<div dir="ltr">Hi Christine,<div><br></div><div style>The only thing I notice is that there don't seem to be P??? processor number prefixes to your yt output. Mine looks like (using yt and enzo-dev tips on RotatingCylinder) :</div>
<div style><div>P001 yt : [DEBUG ] 2013-04-02 20:57:27,208 Received buffer of min 0.0 and max 3.34041847571e-21 (data: 1.66943640208e-23 3.34041847571e-21)</div><div>P000 yt : [DEBUG ] 2013-04-02 20:57:27,209 Received buffer of min 0.0 and max 3.34041847571e-21 (data: 1.66943640208e-23 3.34041847571e-21)</div>
<div>P001 yt : [INFO ] 2013-04-02 20:57:27,306 Added slice of Density at y = 0.5546875 with 'center' = [0.4296875, 0.5546875, 0.4296875]</div><div>P000 yt : [INFO ] 2013-04-02 20:57:27,310 Added slice of Density at y = 0.5546875 with 'center' = [0.4296875, 0.5546875, 0.4296875]</div>
<div>P001 yt : [DEBUG ] 2013-04-02 20:57:27,325 Received buffer of min 0.0 and max 3.34041847571e-21 (data: 1.66943640208e-23 3.34041847571e-21)</div><div>P000 yt : [DEBUG ] 2013-04-02 20:57:27,331 Received buffer of min 0.0 and max 3.34041847571e-21 (data: 1.66943640208e-23 3.34041847571e-21)</div>
<div>P001 yt : [INFO ] 2013-04-02 20:57:27,401 Saved cycle00000001_Slice_y_Density.png</div><div><br></div><div style>I think what this means is that it isn't picking up the parallel part of yt, as you expected. Does running a similar script on a datadump like:</div>
<div style><br></div><div style>mpirun -np 2 python your_script.py --parallel </div><div style><br></div><div style>yield different information in the logs? If you get the same thing (without the P??? prefix), then I'd say try doing pip install mpi4py or re-installing mpi4py some other way and make sure that it picks up the same mpirun that you are running enzo with.</div>
<div style><br></div><div style>Hope that helps,</div><div style>Sam</div><div><br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 2, 2013 at 5:26 PM, Christine Simpson <span dir="ltr"><<a href="mailto:csimpson@astro.columbia.edu" target="_blank">csimpson@astro.columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
I'm not sure what list to send this to since it is about inline yt in<br>
enzo, but I will try it here. I'm trying to do some simple inline tasks<br>
for a non-cosmology problem (one that is not currently in the enzo-dev<br>
repo). I'm trying to do some slices; I eventually want to do some 1-d<br>
profiles and derived quantities.<br>
<br>
I have a script that works on one processor (with MPI on), but when I<br>
try to use more than one processor I get odd results. The slices I get<br>
appear to contain only part of the simulation domain (so there is stuff<br>
in part of the image and the rest is blank) and I get key errors from<br>
some processors saying they can't find the Density field. The error is<br>
pasted below. I'm guessing something about parallel yt is not working<br>
correctly? I should also mention that this run does not use AMR. My yt<br>
script is also pasted below, along with the enzo parameter file (which<br>
is a little jumbled, sorry).<br>
<br>
The yt version I'm using is the current one (I checked out the install<br>
script today). I did have to comment out the following line in<br>
yt-x86_64-shared/src/yt-hg/yt/frontends/enzo/data_structures.py:<br>
<br>
#self.periodicity =<br>
ensure_tuple(self.parameters["LeftFaceBoundaryCondition"] == 3)<br>
<br>
The enzo version I'm using is the tip of the enzo-dev-mom fork which<br>
diverged from enzo-dev after changeset e01ad22. I glanced through the<br>
accepted pull requests, but nothing jumped out at me as being a<br>
solution.<br>
<br>
Any ideas would be appreciated.<br>
<br>
Thanks<br>
Christine<br>
<br>
Error:<br>
<br>
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time<br>
= 4.81533679704e-05<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions<br>
= [98 98 98]<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge<br>
= [ 0. 0. 0.]<br>
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters: domain_right_edge<br>
= [ 1. 1. 1.]<br>
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters:<br>
cosmological_simulation = 0.0<br>
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this<br>
may take a moment.)<br>
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this<br>
may take a moment.)<br>
yt : [INFO ] 2013-04-02 16:00:50,460 Gathering a field list (this<br>
may take a moment.)<br>
Traceback (most recent call last):<br>
File "<string>", line 1, in <module><br>
Traceback (most recent call last):<br>
File "<string>", line 1, in <module><br>
File "./user_script.py", line 19, in main<br>
File "./user_script.py", line 19, in main<br>
pc = PlotCollection(pf)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__<br>
pc = PlotCollection(pf)<br>
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__<br>
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location<br>
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max<br>
source.quantities["MaxLocation"]( field, lazy_reader=True)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__<br>
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location<br>
return self._call_func_lazy(args, kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy<br>
source.quantities["MaxLocation"]( field, lazy_reader=True)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__<br>
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,<br>
**kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation<br>
return self._call_func_lazy(args, kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy<br>
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,<br>
**kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation<br>
if data[field].size > 0:<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__<br>
if data[field].size > 0:<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__<br>
data = self.data_source._get_data_from_grid(self.grid, item)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state<br>
data = self.data_source._get_data_from_grid(self.grid, item)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state<br>
tr = func(self, grid, field, *args, **kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid<br>
tr = func(self, grid, field, *args, **kwargs)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid<br>
tr = grid[field]<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__<br>
tr = grid[field]<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__<br>
self.get_data(key)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data<br>
self.get_data(key)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data<br>
self._generate_field(field)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field<br>
self._generate_field(field)<br>
File<br>
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field<br>
raise exceptions.KeyError(field)<br>
KeyError: raise exceptions.KeyError(field)<br>
'Density'<br>
KeyError: 'Density'<br>
yt : [INFO ] 2013-04-02 16:00:50,892 Max Value is 1.00000e-24 at<br>
0.0051020408163265 0.0051020408163265 0.0051020408163265 in grid<br>
EnzoGrid_0001 at level 0 (0, 0, 0)<br>
yt : [INFO ] 2013-04-02 16:00:50,892 Created plot collection with<br>
default plot-center = [0.0051020408163265302, 0.0051020408163265302,<br>
0.0051020408163265302]<br>
yt : [INFO ] 2013-04-02 16:00:51,222 Added slice of Density at y =<br>
0.00510204081633 with 'center' = [0.0051020408163265302,<br>
0.0051020408163265302, 0.0051020408163265302]<br>
yt : [INFO ] 2013-04-02 16:00:52,250 Saved<br>
cycle00000001_Slice_y_Density.png<br>
['z-velocity', 'Temperature', 'GasEnergy', 'Density', 'TotalEnergy',<br>
'x-velocity', 'y-velocity']<br>
<br>
<br>
python script:<br>
<br>
from yt.mods import *<br>
<br>
def main():<br>
<br>
<br>
pf = EnzoStaticOutputInMemory()<br>
<br>
pc = PlotCollection(pf)<br>
pc.add_slice("Density",1)<br>
pc.save()<br>
<br>
print pf.h.field_list<br>
<br>
enzo parameter file:<br>
#<br>
# AMR PROBLEM DEFINITION FILE: TestStarParticle<br>
<br>
#<br>
PythonTopGridSkip = 1<br>
CellFlaggingMethod = 0<br>
PPMDiffusionParameter = 0<br>
PPMSteepeningParameter = 0<br>
DensityUnits = 1.0e-24<br>
LengthUnits = 3.01802501047e+20<br>
#RadiativeCooling = 1<br>
StarParticleFeedback = 2<br>
RefineBy = 2<br>
CourantSafetyNumber = 0.4<br>
OutputCoolingTime = 1<br>
dtDataDump = 0.1<br>
TopGridDimensions = 98 98 98<br>
TestStarParticleEnergy = 0.00104392468495<br>
MaximumRefinementLevel = 0<br>
Initialdt = 4.81533668755e-05<br>
TestStarParticleDensity = 1.0<br>
ProblemType = 90<br>
PPMFlatteningParameter = 0<br>
StopTime = 0.3<br>
TopGridRank = 3<br>
StarFeedbackKineticFraction = 1.0<br>
StaticHierarchy = 1<br>
Gamma = 1.66667<br>
StarMassEjectionFraction = 0.25<br>
TimeUnits = 3.15e13<br>
TestStarParticleStarMass = 100.0<br>
StarEnergyToThermalFeedback = 5.59e-6<br>
HydroMethod = 0<br>
DualEnergyFormalism = 1<br>
#CycleSkipDataDump = 1<br>
OutputTemperature = 1<br>
<br>
<br>
<br>
<br>
<br>
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</blockquote></div><br></div>