[petsc-users] Appending to vector / numerical continuation / slepc

[Jose E. Roman]

On 11/10/2011, Kevin Green wrote:

> Successfully updated to petsc-3.2 and slepc-dev.
> 
> 
> A note about slepc-dev:
> configure failed, with the error
>  
> Traceback (most recent call last):
>   File "./configure", line 10, in <module>
>     execfile(os.path.join(os.path.dirname(__file__), 'config', 'configure.py'))
>   File "./config/configure.py", line 344, in <module>
>     generatefortranstubs.main(petscconf.BFORT)
> AttributeError: 'module' object has no attribute 'BFORT'
> 
> when I commented out the offending if statement in configure.py, the build worked, but the tests for fortran examples failed... Not really an issue for me, but thought I should point this out.

Yes, this is because sowing is not available (can be fixed with --download-sowing in PETSc or using a mercurial version of PETSc). Now I have added a test in slepc-dev to avoid this error.
Jose

> 
> 
> DMcomposite examples:
> src/snes/examples/tutorials/ex21.c (the example that seems most useful for my purpose) fails to run, as the jacobian isn't set within the code... I thought maybe running it with the -snes_fd option would work, but that results in a null object somewhere within snes.c.  My guess is that an mffd needs to be in place for this.  Or am I missing something?
> 
> 
> Up until this point, I have been setting the jacobian on a 2D (periodic in x and y) DM analytically.  To preallocate the nonzero structure of the jacobian, I use DMDASetBlockFills(...).  Now that I wish to use a DMComposite with the original DM and an array, I presume I'll have to use DMCompositeSetCoupling(...) to preallocate the jacobian structure, but the only example quoted in that documentation points this out, but doesn't actually use it.  So...
> 1.  Can I still manage to use DMDASetBlockFills(...) for the DM part of the composite?
> 2.  How would the array coupling then get "wiggled in" to the structure?
> 3.  It seems like this process could get ugly if the above is not possible... so if I move away from setting the Jacobian explicitly, do things become simpler?
> 
> 
> That's all for now, it seems fairly intuitive on how to make use of the composite once it gets set up.
> 
> Cheers,
> Kevin
> 
> 
> 
> 
> On Wed, Oct 5, 2011 at 10:59 PM, Kevin Green <kevin.richard.green at gmail.com> wrote:
> Jose - Thank you, I'll see if I can get this working.
> 
> Barry - This seems to be exactly what I'm looking for.  Glancing at the documentation briefly, some questions do spring to mind, but I will not ask until I look at some of the examples!
> 
> Mike - Thanks for the updated link, I didn't even notice that Barry's was for 3.0.0.
> 
> In the meantime, I'll update to petsc 3.2, and slepc-dev, and get looking at these examples.  This isn't at the immediate top of my todo list, but I expect I'll have some detailed questions  on DMCOMPOSITE in a week or so.
> 
> Kevin
> 
> 
> 
> On Wed, Oct 5, 2011 at 5:35 PM, Mike McCourt <mccomic at mcs.anl.gov> wrote:
> If you're gonna use PETSc 3.2, make sure to check out the updated documentation:
> 
> http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DM/DMCompositeCreate.html
> 
> It has a more accurate list of examples.
> 
> -Mike
> 
> ----- Original Message -----
> From: "Barry Smith" <bsmith at mcs.anl.gov>
> To: "PETSc users list" <petsc-users at mcs.anl.gov>
> Sent: Wednesday, October 5, 2011 4:29:14 PM
> Subject: Re: [petsc-users] Appending to vector / numerical continuation /       slepc
> 
> 
>  Kevin,
> 
>    The DMCOMPOSITE is designed exactly for this purpose. See the manual page http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.0.0/docs/manualpages/DA/DMCompositeCreate.html#DMCompositeCreate and examples it links to. Essentially you create a DMCOMPOSITE and then use DMCompositeAddDM() to put in the DM which will be parallel and DMCompositeAddArray() for the "k" extra things (like continuation parameters).   After you read the manual pages and look at the examples and start your code using the DMCOMPOSITE, feel free to ask specific questions about its usage.
> 
>   You definitely should switch to PETSc 3.2 before working because the DM has been markedly improved in places for this type of thing,
> 
>   Barry
> 
> 
> 
> On Oct 5, 2011, at 12:46 PM, Kevin Green wrote:
> 
> > Greetings,
> >
> > I was just wondering what the simplest way to create a new N+k dim where the first N come from a DA.  It seems to me that I would have to go the round about way of getting the array, then writing that to the first N components of the new vector... I think there would be a bit of a pain for the parallel case when doing this though, like in managing the change in the local sizes when going from N to N+k... perhaps it's not that tricky.  Also, with DAs I don't have to worry about orderings, correct?
> >
> > Essentially I want to get pseudo-arclength continuation working using the SNES solver.  Another option I'm thinking is that rather than using an extended vector, I could use a MatShell where the added components are located within its context, and updated upon matmult...since k is typically small, this seems reasonable.  Do you know of any code/projects that make use of the SNES module for continuation?  Any thoughts on what would be the better or simpler way of doing this?
> >
> > I'm using petsc-3.1 right now, as I also need slepc...which hasn't been updated to work with 3.2 yet, as far as I know.  I'm fairly new to petsc/slepc... so I have to ask, what is the timescale like between the release of a new petsc, and update of slepc?  Or is there a way to get slepc working with the new release?
> >
> > Cheers,
> > Kevin
> 
> 
>