Re: TFile memory leak?

From: OKUMURA, Akira <oxon_at_astro.isas.jaxa.jp>
Date: Thu, 9 Sep 2010 10:57:17 -0700


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 - 19:57:32 CEST

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