Re: [Rdkit-discuss] Memory leak: new operator in RxnSmartsToChemicalReaction

[Jarod Y. <jar...@ho...>]

Posted the Valgrind HEAP Summary showing the memory allocation in the shared library … When the pointer goes out of scope, that memory must not be deallocated.  Bug?

==10036== HEAP SUMMARY:
==10036==     in use at exit: 2,324,704 bytes in 31,944 blocks
==10036==   total heap usage: 140,499 allocs, 108,555 frees, 8,952,289 bytes allocated
==10036==
==10036== 2,324,704 (15,232 direct, 2,309,472 indirect) bytes in 136 blocks are definitely lost in loss record 93 of 93
==10036==    at 0x4845013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==10036==    by 0x4B0D550: RDKit::RxnSmartsToChemicalReaction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char
_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allo
cator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::
char_traits<char>, std::allocator<char> > > > >*, bool, bool) (in /opt/rdkit-Release_2022_09_2/lib/libRDKitChemReactions.so.1.2022.09.1)
==10036==    by 0x11E943: kMC::Reaction::Reaction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, st
d::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (Reaction.cpp:18)

Sent from my iPhone

On Jul 3, 2023, at 12:48 PM, Jarod Younker <jar...@ho...> wrote:

The function RxnSmartsToChemicalReaction() returns a pointer to a ChemicalReaction object.

Is this pointer a std::unique_ptr?

How does one deallocate said pointer after it goes out of scope?

Valgrind identifies a definite memory loss in libRDKitChemReactions.so from a new(unsigned long)

Thanks,

J

Sent from my iPhone

_______________________________________________
Rdkit-discuss mailing list
Rdk...@li...
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=05%7C01%7C%7C8d25b02bc4ab44cc1ad708db7beda725%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638240032871322956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8Dmfydb9VO9ApXMonLqqRQot3LUvpD4ijtWUmOrUPWw%3D&reserved=0