[vtkusers] Memory leak vtkEnsightGoldReader in Python

[Bernhard Righolt]

Hi Bill,

I added a very small sample data set. I am not sure if the memory problem I
am encountering with my big data-set is measurable for this one.

Anyhow, I would like to repeat that I am using Python 2.6 and VTK 5.10,

Best regards,
Bernhard


On 3 March 2014 19:25, Bill Lorensen <bill.lorensen at gmail.com> wrote:

> 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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> >
> >
> >
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>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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