[yt-users] running out of memory in a loop

[Stephanie Tonnesen]

Thanks!  This didn't work, so I guess it must be Athena.  I would not think
that is the problem because it reads in the second file, makes the
SlicePlot and ProjectionPlot, and just dies with memory while making the
phase_object.  Ah, well, I can work around it.

-Stephanie


On Wed, Oct 23, 2013 at 3:53 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Yup, that's right.
>
>
> On Wed, Oct 23, 2013 at 3:52 PM, Stephanie Tonnesen <stonnes at gmail.com>wrote:
>
>> Okay, so to be totally clear:
>>
>> I put import gc as the first line,
>> and gc.collect() as the last line, but still indented so it is in the
>> loop?
>>
>> import gc
>>
>> import matplotlib.pylab as pl
>> from mpl_toolkits.mplot3d import Axes3D
>> from yt.mods import *
>>
>> ......
>>
>> i = 0
>> while i < len(outstring):
>>     pf = load("id0/rps."+outstring[i]+"
>>
>> .vtk",parameters={"TimeUnits":3.086e14,"LengthUnits":8.0236e22,"DensityUnits":9.999e-30,"VelocityUnits":2.6e8})
>>
>>
>>     p = SlicePlot(pf,"x","Density")
>>     p.set_log("Density", True)
>>     p.save()
>>
>>
>>     p2 = ProjectionPlot(pf,"x","Density")
>>     p2.set_log("Density", True)
>>     p2.save()
>>
>>
>>     alld = pf.h.all_data()
>>
>>     pc = PlotCollection(pf)
>>     tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25",
>> "grid['z'] > 0.04"])
>>     tp25extrema = tracerp25.quantities["Extrema"]("Density")
>>
>> pc.add_phase_object(tracerp25,["zkpc","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds
>> = [-1e8,1.5e8],x_log=False,y_log=False)
>>     pc.set_zlim(10000,1e10)
>>     pc.save()
>>
>>     i = i+1
>>     gc.collect()
>>
>>
>>
>>
>> On Wed, Oct 23, 2013 at 3:36 PM, Matthew Turk <matthewturk at gmail.com>wrote:
>>
>>> Hi Stephanie,
>>>
>>> Can you try adding this at the top of your script:
>>>
>>> import gc
>>>
>>> and just after i + i + 1 putting:
>>>
>>> gc.collect()
>>>
>>> If this fixes the problem, then there may just be extra references
>>> sitting around.  If not, then I suspect there may be an issue with the
>>> Athena frontend hanging onto data.
>>>
>>> -Matt
>>>
>>>
>>> On Wed, Oct 23, 2013 at 3:20 PM, Stephanie Tonnesen <stonnes at gmail.com>wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> Okay, so I am trying to make a SlicePlot, a ProjectionPlot, and a
>>>> phase_object for a bunch of different outputs.  My code keeps using up all
>>>> my memory and dying after the first loop.  I am not using variables, I
>>>> think, so how do I free up my memory at the end of each loop?
>>>>
>>>> See code below.
>>>>
>>>> Thanks,
>>>>
>>>> Stephanie
>>>>
>>>>
>>>> import matplotlib.pylab as pl
>>>> from mpl_toolkits.mplot3d import Axes3D
>>>> from yt.mods import *
>>>>
>>>> def _xkpc(field,data):
>>>>     return(data["x"]*26.)
>>>>
>>>> def _ykpc(field,data):
>>>>     return(data["y"]*26.)
>>>>
>>>> def _zkpc(field,data):
>>>>     return(data["z"]*26.)
>>>>
>>>> def _CellMassSolar(field,data):
>>>>     return(data["CellMass"]/1.99e33)
>>>>
>>>> add_field("xkpc",function=_xkpc,units="kpc")
>>>> add_field("ykpc",function=_ykpc,units="kpc")
>>>> add_field("zkpc",function=_zkpc,units="kpc")
>>>> add_field("CellMassSolar",function=_CellMassSolar,units=r'M$_{\odot}$')
>>>>
>>>> outstring =
>>>> ['0020','0030','0040','0050','0060','0070','0080','0090','0100','0110','0120','0130']
>>>> i = 0
>>>> while i < len(outstring):
>>>>     pf =
>>>> load("id0/rps."+outstring[i]+".vtk",parameters={"TimeUnits":3.086e14,"LengthUnits":8.0236e22,"DensityUnits":9.999e-30,"VelocityUnits":2.6e8})
>>>>
>>>>
>>>>     p = SlicePlot(pf,"x","Density")
>>>>     p.set_log("Density", True)
>>>>     p.save()
>>>>
>>>>
>>>>     p2 = ProjectionPlot(pf,"x","Density")
>>>>     p2.set_log("Density", True)
>>>>     p2.save()
>>>>
>>>>
>>>>     alld = pf.h.all_data()
>>>>
>>>>     pc = PlotCollection(pf)
>>>>     tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25",
>>>> "grid['z'] > 0.04"])
>>>>     tp25extrema = tracerp25.quantities["Extrema"]("Density")
>>>>
>>>> pc.add_phase_object(tracerp25,["zkpc","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds
>>>> = [-1e8,1.5e8],x_log=False,y_log=False)
>>>>     pc.set_zlim(10000,1e10)
>>>>     pc.save()
>>>>
>>>>     i = i+1
>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20131023/aeccb356/attachment.html>