[vtkusers] Memory leak vtkEnsightGoldReader in Python

[Bill Lorensen]

The ensight readers could use more testing. Can you provide a "small"
dataset and program that cause memory leaks?

Bill


On Mon, Mar 3, 2014 at 10:38 AM, Bernhard Righolt
<b.w.righolt at tudelft.nl> wrote:
> Dear all,
>
> A typical case file, looks as follows (ASCII).
>
> $ head -n 20 case.case
> FORMAT
> type: ensight gold
>
> GEOMETRY
> model:        1     sliceCentre.000.mesh
>
> VARIABLE
> vector per node:         1       U       sliceCentre.*****.U
>
> TIME
> time set:                      1
> number of steps:               11550
> filename start number:         1
> filename increment:            1
> time values:
> 0.002
> 0.004
> 0.006
> 0.008
> 0.01
> $
>
> The mesh (snippet only), is as follows:
>
> $ head -n 10 sliceCentre.000.mesh
> Ensight Geometry File
> =====================
> node id assign
> element id assign
> part
>          1
> sliceCentre.000.mesh
> coordinates
>     299028
>  0.00000e+00
> $ sed -n -e 897091,897098p sliceCentre.000.mesh
>  0.00000e+00
>  0.00000e+00
>  0.00000e+00
> tria3
>     595264
>     162106    162714    162799
>     162799    162226    162106
>     162714    162106    162021
>
>
> And the corresponding datafile
> $ head -n 10 sliceCentre.00001.U
> vector
> part
>          1
> coordinates
>  5.33425e-04
>  2.69515e-03
> -1.65164e-03
>  5.33425e-04
>  1.39069e-04
>  2.69515e-03
>
>
> However, I doubt if something is wrong with my datafiles itself, because I
> can easily read them in Paraview for example, the only difference is the
> large amount of data-files, e.g (124GB in this case)
>
> Best regards,
> Bernhard
>
>
> On 27 February 2014 22:28, Berk Geveci <berk.geveci at kitware.com> wrote:
>>
>> Nothing strikes me as obviously wrong in your script. Can you send me
>> your case file? I'll take a look.
>>
>> -berk
>>
>> On Thu, Feb 27, 2014 at 3:20 AM, Bernhard Righolt
>> <b.w.righolt at tudelft.nl> wrote:
>> > Dear all,
>> >
>> > Currently I am using a Python script to process information stored in
>> > the
>> > EnSight Gold format. My Python (2.6) scipt uses VTK (5.10.0) to process
>> > the
>> > file, where I used the vtkEnSightGoldReader for reading the data, and
>> > loop
>> > over time steps.
>> >
>> > In principle this works fine for smaller datasets, however, for large
>> > datasets (i.e. 11k files of 12MB), I see the memory usage (recorded via
>> > top)
>> > increasing with time while the process is running. This filling of the
>> > memory goes slow, but in some cases problems are inevitable. Apparently,
>> > I
>> > am doing some things wrong in my script with respect to memory
>> > management.
>> >
>> > I am using the following script (stripped obviously, but still showing
>> > this
>> > issue)
>> >
>> > import vtk
>> >
>> > reader = vtk.vtkEnSightGoldReader()
>> >
>> > reader.SetCaseFileName("case.case")
>> > reader.Update()
>> >
>> > # Get time values
>> > timeset=reader.GetTimeSets()
>> > time=timeset.GetItem(0)
>> > timesteps=time.GetSize()
>> >
>> > #reader.ReleaseDataFlagOn()
>> >
>> > for j in range(timesteps):
>> >     curTime=time.GetTuple(j)[0]
>> >     print curTime
>> >     reader.SetTimeValue(curTime)
>> >     reader.Update()
>> >
>> >     #reader.RemoveAllInputs()
>> >
>> >
>> > I tried a few things as you can see
>> > - reader.ReleaseDataFlagOn(), without success
>> > - reader.RemoveAllInputs(), did not get it to run
>> > - running gc.collect at the end of the loop, following
>> > http://vtk.1045678.n5.nabble.com/VTK-memory-management-td5715661.html
>> > - Using DeepCopy as suggested here:
>> >
>> > http://vtk.1045678.n5.nabble.com/Memory-leak-in-VTK-Python-module-td1234002.html
>> > However, I am already experiencing this without a call to GetOutput
>> >
>> >
>> > My question is, how can I properly unload/replace the data that is
>> > stored in
>> > the memory, instead of using more memory continuously?
>> >
>> > Best regards,
>> > Bernhard
>> >
>> > _______________________________________________
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>
>
>
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