-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathvalgrind-out.txt
152 lines (152 loc) · 10.8 KB
/
valgrind-out.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
==14588== Memcheck, a memory error detector
==14588== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==14588== Using Valgrind-3.15.0-608cb11914-20190413 and LibVEX; rerun with -h for copyright info
==14588== Command: ./p2s ../converter_prep/1_pod5/output.pod5 sss.blow5
==14588== Parent PID: 357
==14588==
--14588--
--14588-- Valgrind options:
--14588-- --leak-check=full
--14588-- --show-leak-kinds=all
--14588-- --track-origins=yes
--14588-- --verbose
--14588-- --log-file=valgrind-out.txt
--14588-- Contents of /proc/version:
--14588-- Linux version 5.10.16.3-microsoft-standard-WSL2 (oe-user@oe-host) (x86_64-msft-linux-gcc (GCC) 9.3.0, GNU ld (GNU Binutils) 2.34.0.20200220) #1 SMP Fri Apr 2 22:23:49 UTC 2021
--14588--
--14588-- Arch and hwcaps: AMD64, LittleEndian, amd64-cx16-lzcnt-rdtscp-sse3-ssse3-avx-avx2-bmi-f16c-rdrand
--14588-- Page sizes: currently 4096, max supported 4096
--14588-- Valgrind library directory: /usr/lib/x86_64-linux-gnu/valgrind
--14588-- Reading syms from /home/sophia-bhs/slow5_pod5_converter/p2s
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/ld-2.31.so
--14588-- Considering /usr/lib/x86_64-linux-gnu/ld-2.31.so ..
--14588-- .. CRC mismatch (computed 975d0390 wanted 30bd717f)
--14588-- Considering /lib/x86_64-linux-gnu/ld-2.31.so ..
--14588-- .. CRC mismatch (computed 975d0390 wanted 30bd717f)
--14588-- Considering /usr/lib/debug/lib/x86_64-linux-gnu/ld-2.31.so ..
--14588-- .. CRC is valid
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux
--14588-- object doesn't have a symbol table
--14588-- object doesn't have a dynamic symbol table
--14588-- Scheduler: using generic scheduler lock implementation.
--14588-- Reading suppressions file: /usr/lib/x86_64-linux-gnu/valgrind/default.supp
==14588== embedded gdbserver: reading from /tmp/vgdb-pipe-from-vgdb-to-14588-by-sophia-bhs-on-???
==14588== embedded gdbserver: writing to /tmp/vgdb-pipe-to-vgdb-from-14588-by-sophia-bhs-on-???
==14588== embedded gdbserver: shared mem /tmp/vgdb-pipe-shared-mem-vgdb-14588-by-sophia-bhs-on-???
==14588==
==14588== TO CONTROL THIS PROCESS USING vgdb (which you probably
==14588== don't want to do, unless you know exactly what you're doing,
==14588== or are doing some strange experiment):
==14588== /usr/lib/x86_64-linux-gnu/valgrind/../../bin/vgdb --pid=14588 ...command...
==14588==
==14588== TO DEBUG THIS PROCESS USING GDB: start GDB like this
==14588== /path/to/gdb ./p2s
==14588== and then give GDB the following command
==14588== target remote | /usr/lib/x86_64-linux-gnu/valgrind/../../bin/vgdb --pid=14588
==14588== --pid is optional if only one valgrind process is running
==14588==
--14588-- REDIR: 0x4022e10 (ld-linux-x86-64.so.2:strlen) redirected to 0x580c9ce2 (???)
--14588-- REDIR: 0x4022be0 (ld-linux-x86-64.so.2:index) redirected to 0x580c9cfc (???)
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so
--14588-- object doesn't have a symbol table
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so
--14588-- object doesn't have a symbol table
==14588== WARNING: new redirection conflicts with existing -- ignoring it
--14588-- old: 0x04022e10 (strlen ) R-> (0000.0) 0x580c9ce2 ???
--14588-- new: 0x04022e10 (strlen ) R-> (2007.0) 0x0483f060 strlen
--14588-- REDIR: 0x401f5f0 (ld-linux-x86-64.so.2:strcmp) redirected to 0x483ffd0 (strcmp)
--14588-- REDIR: 0x4023370 (ld-linux-x86-64.so.2:mempcpy) redirected to 0x4843a20 (mempcpy)
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
--14588-- object doesn't have a symbol table
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
--14588-- Considering /usr/lib/debug/.build-id/e5/4761f7b554d0fcc1562959665d93dffbebdaf0.debug ..
--14588-- .. build-id is valid
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libjemalloc.so.2
--14588-- object doesn't have a symbol table
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
--14588-- object doesn't have a symbol table
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libm-2.31.so
--14588-- Considering /usr/lib/x86_64-linux-gnu/libm-2.31.so ..
--14588-- .. CRC mismatch (computed fcb42c76 wanted f6c95789)
--14588-- Considering /lib/x86_64-linux-gnu/libm-2.31.so ..
--14588-- .. CRC mismatch (computed fcb42c76 wanted f6c95789)
--14588-- Considering /usr/lib/debug/lib/x86_64-linux-gnu/libm-2.31.so ..
--14588-- .. CRC is valid
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
--14588-- object doesn't have a symbol table
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libc-2.31.so
--14588-- Considering /usr/lib/x86_64-linux-gnu/libc-2.31.so ..
--14588-- .. CRC mismatch (computed 86b78530 wanted e380f01c)
--14588-- Considering /lib/x86_64-linux-gnu/libc-2.31.so ..
--14588-- .. CRC mismatch (computed 86b78530 wanted e380f01c)
--14588-- Considering /usr/lib/debug/lib/x86_64-linux-gnu/libc-2.31.so ..
--14588-- .. CRC is valid
--14588-- Reading syms from /usr/lib/x86_64-linux-gnu/libdl-2.31.so
--14588-- Considering /usr/lib/x86_64-linux-gnu/libdl-2.31.so ..
--14588-- .. CRC mismatch (computed b5d487d3 wanted 6ef97e7c)
--14588-- Considering /lib/x86_64-linux-gnu/libdl-2.31.so ..
--14588-- .. CRC mismatch (computed b5d487d3 wanted 6ef97e7c)
--14588-- Considering /usr/lib/debug/lib/x86_64-linux-gnu/libdl-2.31.so ..
--14588-- .. CRC is valid
--14588-- REDIR: 0x4f60600 (libc.so.6:memmove) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f900 (libc.so.6:strncpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60930 (libc.so.6:strcasecmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f220 (libc.so.6:strcat) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f960 (libc.so.6:rindex) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f61dd0 (libc.so.6:rawmemchr) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7ce60 (libc.so.6:wmemchr) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7c9a0 (libc.so.6:wcscmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60760 (libc.so.6:mempcpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60590 (libc.so.6:bcmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f890 (libc.so.6:strncmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f2d0 (libc.so.6:strcmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f606c0 (libc.so.6:memset) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7c960 (libc.so.6:wcschr) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f7f0 (libc.so.6:strnlen) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f3b0 (libc.so.6:strcspn) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60980 (libc.so.6:strncasecmp) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f350 (libc.so.6:strcpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60ad0 (libc.so.6:memcpy@@GLIBC_2.14) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7e0d0 (libc.so.6:wcsnlen) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7c9e0 (libc.so.6:wcscpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f9a0 (libc.so.6:strpbrk) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f280 (libc.so.6:index) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5f7b0 (libc.so.6:strlen) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f68d20 (libc.so.6:memrchr) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f609d0 (libc.so.6:strcasecmp_l) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60550 (libc.so.6:memchr) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f7cab0 (libc.so.6:wcslen) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f5fc60 (libc.so.6:strspn) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f608d0 (libc.so.6:stpncpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60870 (libc.so.6:stpcpy) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f61e10 (libc.so.6:strchrnul) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x4f60a20 (libc.so.6:strncasecmp_l) redirected to 0x48311d0 (_vgnU_ifunc_wrapper)
--14588-- REDIR: 0x5048490 (libc.so.6:__strrchr_avx2) redirected to 0x483ea10 (rindex)
--14588-- REDIR: 0x48a8910 (libjemalloc.so.2:malloc) redirected to 0x483b780 (malloc)
--14588-- REDIR: 0x5048660 (libc.so.6:__strlen_avx2) redirected to 0x483ef40 (strlen)
--14588-- REDIR: 0x5043fa0 (libc.so.6:__strncmp_avx2) redirected to 0x483f670 (strncmp)
--14588-- REDIR: 0x504baf0 (libc.so.6:__memset_avx2_unaligned_erms) redirected to 0x48428e0 (memset)
--14588-- REDIR: 0x504b670 (libc.so.6:__memcpy_avx_unaligned_erms) redirected to 0x48429f0 (memmove)
--14588-- REDIR: 0x5044c50 (libc.so.6:__memcmp_avx2_movbe) redirected to 0x48421e0 (bcmp)
--14588-- REDIR: 0x5043b60 (libc.so.6:__strcmp_avx2) redirected to 0x483fed0 (strcmp)
--14588-- REDIR: 0x4932c10 (libjemalloc.so.2:operator new(unsigned long)) redirected to 0x483bdf0 (operator new(unsigned long))
--14588-- REDIR: 0x4932c90 (libjemalloc.so.2:operator delete(void*)) redirected to 0x483cf50 (operator delete(void*))
--14588-- REDIR: 0x4932cd0 (libjemalloc.so.2:operator delete(void*, unsigned long)) redirected to 0x483d160 (operator delete(void*, unsigned long))
--14588-- REDIR: 0x48aa430 (libjemalloc.so.2:calloc) redirected to 0x483dce0 (calloc)
--14588-- REDIR: 0x50444c0 (libc.so.6:__memchr_avx2) redirected to 0x4840050 (memchr)
==14588== Warning: set address range perms: large range [0x5e00000, 0x16fca000) (defined)
--14588-- REDIR: 0x48adb10 (libjemalloc.so.2:free) redirected to 0x483c9d0 (free)
--14588-- REDIR: 0x50482a0 (libc.so.6:__strchrnul_avx2) redirected to 0x4843540 (strchrnul)
--14588-- REDIR: 0x4f60120 (libc.so.6:__GI_strstr) redirected to 0x4843ca0 (__strstr_sse2)
--14588-- REDIR: 0x48a18d0 (libjemalloc.so.2:realloc) redirected to 0x483df30 (realloc)
--14588-- REDIR: 0x504b650 (libc.so.6:__mempcpy_avx_unaligned_erms) redirected to 0x4843660 (mempcpy)
--14588-- REDIR: 0x50437b0 (libc.so.6:__strcspn_sse42) redirected to 0x4843e10 (strcspn)
==14588== Warning: set address range perms: large range [0x5e00000, 0x16fca000) (noaccess)
==14588==
==14588== HEAP SUMMARY:
==14588== in use at exit: 0 bytes in 0 blocks
==14588== total heap usage: 1,144,607 allocs, 1,144,607 frees, 11,821,862,079 bytes allocated
==14588==
==14588== All heap blocks were freed -- no leaks are possible
==14588==
==14588== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)