Re: [yt-dev] Revising the skeleton frontend

Hi Matt, Thanks for the comments. I 'll add them to the revised skeleton frontend. Sincerely, Justin On Fri, May 6, 2016 at 11:02 AM, Matthew Turk wrote:

Hi Hsi-Yu,

Thanks for going through this!

On Wed, Apr 27, 2016 at 7:47 PM, Hsi-Yu Schive wrote:

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Hi all,

I just finish the GAMER frontend for YT, and below I want to summarize some issues and things that might be confusing in the current skeleton frontend. I appreciate if you could help validate these issues and/or clarify some points in the section "Things to be clarified". Hopefully it will make frontend implementation easier in the future. I'll collect all comments and issue a PR for the revised skeleton. It will be complementary to the recent PR #2130 by Jonah Miller, which provides an extremely helpful example frontend.

*Things to be clarified:*============================ 1. Difference between *FieldInfoContainer.known_other_fields* and *GridIndex._detect_output_field*: => known_other_fields contains fields that *might* be in an output, and lists their units and aliases. _detect_output_fields finds the fields that are defined in the currently loaded dataset.

Sounds right.

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2. *Dataset.unique_identifier*: => ??

This just needs to be unique; for some codes it's a UUID output at runtime. A combination of hash and ctime might work for your data, or even just a random number.

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3. Set *AMRGridPatch.Parent = None* for grids without parents, and *AMRGridPatch.Children = []* for grids without children

Yes, but creating lots of lists can be slow, so some frontends also make it on-demand if Children is None. Some frontends also allow for multiple parents, so that can be a list.

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4. Field array returned by *BaseIOHandler._read_fluid_selection* should be contiguous along the z instead of x direction. Therefore, for C-like array with the dimension [x][y][z] and for Fortran-like array with the the dimension (z,y,x), a matrix transpose is required (e.g., using np_array.transpose() or np_array.swapaxes(0,2))

Yes, unless you swap your coordinate systems in the indexing scheme, which is also possible. You may try doing this my supplying geometry = ("cartesian", ("z", "y", "x")) and not transposing. It may not work, but I think it should.

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5. *start_index, stop_index, *and *ActiveDimension*s in the AMRGridPatch objects => ?? (1) It looks like stop_index is not used anymore

I think that's correct.

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(2) ActiveDimensions will be set by AMRGridPatch._prepare_grid. So perhaps frontend does not need to set it explicitly anymore

Also correct, unless you can do it faster.

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(3) It seems that start_index is also calculated automatically

Yes, but this can be overridden, as I think the boxlib frontends do.

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6. *chunk, selector, *and *_read_chunk_data* in io.py. => ?? Also the following comment about caching is confusing: def _read_chunk_data(self, chunk, fields): # This reads the data from a single chunk, and is only used for caching.

That is confusing; it's designed to be a "read data from this chunk without doing any selection" -- then it can be used for caching data that might be used by multiple different selectors later. For instance, this can speed up ghost zone computation.

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7. float type: (1) *GridIndex.float_type* is the float type for left and right simulation edges and must be float64 now (2) *BaseIOHandler._read_fluid_selection* should always return float64 now even if the on-disk data are stored in single precision

Yes, that's presently the case.

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8. Difference between *add_output_field *and *add_field *used in FieldInfoContainer.setup_fluid_fields:

One means on-disk, the other is not necessarily on-disk.

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9. Dataset._parse_parameter_file: what does the following comment mean "Note that these are all assumed to be in code units; domain_left_edge and domain_right_edge will be updated to be in code units at a later time" => Perhaps it means that "domain_left_edge and domain_right_edge will be converted to YTArray automatically at a later time"?

Yes, that's what it means.

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*Missing procedure*============================ 1. Add the new frontend in *frontends/api.py* 2. Set *GridIndex.max_level* 3. Set *Dataset.refine_by*

*Bugin the current skeleton frontend* ============================ 1. data_structures.py: *self.dataset* is not set in GridIndex.__init__ when calling self.index_filename = self.dataset.parameter_filename 2. data_structures.py: replace self.Parent=[] by *self.Parent = None* 3. fields.py: the *field_list *argument is missing in FieldInfoContainer.__init__. This issue has been fixed in Jonah's PR. def __init__(self, ds, field_list): super(SkeletonFieldInfo, self).__init__(ds, field_list)

Sincerely, Hsi-Yu (Justin)

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