[gnuastro-devel] [bug #49347] Invalid writes and reads in Table

[Mohammad Akhlaghi]

URL:
  <http://savannah.gnu.org/bugs/?49347>

                 Summary: Invalid writes and reads in Table
                 Project: GNU Astronomy Utilities
            Submitted by: makhlaghi
            Submitted on: Sat 15 Oct 2016 09:59:05 AM JST
                Category: Table
                Severity: 4 - Important
              Item Group: Crash
                  Status: Confirmed
                 Privacy: Public
             Assigned to: None
             Open/Closed: Open
         Discussion Lock: Any

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Details:

After inspecting the output of the GNU Hydra
<http://hydra.gnu.org/build/1511760/nixlog/1> for Gnuastro 0.2, it was
interesting to see issues errors on 32-bit systems. 

The first thing that grabs most attention are the numerous warnings are for
using `%lu' for size_t values. So in This commit
<http://git.savannah.gnu.org/cgit/gnuastro.git/commit/?id=bcd59d5b>, `%lu' was
replaced with `%zu' (from C99 for dealing with `size_t' on both 32-bit and
64-bit systems).

After compilation and in `make check' the two `table/asciitobinary.sh' and
`table/binarytoascii.sh' have failed. Alan Lefor also kindly tested it on his
32-bit Raspberry Pi and was able to reproduce this failure. The second depends
on the first, so fixing the error in the first will probably fix the second
failure too.

So I tried valgrind on `table/asciitobinary.sh' and was surprized to see
multiple cases of invalid reads and writes (see below). These invalid reads
and writes are probably causing this failure on 32-bit systems and are somehow
not an issue on 64-bit systems. But we have to fix them any way.

I currently don't have time to look into them. But if anyone has the chance to
look into this it would be great.


==9389== Memcheck, a memory error detector
==9389== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==9389== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==9389== Command: ../bin/table/asttable
/path/to/gnuastro/tests/table/asciitobinary.txt --output=asciitobinary.fits
==9389== 
==9389== Invalid write of size 8
==9389==    at 0x409058: readinputcols (table.c:203)
==9389==    by 0x409CA6: table (table.c:431)
==9389==    by 0x405756: main (main.c:47)
==9389==  Address 0x89c7d70 is 0 bytes inside a block of size 2 alloc'd
==9389==    at 0x4C29BBE: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x408FC9: readinputcols (table.c:197)
==9389==    by 0x409CA6: table (table.c:431)
==9389==    by 0x405756: main (main.c:47)
==9389== 
==9389== Conditional jump or move depends on uninitialised value(s)
==9389==    at 0x499833: ffpcnd (putcold.c:657)
==9389==    by 0x4949E3: ffpcn (putcol.c:829)
==9389==    by 0x40946C: saveouttofits (table.c:283)
==9389==    by 0x409CC0: table (table.c:434)
==9389==    by 0x405756: main (main.c:47)
==9389== 
==9389== Invalid read of size 8
==9389==    at 0x49982C: ffpcnd (putcold.c:657)
==9389==    by 0x4949E3: ffpcn (putcol.c:829)
==9389==    by 0x40946C: saveouttofits (table.c:283)
==9389==    by 0x409CC0: table (table.c:434)
==9389==    by 0x405756: main (main.c:47)
==9389==  Address 0x89c7d78 is 6 bytes after a block of size 2 alloc'd
==9389==    at 0x4C29BBE: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x408FC9: readinputcols (table.c:197)
==9389==    by 0x409CA6: table (table.c:431)
==9389==    by 0x405756: main (main.c:47)
==9389== 
==9389== Invalid read of size 8
==9389==    at 0x4C305F0: memmove (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x49882B: ffr8fr8 (putcold.c:1007)
==9389==    by 0x498C61: ffpcld.part.0 (putcold.c:441)
==9389==    by 0x499933: ffpcnd (putcold.c:711)
==9389==    by 0x4949E3: ffpcn (putcol.c:829)
==9389==    by 0x40946C: saveouttofits (table.c:283)
==9389==    by 0x409CC0: table (table.c:434)
==9389==    by 0x405756: main (main.c:47)
==9389==  Address 0x89c7d78 is 6 bytes after a block of size 2 alloc'd
==9389==    at 0x4C29BBE: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x408FC9: readinputcols (table.c:197)
==9389==    by 0x409CA6: table (table.c:431)
==9389==    by 0x405756: main (main.c:47)
==9389== 
==9389== Syscall param write(buf) points to uninitialised byte(s)
==9389==    at 0x638E530: __write_nocancel (in /usr/lib/libc-2.24.so)
==9389==    by 0x6325866: _IO_file_write@@GLIBC_2.2.5 (in
/usr/lib/libc-2.24.so)
==9389==    by 0x6324BB1: new_do_write (in /usr/lib/libc-2.24.so)
==9389==    by 0x6326938: _IO_do_write@@GLIBC_2.2.5 (in
/usr/lib/libc-2.24.so)
==9389==    by 0x6325F05: _IO_file_xsputn@@GLIBC_2.2.5 (in
/usr/lib/libc-2.24.so)
==9389==    by 0x631B0FA: fwrite (in /usr/lib/libc-2.24.so)
==9389==    by 0x426E74: file_write (drvrfile.c:669)
==9389==    by 0x4220C3: ffwrite (cfileio.c:7083)
==9389==    by 0x4E2BA4: ffbfwt (buffers.c:676)
==9389==    by 0x4E3EA9: ffflsh (buffers.c:608)
==9389==    by 0x42161F: ffclos (cfileio.c:6923)
==9389==    by 0x4094B3: saveouttofits (table.c:288)
==9389==  Address 0x8ef3310 is 1,664 bytes inside a block of size 4,096
alloc'd
==9389==    at 0x4C29BBE: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x6319AB1: _IO_file_doallocate (in /usr/lib/libc-2.24.so)
==9389==    by 0x6327AD5: _IO_doallocbuf (in /usr/lib/libc-2.24.so)
==9389==    by 0x6326E37: _IO_file_overflow@@GLIBC_2.2.5 (in
/usr/lib/libc-2.24.so)
==9389==    by 0x6325F05: _IO_file_xsputn@@GLIBC_2.2.5 (in
/usr/lib/libc-2.24.so)
==9389==    by 0x631B0FA: fwrite (in /usr/lib/libc-2.24.so)
==9389==    by 0x426E74: file_write (drvrfile.c:669)
==9389==    by 0x4220C3: ffwrite (cfileio.c:7083)
==9389==    by 0x4E2BA4: ffbfwt (buffers.c:676)
==9389==    by 0x4E3EA9: ffflsh (buffers.c:608)
==9389==    by 0x42161F: ffclos (cfileio.c:6923)
==9389==    by 0x4094B3: saveouttofits (table.c:288)
==9389== 
==9389== 
==9389== HEAP SUMMARY:
==9389==     in use at exit: 98,840 bytes in 3,272 blocks
==9389==   total heap usage: 38,220 allocs, 34,948 frees, 2,759,099 bytes
allocated
==9389== 
==9389== 48 bytes in 1 blocks are definitely lost in loss record 590 of 658
==9389==    at 0x4C29BBE: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9389==    by 0x41A6F7: gal_txtarray_txt_to_array (txtarray.c:264)
==9389==    by 0x407C40: sanitycheck (ui.c:687)
==9389==    by 0x408789: setparams (ui.c:970)
==9389==    by 0x405747: main (main.c:44)
==9389== 
==9389== LEAK SUMMARY:
==9389==    definitely lost: 48 bytes in 1 blocks
==9389==    indirectly lost: 0 bytes in 0 blocks
==9389==      possibly lost: 0 bytes in 0 blocks
==9389==    still reachable: 98,792 bytes in 3,271 blocks
==9389==         suppressed: 0 bytes in 0 blocks
==9389== Reachable blocks (those to which a pointer was found) are not shown.
==9389== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==9389== 
==9389== For counts of detected and suppressed errors, rerun with: -v
==9389== Use --track-origins=yes to see where uninitialised values come from
==9389== ERROR SUMMARY: 17 errors from 6 contexts (suppressed: 0 from 0)
PASS table/asciitobinary.sh (exit status: 0)





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