[yt-users] inline yt in parallel
Christine Simpson
csimpson at astro.columbia.edu
Tue Apr 2 16:26:52 PDT 2013
Hi all,
I'm not sure what list to send this to since it is about inline yt in
enzo, but I will try it here. I'm trying to do some simple inline tasks
for a non-cosmology problem (one that is not currently in the enzo-dev
repo). I'm trying to do some slices; I eventually want to do some 1-d
profiles and derived quantities.
I have a script that works on one processor (with MPI on), but when I
try to use more than one processor I get odd results. The slices I get
appear to contain only part of the simulation domain (so there is stuff
in part of the image and the rest is blank) and I get key errors from
some processors saying they can't find the Density field. The error is
pasted below. I'm guessing something about parallel yt is not working
correctly? I should also mention that this run does not use AMR. My yt
script is also pasted below, along with the enzo parameter file (which
is a little jumbled, sorry).
The yt version I'm using is the current one (I checked out the install
script today). I did have to comment out the following line in
yt-x86_64-shared/src/yt-hg/yt/frontends/enzo/data_structures.py:
#self.periodicity =
ensure_tuple(self.parameters["LeftFaceBoundaryCondition"] == 3)
The enzo version I'm using is the tip of the enzo-dev-mom fork which
diverged from enzo-dev after changeset e01ad22. I glanced through the
accepted pull requests, but nothing jumped out at me as being a
solution.
Any ideas would be appreciated.
Thanks
Christine
Error:
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this
may take a moment.)
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this
may take a moment.)
yt : [INFO ] 2013-04-02 16:00:50,460 Gathering a field list (this
may take a moment.)
Traceback (most recent call last):
File "<string>", line 1, in <module>
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "./user_script.py", line 19, in main
File "./user_script.py", line 19, in main
pc = PlotCollection(pf)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__
pc = PlotCollection(pf)
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max
source.quantities["MaxLocation"]( field, lazy_reader=True)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location
return self._call_func_lazy(args, kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy
source.quantities["MaxLocation"]( field, lazy_reader=True)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,
**kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation
return self._call_func_lazy(args, kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,
**kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation
if data[field].size > 0:
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__
if data[field].size > 0:
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__
data = self.data_source._get_data_from_grid(self.grid, item)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state
data = self.data_source._get_data_from_grid(self.grid, item)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state
tr = func(self, grid, field, *args, **kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid
tr = func(self, grid, field, *args, **kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid
tr = grid[field]
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__
tr = grid[field]
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__
self.get_data(key)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data
self.get_data(key)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data
self._generate_field(field)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field
self._generate_field(field)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field
raise exceptions.KeyError(field)
KeyError: raise exceptions.KeyError(field)
'Density'
KeyError: 'Density'
yt : [INFO ] 2013-04-02 16:00:50,892 Max Value is 1.00000e-24 at
0.0051020408163265 0.0051020408163265 0.0051020408163265 in grid
EnzoGrid_0001 at level 0 (0, 0, 0)
yt : [INFO ] 2013-04-02 16:00:50,892 Created plot collection with
default plot-center = [0.0051020408163265302, 0.0051020408163265302,
0.0051020408163265302]
yt : [INFO ] 2013-04-02 16:00:51,222 Added slice of Density at y =
0.00510204081633 with 'center' = [0.0051020408163265302,
0.0051020408163265302, 0.0051020408163265302]
yt : [INFO ] 2013-04-02 16:00:52,250 Saved
cycle00000001_Slice_y_Density.png
['z-velocity', 'Temperature', 'GasEnergy', 'Density', 'TotalEnergy',
'x-velocity', 'y-velocity']
python script:
from yt.mods import *
def main():
pf = EnzoStaticOutputInMemory()
pc = PlotCollection(pf)
pc.add_slice("Density",1)
pc.save()
print pf.h.field_list
enzo parameter file:
#
# AMR PROBLEM DEFINITION FILE: TestStarParticle
#
PythonTopGridSkip = 1
CellFlaggingMethod = 0
PPMDiffusionParameter = 0
PPMSteepeningParameter = 0
DensityUnits = 1.0e-24
LengthUnits = 3.01802501047e+20
#RadiativeCooling = 1
StarParticleFeedback = 2
RefineBy = 2
CourantSafetyNumber = 0.4
OutputCoolingTime = 1
dtDataDump = 0.1
TopGridDimensions = 98 98 98
TestStarParticleEnergy = 0.00104392468495
MaximumRefinementLevel = 0
Initialdt = 4.81533668755e-05
TestStarParticleDensity = 1.0
ProblemType = 90
PPMFlatteningParameter = 0
StopTime = 0.3
TopGridRank = 3
StarFeedbackKineticFraction = 1.0
StaticHierarchy = 1
Gamma = 1.66667
StarMassEjectionFraction = 0.25
TimeUnits = 3.15e13
TestStarParticleStarMass = 100.0
StarEnergyToThermalFeedback = 5.59e-6
HydroMethod = 0
DualEnergyFormalism = 1
#CycleSkipDataDump = 1
OutputTemperature = 1
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