[FLASH-USERS] Bug fixes for active particles unit

[seyit]

Hi Chris,

> The error you show should be unrelated to the recent patch.
That's unfortunate. I was hoping that would be my solution.

> Do you use a custom gr_markRefineDerefine or
> Grid_markRefineDerefine?
Yes, but nothing really weird is happening there.  


> Does the error appear with both
> Paramesh-4.0 and Paramesh-4dev?  
Don't know, haven't tested it.

> If you manually add an extra
> call to gr_checkGridConsistency before amr_refine_derefine in
> gr_updateRefinement, does the abort also happen before the
> refinement/derefinement?
I could check this.

Thanks,
Seyit



On Wed, 02 Feb 2011 11:41:37 -0600, Chris Daley <cdaley at flash.uchicago.edu>
wrote:
> Hi Seyit,
> 
> The error you show should be unrelated to the recent patch.
> 
> You are seeing a controlled abort in gr_checkGridConsistency
> after a Grid consistency check fails.  This subroutine is called
> in gr_updateRefinement after a refinement/derefinement happens in
> amr_refine_derefine.
> 
> Some questions that may be useful:
> 
> Do you use a custom gr_markRefineDerefine or
> Grid_markRefineDerefine?  Does the error appear with both
> Paramesh-4.0 and Paramesh-4dev?  If you manually add an extra
> call to gr_checkGridConsistency before amr_refine_derefine in
> gr_updateRefinement, does the abort also happen before the
> refinement/derefinement?
> 
> Chris
> 
> 
> Seyit Hocuk wrote:
>> Hi Chris,
>>
>> After applying your patch, I still get the error as shown below when
>> using active particles. This is a restart from a running simulation
>> which was crashing at the same point. I was hoping that this would now
>> be solved, alas.
>>
>> Kind regards,
>> Seyit
>>
>>
>> refined: total blocks =         3145
>> Missing neighbors on PE    2, lb=  8,surrblks=(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(   8,   2, 2)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)
>> Missing neighbors on PE    2, lb=  8,surrblks=(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(   8,   2, 2)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,  -1,-1)(  -1,
>> -1,-1)
>> *** Wrote plotfile to xSHx_hdf5_plt_cnt_0001 ****
>> DRIVER_ABORT: missing neighbor!
>>
>>
>>
>>
>>
>> Chris Daley wrote:
>>> To FLASH users,
>>>
>>> We have recently become aware of two bugs in the active particles unit
>>> of FLASH.  These bugs do not affect tracer particles.
>>>
>>> 1). There is an error when mapping a portion of a particle's mass to a
>>> neighboring block that is at a coarser refinement level.  The bug only
>>> happens when a particle is within a zone that is next to a fine-coarse
>>> block boundary.  It causes integrated PDEN mass on the grid to differ
>>> from the total particle mass.
>>>
>>> 2). There is an error in the calculated size of a receive buffer which
>>> can lead to out-of-bounds accesses.  The bug can only happen in
>>> applications which have explicitly included the non-default
>>> point-to-point map particles to mesh implementation (i.e. using
>>> -unit=Grid/GridParticles/GridParticlesMapToMesh/Paramesh/PttoPt).
>>>
>>>
>>> The bugs can be fixed by applying the patch attached to this email.
>>> Navigate to the top level directory of an untouched version of
>>> FLASH3.3 and enter the command:
>>>
>>> patch -p0 < fix_particle_map_jan_2011.diff
>>>
>>> Additional information about the fixes is provided in the file
>>> svn_log_messages.txt.  A copy of all the attachments are at
>>>
>
http://www.flash.uchicago.edu/~cdaley/FLASH3.3_patches/fix_particle_map_jan_2011/
>>>
>>>
>>> Regards,
>>> Chris