Commits on Oct 8, 2017

1. main:cpp: Fix thread race …

   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 committed Oct 8, 2017
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