Date: Thu, 07 Jan 2010 09:02:36 +0000 From: "O. Hartmann" <ohartman@zedat.fu-berlin.de> To: Pieter de Goeje <pieter@degoeje.nl> Cc: freebsd-questions@freebsd.org, freebsd-ports@freebsd.org Subject: Re: ports/devel/protobuf: Segmentation fault in mmap in some applications Message-ID: <4B45A32C.2070708@zedat.fu-berlin.de> In-Reply-To: <201001070241.18190.pieter@degoeje.nl> References: <4B448CB4.5000105@zedat.fu-berlin.de> <201001070241.18190.pieter@degoeje.nl>
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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 ?? () #14 0x0000000000000000 in ?? () #15 0x0000000000000000 in ?? () #16 0x0000000000000000 in ?? () #17 0x0000000000000001 in ?? () #18 0x00007fffffffe800 in ?? () #19 0x0000000000000000 in ?? () #20 0x00007fffffffe806 in ?? () #21 0x00007fffffffe822 in ?? () #22 0x00007fffffffe847 in ?? () #23 0x00007fffffffe852 in ?? () #24 0x00007fffffffe86c in ?? () #25 0x00007fffffffe879 in ?? () #26 0x00007fffffffe899 in ?? () #27 0x00007fffffffe8c7 in ?? () #28 0x00007fffffffe8d9 in ?? () #29 0x00007fffffffe8f0 in ?? () #30 0x00007fffffffe907 in ?? () #31 0x00007fffffffe927 in ?? () #32 0x00007fffffffe936 in ?? () #33 0x00007fffffffe943 in ?? () #34 0x00007fffffffe95d in ?? () #35 0x00007fffffffec8e in ?? () #36 0x00007fffffffecb1 in ?? 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() #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
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