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donald
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Oct 8, 2017
There is some a global variable read_time which is updated by
all threads without proper synchronization.
WARNING: ThreadSanitizer: data race (pid=15896)
Read of size 4 at 0x00000066d53c by thread T7:
#0 t_PairAlign(void*) /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:118 (bsmap+0x00000042c4f2)
Previous write of size 4 at 0x00000066d53c by thread T6:
[failed to restore the stack]
Location is global 'read_time' of size 4 at 0x00000066d53c (bsmap+0x00000066d53c)
Thread T7 (tid=15960, running) created by main thread at:
#0 pthread_create /scratch/local/bee-root/gcc/gcc-5.3.0-0/source/libsanitizer/tsan/tsan_interceptors.cc:895 (libtsan.so.0+0x000000026c44)
#1 Do_PairAlign() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:128 (bsmap+0x00000042c613)
#2 RunProcess() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:499 (bsmap+0x0000004306b0)
#3 main /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:611 (bsmap+0x0000004320ae)
Thread T6 (tid=15959, finished) created by main thread at:
#0 pthread_create /scratch/local/bee-root/gcc/gcc-5.3.0-0/source/libsanitizer/tsan/tsan_interceptors.cc:895 (libtsan.so.0+0x000000026c44)
#1 Do_PairAlign() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:128 (bsmap+0x00000042c613)
#2 RunProcess() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:499 (bsmap+0x0000004306b0)
#3 main /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:611 (bsmap+0x0000004320ae)
SUMMARY: ThreadSanitizer: data race /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:118 t_PairAlign(void*)
==================
This is not a real issue, because the value is not currently
used. But because we are holding the mutex_fout mutex at this point
in code anyway, swap the order and work in the global first, then
release the mutex. This puts read_time under the protection of
mutex_fout.
donald
added a commit
that referenced
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Oct 9, 2017
This fixed size array, which overflows when more than 64 threads
are requested, is not used. Remove it.
Bug identified by address sanitizer:
#0 0x449813 in Do_PairAlign() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:129
#1 0x4527e4 in RunProcess() /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:498
#2 0x40613c in main /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:609
#3 0x7f0dff71803f in __libc_start_main ../csu/libc-start.c:308
#4 0x40a0c9 in _start (/scratch/cluster02/buczek/bsmap/bsmap.git/bsmap+0x40a0c9)
0x00000069b9e0 is located 32 bytes to the left of global variable 'read_time' defined in 'main.cpp:45:19' (0x69ba00) of size 4
0x00000069b9e0 is located 0 bytes to the right of global variable 'tid' defined in 'main.cpp:46:9' (0x69b960) of size 128
SUMMARY: AddressSanitizer: global-buffer-overflow /scratch/cluster/buczek/bsmap/bsmap.git/main.cpp:129 in Do_PairAlign()
Shadow bytes around the buggy address:
0x0000800cb6e0: 00 00 00 00 00 f9 f9 f9 f9 f9 f9 f9 00 00 00 00
0x0000800cb6f0: 00 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 00 00 00 00
0x0000800cb700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x0000800cb710: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x0000800cb720: 00 00 00 00 00 00 00 f9 f9 f9 f9 f9 00 00 00 00
=>0x0000800cb730: 00 00 00 00 00 00 00 00 00 00 00 00[f9]f9 f9 f9
0x0000800cb740: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
0x0000800cb750: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
0x0000800cb760: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
0x0000800cb770: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
0x0000800cb780: 04 f9 f9 f9 f9 f9 f9 f9 04 f9 f9 f9 f9 f9 f9 f9
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
==6441==ABORTING
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