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BugsBugs that only solvable with sufficient knowledge of DFTBugs that only solvable with sufficient knowledge of DFTMemoryMemory issuesMemory issues
Description
Describe the bug
Test case 601_NO_TDDFT_CO
On process id asan.101435
=================================================================
==101435==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x604000114740 at pc 0x5565d8400555 bp 0x7ffc6b2794a0 sp 0x7ffc6b279490
READ of size 8 at 0x604000114740 thread T0
#0 0x5565d8400554 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const /usr/include/c++/11/bits/basic_string.h:921
#1 0x5565d8400554 in std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char>, std::allocator<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) /usr/include/c++/11/bits/basic_string.h:6536
#2 0x5565d8400554 in MD_func::dump_info(int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, UnitCell const&, Parameter const&, ModuleBase::matrix const&, ModuleBase::Vector3<double> const*, ModuleBase::Vector3<double> const*) /__w/abacus-develop/abacus-develop/source/module_md/md_func.cpp:385
#3 0x5565d841ec9a in Run_MD::md_line(UnitCell&, ModuleESolver::ESolver*, Parameter const&) /__w/abacus-develop/abacus-develop/source/module_md/run_md.cpp:89
#4 0x5565d89d84a7 in Driver::driver_run() /__w/abacus-develop/abacus-develop/source/driver_run.cpp:63
#5 0x5565d89d1bbe in Driver::atomic_world() /__w/abacus-develop/abacus-develop/source/driver.cpp:186
#6 0x5565d89d6f36 in Driver::init() /__w/abacus-develop/abacus-develop/source/driver.cpp:40
#7 0x5565d7fe731a in main /__w/abacus-develop/abacus-develop/source/main.cpp:42
#8 0x7fbf24b48d8f (/lib/x86_64-linux-gnu/libc.so.6+0x29d8f)
#9 0x7fbf24b48e3f in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29e3f)
#10 0x5565d801e5a4 in _start (/usr/local/bin/abacus+0x29c5a4)
0x604000114740 is located 8 bytes to the right of 40-byte region [0x604000114710,0x604000114738)
allocated by thread T0 here:
#0 0x7fbf3fb97357 in operator new[](unsigned long) ../../../../src/libsanitizer/asan/asan_new_delete.cpp:102
#1 0x5565d82b0533 in UnitCell::UnitCell() /__w/abacus-develop/abacus-develop/source/module_cell/unitcell.cpp:64
#2 0x5565d800e405 in __static_initialization_and_destruction_0 /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:11
#3 0x5565d800e405 in _GLOBAL__sub_I__ZN7GlobalC6ppcellE /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:15
#4 0x7fbf24b48eba in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29eba)
SUMMARY: AddressSanitizer: heap-buffer-overflow /usr/include/c++/11/bits/basic_string.h:921 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const
Shadow bytes around the buggy address:
0x0c088001a890: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8a0: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8b0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8c0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8d0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
=>0x0c088001a8e0: fa fa 00 00 00 00 00 fa[fa]fa 00 00 00 00 00 fa
0x0c088001a8f0: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 fa
0x0c088001a900: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a910: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a920: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 06 fa
0x0c088001a930: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 00 02
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
Shadow gap: cc
==101435==ABORTING
Test case 601_NO_TDDFT_CO_occ
On process id asan.101552
=================================================================
==101552==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x604000114740 at pc 0x555f78191555 bp 0x7ffcef8b4540 sp 0x7ffcef8b4530
READ of size 8 at 0x604000114740 thread T0
#0 0x555f78191554 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const /usr/include/c++/11/bits/basic_string.h:921
#1 0x555f78191554 in std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char>, std::allocator<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) /usr/include/c++/11/bits/basic_string.h:6536
#2 0x555f78191554 in MD_func::dump_info(int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, UnitCell const&, Parameter const&, ModuleBase::matrix const&, ModuleBase::Vector3<double> const*, ModuleBase::Vector3<double> const*) /__w/abacus-develop/abacus-develop/source/module_md/md_func.cpp:385
#3 0x555f781afc9a in Run_MD::md_line(UnitCell&, ModuleESolver::ESolver*, Parameter const&) /__w/abacus-develop/abacus-develop/source/module_md/run_md.cpp:89
#4 0x555f787694a7 in Driver::driver_run() /__w/abacus-develop/abacus-develop/source/driver_run.cpp:63
#5 0x555f78762bbe in Driver::atomic_world() /__w/abacus-develop/abacus-develop/source/driver.cpp:186
#6 0x555f78767f36 in Driver::init() /__w/abacus-develop/abacus-develop/source/driver.cpp:40
#7 0x555f77d7831a in main /__w/abacus-develop/abacus-develop/source/main.cpp:42
#8 0x7f1b63800d8f (/lib/x86_64-linux-gnu/libc.so.6+0x29d8f)
#9 0x7f1b63800e3f in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29e3f)
#10 0x555f77daf5a4 in _start (/usr/local/bin/abacus+0x29c5a4)
0x604000114740 is located 8 bytes to the right of 40-byte region [0x604000114710,0x604000114738)
allocated by thread T0 here:
#0 0x7f1b7e84b357 in operator new[](unsigned long) ../../../../src/libsanitizer/asan/asan_new_delete.cpp:102
#1 0x555f78041533 in UnitCell::UnitCell() /__w/abacus-develop/abacus-develop/source/module_cell/unitcell.cpp:64
#2 0x555f77d9f405 in __static_initialization_and_destruction_0 /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:11
#3 0x555f77d9f405 in _GLOBAL__sub_I__ZN7GlobalC6ppcellE /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:15
#4 0x7f1b63800eba in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29eba)
SUMMARY: AddressSanitizer: heap-buffer-overflow /usr/include/c++/11/bits/basic_string.h:921 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const
Shadow bytes around the buggy address:
0x0c088001a890: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8a0: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8b0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8c0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8d0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
=>0x0c088001a8e0: fa fa 00 00 00 00 00 fa[fa]fa 00 00 00 00 00 fa
0x0c088001a8f0: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 fa
0x0c088001a900: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a910: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a920: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 06 fa
0x0c088001a930: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 00 02
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
Shadow gap: cc
==101552==ABORTING
Test case 601_NO_TDDFT_graphene_kpoint
On process id asan.101669
=================================================================
==101669==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x604000114740 at pc 0x557e16625555 bp 0x7ffdee1d9f20 sp 0x7ffdee1d9f10
READ of size 8 at 0x604000114740 thread T0
#0 0x557e16625554 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const /usr/include/c++/11/bits/basic_string.h:921
#1 0x557e16625554 in std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char>, std::allocator<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) /usr/include/c++/11/bits/basic_string.h:6536
#2 0x557e16625554 in MD_func::dump_info(int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, UnitCell const&, Parameter const&, ModuleBase::matrix const&, ModuleBase::Vector3<double> const*, ModuleBase::Vector3<double> const*) /__w/abacus-develop/abacus-develop/source/module_md/md_func.cpp:385
#3 0x557e16643c9a in Run_MD::md_line(UnitCell&, ModuleESolver::ESolver*, Parameter const&) /__w/abacus-develop/abacus-develop/source/module_md/run_md.cpp:89
#4 0x557e16bfd4a7 in Driver::driver_run() /__w/abacus-develop/abacus-develop/source/driver_run.cpp:63
#5 0x557e16bf6bbe in Driver::atomic_world() /__w/abacus-develop/abacus-develop/source/driver.cpp:186
#6 0x557e16bfbf36 in Driver::init() /__w/abacus-develop/abacus-develop/source/driver.cpp:40
#7 0x557e1620c31a in main /__w/abacus-develop/abacus-develop/source/main.cpp:42
#8 0x7f1e23338d8f (/lib/x86_64-linux-gnu/libc.so.6+0x29d8f)
#9 0x7f1e23338e3f in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29e3f)
#10 0x557e162435a4 in _start (/usr/local/bin/abacus+0x29c5a4)
0x604000114740 is located 8 bytes to the right of 40-byte region [0x604000114710,0x604000114738)
allocated by thread T0 here:
#0 0x7f1e3e385357 in operator new[](unsigned long) ../../../../src/libsanitizer/asan/asan_new_delete.cpp:102
#1 0x557e164d5533 in UnitCell::UnitCell() /__w/abacus-develop/abacus-develop/source/module_cell/unitcell.cpp:64
#2 0x557e16233405 in __static_initialization_and_destruction_0 /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:11
#3 0x557e16233405 in _GLOBAL__sub_I__ZN7GlobalC6ppcellE /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:15
#4 0x7f1e23338eba in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29eba)
SUMMARY: AddressSanitizer: heap-buffer-overflow /usr/include/c++/11/bits/basic_string.h:921 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const
Shadow bytes around the buggy address:
0x0c088001a890: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8a0: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8b0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8c0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8d0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
=>0x0c088001a8e0: fa fa 00 00 00 00 00 fa[fa]fa 00 00 00 00 00 fa
0x0c088001a8f0: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 fa
0x0c088001a900: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a910: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a920: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 06 fa
0x0c088001a930: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 00 02
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
Shadow gap: cc
==101669==ABORTING
Test case 601_NO_TDDFT_graphene_kpoint
On process id asan.101669
=================================================================
==101669==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x604000114740 at pc 0x557e16625555 bp 0x7ffdee1d9f20 sp 0x7ffdee1d9f10
READ of size 8 at 0x604000114740 thread T0
#0 0x557e16625554 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const /usr/include/c++/11/bits/basic_string.h:921
#1 0x557e16625554 in std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char>, std::allocator<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) /usr/include/c++/11/bits/basic_string.h:6536
#2 0x557e16625554 in MD_func::dump_info(int const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, UnitCell const&, Parameter const&, ModuleBase::matrix const&, ModuleBase::Vector3<double> const*, ModuleBase::Vector3<double> const*) /__w/abacus-develop/abacus-develop/source/module_md/md_func.cpp:385
#3 0x557e16643c9a in Run_MD::md_line(UnitCell&, ModuleESolver::ESolver*, Parameter const&) /__w/abacus-develop/abacus-develop/source/module_md/run_md.cpp:89
#4 0x557e16bfd4a7 in Driver::driver_run() /__w/abacus-develop/abacus-develop/source/driver_run.cpp:63
#5 0x557e16bf6bbe in Driver::atomic_world() /__w/abacus-develop/abacus-develop/source/driver.cpp:186
#6 0x557e16bfbf36 in Driver::init() /__w/abacus-develop/abacus-develop/source/driver.cpp:40
#7 0x557e1620c31a in main /__w/abacus-develop/abacus-develop/source/main.cpp:42
#8 0x7f1e23338d8f (/lib/x86_64-linux-gnu/libc.so.6+0x29d8f)
#9 0x7f1e23338e3f in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29e3f)
#10 0x557e162435a4 in _start (/usr/local/bin/abacus+0x29c5a4)
0x604000114740 is located 8 bytes to the right of 40-byte region [0x604000114710,0x604000114738)
allocated by thread T0 here:
#0 0x7f1e3e385357 in operator new[](unsigned long) ../../../../src/libsanitizer/asan/asan_new_delete.cpp:102
#1 0x557e164d5533 in UnitCell::UnitCell() /__w/abacus-develop/abacus-develop/source/module_cell/unitcell.cpp:64
#2 0x557e16233405 in __static_initialization_and_destruction_0 /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:11
#3 0x557e16233405 in _GLOBAL__sub_I__ZN7GlobalC6ppcellE /__w/abacus-develop/abacus-develop/source/module_hamilt_pw/hamilt_pwdft/global.cpp:15
#4 0x7f1e23338eba in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x29eba)
SUMMARY: AddressSanitizer: heap-buffer-overflow /usr/include/c++/11/bits/basic_string.h:921 in std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const
Shadow bytes around the buggy address:
0x0c088001a890: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8a0: fa fa 00 00 00 00 00 04 fa fa 00 00 00 00 00 04
0x0c088001a8b0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8c0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
0x0c088001a8d0: fa fa 00 00 00 00 00 00 fa fa 00 00 00 00 00 00
=>0x0c088001a8e0: fa fa 00 00 00 00 00 fa[fa]fa 00 00 00 00 00 fa
0x0c088001a8f0: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 fa
0x0c088001a900: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a910: fa fa 00 00 00 00 00 fa fa fa 00 00 00 00 00 00
0x0c088001a920: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 06 fa
0x0c088001a930: fa fa fd fd fd fd fd fa fa fa 00 00 00 00 00 02
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
Shadow gap: cc
==101669==ABORTING
Expected behavior
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To Reproduce
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Environment
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Additional Context
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BugsBugs that only solvable with sufficient knowledge of DFTBugs that only solvable with sufficient knowledge of DFTMemoryMemory issuesMemory issues