Hi Matt,

I updated yt via 'yt update' and the change set is the one I specified before. To do a direct pull from the tip, I tried:

cd src/yt-hg
hg pull -r 1a67d558b51c

but just got:

"abort: requirement 'dotencode' not supported!"

What should I have done? (It might be handy to add this 'how to' to the docs, since surely many people use the handy install script and then don't know how to pull from the tip?)

E. 


On 25 April 2014 17:44, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Elizabeth,

On Fri, Apr 25, 2014 at 4:38 AM, Elizabeth Tasker
<tasker@astro1.sci.hokudai.ac.jp> wrote:
> Hi Matt,
>
> Thanks! This is:
>
> yt module located at:
>     /home/tasker/yt-new2/src/yt-hg
>
> The current version of the code is:
>
> ---
> 81c2f6f5f983
> ---
>
>
> Elizabeth

I've just checked, and I am able to replicate the error with this
changeset using this script:

from yt.mods import *
pf = load("IsolatedGalaxy/galaxy0030/galaxy0030")
level = 0
left = [0.0, 0.0, 0.0]
dims = [16, 16, 16]
cgrid = pf.h.covering_grid(level, left_edge = left, dims=dims,
num_ghost_zones=2)

However, when I update to the current tip of the yt branch,
1a67d558b51c, it works.  :)

-Matt

>
>
> On 25 April 2014 17:34, Matthew Turk <matthewturk@gmail.com> wrote:
>>
>> Hi Elizabeth,
>>
>> On Fri, Apr 25, 2014 at 3:40 AM, Elizabeth Tasker
>> <tasker@astro1.sci.hokudai.ac.jp> wrote:
>> > Hi,
>> >
>> > I've hit a problem with the latest version of yt and covering grid that
>> > is
>> > linked with the number of ghostzones. My code looked like:
>> >
>> > for dim in range(3):
>> >
>> >       left.append(cloud_position[c][dim] - 0.5*width[dim])
>> >       right.append(cloud_position[c][dim] + 0.5*width[dim])
>> >       dims.append(int(round((right[dim]-left[dim])/cellsize)))
>> >
>> >     cgrid = pf.h.covering_grid(level,
>> >                                left_edge = left,
>> >                                dims=dims,
>> >                                num_ghost_zones=2)
>> >
>> >
>> > but gives me:
>> >
>> > TypeError                                 Traceback (most recent call
>> > last)
>> > /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
>> > ----> 1 execfile("export_hdf5_cube.py")
>> >
>> > /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
>> >      51                                left_edge = left,
>> >      52                                dims=dims,
>> > ---> 53                                num_ghost_zones=2)
>> >      54
>> >      55
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
>> > __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones,
>> > use_pbar, **kwargs)
>> >    3689         self.level = level
>> >    3690         rdx = self.pf.domain_dimensions*self.pf.refine_by**level
>> > -> 3691         rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1   #
>> > issue
>> > 602
>> >    3692         self.dds = self.pf.domain_width / rdx.astype("float64")
>> >    3693         self.ActiveDimensions = np.array(dims, dtype='int32')
>> >
>> > TypeError: unsupported operand type(s) for -: 'list' and 'int'
>> >
>> >
>> >
>> >
>> > This happens regardless of whether I use num_ghost_zones or not. If I
>> > don't
>> > have ghost_zones set, the error occurs at line 52, but still points to
>> > line
>> > 3691. Dims and left look fine:
>> >
>> > In [9]: dims
>> > Out[9]: [64, 64, 64]
>> >
>> > In [10]: left
>> > Out[10]: [20.424700000000001, 11.512700000000001, 15.7158]
>> >
>> > In [11]: level
>> > Out[11]: 5
>> >
>> > In [14]: rdx = pf.domain_dimensions*pf.refine_by**level
>> > In [15]: rdx
>> > Out[15]: array([4096, 4096, 4096])
>> >
>> >
>> > If I set num_ghost_zones = na.array([0,0,0]) then it runs. However, if I
>> > then try
>> >
>> >  cgrid["x"]
>> >
>> > I hit more problems circulating around the same area:
>> >
>> > ValueError                                Traceback (most recent call
>> > last)
>> > /home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
>> > ----> 1 cgrid["y"]
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
>> > __getitem__(self, key)
>> >     316             if key not in self.fields:
>> >     317                 self.fields.append(key)
>> > --> 318             self.get_data(key)
>> >     319         return self.field_data[key]
>> >     320
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
>> > get_data(self, fields)
>> >    3733                 try:
>> >    3734                     #print "Generating", field
>> > -> 3735                     self._generate_field(field)
>> >    3736                     continue
>> >    3737                 except NeedsOriginalGrid, ngt_exception:
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
>> > _generate_field(self, field)
>> >    3764         if self.pf.field_info.has_key(field):
>> >    3765             # First we check the validator; this might even
>> > raise!
>> > -> 3766             self.pf.field_info[field].check_available(self)
>> >    3767             self[field] = self.pf.field_info[field](self)
>> >    3768         else: # Can't find the field, try as it might
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc
>> > in
>> > check_available(self, data)
>> >     354         """
>> >     355         for validator in self.validators:
>> > --> 356             validator(data)
>> >     357         # If we don't get an exception, we're good to go
>> >     358         return True
>> >
>> > /home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc
>> > in
>> > __call__(self, data)
>> >     482         if not data._spatial:
>> >     483             raise NeedsGridType(self.ghost_zones,self.fields)
>> > --> 484         if self.ghost_zones <= data._num_ghost_zones:
>> >     485             return True
>> >     486         raise NeedsGridType(self.ghost_zones,self.fields)
>> >
>> > ValueError: The truth value of an array with more than one element is
>> > ambiguous. Use a.any() or a.all()
>> >
>> >
>> > cgrid["Density"] and the velocities are fine.
>> >
>> > I'm suspecting this is because the position calculation in the code is
>> > not
>> > expecting an array for the ghost zone number?
>> >
>> > Oddly, I see from the mailing list is this reminiscent of a problem nyx
>> > was
>> > having.
>>
>> Yes, and it feels like this exact issue -- where dims are lists, not
>> arrays -- gets fixed over and over and over again.  :(  Can you report
>> which changeset you're on, and I'll push a fix?
>>
>> -Matt
>>
>> >
>> > Elizabeth
>> >
>> > _______________________________________________
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>> >
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