Re: TFile memory leak?

From: OKUMURA, Akira <oxon_at_astro.isas.jaxa.jp>
Date: Thu, 9 Sep 2010 12:32:43 -0700


Hello Philippe,

Thanks again for your advise. kCanDelete works fine in my actual longer script.

Regards,

--
OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu}
Institute of Space and Astronautical Science (ISAS/JAXA)
Now at KIPAC/SLAC/Stanford
Varian Physics #306
382 Via Pueblo Mall, MC 406 Stanford, CA94305
TEL 650-736-0971/FAX 650-724-5065
Skype : okumura.akira

On 2010/09/09, at 11:07, Philippe Canal wrote:

> Hi,
> 
> If you know that a file has a canvas which needs to own its content simply do:
> 
>   TFile f("tmp.root");
>   TCanvas* c = (TCanvas*)f.Get("can");
>   TIter next( c->GetListOfPrimitives() );
>   TObject *obj;
>   while( (obj = next() ) {
>     obj->SetBit(TObject::kCanDelete()); // Add missing ownership delegation
>   }
> 
> Cheers,
> Philippe.
> 
> 
> On 9/9/10 12:57 PM, OKUMURA, Akira wrote:
>> Hello Philippe,
>> 
>> Thank you for your detailed explanation. I now understand that it was my mistake and how I should save canvases in ROOT files.
>> 
>> In addition, I would like to know how I can delete the allocated memory with the bad files which have been already created in my HDD. I have many files which were created without caring about ownership delegation. Of course, I can recreate the files with small modification, but do you have any easy solution?
>> 
>> Regards,
>> 
>> --
>> OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu}
>> Institute of Space and Astronautical Science (ISAS/JAXA)
>> Now at KIPAC/SLAC/Stanford
>> Varian Physics #306
>> 382 Via Pueblo Mall, MC 406 Stanford, CA94305
>> TEL 650-736-0971/FAX 650-724-5065
>> Skype : okumura.akira
>> 
>> On 2010/09/09, at 10:32, Philippe Canal wrote:
>> 

>>> Hi Akira,
>>>
>>> The issue is the ownership of the histogram object. The simplest fix is to use:
>>>
>>> TCanvas can("can", "can");
>>> TH2D h("h", "h", 100, -3, 3, 100, -3, 3);
>>> h.FillRandom("gaus", 100000);
>>> h.DrawCopy("col");
>>> can.SaveAs("tmp.root");
>>>
>>> The issue is that when you do h.Draw, it does associate the histogram with
>>> the Canvas but it __correctly__ (especially in your case) does not delegate
>>> ownership of the histogram to the Canvas. Since you did not delegate
>>> ownership of the histogram to the Canvas, the Canvas __must__ assume
>>> that you will store the histogram independently and thus upon reading
>>> the file, the Canvas does not take ownership of the histogram and do
>>> not delete it when you delete the Canvas.
>>>
>>> By using DrawCopy you create a new histogram and delegate its
>>> ownership to the Canvas.
>>>
>>> Note that you of course need to delete the Canvas in the reading
>>> loop in order to really get rid of the leak (this is because Canvas
>>> are __not__ owned by the TFile they are read from).
>>>
>>> Cheers,
>>> Philippe.
>>>
>>> PS. A slightly more cpu efficient option is:
>>>
>>> TCanvas can("can", "can");
>>> TH2D *h = new TH2D("h", "h", 100, -3, 3, 100, -3, 3);
>>> h->FillRandom("gaus", 100000);
>>> h->Draw("col");
>>> h->SetBit(TObject::kCanDelete); // Delegate ownership to the Canvas.
>>> can.SaveAs("tmp.root");
>>>
>>> On 9/9/10 10:34 AM, OKUMURA, Akira wrote:
>>>> Hello all, >>>> >>>> Here is a minimum example. You don't need to download http://slac.stanford.edu/~oxon/tmp.tgz >>>> >>>> ============================== >>>> #include<TFile.h> >>>> #include<TCanvas.h> >>>> #include<TH2D.h> >>>> #include<iostream> >>>> >>>> int main(int argc, char** argv) >>>> { >>>> TCanvas can("can", "can"); >>>> TH2D h("h", "h", 100, -3, 3, 100, -3, 3); >>>> h.FillRandom("gaus", 100000); >>>> h.Draw("col"); >>>> can.SaveAs("tmp.root"); >>>> >>>> const Int_t kN = 10000; >>>> for(Int_t i = 0; i< kN; i++){ >>>> TFile f("tmp.root"); >>>> std::cout<< "Reading"<< f.GetName()<< "...\n"; >>>> TCanvas* c = (TCanvas*)f.Get("can"); >>>> f.Close(); >>>> } // i >>>> >>>> return 0; >>>> } >>>> ============================== >>>> >>>> I would like to know how to delete the allocated memory to TCanvas* c. C++'s delete does not work. >>>> >>>> Regards, >>>> >>>> -- >>>> OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu} >>>> Institute of Space and Astronautical Science (ISAS/JAXA) >>>> Now at KIPAC/SLAC/Stanford >>>> Varian Physics #306 >>>> 382 Via Pueblo Mall, MC 406 Stanford, CA94305 >>>> TEL 650-736-0971/FAX 650-724-5065 >>>> Skype : okumura.akira >>>> >>>> On 2010/09/09, at 8:20, OKUMURA, Akira wrote: >>>> >>>>> Hello John and all, >>>>> >>>>> I uploaded the log file here. >>>>> http://slac.stanford.edu/~oxon/valgrind.log >>>>> >>>>> Regards, >>>>> >>>>> -- >>>>> OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu} >>>>> Institute of Space and Astronautical Science (ISAS/JAXA) >>>>> Now at KIPAC/SLAC/Stanford >>>>> Varian Physics #306 >>>>> 382 Via Pueblo Mall, MC 406 Stanford, CA94305 >>>>> TEL 650-736-0971/FAX 650-724-5065 >>>>> Skype : okumura.akira >>>>> >>>>> On 2010/09/09, at 2:06, John Idarraga wrote: >>>>> >>>>>> Hello Akira >>>>>> >>>>>> Can you&> that to a log file and send it ? >>>>>> >>>>>> John >>>>>> >>>>>> OKUMURA, Akira wrote: >>>>>>> Hello Claudi and all, >>>>>>> >>>>>>> Thank you for your advice. I attach a part of the valgrind output. Even though this is a first time to use valgrind for me, the output seems that there is memory leak. >>>>>>> >>>>>>> ==17737== 5,189,819 (27,328 direct, 5,162,491 indirect) bytes in 61 blocks are definitely lost in loss record 45,809 of 45,811 >>>>>>> ==17737== at 0x1000146CE: operator new(unsigned long) (vg_replace_malloc.c:261) >>>>>>> ==17737== by 0x1000386C9: TStorage::ObjectAlloc(unsigned long) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x100233BB4: TObject::operator new(unsigned long) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x102DE6955: ROOT::new_TPaletteAxis(void*) (in /usr/local/root_svn/lib/libHistPainter.so) >>>>>>> ==17737== by 0x10010AAA5: TClass::New(TClass::ENewType) const (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x100FEB2BF: TBufferFile::ReadObjectAny(TClass const*) (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x1000EF390: TBuffer& operator>><TObject>(TBuffer&, TObject*&) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x1000F2C22: TList::Streamer(TBuffer&) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x100FE8A18: TBufferFile::ReadFastArray(void**, TClass const*, int, bool, TMemberStreamer*, TClass const*) (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x1010A1864: int TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, int, int, int, int) (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x100FE9C15: TBufferFile::ReadClassBuffer(TClass const*, void*, int, unsigned int, unsigned int, TClass const*) (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x101363C23: TH1::Streamer(TBuffer&) (in /usr/local/root_svn/lib/libHist.so) >>>>>>> ==17737== ==17737== 69,739,543 (823,176 direct, 68,916,367 indirect) bytes in 999 blocks are definitely lost in loss record 45,810 of 45,811 >>>>>>> ==17737== at 0x1000146CE: operator new(unsigned long) (vg_replace_malloc.c:261) >>>>>>> ==17737== by 0x1000386C9: TStorage::ObjectAlloc(unsigned long) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x100233BB4: TObject::operator new(unsigned long) (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x101A9EA7E: ROOT::new_TCanvas(void*) (in /usr/local/root_svn/lib/libGpad.so) >>>>>>> ==17737== by 0x10010AAA5: TClass::New(TClass::ENewType) const (in /usr/local/root_svn/lib/libCore.so) >>>>>>> ==17737== by 0x101013FBB: TKey::ReadObj() (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x100FF5AEE: TDirectoryFile::Get(char const*) (in /usr/local/root_svn/lib/libRIO.so) >>>>>>> ==17737== by 0x100000EFC: main (test.C:19) >>>>>>> ==17737== ==17737== LEAK SUMMARY: >>>>>>> ==17737== definitely lost: 859,176 bytes in 1,222 blocks >>>>>>> ==17737== indirectly lost: 85,444,368 bytes in 14,771 blocks >>>>>>> ==17737== possibly lost: 387,824 bytes in 1,534 blocks >>>>>>> ==17737== still reachable: 9,549,367 bytes in 84,421 blocks >>>>>>> ==17737== suppressed: 852,204 bytes in 23,733 blocks >>>>>>> ==17737== Reachable blocks (those to which a pointer was found) are not shown. >>>>>>> ==17737== To see them, rerun with: --leak-check=full --show-reachable=yes >>>>>>> ==17737== ==17737== For counts of detected and suppressed errors, rerun with: -v >>>>>>> ==17737== Use --track-origins=yes to see where uninitialised values come from >>>>>>> ==17737== ERROR SUMMARY: 705 errors from 705 contexts (suppressed: 1692 from 1692) >>>>>>> >>>>>>> Regards, >>>>>>> >>>>>>> -- >>>>>>> OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu} >>>>>>> Institute of Space and Astronautical Science (ISAS/JAXA) >>>>>>> Now at KIPAC/SLAC/Stanford >>>>>>> Varian Physics #306 >>>>>>> 382 Via Pueblo Mall, MC 406 Stanford, CA94305 >>>>>>> TEL 650-736-0971/FAX 650-724-5065 >>>>>>> Skype : okumura.akira >>>>>>> >>>>>>> >>>>>>> On 2010/09/08, at 14:31, Claudi Astres wrote: >>>>>>> >>>>>>> >>>>>>>> Hi Akira, >>>>>>>> You could use "valgrind" utility to check whether the problem is really a memory leak. Maybe you already knew it. >>>>>>>> Valgrind has become crucial for me: http://valgrind.org/ >>>>>>>> >>>>>>>> Regards. >>>>>>>> Claudi >>>>>>>> >>>>>>>> >>>>>>>> El 08/09/2010, a las 22:14, OKUMURA, Akira escribió: >>>>>>>> >>>>>>>> >>>>>>>>> Hello ROOTers, >>>>>>>>> >>>>>>>>> This question may be a very basic one but I could not find similar questions on the web. >>>>>>>>> >>>>>>>>> http://slac.stanford.edu/~oxon/tmp.tgz >>>>>>>>> >>>>>>>>> This tgz file includes a .root file and a very simple script which opens TFile 10000 times. When I execute the script, >>>>>>>>> >>>>>>>>> root [0] .x test.C >>>>>>>>> >>>>>>>>> the memory usage of the process becomes more than 1 GB while all TFile instances are closed. >>>>>>>>> >>>>>>>>> The .root file was created via TPad::SaveAs, as follows. >>>>>>>>> >>>>>>>>> root [0] TCanvas can("can", "can") >>>>>>>>> root [1] TH2D* h = new TH2D("h", "h", 100, -3, 3, 100, -3, 3) >>>>>>>>> root [2] h->FillRandom("gaus", 1000000) >>>>>>>>> root [3] h->Draw() >>>>>>>>> root [4] can.SaveAs("aho.root") >>>>>>>>> >>>>>>>>> How can I suppress this large memory consumption? I am not sure if this is an intended behavior or memory leak. >>>>>>>>> >>>>>>>>> I am using svn trunk on Snow Leopard and SL 5. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> >>>>>>>>> -- >>>>>>>>> OKUMURA, Akira oxon@{astro.isas.jaxa.jp,stanford.edu} >>>>>>>>> Institute of Space and Astronautical Science (ISAS/JAXA) >>>>>>>>> Now at KIPAC/SLAC/Stanford >>>>>>>>> Varian Physics #306 >>>>>>>>> 382 Via Pueblo Mall, MC 406 Stanford, CA94305 >>>>>>>>> TEL 650-736-0971/FAX 650-724-5065 >>>>>>>>> Skype : okumura.akira >>>>>>>>> >>>>>>>>> >
Received on Thu Sep 09 2010 - 21:32:58 CEST

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