Compiling with KPP - where are the libraries??

[hmacintyre]

I have a mysterious error that I cannot seem to find a solution for.

I am using WRFV3.8.1 with 3.8.1 chemistry. I can compile successfully without KPP, but with KPP it seems to fall almost at the first step.

running chem/KPP/configure_kpp gives:

Code: Select all

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

  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: /home/helen.macintyre/LIBRARIES/flex/lib/libfl.a
OMPCC = # -fopenmp CCOMP = gcc CC = $(DM_CC) -DFSEEKO64_OK
DESCRIPTION = GNU ($SFC/$SCC) SCC = gcc DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT CC_TOOLS = $(SCC) CC="$(SCC)" CFLAGS="$(CFLAGS)" \
writing chem//configure.kpp
/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3
-----------------------------------------


then chem/KPP/compile_wkc:

Code: Select all

====================================================
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: /home/helen.macintyre/LIBRARIES/flex/lib/libfl.a
OMPCC = # -fopenmp CCOMP = gcc CC = $(DM_CC) -DFSEEKO64_OK
DESCRIPTION = GNU ($SFC/$SCC) SCC = gcc DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT CC_TOOLS = $(SCC) CC="$(SCC)" CFLAGS="$(CFLAGS)" \
writing chem/KPP/configure.kpp
/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3
-----------------------------------------
compile kpp
make[1]: Entering directory `/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/src'
  gcc -O -lm 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 -L/home/helen.macintyre/LIBRARIES/flex/lib -lfl -o kpp
make[1]: Leaving directory `/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/src'
-----------------------------------------
compile the coupler
gcc -I../../../../inc  -c -g  gen_kpp.c
gcc -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
-----------------------------------------
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
/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp cb05_sorg_aq.kpp
/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp: error while loading shared libraries: libfl.so.2: cannot open shared object file: No such file or directory
make: *** [cb05_sorg_aq_Integrator.f90] Error 127
WARNING: If kpp fails here the path to WRF-Chem might be too long for yacc ...
grep: ../../../module_kpp_cb05_sorg_aq_Integr.F: No such file or directory
Makefile:50: warning: overriding recipe for target `.F.o'
../../../../configure.wrf:334: warning: ignoring old recipe for target `.F.o'
Makefile:58: warning: overriding recipe for target `.c.o'
../../../../configure.wrf:361: warning: ignoring old recipe for target `.c.o'
rm -f decomp_uses.inc


... and so on with errors.

I have gone through the solutions here (http://forum.wrfforum.com/viewtopic.php?f=39&t=3302) but none have solved the issue.

I have a feeling that the kpp binary is not pointing to the correct flex libraries, but the code tells me that it is. I have explicitly set FLEX and FLEX_LIB_DIR to my locally installed version. I have also edited my files according to the solution here http://ruc.noaa.gov/wrf/wrf-chem/KPP_yacc_flex_problems.pdf

I've gone through executing the make scripts line by line and the first instance that kpp is run, I get the error about not locating shared libraries :

Code: Select all

/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp cb05_sorg_aq.kpp
/home/helen.macintyre/WRFv3.8.1/Build_WRF/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp: error while loading shared libraries: libfl.so.2: cannot open shared object file: No such file or directory
make: *** [cb05_sorg_aq_Integrator.f90] Error 127

Feeling very confused, any help appreciated.

[hmacintyre]

Hi,
Just to update, I did not manage to get the original error fixed, but instead used the flex library files already installed on the system.
The odd thing is that the missing file libfl.so.2 is not part of the system flex libraries, but it seems to not matter now....??

It turned out I was having an issue with yacc not being called properly from within the Makefile. I called it from command line on 'scan.y', copied the files produced ('y.tab.c' and 'y.tab.h') to the appropriate directory, and then did a configure and compile again (with WRF_KPP=1 from WRFV3/), and it seems to have compiled with no errors.

Rather unusual.

[ultidream]

Hi hmacintyre,

Thanks for updating the solution. I met the same problem. I am trying what you did but have simple questions.

I can call it from command line on scan.y and generated y.tab.c and y.tab.h, but what is the "appropriate directory" to copy them?

Thanks,

Hi,
Just to update, I did not manage to get the original error fixed, but instead used the flex library files already installed on the system.
The odd thing is that the missing file libfl.so.2 is not part of the system flex libraries, but it seems to not matter now....??

It turned out I was having an issue with yacc not being called properly from within the Makefile. I called it from command line on 'scan.y', copied the files produced ('y.tab.c' and 'y.tab.h') to the appropriate directory, and then did a configure and compile again (with WRF_KPP=1 from WRFV3/), and it seems to have compiled with no errors.

Rather unusual.

[yang]

I am having the same issue could kindly guide me through, how you used scan Y and where did you place it, which directory.

Thanks &regards,
Yang

[jazzyl]

Hi all, I don't know if you solved this, but I managed to solve it when I installed WRF-Chem 3.8.1 on my Ubuntu 16.04.
The trick is to check the compiling log of the command "./compile em_real >&checkwrf.log". You will see that the compiling first started with
"/usr/local/yacc/yacc -d scan.y
...
gcc -O -c y.tab.c
...",
then error occurred with the following line:
"gcc -O -lm 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 -L/usr/local/flex/lib -lfl -ll -o kpp"
The log file will say:
"/usr/bin/ld: cannot find -ll
collect2: error: ld returned 1 exit status
Makefile:66: recipe for target 'kpp' failed
make[1]: *** [kpp] Error 1
make[1]: Leaving directory '/home/models/WRFV3/chem/KPP/kpp/kpp-2.1/src'"

It means that the compiling procedure cannot find the libl.a file in the flex library. So the solution is to provide a flex with the libl.a file. On my Ubuntu 16.04, the solution is simply "apt-get install flex", then set the two environment variables:
export FLEX=/usr/bin/flex
export FLEX_LIB_DIR=/usr/lib/x86_64-linux-gnu

Finally, recompiled it and it worked. Hope this help.