Mailman 3 Re: [yt-users] Parallel Broadcasting in yt - yt-users

May 7, 2014


      mpi_bcast was what I was looking for! Thank you

-Claire


On Tue, May 6, 2014 at 2:05 PM, <yt-users-request@lists.spacepope.org>wrote:
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Today's Topics:
1. Parallel Broadcasting in yt (Claire Kopenhafer)
   2. Re: Parallel Broadcasting in yt (Britton Smith)
   3. fractional keyword in profile plot (Chang-Goo Kim)
   4. total mass (Chang-Goo Kim)
   5. Re: total mass (Matthew Turk)
---------- Forwarded message ----------
From: Claire Kopenhafer <clairekope@gmail.com>
To: yt-users@lists.spacepope.org
Cc:
Date: Mon, 5 May 2014 15:56:29 -0400
Subject: [yt-users] Parallel Broadcasting in yt
Hello all,
I've got a code that reads in a dictionary from file and then operates on
it, and I'd like to run it in parallel. My best thought is to have the root
process read in the dict and then broadcast it to all the rest, but I am
not sure how best to do this within yt. Any suggestions? Thanks!
-Claire
---------- Forwarded message ----------
From: Britton Smith <brittonsmith@gmail.com>
To: Discussion of the yt analysis package <yt-users@lists.spacepope.org>
Cc:
Date: Mon, 5 May 2014 16:50:06 -0400
Subject: Re: [yt-users] Parallel Broadcasting in yt
Hi Claire,
You might want to have a look at the function called mpi_bcast
in yt/utilities/parallel_tools/parallel_analysis_interface.py.  This should
do a standard mpi broadcast from the root process to all of the
subprocesses.  Alternatively, if the dictionary is something that can be
loaded in in parts by each of the processors and then combined, you might
also want to check par_combine_object in the same file.
Britton
On Mon, May 5, 2014 at 3:56 PM, Claire Kopenhafer <clairekope@gmail.com>wrote:
...
Hello all,
I've got a code that reads in a dictionary from file and then operates on
it, and I'd like to run it in parallel. My best thought is to have the root
process read in the dict and then broadcast it to all the rest, but I am
not sure how best to do this within yt. Any suggestions? Thanks!
-Claire
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---------- Forwarded message ----------
From: Chang-Goo Kim <cgkim@astro.princeton.edu>
To: Discussion of the yt analysis package <yt-users@lists.spacepope.org>
Cc:
Date: Tue, 6 May 2014 13:43:39 -0400
Subject: [yt-users] fractional keyword in profile plot
Hi all,
I tried to draw PDFs using ProfilePlot with "fractional" keyword. But, it
returned unit incompatibility. I have looked at the code, and realized that
the fractional keyword makes field_data dimensionless, while it tried to
return data with units of original data. I think it must be easy to fix.
Error message is attached below.
Thanks,
Chang-Goo
---------------------------------------------------------------------------YTUnitConversionError                     Traceback (most recent call last)<ipython-input-137-18016774c3d0> in <module>()----> 1 pdf=ProfilePlot(dd,"temp",['cell_mass','cell_volume'],weight_field=None,fractional=True)      2 pdf.show()
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in __init__(self, data_source, x_field, y_fields, weight_field, n_bins, accumulation, fractional, label, plot_spec, profiles)    216             self.plot_spec = [self.plot_spec.copy() for p in self.profiles]    217 --> 218         self._setup_plots()    219     220     def save(self, name=None):
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc in _setup_plots(self)    309         self.axes = AxesContainer(self.figures)    310         for i, profile in enumerate(self.profiles):--> 311             for field, field_data in profile.items():    312                 self.axes[field].plot(np.array(profile.x),    313                                       np.array(field_data),
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in items(self)    854     855     def items(self):--> 856         return [(k,self[k]) for k in self.field_data.keys()]    857     858     def __iter__(self):
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc in __getitem__(self, field)    851             raise KeyError(field)    852         else:--> 853             return self.field_data[fname].in_units(self.field_units[fname])    854     855     def items(self):
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in in_units(self, units)    358     359         """--> 360         new_units = self._unit_repr_check_same(units)    361         conversion_factor = self.units.get_conversion_factor(new_units)    362
/u/cgkim/Sources/yt-x86_64/src/yt-hg/yt/units/yt_array.pyc in _unit_repr_check_same(self, units)    315         if not self.units.same_dimensions_as(units):    316             raise YTUnitConversionError(--> 317                 self.units, self.units.dimensions, units, units.dimensions)    318     319         return units
YTUnitConversionError: Unit dimensionalities do not match. Tried to convert between dimensionless (dim 1) and code_length**3 (dim (length)**3).
---------- Forwarded message ----------
From: Chang-Goo Kim <cgkim@astro.princeton.edu>
To: Discussion of the yt analysis package <yt-users@lists.spacepope.org>
Cc:
Date: Tue, 6 May 2014 13:50:47 -0400
Subject: [yt-users] total mass
Hi all again,
I tried to find mass fraction of each temperature component, but I got
inconsistent results as below:
==
dd=pf.all_data()
hot=dd.cut_region(["obj['temperature'] >= 1.e4"])
wnm=dd.cut_region(["obj['temperature'] < 1.e4"])
print dd.quantities.total_mass()
print wnm.quantities.total_mass()+hot.quantities.total_mass()
2.88677799841e+38 g
2.91575727709e+38 g
==
I can't understand why those two are different. Have any idea?
Chang-Goo
---------- Forwarded message ----------
From: Matthew Turk <matthewturk@gmail.com>
To: Discussion of the yt analysis package <yt-users@lists.spacepope.org>
Cc:
Date: Tue, 6 May 2014 13:53:45 -0400
Subject: Re: [yt-users] total mass
Hi Chang-Goo,
On Tue, May 6, 2014 at 1:50 PM, Chang-Goo Kim <cgkim@astro.princeton.edu>
wrote:
...
Hi all again,
I tried to find mass fraction of each temperature component, but I got
inconsistent results as below:
==
dd=pf.all_data()
hot=dd.cut_region(["obj['temperature'] >= 1.e4"])
wnm=dd.cut_region(["obj['temperature'] < 1.e4"])
print dd.quantities.total_mass()
print wnm.quantities.total_mass()+hot.quantities.total_mass()
The total_mass includes particle fields, which will be incorrectly cut
by the cut_region.  We're trying to figure out a way to make this
clearer, but you should get identical results if you use the
.total_quantity("cell_mass") function.  This was the subject of a
recent bug report and discussion, as well:
https://bitbucket.org/yt_analysis/yt/issue/812/derived-quantities-on-cut_reg...
I thought we'd had a pull request discussion, too, but I can't find it
right now.
-Matt
...
2.88677799841e+38 g
2.91575727709e+38 g
==
I can't understand why those two are different. Have any idea?
Chang-Goo
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Re: [yt-users] Parallel Broadcasting in yt

Claire Kopenhafer

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