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vGate9.3 maybe with memory leak #615

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Fantasticlyy opened this issue Jun 1, 2023 · 5 comments
Closed

vGate9.3 maybe with memory leak #615

Fantasticlyy opened this issue Jun 1, 2023 · 5 comments

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@Fantasticlyy
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Describe the bug
use the vGate 9.3,while use digitizer and enable the “/gate/output/” ，when run a simulation ,the RAM will be raise by follow time,I thin may be enable the “/gate/output/” with memory leak,this issue only appear in vGate9.3 ,the other version not appear.
Desktop (please complete the following information):
vGate9.3 VirtualBox 7.06

#############

DIGITIZER

#############
/gate/digitizerMgr/name LESingles
/gate/digitizerMgr/chooseSD pixel
/gate/digitizerMgr/insert SinglesDigitizer
/gate/digitizerMgr/pixel/SinglesDigitizer/LESingles/setInputCollection Singles
/gate/digitizerMgr/pixel/SinglesDigitizer/LESingles/insert energyFraming
/gate/digitizerMgr/pixel/SinglesDigitizer/LESingles/energyFraming/setMin 0. keV
/gate/digitizerMgr/pixel/SinglesDigitizer/LESingles/energyFraming/setMax 6000. keV

########

OUTPUT

########
/gate/output/tree/enable
/gate/output/tree/addFileName output/LHCsI.txt
/gate/output/tree/hits/enable
/gate/output/tree/addCollection LESingles
/gate/output/tree/addCollection Singles
@tontyoutoure
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tontyoutoure commented Jun 3, 2023 •
edited
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Can confirm.
I ran valgrind and the following part is what increases as duration of simulation increase:

parts of valgrind output 
==72618== 2,844,528 bytes in 118,522 blocks are definitely lost in loss record 22,855 of 22,861
==72618==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==72618==    by 0x359D45: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:114)
==72618==    by 0x358F84: std::allocator_traits<std::allocator<int> >::allocate(std::allocator<int>&, unsigned long) (alloc_traits.h:443)
==72618==    by 0x3584AD: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:343)
==72618==    by 0x37E712: std::_Vector_base<int, std::allocator<int> >::_M_create_storage(unsigned long) (stl_vector.h:358)
==72618==    by 0x37E1CA: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:302)
==72618==    by 0x3A0AFA: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:521)
==72618==    by 0x3A0203: GateOutputVolumeID::GateOutputVolumeID(unsigned long) (GateOutputVolumeID.hh:56)
==72618==    by 0x417BA6: GateDigi::GateDigi(void const*) (GateDigi.cc:45)
==72618==    by 0x5F2AC7: GateReadout::Digitize() (GateReadout.cc:225)
==72618==    by 0x42AC40: GateDigitizerMgr::RunDigitizers() (GateDigitizerMgr.cc:427)
==72618==    by 0x3833AA: GateAnalysis::RecordEndOfEvent(G4Event const*) (GateAnalysis.cc:479)
==72618== 
==72618== 2,844,552 bytes in 118,523 blocks are definitely lost in loss record 22,856 of 22,861
==72618==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==72618==    by 0x359D45: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:114)
==72618==    by 0x358F84: std::allocator_traits<std::allocator<int> >::allocate(std::allocator<int>&, unsigned long) (alloc_traits.h:443)
==72618==    by 0x3584AD: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:343)
==72618==    by 0x37E712: std::_Vector_base<int, std::allocator<int> >::_M_create_storage(unsigned long) (stl_vector.h:358)
==72618==    by 0x37E1CA: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:302)
==72618==    by 0x3A0AFA: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:521)
==72618==    by 0x3A0203: GateOutputVolumeID::GateOutputVolumeID(unsigned long) (GateOutputVolumeID.hh:56)
==72618==    by 0x417BA6: GateDigi::GateDigi(void const*) (GateDigi.cc:45)
==72618==    by 0x61C6F8: GateSpatialResolution::Digitize() (GateSpatialResolution.cc:115)
==72618==    by 0x42AC40: GateDigitizerMgr::RunDigitizers() (GateDigitizerMgr.cc:427)
==72618==    by 0x3833AA: GateAnalysis::RecordEndOfEvent(G4Event const*) (GateAnalysis.cc:479)
==72618== 
==72618== 2,844,624 bytes in 118,526 blocks are definitely lost in loss record 22,857 of 22,861
==72618==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==72618==    by 0x359D45: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:114)
==72618==    by 0x358F84: std::allocator_traits<std::allocator<int> >::allocate(std::allocator<int>&, unsigned long) (alloc_traits.h:443)
==72618==    by 0x3584AD: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:343)
==72618==    by 0x37E712: std::_Vector_base<int, std::allocator<int> >::_M_create_storage(unsigned long) (stl_vector.h:358)
==72618==    by 0x37E1CA: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:302)
==72618==    by 0x3A0AFA: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:521)
==72618==    by 0x3A0203: GateOutputVolumeID::GateOutputVolumeID(unsigned long) (GateOutputVolumeID.hh:56)
==72618==    by 0x417BA6: GateDigi::GateDigi(void const*) (GateDigi.cc:45)
==72618==    by 0x48549F: GateEnergyResolution::Digitize() (GateEnergyResolution.cc:96)
==72618==    by 0x42AC40: GateDigitizerMgr::RunDigitizers() (GateDigitizerMgr.cc:427)
==72618==    by 0x3833AA: GateAnalysis::RecordEndOfEvent(G4Event const*) (GateAnalysis.cc:479)
==72618== 
==72618== 2,844,696 bytes in 118,529 blocks are definitely lost in loss record 22,858 of 22,861
==72618==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==72618==    by 0x359D45: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:114)
==72618==    by 0x358F84: std::allocator_traits<std::allocator<int> >::allocate(std::allocator<int>&, unsigned long) (alloc_traits.h:443)
==72618==    by 0x3584AD: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:343)
==72618==    by 0x37E712: std::_Vector_base<int, std::allocator<int> >::_M_create_storage(unsigned long) (stl_vector.h:358)
==72618==    by 0x37E1CA: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:302)
==72618==    by 0x3A0AFA: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:521)
==72618==    by 0x3A0203: GateOutputVolumeID::GateOutputVolumeID(unsigned long) (GateOutputVolumeID.hh:56)
==72618==    by 0x417BA6: GateDigi::GateDigi(void const*) (GateDigi.cc:45)
==72618==    by 0x37C84A: GateAdder::Digitize() (GateAdder.cc:70)
==72618==    by 0x42AC40: GateDigitizerMgr::RunDigitizers() (GateDigitizerMgr.cc:427)
==72618==    by 0x3833AA: GateAnalysis::RecordEndOfEvent(G4Event const*) (GateAnalysis.cc:479)
==72618== 
==72618== 2,844,696 bytes in 118,529 blocks are definitely lost in loss record 22,859 of 22,861
==72618==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==72618==    by 0x359D45: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:114)
==72618==    by 0x358F84: std::allocator_traits<std::allocator<int> >::allocate(std::allocator<int>&, unsigned long) (alloc_traits.h:443)
==72618==    by 0x3584AD: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:343)
==72618==    by 0x37E712: std::_Vector_base<int, std::allocator<int> >::_M_create_storage(unsigned long) (stl_vector.h:358)
==72618==    by 0x37E1CA: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:302)
==72618==    by 0x3A0AFA: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:521)
==72618==    by 0x3A0203: GateOutputVolumeID::GateOutputVolumeID(unsigned long) (GateOutputVolumeID.hh:56)
==72618==    by 0x417BA6: GateDigi::GateDigi(void const*) (GateDigi.cc:45)
==72618==    by 0x483461: GateEnergyFraming::Digitize() (GateEnergyFraming.cc:86)
==72618==    by 0x42AC40: GateDigitizerMgr::RunDigitizers() (GateDigitizerMgr.cc:427)
==72618==    by 0x3833AA: GateAnalysis::RecordEndOfEvent(G4Event const*) (GateAnalysis.cc:479)
After a while I realize the cause of the problem is kind simple. A lot of digitizer ( not sure if it's all of them) said 
GateDigi* inputDigi = new GateDigi();

in their ::Digitize() method. And without delete.

It could be patched with ease.

tontyoutoure pushed a commit to tontyoutoure/Gate that referenced this issue Jun 3, 2023
fix memory leak in digitizer, issue OpenGATE#615
37863bc
@tontyoutoure
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Wow it turn outs that this pointer will be assigned other values and should not allocate anything in the first place.
Make a PR hope it will be merged asap.

@tontyoutoure
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tontyoutoure commented Jun 3, 2023 •
edited
Loading

It seems there are more leak other than the one showed above. I'll try to find it.

Edit: Turns out to be it's something else. The fix above should be sufficient.

kochebina added a commit that referenced this issue Jun 7, 2023
@kochebina
Merge pull request #619 from tontyoutoure/tontyoutoure_fix_memleak
e73015d 
fix memory leak in digitizer, issue #615
@tontyoutoure
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You can now git pull origin develop in your virtual machine ~/Software/Gate/src dir and make in ~/Software/Gate/bin dir to fix the problem. @Fantasticlyy

@dsarrut
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dsarrut commented Jun 8, 2023

done #619

@dsarrut dsarrut closed this as completed Jun 8, 2023
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@dsarrut @tontyoutoure @Fantasticlyy