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

[Stephanie Tonnesen]

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
>>
>>
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>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
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