[vtkusers] problems with java memory management
Mark Roden
mmroden at gmail.com
Wed Nov 24 16:14:14 EST 2010
Hi Sebastien,
I've made the changes, as in:
vtkPolyData marchingoutput = marching.GetOutput();
stripper.SetInput(marchingoutput);
instead of
stripper.SetInput(marching.GetOutput());
But in order for this to be effective, do I need to correct lines like
renWin.GetRenderer().AddActor(outlineActor);
Should that be split, or can I continue to have multiple command stacked
like that? Could the renWin.GetRenderer() leak in the above line?
How about a method that returns something like
return stripper.GetOutput();
Will that leak?
or
for (int j=0; j<cell.GetNumberOfPoints()-1; j++)
I have a lot of inlining (if that's the proper term in this context) in my
code. If the only way to solve this problem is to have each individual vtk
call be its own call, that's a pretty big refactor. So are there certain
rules I can use to avoid this? If it's just making sure that one output
doesn't directly go into another input, that's straightforward. Buf it it's
'every time a function with .get' is called, then I need to fix quite a bit
more.
This approach does look like it's pulled the leak down somewhat, but not
entirely.
Mark
On Wed, Nov 24, 2010 at 12:56 PM, Sebastien Jourdain <
sebastien.jourdain at kitware.com> wrote:
> Hi Mark,
>
> I agree it is a common habit in Java. But this problem ONLY if object
> is a vtkObject. If it's one of your Java object, this is not a
> problem.
>
> Seb
>
> On Wed, Nov 24, 2010 at 3:11 PM, Mark Roden <mmroden at gmail.com> wrote:
> > Hi Sebastian,
> >
> > Thanks for giving me a place to start. I'll take a look at my various
> > pipelines and see where/if I'm doing things like that. I probably am,
> since
> > that kind of line saving is just what I'd do.
> >
> > I'll let you and the list know.
> >
> > Mark
> >
> > On Wed, Nov 24, 2010 at 9:37 AM, Sebastien Jourdain
> > <sebastien.jourdain at kitware.com> wrote:
> >>
> >> Hi Mark,
> >>
> >> it might be related to the way you bind vtk object together. I mean by
> >> bind something like the following expression.
> >>
> >> actor.SetMapper( object.GetMapper() );
> >>
> >> In fact VTK can have some issue with reference count if you provide a
> >> VTK object reference across the C++ layer without going through the
> >> Java object layer. (Sorry it is not very clear, but it is quite
> >> difficult to explain.)
> >>
> >> So to solve this problem, you should rewrite the above expression like
> >> that.
> >>
> >> vtkDataSetMapper mapper = object.GetMapper();
> >> actor.SetMapper( mapper );
> >>
> >> Hope that helped and please let us know if that solved your problem.
> >>
> >> Seb
> >>
> >>
> >> On Tue, Nov 23, 2010 at 11:15 PM, Mark Roden <mmroden at gmail.com> wrote:
> >> > Hi all,
> >> >
> >> > I'm having problems with memory management in java (windows 7, 64 bit
> >> > and 32
> >> > bit, vtk 5.6).
> >> >
> >> > The application loads ~150mb of dicom images (varies from patient to
> >> > patient), allocates between 1 to 10 binary masks on top of those
> images,
> >> > and
> >> > then Does Things, things that include PolyData contours.
> >> >
> >> > Once I'm done with an image, I want to completely wipe all instances
> of
> >> > vtk
> >> > and start afresh with a new image.
> >> >
> >> > So, I'm calling
> >> >
> >> > vtkGlobalJavaHash.GC();
> >> >
> >> > But that doesn't work, even after I delete all windows and data
> holders.
> >> >
> >> > So, I go ahead and get more aggressive, calling
> >> >
> >> > vtkGlobalJavaHash.DeleteAll();
> >> >
> >> > This call works somewhat better, but appears to leave ~150 mb behind
> >> > (coincidentally, the size of the original image). When I use the
> >> > netbeans
> >> > memory profiler at this point, I get no indication that this memory is
> >> > actually in use; I'm seeing the memory allocations via the system
> >> > resources
> >> > in the task manager.
> >> >
> >> > I then try something a bit more drastic:
> >> >
> >> > private int DeleteAllVTKObjects(){
> >> > int deleted = 0;
> >> > Set entries = vtkGlobalJavaHash.PointerToReference.entrySet();
> >> > Iterator iter = entries.iterator();
> >> > while (iter.hasNext()) {
> >> > Map.Entry entry = (Map.Entry) iter.next();
> >> > vtkObjectBase obj = (vtkObjectBase) ((WeakReference)
> >> > entry.getValue()).get();
> >> > if (obj == null) {
> >> > // Delete a garbage collected object using the raw C++
> >> > pointer.
> >> > long id = ((Long)entry.getKey()).longValue();
> >> > vtkObjectBase.VTKDeleteReference(id);
> >> > entries.remove(entry);
> >> > deleted++;
> >> > }
> >> > else if (obj != null){
> >> > // Delete a non-garbage collected object.
> >> > // We use Delete() which will call the "real" C++
> >> > Delete()
> >> > // unless Delete() has been called on this Java object
> >> > before.
> >> > // Delete() will remove from the map so we don't have
> >> > to.
> >> > obj.Delete();
> >> > deleted++;
> >> > }
> >> > }
> >> > return deleted;
> >> > }
> >> >
> >> > But that appears to be the same (or no better than)
> >> > vtkGlobalJavaHash.DeleteAll().
> >> >
> >> > So here's the deal: I've got ~140 mb leaking with each image that I
> >> > open,
> >> > and the profiler indicates that the leak is not in Java.
> >> >
> >> > I'm using the vtkGDCMImageReader to read in images, and this object
> does
> >> > not
> >> > (as far as I can see) have a dispose method. I'm using vtkPolyData
> >> > objects,
> >> > but again, I'm not seeing dispose methods. I'm using
> >> > vtkGDCMPolyDataReader
> >> > and to handle contours, again, no dispose method present.
> >> >
> >> > So right now, I'm thinking that either those particular classes have
> >> > leaks
> >> > on the C++ side, or some memory is just not getting handled and
> removed
> >> > by
> >> > the above calls to vtk.
> >> >
> >> > Are there other ways I can debug this issue? I want the user to be
> able
> >> > to
> >> > open and close as many images as they want, rather than having to
> >> > restart
> >> > the program every ~10 or so images due to instabilities from the leak.
> >> >
> >> > Also, due to problems I mentioned previously on the list with changes
> in
> >> > the
> >> > vtk libraries, I can't move to the head version of vtk. If the head
> >> > version
> >> > has a fix, I can try it, but right now, gdcm and vtk head do not play
> >> > well
> >> > together at all. It seems that the vtkStringArrays necessary to read
> in
> >> > files on the gdcm side are empty when passed through the java layer in
> >> > 5.7,
> >> > but not in 5.6 (which I discovered through that error << trick from
> >> > Monday,
> >> > thanks for that). I don't know why that is, but since 5.6 works with
> >> > gdcm
> >> > git head, that's the version I have.
> >> >
> >> > Thanks,
> >> > Mark
> >> >
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>
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