ports/devel/protobuf: Segmentation fault in mmap in some applications

[O. Hartmann]

On 01/07/10 01:41, Pieter de Goeje wrote:
> On Wednesday 06 January 2010 14:14:28 O. Hartmann wrote:
>> Dear Sirs,
>> We use a software package for scientific imagery processing from USGS,
>> ISIS3 (http://isis.astrogeology.usgs.gov/). The most recent version is
>> 3.1.21 and since this version, the software intensively uses
>> libprotobuf.so.
>>
>> While we can use ISIS 3.1.20 very well under FreeBSD 8.0/amd64, it is
>> impossible to use the software with version no. 3.1.21, which seems to
>> have some issues wih libprotobuf.so. Every client out of this ISIS3
>> package crashes with a segmentation fault and as far as I can judge the
>> situation, there is a problem with libprotobuf.so, against which all
>> clients out of ISIS 3.1.21 are linked.
>
> Perhaps the ISIS package was developed using a different (older?) version of
> Google's protocol buffers. Compiling protobuf from source is quite easy on
> FreeBSD. You can find the source here:
> http://code.google.com/p/protobuf/downloads/list
> I would start by trying version 2.1.0 and 2.2.0a.
>
>>
>> I searched for help on the ISIS3-support forum and realised that some
>> Apple OS X guys have had similar problems, but those threads where
>> closed immediately or got relative senseless response.
>>
>> In our case, we compile every necessary library and prerequisite
>> software package (mostly Qt4 libs) from ports. This works great with
>> some tweaks for FreeBSD in make/config.freebsd (which I derived from
>> some linux and/or OS X config files).
>>
>> Now I'm floating like a dead man i the water. Below I provide q gdb
>> output of the qview-client (the same is with all other clients, like
>> photrim etc. for those familiar with the software package).
>
> A backtrace ('bt' at the gdb prompt) might contain more useful information.
>
>>
>> Additionaly, I provide a truss-output, that stops at mmap issues.
>>
>> Well, if someone could provide me with some advance debugging hints I
>> would appreaciate them. I'm pretty sure he problem is located within the
>> libprotobuf library or the way it is treated, but this is a guess of a
>> non-developer.
>>
>> Thanks very much in advance.
>> Please reply also to this email address, since I'm not subscriber of the
>> list I post to.
>>
>> Oliver
>
> - Pieter


Hello Pieter,

ISIS3 utilises the very same revision of libprotobuf as FreeBSD has in 
the ports repositorium (libprotobuf.so.4.0.0, aka protobuf-2.2.0). The 
backtrace follows, it is a little bit lengthy ...


(gdb) bt
#0  0x0000000805a2f2c8 in std::_Rb_tree<std::string, 
std::pair<std::string const, std::pair<void const*, int> >, 
std::_Select1st<std::pair<std:: tring const, std::pair<void const*, int> 
 > >, std::less<std::string>, std::allocator<std::pair<std::string 
const, std::pair<void const*, int> >   >::_M_insert_unique () from 
/usr/local/lib/libprotobuf.so.4
#1  0x0000000805a326c6 in 
google::protobuf::InsertIfNotPresent<std::map<std::string, 
std::pair<void const*, int>, std::less<std::string>, std::a 
locator<std::pair<std::string const, std::pair<void const*, int> > > >, 
std::string, std::pair<void const*, int> > ()
    from /usr/local/lib/libprotobuf.so.4
#2  0x0000000805a32d4f in 
google::protobuf::SimpleDescriptorDatabase::DescriptorIndex<std::pair<void 
const*, int> >::AddFile ()
    from /usr/local/lib/libprotobuf.so.4
#3  0x0000000805a2df86 in 
google::protobuf::EncodedDescriptorDatabase::Add () from 
/usr/local/lib/libprotobuf.so.4
#4  0x00000008059ed8fd in 
google::protobuf::DescriptorPool::InternalAddGeneratedFile () from 
/usr/local/lib/libprotobuf.so.4
#5  0x0000000805a16218 in 
google::protobuf::protobuf_AddDesc_google_2fprotobuf_2fdescriptor_2eproto () 
from /usr/local/lib/libprotobuf.so.4
#6  0x0000000805a168a5 in __static_initialization_and_destruction_0 () 
from /usr/local/lib/libprotobuf.so.4
#7  0x0000000805a64aab in __do_global_ctors_aux () from 
/usr/local/lib/libprotobuf.so.4
#8  0x00000008059d00f6 in _init () from /usr/local/lib/libprotobuf.so.4
#9  0x000000080064bc70 in ?? () from /libexec/ld-elf.so.1
#10 0x000000080052582b in dlsym () from /libexec/ld-elf.so.1
#11 0x0000000800526b85 in dlopen () from /libexec/ld-elf.so.1
#12 0x00000008005217a9 in ?? () from /libexec/ld-elf.so.1
#13 0x0000000000000000 in ?? ()
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---Type <return> to continue, or q <return> to quit---
#436 0x0000000000000000 in ?? ()
#437 0x0000000000000000 in ?? ()
#438 0x0000000000000000 in ?? ()
#439 0x0000000000000000 in ?? ()
#440 0x0000000000000000 in ?? ()
#441 0x0000000000000000 in ?? ()
#442 0x0000000000000000 in ?? ()
#443 0x0000000000000000 in ?? ()
#444 0x0000000000000000 in ?? ()
#445 0x0000000000000000 in ?? ()
#446 0x0000000000000000 in ?? ()
#447 0x0000000000000000 in ?? ()
#448 0x0000000000000000 in ?? ()
#449 0x0000000000000000 in ?? ()

#450 0x0000000000000000 in ?? ()
#451 0x0000000000000000 in ?? ()
#452 0x0000000000000000 in ?? ()
#453 0x0000000000000000 in ?? ()
#454 0x0000000000000000 in ?? ()
#455 0x0000000000000000 in ?? ()
#456 0x0000000000000000 in ?? ()
#457 0x0000000000000000 in ?? ()
#458 0x0000000000000000 in ?? ()
#459 0x0000000000000000 in ?? ()
#460 0x0000000000000000 in ?? ()
#461 0x0000000000000000 in ?? ()
#462 0x0000000000000000 in ?? ()
#463 0x0000000000000000 in ?? ()
#464 0x0000000000000000 in ?? ()
#465 0x0000000000000000 in ?? ()
#466 0x0000000000000000 in ?? ()
#467 0x0000000000000000 in ?? ()
#468 0x0000000000000000 in ?? ()
#469 0x0000000000000000 in ?? ()
#470 0x0000000000000000 in ?? ()
#471 0x0000000000000000 in ?? ()
#472 0x0000000000000000 in ?? ()
#473 0x0000000000000000 in ?? ()
#474 0x0000000000000000 in ?? ()
#475 0x0000000000000000 in ?? ()
#476 0x0000000000000000 in ?? ()
#477 0x0000000000000000 in ?? ()
#478 0x0000000000000000 in ?? ()
#479 0x0000000000000000 in ?? ()
#480 0x0000000000000000 in ?? ()

#481 0x0000000000000000 in ?? ()
#482 0x0000000000000000 in ?? ()
#483 0x0000000000000000 in ?? ()
#484 0x0000000000000000 in ?? ()
---Type <return> to continue, or q <return> to quit---
#485 0x0000000000000000 in ?? ()
#486 0x0000000000000000 in ?? ()
#487 0x0000000000000000 in ?? ()
[...] SNIP (#488 - #876 ==>> 0x0000000000000000 in ?? ()

---Type <return> to continue, or q <return> to quit---
#877 0x0000000000000000 in ?? ()
#878 0x0000000000000000 in ?? ()
#879 0x0000000000000000 in ?? ()
#880 0x0000000000000000 in ?? ()
#881 0x0000000000000000 in ?? ()
#882 0x0000000000000000 in ?? ()
#883 0x0000000000000000 in ?? ()
#884 0x2f00000000000000 in ?? ()

#885 0x61636f6c2f727375 in ?? ()
#886 0x332f736973692f6c in ?? ()
#887 0x69622f31322e312e in ?? ()
#888 0x0077656976712f6e in ?? ()
#889 0x247c8d48002454ff in ?? ()
#890 0x01a1c0c748006a10 in ?? ()
#891 0x66fdebf4050f0000 in ?? ()
#892 0x9066669066669066 in ?? ()
#893 0x00007fffffffe488 in ?? ()
#894 0x0000000000000001 in ?? ()
#895 0x00007fffffffe498 in ?? ()
#896 0x000000000000002b in ?? ()
Cannot access memory at address 0x800000000000
(gdb)

-- 
Oliver Hartmann
Freie Universitaet Berlin
Planetologie und Fernerkundung
Malteserstr. 74 - 100/Haus D
D-12249 Berlin

Tel.: +49 (0) 30 838 70 508
FAX:  +49 (0) 30 838 70 539