[Debian-med-packaging] Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

[Andreas Tille]

On Thu, Apr 30, 2020 at 07:17:50AM -0700, Matthew Fernandez wrote:
> 
> Valgrind, in its default mode, checks for a variety of memory issues (use-after-free, write out-of bounds, …). You don’t need any special configure/build options, but you probably want to enable debug symbols (`export CFLAGS=-g; export CXXFLAGS=-g`). Then you can prefix the test you’re running with Valgrind: `valgrind ./src/clustalo -i debian/tests/biopython_testdata/f002 …`.


Running on mipsel:

(sid_mipsel-dchroot)tille at eller:~/clustalo$ valgrind src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
==15149== Memcheck, a memory error detector
==15149== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==15149== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==15149== Command: src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
==15149== 
==15149== Conditional jump or move depends on uninitialised value(s)
==15149==    at 0x4007828: cached_fpabi_reject_phdr_p (dl-machine-reject-phdr.h:57)
==15149==    by 0x4007828: elf_machine_reject_phdr_p (dl-machine-reject-phdr.h:217)
==15149==    by 0x4008080: open_verify.constprop.0 (dl-load.c:1688)
==15149==    by 0x4009D7C: _dl_map_object (dl-load.c:2181)
==15149==    by 0x40011F8: map_doit (rtld.c:607)
==15149==    by 0x401B2A8: _dl_catch_exception (dl-error-skeleton.c:196)
==15149==    by 0x401B334: _dl_catch_error (dl-error-skeleton.c:215)
==15149==    by 0x4001138: do_preload (rtld.c:778)
==15149==    by 0x4002560: handle_preload_list (rtld.c:879)
==15149==    by 0x4005B08: dl_main (rtld.c:1684)
==15149==    by 0x401A094: _dl_sysdep_start (dl-sysdep.c:253)
==15149==    by 0x400199C: _dl_start_final (rtld.c:447)
==15149==    by 0x4001D44: _dl_start (rtld.c:539)
==15149== 
==15149== Invalid read of size 1
==15149==    at 0x486F558: ??? (in /usr/lib/mipsel-linux-gnu/libargtable2.so.0.1.8)
==15149==    by 0x486F5F0: ??? (in /usr/lib/mipsel-linux-gnu/libargtable2.so.0.1.8)
==15149==  Address 0x4d655c5 is 0 bytes after a block of size 37 alloc'd
==15149==    at 0x484B89C: malloc (in /usr/lib/mipsel-linux-gnu/valgrind/vgpreload_memcheck-mips32-linux.so)
==15149==    by 0x126674: CkMalloc (util.c:83)
==15149==    by 0x126864: CkStrdup (util.c:213)
==15149==    by 0x1108F4: ConvertOldCmdline(int*, char***, int, char**) (main.cpp:358)
==15149==    by 0x10FCDC: main (main.cpp:467)
==15149== 
==15149== Invalid read of size 4
==15149==    at 0x1221B8: PairDistances (pair_dist.c:346)
==15149==    by 0x114774: AlignmentOrder (clustal-omega.c:835)
==15149==    by 0x115024: Align (clustal-omega.c:1221)
==15149==    by 0x112EB4: MyMain (mymain.c:1192)
==15149==    by 0x10FCF0: main (main.cpp:469)
==15149==  Address 0xffff83b0 is not stack'd, malloc'd or (recently) free'd
==15149== 
==15149== 
==15149== Process terminating with default action of signal 10 (SIGBUS)
==15149==    at 0x1221B8: PairDistances (pair_dist.c:346)
==15149==    by 0x114774: AlignmentOrder (clustal-omega.c:835)
==15149==    by 0x115024: Align (clustal-omega.c:1221)
==15149==    by 0x112EB4: MyMain (mymain.c:1192)
==15149==    by 0x10FCF0: main (main.cpp:469)
==15149== 
==15149== HEAP SUMMARY:
==15149==     in use at exit: 8,039 bytes in 34 blocks
==15149==   total heap usage: 112 allocs, 78 frees, 77,811 bytes allocated
==15149== 
==15149== LEAK SUMMARY:
==15149==    definitely lost: 128 bytes in 2 blocks
==15149==    indirectly lost: 0 bytes in 0 blocks
==15149==      possibly lost: 0 bytes in 0 blocks
==15149==    still reachable: 7,911 bytes in 32 blocks
==15149==         suppressed: 0 bytes in 0 blocks
==15149== Rerun with --leak-check=full to see details of leaked memory
==15149== 
==15149== Use --track-origins=yes to see where uninitialised values come from
==15149== For lists of detected and suppressed errors, rerun with: -s
==15149== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 0 from 0)
Bus error


Is this different from your tests on amd64?

 
> > On the other hand:  Is valgrind possibly able to uncover issues also
> > on any other architecture?
> 
> You mean if we were to use Valgrind to debug this on e.g. x86? In my own experiments on amd64, both ASan and Valgrind found multiple issues in both Clustal Omega and its dependency, argtable2. However I don’t believe any of the remaining ones I was seeing after the last patches I sent you could be causing the mipsel bus error; they were all memory leaks.

Thanks again for your great support and the time you've spent.

Kind regards

     Andreas.

-- 
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