mechanisms/radm2
model radm2
make: 'radm2_Integrator.f90' is up to date.
=========================================================
mechanisms/radm2sorg
model radm2sorg
make: 'radm2sorg_Integrator.f90' is up to date.
=========================================================
mechanisms/saprc99
model saprc99
make: 'saprc99_Integrator.f90' is up to date.
=========================================================
mechanisms/saprc99_mosaic_4bin_vbs2
model saprc99_mosaic_4bin_vbs2
make: 'saprc99_mosaic_4bin_vbs2_Integrator.f90' is up to date.
=========================================================
mechanisms/saprc99_mosaic_8bin_vbs2_aq
model saprc99_mosaic_8bin_vbs2_aq
make: 'saprc99_mosaic_8bin_vbs2_aq_Integrator.f90' is up to date.
=========================================================
mechanisms/t1_mozcart
model t1_mozcart
make: 't1_mozcart_Integrator.f90' is up to date.
tuv_kpp: Argument = t1_mozcart
tuv_kpp: Mechanism = t1_mozcart
tuv_kpp: Argument = LAST
=========================================================
 not running the WRF-Chem KPP coupler
end of compile_wkc
=========================================================
This option is not recognized: emi_conv

I can see the mechanism in WRF/chem/ but I cannot find the *exe.
The log file is returning that the emi_conv is not an option. I am quite lost here. I have tried byacc instead of yacc and I am still having the same problem.
Can anyone shed some light? I am stuck in this step for a while.
Much appreciated for your help in advance.
Thanks,
Sean
 
hi slam:
Recently, i have tried to compile run in WRFv4.1.2 but failed, (when i compile em_real, it works well)and i find the compile.log show that

not running the WRF-Chem KPP coupler
end of compile_wkc
=========================================================
This option is not recognized: run

it seems that it has the same kpp error when you compiled emi_conv . So did you find the way to solve this problem?
looking for your reply.
 
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