New issue 549: Projections should switch off parallel reduction method
https://bitbucket.org/yt_analysis/yt/issue/549/projections-should-switch-of…
Matthew Turk:
For those simulation types where the global mesh is known, we should use the (slightly more scalable) global mesh information to pre-construct the quadtree which is then reduced as an array across all processors. For those simulation types where we do not know the global mesh information, we should fall back on the quadtree reduction method we used before, which is in the routine `merge_quadtree_buffers` in `parallel_analysis_interface`.
This will require a flag or some type of discriminator between global/local mesh simulations.
Responsible: MatthewTurk
Hi all (especially Sam and Stephen, who have done a lot of this type
of debugging),
Christine and I sat down in person, and set up some tracers throughout
the code to see where her inline with yt was dying. It looks like
it's in this call:
communication_system.push_with_ids(ranks)
Can either of you think why this might be a problem? I thought
MVAPICH supported everything we use, but if this is dying, that could
be an issue. Sam, if she's using the Enzo with the refactored
communicator, could that be an issue here? Any ideas?
...all the more reason for an isolated, over-the-wire interface library...
-Matt
New issue 546: Clump finding doesn't use chunks
https://bitbucket.org/yt_analysis/yt/issue/546/clump-finding-doesnt-use-chu…
Christopher Moody:
Clump-finding is broken for the chunk system; currently IsBound returns pot/kin for every chunk. This fails spectacularly when the chunking goes level-by-level, where we only include cells at the same levels in the potential calculation. Instead, it should add every chunk to a persistent octree, and in the combine step it should calculate the binding energy.
Responsible: juxtaposicion
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New issue 545: yt clobbers nose's command line help
https://bitbucket.org/yt_analysis/yt/issue/545/yt-clobbers-noses-command-li…
Nathan Goldbaum:
```
#!bash
$ nosetests --help
usage: nosetests [-h] [--config CONFIG] [--paste] [--paste-detailed]
[--detailed] [--rpdb] [--parallel]
yt command line arguments
optional arguments:
-h, --help show this help message and exit
--config CONFIG Set configuration option, in the form param=value
--paste Paste traceback to paste.yt-project.org
--paste-detailed Paste a detailed traceback with local variables to paste
.yt-project.org
--detailed Display detailed traceback.
--rpdb Enable remote pdb interaction (for parallel debugging).
--parallel Run in MPI-parallel mode (must be launched as an MPI task)
```
Responsible: ngoldbaum
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New issue 544: Chombo answer test results are too big
https://bitbucket.org/yt_analysis/yt/issue/544/chombo-answer-test-results-a…
Nathan Goldbaum:
Right now the chombo answer test results are way too big:
```
#!bash
$ ls -lh gold007_data*
-rw-r--r-- 1 goldbaum staff 104M Mar 30 05:58 gold007_data.0005.3d.hdf5
-rw-r--r-- 1 goldbaum staff 259M Mar 30 05:41 gold007_data.0077.3d.hdf5
```
For comparison:
```
#!bash
$ ls -lh gold007_moving_0010 gold007_galaxy0030
-rw-r--r-- 1 goldbaum staff 23M Mar 30 05:39 gold007_moving7_0010
-rw-r--r-- 1 goldbaum staff 43M Mar 30 05:37 gold007_galaxy0030
```
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New issue 543: annotate_particles doesn't respect periodicity
https://bitbucket.org/yt_analysis/yt/issue/543/annotate_particles-doesnt-re…
Sam Skillman:
Annotating particles should use periodic calculations. This can be seen by setting the center of the plot to something other than the domain:
```
#!python
from yt.mods import *
pf = load('Enzo_64/DD0043/data0043')
p = ProjectionPlot(pf, 0, 'Ones', center=[0.75]*3)
p.annotate_particles(0.1)
p.save()
```
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New issue 542: Standard deviation fields for profiles are undocumented
https://bitbucket.org/yt_analysis/yt/issue/542/standard-deviation-fields-fo…
Nathan Goldbaum:
We should add docs and cookbook recipes on generating profiles of fields that are the standard deviation of an on-disk or derived fields. For me, this is most interesting for calculating velocity dispersion profiles.
This functionality was originally added in PR 114, but unfortunately bitbucket won't render any accompanying information that came with the PR. I've provisionally assigned this to Britton. Britton, please let me know if you're too busy and I'll try to figure it out.
Responsible: brittonsmith
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New issue 541: Docs for Ghost Zone Requiring Covering Grids
https://bitbucket.org/yt_analysis/yt/issue/541/docs-for-ghost-zone-requirin…
Sam Skillman:
We should make it clear how to get a covering grid for fields that require ghost zones. This is primarily a docs issue, but the
By running the cookbook ``extract_fixed_resolution_data.py`` with DivV instead leads to this error:
```
#!python
skillman/test_data:python extract_fixed_resolution_data.py
Traceback (most recent call last):
File "extract_fixed_resolution_data.py", line 19, in <module>
num_ghost_zones=0)
File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3735, in __init__
self._refresh_data()
File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3752, in _refresh_data
AMR3DData._refresh_data(self)
File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 320, in _refresh_data
self.get_data()
File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3770, in get_data
self._generate_field(field)
File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3801, in _generate_field
self.pf.field_info[field].check_available(self)
File "/home/skillman/local/src/yt-hg/yt/data_objects/field_info_container.py", line 364, in check_available
validator(data)
File "/home/skillman/local/src/yt-hg/yt/data_objects/field_info_container.py", line 494, in __call__
raise NeedsGridType(self.ghost_zones,self.fields)
yt.data_objects.field_info_container.NeedsGridType: (1, ['x-velocity', 'y-velocity', 'z-velocity'])
```
We should catch this and report back to the user to require the correct number of ghost zones
Responsible: samskillman
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