<div dir="ltr"><div>Dear Bill,<br><br>With your C++ script, I am indeed facing the same issue (although the python code runs significantly quicker for my case).<br><br>I shared a few files, and a script to create more data here: <a href="https://www.dropbox.com/s/ndg6mwam2xdfmwq/data.tar.gz">https://www.dropbox.com/s/ndg6mwam2xdfmwq/data.tar.gz</a> My experience is that with dissimilar data, the memory leak seems to be larger, but with this data (which just copies the time steps), it is still present,<br>
<br>Best regards,<br>Bernhard<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 4 March 2014 21:27, Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Attached is my C++ program and CMakeLists.txt file. But I don't think<br>
this is a python issue...<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, Mar 4, 2014 at 3:10 PM, Bernhard Righolt <<a href="mailto:b.w.righolt@tudelft.nl">b.w.righolt@tudelft.nl</a>> wrote:<br>
> Dear Bill,<br>
><br>
> I am a C++ speaker, so I don't mind to test your code on my current large<br>
> dataset. Can you maybe share your code, such that I can test it? I've never<br>
> used VTK within C++, if it solves the issues I am experiencing with Python,<br>
> I am very willing to switch. I hope it is not too complicated to link the<br>
> libraries correctly.<br>
><br>
> Bernhard<br>
><br>
><br>
><br>
> On 4 March 2014 21:05, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br>
>><br>
>> Bernhard,<br>
>><br>
>> Thanks for your patience. Since I'm not a python person, I converted<br>
>> your program to C++. I ran valgrind and found no memory leaks.<br>
>><br>
>> Perhaps the small dataset you provided does not exercise the code that<br>
>> is leaking.<br>
>><br>
>> Can you possible place a dataset that you know has leaksat some accessible<br>
>> site?<br>
>><br>
>> I will say, that I don't think any of the current ensight tests access<br>
>> multiple time steps. Your data and test script will be a good starting<br>
>> point for such a test.<br>
>><br>
>> Bill<br>
>><br>
>> On Tue, Mar 4, 2014 at 12:08 AM, Bernhard Righolt<br>
>> <<a href="mailto:b.w.righolt@tudelft.nl">b.w.righolt@tudelft.nl</a>> wrote:<br>
>> > Therr is a python script inside the archive which is the same script<br>
>> > that I<br>
>> > used on the large case.<br>
>> ><br>
>> > Bernhard<br>
>> ><br>
>> ><br>
>> > On Mar 4, 2014 12:22 AM, "Bill Lorensen" <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>> > wrote:<br>
>> >><br>
>> >> This is great. Can you send a complete python script that illustrates<br>
>> >> the<br>
>> >> problem.?<br>
>> >><br>
>> >> On Mar 3, 2014 2:47 PM, "Bernhard Righolt" <<a href="mailto:b.w.righolt@tudelft.nl">b.w.righolt@tudelft.nl</a>><br>
>> >> wrote:<br>
>> >> ><br>
>> >> > Hi Bill,<br>
>> >> ><br>
>> >> > I added a very small sample data set. I am not sure if the memory<br>
>> >> > problem I am encountering with my big data-set is measurable for this<br>
>> >> > one.<br>
>> >> ><br>
>> >> > Anyhow, I would like to repeat that I am using Python 2.6 and VTK<br>
>> >> > 5.10,<br>
>> >> ><br>
>> >> > Best regards,<br>
>> >> > Bernhard<br>
>> >> ><br>
>> >> ><br>
>> >> > On 3 March 2014 19:25, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br>
>> >> >><br>
>> >> >> The ensight readers could use more testing. Can you provide a<br>
>> >> >> "small"<br>
>> >> >> dataset and program that cause memory leaks?<br>
>> >> >><br>
>> >> >> Bill<br>
>> >> >><br>
>> >> >><br>
>> >> >> On Mon, Mar 3, 2014 at 10:38 AM, Bernhard Righolt<br>
>> >> >> <<a href="mailto:b.w.righolt@tudelft.nl">b.w.righolt@tudelft.nl</a>> wrote:<br>
>> >> >> > Dear all,<br>
>> >> >> ><br>
>> >> >> > A typical case file, looks as follows (ASCII).<br>
>> >> >> ><br>
>> >> >> > $ head -n 20 case.case<br>
>> >> >> > FORMAT<br>
>> >> >> > type: ensight gold<br>
>> >> >> ><br>
>> >> >> > GEOMETRY<br>
>> >> >> > model: 1 sliceCentre.000.mesh<br>
>> >> >> ><br>
>> >> >> > VARIABLE<br>
>> >> >> > vector per node: 1 U sliceCentre.*****.U<br>
>> >> >> ><br>
>> >> >> > TIME<br>
>> >> >> > time set: 1<br>
>> >> >> > number of steps: 11550<br>
>> >> >> > filename start number: 1<br>
>> >> >> > filename increment: 1<br>
>> >> >> > time values:<br>
>> >> >> > 0.002<br>
>> >> >> > 0.004<br>
>> >> >> > 0.006<br>
>> >> >> > 0.008<br>
>> >> >> > 0.01<br>
>> >> >> > $<br>
>> >> >> ><br>
>> >> >> > The mesh (snippet only), is as follows:<br>
>> >> >> ><br>
>> >> >> > $ head -n 10 sliceCentre.000.mesh<br>
>> >> >> > Ensight Geometry File<br>
>> >> >> > =====================<br>
>> >> >> > node id assign<br>
>> >> >> > element id assign<br>
>> >> >> > part<br>
>> >> >> > 1<br>
>> >> >> > sliceCentre.000.mesh<br>
>> >> >> > coordinates<br>
>> >> >> > 299028<br>
>> >> >> > 0.00000e+00<br>
>> >> >> > $ sed -n -e 897091,897098p sliceCentre.000.mesh<br>
>> >> >> > 0.00000e+00<br>
>> >> >> > 0.00000e+00<br>
>> >> >> > 0.00000e+00<br>
>> >> >> > tria3<br>
>> >> >> > 595264<br>
>> >> >> > 162106 162714 162799<br>
>> >> >> > 162799 162226 162106<br>
>> >> >> > 162714 162106 162021<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > And the corresponding datafile<br>
>> >> >> > $ head -n 10 sliceCentre.00001.U<br>
>> >> >> > vector<br>
>> >> >> > part<br>
>> >> >> > 1<br>
>> >> >> > coordinates<br>
>> >> >> > 5.33425e-04<br>
>> >> >> > 2.69515e-03<br>
>> >> >> > -1.65164e-03<br>
>> >> >> > 5.33425e-04<br>
>> >> >> > 1.39069e-04<br>
>> >> >> > 2.69515e-03<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > However, I doubt if something is wrong with my datafiles itself,<br>
>> >> >> > because I<br>
>> >> >> > can easily read them in Paraview for example, the only difference<br>
>> >> >> > is<br>
>> >> >> > the<br>
>> >> >> > large amount of data-files, e.g (124GB in this case)<br>
>> >> >> ><br>
>> >> >> > Best regards,<br>
>> >> >> > Bernhard<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > On 27 February 2014 22:28, Berk Geveci <<a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a>><br>
>> >> >> > wrote:<br>
>> >> >> >><br>
>> >> >> >> Nothing strikes me as obviously wrong in your script. Can you<br>
>> >> >> >> send<br>
>> >> >> >> me<br>
>> >> >> >> your case file? I'll take a look.<br>
>> >> >> >><br>
>> >> >> >> -berk<br>
>> >> >> >><br>
>> >> >> >> On Thu, Feb 27, 2014 at 3:20 AM, Bernhard Righolt<br>
>> >> >> >> <<a href="mailto:b.w.righolt@tudelft.nl">b.w.righolt@tudelft.nl</a>> wrote:<br>
>> >> >> >> > Dear all,<br>
>> >> >> >> ><br>
>> >> >> >> > Currently I am using a Python script to process information<br>
>> >> >> >> > stored<br>
>> >> >> >> > in<br>
>> >> >> >> > the<br>
>> >> >> >> > EnSight Gold format. My Python (2.6) scipt uses VTK (5.10.0) to<br>
>> >> >> >> > process<br>
>> >> >> >> > the<br>
>> >> >> >> > file, where I used the vtkEnSightGoldReader for reading the<br>
>> >> >> >> > data,<br>
>> >> >> >> > and<br>
>> >> >> >> > loop<br>
>> >> >> >> > over time steps.<br>
>> >> >> >> ><br>
>> >> >> >> > In principle this works fine for smaller datasets, however, for<br>
>> >> >> >> > large<br>
>> >> >> >> > datasets (i.e. 11k files of 12MB), I see the memory usage<br>
>> >> >> >> > (recorded via<br>
>> >> >> >> > top)<br>
>> >> >> >> > increasing with time while the process is running. This filling<br>
>> >> >> >> > of<br>
>> >> >> >> > the<br>
>> >> >> >> > memory goes slow, but in some cases problems are inevitable.<br>
>> >> >> >> > Apparently,<br>
>> >> >> >> > I<br>
>> >> >> >> > am doing some things wrong in my script with respect to memory<br>
>> >> >> >> > management.<br>
>> >> >> >> ><br>
>> >> >> >> > I am using the following script (stripped obviously, but still<br>
>> >> >> >> > showing<br>
>> >> >> >> > this<br>
>> >> >> >> > issue)<br>
>> >> >> >> ><br>
>> >> >> >> > import vtk<br>
>> >> >> >> ><br>
>> >> >> >> > reader = vtk.vtkEnSightGoldReader()<br>
>> >> >> >> ><br>
>> >> >> >> > reader.SetCaseFileName("case.case")<br>
>> >> >> >> > reader.Update()<br>
>> >> >> >> ><br>
>> >> >> >> > # Get time values<br>
>> >> >> >> > timeset=reader.GetTimeSets()<br>
>> >> >> >> > time=timeset.GetItem(0)<br>
>> >> >> >> > timesteps=time.GetSize()<br>
>> >> >> >> ><br>
>> >> >> >> > #reader.ReleaseDataFlagOn()<br>
>> >> >> >> ><br>
>> >> >> >> > for j in range(timesteps):<br>
>> >> >> >> > curTime=time.GetTuple(j)[0]<br>
>> >> >> >> > print curTime<br>
>> >> >> >> > reader.SetTimeValue(curTime)<br>
>> >> >> >> > reader.Update()<br>
>> >> >> >> ><br>
>> >> >> >> > #reader.RemoveAllInputs()<br>
>> >> >> >> ><br>
>> >> >> >> ><br>
>> >> >> >> > I tried a few things as you can see<br>
>> >> >> >> > - reader.ReleaseDataFlagOn(), without success<br>
>> >> >> >> > - reader.RemoveAllInputs(), did not get it to run<br>
>> >> >> >> > - running gc.collect at the end of the loop, following<br>
>> >> >> >> ><br>
>> >> >> >> ><br>
>> >> >> >> > <a href="http://vtk.1045678.n5.nabble.com/VTK-memory-management-td5715661.html" target="_blank">http://vtk.1045678.n5.nabble.com/VTK-memory-management-td5715661.html</a><br>
>> >> >> >> > - Using DeepCopy as suggested here:<br>
>> >> >> >> ><br>
>> >> >> >> ><br>
>> >> >> >> ><br>
>> >> >> >> > <a href="http://vtk.1045678.n5.nabble.com/Memory-leak-in-VTK-Python-module-td1234002.html" target="_blank">http://vtk.1045678.n5.nabble.com/Memory-leak-in-VTK-Python-module-td1234002.html</a><br>
>> >> >> >> > However, I am already experiencing this without a call to<br>
>> >> >> >> > GetOutput<br>
>> >> >> >> ><br>
>> >> >> >> ><br>
>> >> >> >> > My question is, how can I properly unload/replace the data that<br>
>> >> >> >> > is<br>
>> >> >> >> > stored in<br>
>> >> >> >> > the memory, instead of using more memory continuously?<br>
>> >> >> >> ><br>
>> >> >> >> > Best regards,<br>
>> >> >> >> > Bernhard<br>
>> >> >> >> ><br>
>> >> >> >> > _______________________________________________<br>
>> >> >> >> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>> >> >> >> ><br>
>> >> >> >> > Visit other Kitware open-source projects at<br>
>> >> >> >> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >> >> >> ><br>
>> >> >> >> > Please keep messages on-topic and check the VTK FAQ at:<br>
>> >> >> >> > <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">http://www.vtk.org/Wiki/VTK_FAQ</a><br>
>> >> >> >> ><br>
>> >> >> >> > Follow this link to subscribe/unsubscribe:<br>
>> >> >> >> > <a href="http://www.vtk.org/mailman/listinfo/vtkusers" target="_blank">http://www.vtk.org/mailman/listinfo/vtkusers</a><br>
>> >> >> >> ><br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > _______________________________________________<br>
>> >> >> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>> >> >> ><br>
>> >> >> > Visit other Kitware open-source projects at<br>
>> >> >> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >> >> ><br>
>> >> >> > Please keep messages on-topic and check the VTK FAQ at:<br>
>> >> >> > <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">http://www.vtk.org/Wiki/VTK_FAQ</a><br>
>> >> >> ><br>
>> >> >> > Follow this link to subscribe/unsubscribe:<br>
>> >> >> > <a href="http://www.vtk.org/mailman/listinfo/vtkusers" target="_blank">http://www.vtk.org/mailman/listinfo/vtkusers</a><br>
>> >> >> ><br>
>> >> >><br>
>> >> >><br>
>> >> >><br>
>> >> >> --<br>
>> >> >> Unpaid intern in BillsBasement at noware dot com<br>
>> >> ><br>
>> >> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Unpaid intern in BillsBasement at noware dot com<br>
><br>
><br>
<br>
<br>
<br>
--<br>
Unpaid intern in BillsBasement at noware dot com<br>
</div></div></blockquote></div><br></div>