[vtkusers] Memory leak vtkEnsightGoldReader in Python
Bill Lorensen
bill.lorensen at gmail.com
Tue Mar 4 15:05:28 EST 2014
Bernhard,
Thanks for your patience. Since I'm not a python person, I converted
your program to C++. I ran valgrind and found no memory leaks.
Perhaps the small dataset you provided does not exercise the code that
is leaking.
Can you possible place a dataset that you know has leaksat some accessible site?
I will say, that I don't think any of the current ensight tests access
multiple time steps. Your data and test script will be a good starting
point for such a test.
Bill
On Tue, Mar 4, 2014 at 12:08 AM, Bernhard Righolt
<b.w.righolt at tudelft.nl> wrote:
> Therr is a python script inside the archive which is the same script that I
> used on the large case.
>
> Bernhard
>
>
> On Mar 4, 2014 12:22 AM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:
>>
>> This is great. Can you send a complete python script that illustrates the
>> problem.?
>>
>> On Mar 3, 2014 2:47 PM, "Bernhard Righolt" <b.w.righolt at tudelft.nl> wrote:
>> >
>> > 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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>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
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>> >> >
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>> >> >
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>> >>
>> >>
>> >> --
>> >> Unpaid intern in BillsBasement at noware dot com
>> >
>> >
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Unpaid intern in BillsBasement at noware dot com
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