#565 closed defect (fixed)
r.colors: glibc double free or corruption with -ae
| Reported by: | hamish | Owned by: | |
|---|---|---|---|
| Priority: | minor | Milestone: | 6.5.0 |
| Component: | Raster | Version: | svn-develbranch6 |
| Keywords: | r.colors | Cc: | |
| CPU: | x86-32 | Platform: | Linux |
Description
Hi,
I'm unable to recreate it right now, but yesterday I was consistently getting a rather ugly *** glibc ... error which said something about an invalid double free().
looked rather worse than a standard segfault and not something I've seen much of before. this is on the 20 month old version of Debian/stable and I haven't changed anything so expect glibc versions is as stable & well tested as it ever could be.
the command line looked like
r.colors map1 color=bcyr -ae
the input map is gone now and I've changed r.surf.volcano enough that I don't get it anymore, but it can be assumed that there were 0.0s in the map. (-g blocks 0s but -a doesn't?)
Hamish
Change History (9)
follow-up: 4 comment:1 by , 16 years ago
| Summary: | r.colors: glibc double free error with -ae → r.colors: glibc double free or corruption with -ae |
|---|
comment:2 by , 16 years ago
..., even with maps created with the same params which do run to 100% on the standard command line will barf in valgrind at the same 72% complete stage.
Same if I do 'g.region -d' first, so that's probably a red herring (I mentioned it because the volcano alg calcs distance from the map center so you can get an div0 anomaly there if the cells line up).
I can simplify the map creation line to:
r.surf.volcano -r map3
and it still breaks with valgrind. If I remove the -r rough-it-up flag (which sends the surface slightly negative) the min becomes 1.2345e-91 and valgrind runs to completion. it still complains about the same "Invalid read of size 4" and "Invalid write of size 4" errors though.
Hamish
comment:3 by , 16 years ago
G65> CMD="r.colors map3 color=bcyr -ae" G65> LD_PRELOAD=libefence.so.0.0 $CMD --v Electric Fence 2.1 Copyright (C) 1987-1998 Bruce Perens. Reading raster map <map3@user7>... Segmentation fault
it makes electric-fence segfault. that's not encouraging at all.
Hamish
comment:4 by , 16 years ago
Replying to hamish:
here we go, happened again..
G> r.univar -g map1 ... min=-23.8941449919674 max=1999.8932486971 ...
...
#7 0x0804b386 in get_fp_stats (name=0x9b72640 "map1", mapset=0x9b72030 "user7",
statf=0xbfd05f94, min=3.2146326349358647, max=7.601348984183665, geometric=0,
geom_abs=1) at stats.c:136
If any of the raster values lie outside of the range specified by the min/max parameters, memory corruption will occur due to modifying an out-of-range array element.
FWIW, I have noticed a bug in get_fp_stats(...,geom_abs=1): if the range is signed, values which are closer to zero than both min and max will also modify an out-of-range array element.
I'll fix that one shortly, but it won't help if the min/max parameters are bogus.
comment:5 by , 16 years ago
| Resolution: | → fixed |
|---|---|
| Status: | new → closed |
G> r.univar -g map1 ... min=-23.8941449919674 max=1999.8932486971 ...
...
#7 0x0804b386 in get_fp_stats (name=0x9b72640 "map1", mapset=0x9b72030 "user7",
statf=0xbfd05f94, min=3.2146326349358647, max=7.601348984183665, geometric=0,
geom_abs=1) at stats.c:136
Glynn:
If any of the raster values lie outside of the range specified by the min/max parameters, memory corruption will occur due to modifying an out-of-range array element.
FWIW, I have noticed a bug in get_fp_stats(...,geom_abs=1): if the range is signed, values which are closer to zero than both min and max will also modify an out-of-range array element.
I'll fix that one shortly, but it won't help if the min/max parameters are bogus.
thanks, that solved the problem. backported to 6.4.0 and devbr6.
are the min/max values really bogus? r.univar and 'r.info -r' both give (-23,1999) for those values. The 'max' value seen in gdb frame # 7 (ie 7.60) is simply the natural log of the max value in the map (1999). The min value in frame # 7 (3.2146) is a bit weirder. AFAICT it comes from ln(abs(min)+1). But hopefully that weirdness was just product of this bug.
closing ticket, "thanks heaps"
Hamish
follow-up: 8 comment:6 by , 16 years ago
fwiw, valgrind still reports an error, but now it is slightly different:
... --3098-- REDIR: 0x4141680 (memset) redirected to 0x401E4F0 (memset) ==3098== Invalid read of size 4 ==3098== at 0x804B344: get_fp_stats (stats.c:132) ==3098== by 0x804A654: main (main.c:385) ==3098== Address 0x4224FA8 is 0 bytes after a block of size 4,000 alloc'd ==3098== at 0x401C6CA: calloc (vg_replace_malloc.c:279) ==3098== by 0x402EC00: G__calloc (alloc.c:74) ==3098== by 0x804B1DA: get_fp_stats (stats.c:104) ==3098== by 0x804A654: main (main.c:385) ==3098== ==3098== Invalid write of size 4 ==3098== at 0x804B349: get_fp_stats (stats.c:132) ==3098== by 0x804A654: main (main.c:385) ==3098== Address 0x4224FA8 is 0 bytes after a block of size 4,000 alloc'd ==3098== at 0x401C6CA: calloc (vg_replace_malloc.c:279) ==3098== by 0x402EC00: G__calloc (alloc.c:74) ==3098== by 0x804B1DA: get_fp_stats (stats.c:104) ==3098== by 0x804A654: main (main.c:385) 100% Color table for raster map <map1> set to 'bcyr' ==3098== ==3098== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 21 from 1) ==3098== ==3098== 1 errors in context 1 of 2: ==3098== Invalid write of size 4 ==3098== at 0x804B349: get_fp_stats (stats.c:132) ==3098== by 0x804A654: main (main.c:385) ==3098== Address 0x4224FA8 is 0 bytes after a block of size 4,000 alloc'd ==3098== at 0x401C6CA: calloc (vg_replace_malloc.c:279) ==3098== by 0x402EC00: G__calloc (alloc.c:74) ==3098== by 0x804B1DA: get_fp_stats (stats.c:104) ==3098== by 0x804A654: main (main.c:385) ==3098== ==3098== 1 errors in context 2 of 2: ==3098== Invalid read of size 4 ==3098== at 0x804B344: get_fp_stats (stats.c:132) ==3098== by 0x804A654: main (main.c:385) ==3098== Address 0x4224FA8 is 0 bytes after a block of size 4,000 alloc'd ==3098== at 0x401C6CA: calloc (vg_replace_malloc.c:279) ==3098== by 0x402EC00: G__calloc (alloc.c:74) ==3098== by 0x804B1DA: get_fp_stats (stats.c:104) ==3098== by 0x804A654: main (main.c:385) --3098-- --3098-- supp: 21 Debian libc6 (2.3.x) stripped dynamic linker ==3098== ==3098== IN SUMMARY: 2 errors from 2 contexts (suppressed: 21 from 1) ==3098== ==3098== malloc/free: in use at exit: 84,827 bytes in 1,460 blocks. ==3098== malloc/free: 3,367 allocs, 1,907 frees, 7,063,699 bytes allocated. ==3098== ==3098== searching for pointers to 1,460 not-freed blocks. ==3098== checked 164,128 bytes. ==3098== ...
ie before it read
Address 0x4223EDC is 12 bytes before a block of size 4,000 alloc'd
now it reads ... is 0 bytes after a block of size 4,000 alloc'd.
? Hamish
comment:7 by , 16 years ago
..., and running with different combinations of -ae, -a, -e shows that the remaining valgrind error is only seen when using -e. If just -a alone then it's error free.
Hamish
comment:8 by , 16 years ago
Replying to hamish:
fwiw, valgrind still reports an error, but now it is slightly different:
ie before it read
Address 0x4223EDC is 12 bytes before a block of size 4,000 alloc'd
now it reads
... is 0 bytes after a block of size 4,000 alloc'd
?
Fencepost error. If x == statf->max, then i == statf->count, which overruns. The array needs to have statf->count+1 elements. Fixed in r36862.
are the min/max values really bogus? r.univar and 'r.info -r' both give (-23,1999) for those values. The 'max' value seen in gdb frame # 7 (ie 7.60) is simply the natural log of the max value in the map (1999).
Right; get_fp_stats() overwrites min/max with the log/log-abs values, and gdb is showing the updated values.
So, yes, the bug was due to failing to account for the fact that log-abs needs to include zero in the range calculation as well as min and max.
comment:9 by , 16 years ago
thanks, it now passes valgrind and electric-fence tests without errors. fix backported.
Hamish
here we go, happened again..
G> gdb `which r.colors` (gdb) run gauss color=bcyr -ae Starting program: [...]/dist.i686-pc-linux-gnu/bin/r.colors map1 color=bcyr -ae 100% *** glibc detected *** double free or corruption (!prev): 0x08e40a18 *** Program received signal SIGABRT, Aborted. 0xb7f18424 in __kernel_vsyscall () (gdb) bt #0 0xb7ef0424 in __kernel_vsyscall () #1 0xb7d31811 in raise () from /lib/tls/i686/cmov/libc.so.6 #2 0xb7d32fb9 in abort () from /lib/tls/i686/cmov/libc.so.6 #3 0xb7d66dfa in __fsetlocking () from /lib/tls/i686/cmov/libc.so.6 #4 0xb7d6e68f in mallopt () from /lib/tls/i686/cmov/libc.so.6 #5 0xb7d6e732 in free () from /lib/tls/i686/cmov/libc.so.6 #6 0xb7ea2cd6 in G_free (buf=0x9b7ba18) at alloc.c:129 #7 0x0804b386 in get_fp_stats (name=0x9b72640 "map1", mapset=0x9b72030 "user7", statf=0xbfd05f94, min=3.2146326349358647, max=7.601348984183665, geometric=0, geom_abs=1) at stats.c:136 #8 0x0804a655 in main (argc=Cannot access memory at address 0x13d8 ) at main.c:385 (gdb) frame 7 #7 0x0804b386 in get_fp_stats (name=0x9b72640 "map1", mapset=0x9b72030 "user7", statf=0xbfd05f94, min=3.2146326349358647, max=7.601348984183665, geometric=0, geom_abs=1) at stats.c:136 136 G_free(dcell); (gdb) list 131 } 132 } 133 134 G_percent(row, nrows, 2); 135 G_close_cell(fd); 136 G_free(dcell); 137 } (gdb) bt full ... #6 0xb7ea2cd6 in G_free (buf=0x9b7ba18) at alloc.c:129 No locals. #7 0x0804b386 in get_fp_stats (name=0x9b72640 "map1", mapset=0x9b72030 "user7", statf=0xbfd05f94, min=3.2146326349358647, max=7.601348984183665, geometric=0, geom_abs=1) at stats.c:136 dcell = (DCELL *) 0x9b7ba18 row = 477 col = 633 nrows = 477 ncols = 633 fd = 7 #8 0x0804a655 in main (argc=Cannot access memory at address 0x13d8 ) at main.c:385 fpstats = {geometric = 0, geom_abs = 1, flip = 0, count = 1000, min = 3.2146326349358647, max = 7.601348984183665, stats = 0x9b7cdf0, total = 301941} overwrite = 1 interactive = 0 ...this map was created with:
but that uses r.surf.gauss which changes each time you run it. The same r.colors command runs to 100% with no problem with the exact same call to r.surf.volcano.
r.mapcalc found no values exactly matching 0.00000 in the map.
It consistently breaks with this map, I can .tgz it if needed.
Here's the valgrind output:
Hamish