Re: TFile memory leak?

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
>>>>>>> 
>>>>>>> 
>>>>> 


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