KPP is parsing the equation file.Error :aqchem.spc:27: Misplaced ';'

[gmichals]

Hi,
We have been running kpp with success but have run into a road block. We are running version 2.2.3 because this version was used by Fahey et al. 2006 for their box model wrap of kpp to test for use in CMAQ. We are building new mechanisms and using the same tests. Through much effort we were able to get it working in the Fall but on a new mechanism was getting segment faults that we traced to kpp build using VAR pointers instead of defined VAR. I thought this might be a version issue, so I reloaded 2.2.3. Now using the same files that worked before I reinstalled the .spc will not parse giving a KPP a "Error :aqchem.spc: Misplaced ';'. Ive gone through it for hidden characters, re written it, deleted suspects lines, you name it but I can find no error. Any idea?

aqchem.txt

[yantosca]

Thanks for writing @gmichals. I was able to do the following:

1. git clone https://github.com/KineticPreProcessor/KPP
2. cd KPP
3. git checkout tags/2.2.3
4. git checkout -b version_2.2.3
5. mkdir bin
6. export KPP_HOME=/path/to/KPP
7. cd src
8. make

Then I copied your aqchem.txt to a folder and added the line #LANGUAGE Fortran90 at the top. This is because we no longer have access to the old G77 compiler.

8. cd /path/where/aqchem.kpp/lives
9. $KPP_HOME/bin/kpp aqchem.kpp

I get this output:

This is KPP-2.2.3.

KPP is parsing the equation file.
KPP is computing Jacobian sparsity structure.
KPP is starting the code generation.
KPP is initializing the code generation.
KPP is generating the monitor data:
    - aqchem_Monitor
KPP is generating the utility data:
    - aqchem_Util
KPP is generating the global declarations:
    - aqchem_Main
KPP is generating the ODE function:
    - aqchem_Function
KPP is generating the ODE Jacobian:
    - aqchem_Jacobian
    - aqchem_JacobianSP
KPP is generating the linear algebra routines:
    - aqchem_LinearAlgebra
KPP is generating the Hessian:
    - aqchem_Hessian
    - aqchem_HessianSP
KPP is generating the utility functions:
    - aqchem_Util
KPP is generating the rate laws:
    - aqchem_Rates
KPP is generating the parameters:
    - aqchem_Parameters
KPP is generating the global data:
    - aqchem_Global
KPP is generating the stoichiometric description files:
    - aqchem_Stoichiom
    - aqchem_StoichiomSP
KPP is generating the driver from none.f90:
    - aqchem_Main
KPP is starting the code post-processing.

KPP has succesfully created the model "aqchem".

But when I try to compile the Fortran code

$ make -f Makefile_aqchem

I get this error:

aqchem_Stoichiom.f90:118:34:

  118 |       REAL(kind=dp) JV_RPROD(NJVRP)
      |                                  1
Error: Symbol ‘njvrp’ at (1) has no IMPLICIT type
aqchem_Stoichiom.f90:138:37:

  138 |              aj = aj + JV_RPROD(k)*U(ICOL_JVRP(k))
      |                                     1
Error: Function ‘icol_jvrp’ at (1) has no IMPLICIT type
aqchem_Stoichiom.f90:137:14:

  137 |          DO k=CROW_JVRP(JCOEFF(j)),CROW_JVRP(JCOEFF(j)+1)-1
      |              1
Error: Function ‘crow_jvrp’ at (1) has no IMPLICIT type

I don't know if I'm missing a file where NJVRP is defined. But it looks even code 2.3.3 (at least the version from the Git repo and maybe not the tarball on the old KPP site) can parse the mechanism.

Also tagging @RolfSander

[yantosca]

@gmichals Here is a zip folder with the output from KPP 2.3.3.

test_kpp_2.3.3.zip

[gmichals]

Hmmm...I did all that successfully but still getting the same error...
gmichals@login06.negishi:[Sulfur 33 (W)] $ kpp aqchem.kpp
This is KPP-2.2.3.
KPP is parsing the equation file.Error :aqchem.spc:28: Misplaced ';'
Fatal error : 1 errors and 0 warnings encountered.
Program aborted
gmichals@login06.negishi:[Sulfur 33 (W)] $

Even deleted the spc file and pasted the one in the zip...

[gmichals]

And it happens to any .spc file

[gmichals]

EPAmodel.zip
attached kpp, spc and eqn im using

[yantosca]

Thanks @gmichals. I'm missing an integr.kpp file that is included by aqchem.kpp.

Also, here are the KPP dependencies that I am using:

$ gcc --version
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ gfortran --version
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ flex --version
flex 2.6.4

$ bison --version
bison (GNU Bison) 3.8.2
Written by Robert Corbett and Richard Stallman.

Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[yantosca]

@gmichals: As a workaround I replaced the #INCLUDE integr.kpp with #INTEGRATOR rosenbrock and recompiled KPP. I got this error:

$ kpp aqchem.kpp

This is KPP-2.2.3.

KPP is parsing the equation file.Error :aqchem.eqn:336: 
Inline code for F90_RATES is too long (10019>10000).
Increase MAX_INLINE in scan.h and recompile kpp!
malloc(): invalid size (unsorted)
Aborted (core dumped)

So I then changed MAX_INLINE to 100000 and then recompiled KPP. I then was able to build the mechanism:

$ kpp aqchem.kpp

This is KPP-2.2.3.

KPP is parsing the equation file.***************************
KPP is computing Jacobian sparsity structure.
KPP is starting the code generation.
KPP is initializing the code generation.
KPP is generating the monitor data:
    - aqchem_Monitor
KPP is generating the utility data:
    - aqchem_Util
KPP is generating the global declarations:
    - aqchem_Main
KPP is generating the ODE function:
    - aqchem_Function
KPP is generating the ODE Jacobian:
    - aqchem_Jacobian
    - aqchem_JacobianSP
KPP is generating the linear algebra routines:
    - aqchem_LinearAlgebra
KPP is generating the utility functions:
    - aqchem_Util
KPP is generating the rate laws:
    - aqchem_Rates
KPP is generating the parameters:
    - aqchem_Parameters
KPP is generating the global data:
    - aqchem_Global
KPP is generating the driver from general.f90:
    - aqchem_Main
KPP is starting the code post-processing.

KPP has succesfully created the model "aqchem".

Wondering if your error is caused by an older versions of GCC, flex, and/or bison. Or have you built KPP with another compiler like ifort?

[yantosca]

@gmichals: Also in the most recent KPP we now use #define MAX_INLINE 200000.