[Yt-dev] Packed AMR hierarchy problem

Matthew Turk matthewturk at gmail.com
Wed Nov 18 20:55:56 PST 2009


Hi Stephen,

This is the same problem Britton reported.  cpu_map is unused, but it
gets created anyway.  The current trunk hierarchy is not great.

Can you try commenting out the call to __obtain_filenames inside
populate_hierarchy, and also try with the current mercurial tip, to
see if either or both of those things fix the problem?

-Matt

On Wed, Nov 18, 2009 at 8:52 PM, Stephen Skory <stephenskory at yahoo.com> wrote:
> Hi (Matt, mainly),
>
> I have a packed AMR, dm-only dataset that is giving me some odd issues with the hierarchy. The grids are not being referenced to the correct AMR HDF5 file. These commands:
>
> from yt.mods import *
> pf = load('RedshiftOutput0005', data_style="enzo_packed_3d")
> pf.h.cpu_map['/mirage/sskory/reddead-survey-amr/RD0005/RedshiftOutput0005.cpu0004'][:10]
>
> give:
> [EnzoGrid_0005,
>  EnzoGrid_1867,
>  EnzoGrid_1868,
>  EnzoGrid_1869,
>  EnzoGrid_1870,
>  EnzoGrid_1871,
>  EnzoGrid_1872,
>  EnzoGrid_1873,
>  EnzoGrid_1874,
>  EnzoGrid_1875]
>
> This shows that grid 1867 is owned by cpu 4. But here's what the .hierarchy file says about Grid 1867, that it's owned by cpu0005. A manual inspection shows that it is indeed inside of the cpu0005 HDF5 file.
>
> Grid = 1867
> Task              = 5
> GridRank          = 3
> GridDimension     = 12 12 12
> GridStartIndex    = 3 3 3
> GridEndIndex      = 8 8 8
> GridLeftEdge      = 0.5078125 0.521484375 0.337890625
> GridRightEdge     = 0.513671875 0.52734375 0.34375
> Time              = 646.75066015177
> SubgridsAreStatic = 0
> NumberOfBaryonFields = 0
> NumberOfParticles   = 96
> ParticleFileName = /mirage/sskory/reddead-survey-amr/RD0005/RedshiftOutput0005.cpu0005
> GravityBoundaryType = 2
> Pointer: Grid[1867]->NextGridThisLevel = 0
> Pointer: Grid[1867]->NextGridNextLevel = 0
> Pointer: Grid[5]->NextGridNextLevel = 1868
>
> I'm using the latest trunk, and the files should be world-readable. Any ideas why this is happening?
>
> Thanks!
>
>  _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
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