[petsc-dev] proposed patch: YAML parser

[Blaise Bourdin]

Responding to myself:

- the attached patch (yaml-3.patch) replaces the first one I sent yesterday and adds fortran binding for PetscOptionsInsertFile_YAML

- The reason why calling PetscOptionsInsertFile_YAML is not working when called from inside PetscInitialize is that I use PetscViewerStringOpen to print the generated options list to a string then MPI_Bcast it, but PetscViewerStringOpen is not available until after PetscInitialize. I have modified pinit.c and options.c so that PetscOptionsInsertFile_YAML is called later on, after logging has been enabled. This is enabled in yaml-4.patch

Are these patches suitable?

Blaise

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On Jul 23, 2012, at 11:39 PM, Blaise Bourdin wrote:

> Hi,
> 
> After trying to get the current yaml parser in petsc to work, I finally gave up and rewrote a very basic one. It supports only a subset of the standard and lacks support or sequences and aliases , for instance (would that be JSON?). Would you consider applying this patch (yaml-1.patch) to 3.3 and dev? The fortran binding also does not work, I think that I am still missing the proper headers in include/finclude, but I am getting a bit lost.
> 
> I also tried to modify options.c in order to add a global flag -yaml_file (this is probably a bad name, I agree), but I can't figure out why it doesn't work (I can't even get a stack trace). The changes are in yaml-2.patch
> (gdb) run -yaml_file petsc.yaml
> Starting program: /opt/HPC/petsc-3.3/src/sys/examples/tutorials/ex79 -yaml_file petsc.yaml
> Reading symbols for shared libraries ++++++++++++++++++++++............................ done
> PETSC ERROR: Logging has not been enabled.
> You might have forgotten to call PetscInitialize().
> application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0
> 
> Program exited with code 070.
> (gdb) where
> No stack.
> 
> Would anybody be willing to have a look at the second patch?
> 
> Regards,
> 
> Blaise
> <yaml-1.patch><yaml-2.patch>
> -- 
> Department of Mathematics and Center for Computation & Technology
> Louisiana State University, Baton Rouge, LA 70803, USA
> Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin
> 
> 
> 
> 
> 
> 
> 

-- 
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin