[petsc-dev] Integrating PFLOTRAN, PETSC & SAMRAI

[Bobby Philip]

What usually breaks for me is VecNorm caching, arguments for functions, 
and introduction of new functions. Once in a while the PETScObject structure
changes and that causes trouble too. But this is my usual list.

Any time petsc-dev changes, I end up having to build:

1. SAMRAI
2. SAMRUtils
3. SAMRSolvers
4. PFLOTRAN

with stops along the way to fix anything that broke mainly in 1 and 4. Also, SAMRAI
continues to only want to support version 2.3.3 of PETSc so I end up keeping tabs
on what needs to be changed with each new SAMRAI version. A set of automated
tests I hope might be the right catalyst to move them to the present generation(s) of PETSc.

Bobby

On Jun 4, 2011, at 9:09 AM, Matthew Knepley wrote:

> On Sat, Jun 4, 2011 at 8:03 AM, Bobby Philip <philipb at ornl.gov> wrote:
> 
>> Barry:
>> 
>> I heartily agree with all that you have said. Thanks for your suggestions.
>> I do believe what you have suggested is the best both in the shorter and
>> longer term. As a clarification on freezing the petsc-dev version, my
>> suggestion was to freeze
>> the version for a few months at a time as it reduces the burden on me on
>> fixing frequent breakages.
>> 
> 
> We don't have to bog down pflotran-dev with particulars, but can you
> characterize what breaks
> most often for you, or what you find yourself doing most often for SAMRAI?
> 
>  Thanks,
> 
>     Matt
> 
> 
>> Regards,
>> Bobby
>> 
>> 
>>> 
>>> Peter,
>>> 
>>>   In the mid to longer term we need to make sure that SAMRAI has more
>> resources than a one man operation, so this is something that needs coverage
>> in the next round of SciDAC.
>>> 
>>>   When dealing with tracking package changes I've found the best way is
>> to track them continuously so each new issue (due to a change) gets fixed
>> immediately rather than waiting until a bunch of stuff is broken before
>> fixing it.  This way determining what change broke what, is much easier.
>> This means we should set up nightly tests of PETSc+SAMRAI+PFLOTRAN and deal
>> with each issue the day after it breaks instead of weeks later. Probably
>> Richard could set up such a test and have it send email to say Richard,
>> Bobby and I each time a breakage occurs.
>>> 
>>> 
>>>  Barry
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Jun 3, 2011, at 5:49 PM, Lichtner, Peter C wrote:
>>> 
>>>> Folks: we have a problem trying to integrate PFLOTRAN with PETSc and
>> SAMRAI. The basic problem is that when PETSc is updated it often breaks
>> SAMRAI in nontrivial ways. For PFLOTRAN itself the changes needed are
>> usually minor to bring PFLOTRAN back in sync with PETSc. But this is not the
>> case for SAMRAI. Bobby Philip, the lead on SAMRAI, does not have the
>> resources to develop the PFLOTRAN implementation of SAMRAI and keep it up to
>> date with changes in PETSc. The question is how to resolve this difficulty.
>> We have expended a considerable effort in adding SAMRAI to PFLOTRAN and
>> several directions of PFLOTRAN development rely on SAMRAI including
>> applications to CO2 sequestration, the Hanford uranium plume, and a hybrid
>> model using the lattice Boltzmann method at the pore scale coupled to the
>> Darcy continuum scale with SAMRAI providing the bridge between the two
>> scales. Bobby has suggested freezing the PETSc developer version used in
>> PFLOTRAN. However, this would potentially limit the development of PFLOTRAN.
>> An alternative approach is to create a separate branch of PFLOTRAN for use
>> with SAMRAI. However, this would limit our ability to develop a hybrid
>> model, not to mention causing difficulties down the road when the two
>> branches are finally merged. Any thoughts, suggestions, comments, etc.
>> appreciated on how we can best resolve this issue.
>>>> Thanks, ...Peter
>>>> <><><><><><><><><><><><><><><><><><><><><>
>>>> Peter C. Lichtner (lichtner at lanl.gov)
>>>> LANL EES-16: MS D469
>>>> (505) 667-3420 (o), 665-3285 (fax), 795-2881 (cell)
>>>> Los Alamos National Laboratory
>>>> SM-30 Bikini Atoll Road
>>>> Los Alamos, NM 87545
>>>> blockedblockedhttp://www.ees.lanl.gov/pflotran/
>>>> <><><><><><><><><><><><><><><><><><><><><>
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 
> -- 
> What most experimenters take for granted before they begin their experiments
> is infinitely more interesting than any results to which their experiments
> lead.
> -- Norbert Wiener