From 9075ce8ad14f4c1dd45f44be63ab0b567194bf9b Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sat, 7 Oct 2017 15:54:26 +0200
Subject: [PATCH] main.cpp: Remove fixed size tid array

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
---
 main.cpp | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/main.cpp b/main.cpp
index aeba443..45486cf 100644
--- a/main.cpp
+++ b/main.cpp
@@ -43,7 +43,6 @@ bit32_t n_aligned_pairs=0, n_unique_pairs=0, n_multiple_pairs=0;  //number of pa
 bit32_t n_aligned_a=0, n_unique_a=0, n_multiple_a=0;  //number of a reads aligned
 bit32_t n_aligned_b=0, n_unique_b=0, n_multiple_b=0;  //number of b reads aligned
 bit32_t ref_time, read_time;
-bit16_t tid[64];
 char version[] = "2.90";
 ostringstream message;
 
@@ -56,7 +55,7 @@ void info(int level) {
 pthread_mutex_t mutex_fin=PTHREAD_MUTEX_INITIALIZER;
 pthread_mutex_t mutex_fout=PTHREAD_MUTEX_INITIALIZER;
 
-void *t_SingleAlign(void *tid) {
+void *t_SingleAlign(void *) {
 	SingleAlign a;
 	int n;
 	bit32_t cur_at;
@@ -85,13 +84,13 @@ void *t_SingleAlign(void *tid) {
 void Do_SingleAlign() {
 	vector<pthread_t> pthread_ids(param.num_procs);
 	for(int i=0; i<param.num_procs; i++) {
-		tid[i]=i; pthread_create(&pthread_ids[i], NULL, t_SingleAlign, (void*)&tid[i]);
+		pthread_create(&pthread_ids[i], NULL, t_SingleAlign,NULL);
 	}
 	for(int i=0; i<param.num_procs; i++) pthread_join(pthread_ids[i], NULL);
 };
 
 
-void *t_PairAlign(void *tid) {
+void *t_PairAlign(void *) {
 	PairAlign a;
 	int n1, n2;
 	bit32_t cur_at;
@@ -126,7 +125,7 @@ void Do_PairAlign() {
 	//create
 	//cout <<param.num_procs<<"num_procs\n";
 	for(int i=0; i<param.num_procs; i++) {
-		tid[i]=i; pthread_create(&pthread_ids[i], NULL, t_PairAlign, (void*)&tid[i]);
+		pthread_create(&pthread_ids[i], NULL, t_PairAlign,NULL);
 	}
 	for(int i=0; i<param.num_procs; i++) pthread_join(pthread_ids[i], NULL);
 };