On Apr 22, 2010, at 3:28 AM, Sean Gillies wrote: > On Tue, Apr 20, 2010 at 3:48 PM, Jean-Baptiste Quenot <[email protected]> > wrote: >> Hi there, >> >> First, thanks for the great piece of software! >> >> I am a happy user of Shapely since a few years, but since I upgraded >> my server to Ubuntu 9.10 I notice the following message everytime I my >> Python application ends: >> >> *** glibc detected *** python: double free or corruption (!prev): >> 0x00000000018839b0 *** >> >> Also, the process hangs and never completes. This problem is >> particularly painful when Python is run as a CGI within Apache, as >> HTTP requests will never complete. Otherwise on the command-line, I >> just issue a CTRL-C to stop it. >> >> Software that has changed during the Ubuntu upgrade includes: >> >> * Python, from 2.6.2 to 2.6.4 >> * Libgeos, from 3.0.0 to 3.1.0 >> >> I tried to upgrade shapely from 1.0.11 to 1.0.14 with no luck. >> >> Note that I also use python-mapscript, the package that comes with >> mapserver, also using libgeos. I verified that only one version of >> libgeos is installed and used. >> >> Here is the gdb backtrace during the hang: >> >> #0 __lll_lock_wait_private () at >> ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:97 >> #1 0x00007f238c6c7b11 in _L_lock_9274 () from /lib/libc.so.6 >> #2 0x00007f238c6c5741 in *__GI___libc_free (mem=0x7f238c9b5e40) at >> malloc.c:3714 >> #3 0x00007f238d48ab32 in _dl_scope_free (old=0xf6e5b0) at dl-open.c:175 >> #4 0x00007f238d485035 in _dl_map_object_deps (map=0x7f238d697530, >> preloads=<value optimized out>, npreloads=<value optimized out>, >> trace_mode=<value optimized out>, open_mode=<value optimized out>) at >> dl-deps.c:668 >> #5 0x00007f238d48ada3 in dl_open_worker (a=<value optimized out>) at >> dl-open.c:326 >> #6 0x00007f238d486386 in _dl_catch_error (objname=<value optimized >> out>, errstring=<value optimized out>, mallocedp=<value optimized >> out>, operate=<value optimized out>, args=<value optimized out>) at >> dl-error.c:178 >> #7 0x00007f238d48a6c7 in _dl_open (file=0x7f238c77e2ae >> "libgcc_s.so.1", mode=-2147483647, caller_dlopen=0x0, nsid=-2, argc=1, >> argv=0x18, env=0xafed90) at dl-open.c:615 >> #8 0x00007f238c767c00 in do_dlopen (ptr=0x7ffff3913b10) at dl-libc.c:86 >> #9 0x00007f238d486386 in _dl_catch_error (objname=<value optimized >> out>, errstring=<value optimized out>, mallocedp=<value optimized >> out>, operate=<value optimized out>, args=<value optimized out>) at >> dl-error.c:178 >> #10 0x00007f238c767d57 in dlerror_run (name=<value optimized out>, >> mode=<value optimized out>) at dl-libc.c:47 >> #11 *__GI___libc_dlopen_mode (name=<value optimized out>, mode=<value >> optimized out>) at dl-libc.c:160 >> #12 0x00007f238c7426e5 in init () at ../sysdeps/x86_64/../ia64/backtrace.c:41 >> #13 0x00007f238d2687a3 in pthread_once () at >> ../nptl/sysdeps/unix/sysv/linux/x86_64/pthread_once.S:94 >> #14 0x00007f238c7427e4 in *__GI___backtrace (array=<value optimized >> out>, size=64) at ../sysdeps/x86_64/../ia64/backtrace.c:79 >> #15 0x00007f238c6b6cab in __libc_message (do_abort=<value optimized >> out>, fmt=<value optimized out>) at >> ../sysdeps/unix/sysv/linux/libc_fatal.c:168 >> #16 0x00007f238c6c0dd6 in malloc_printerr (action=3, >> str=0x7f238c7827b0 "double free or corruption (!prev)", ptr=<value >> optimized out>) at malloc.c:6217 >> #17 0x00007f238c6c574c in *__GI___libc_free (mem=<value optimized >> out>) at malloc.c:3716 >> #18 0x00007f2384a5130b in msGEOSCleanup () from >> /usr/lib/python2.6/dist-packages/_mapscript.so >> #19 0x00007f2384969fda in msCleanup () from >> /usr/lib/python2.6/dist-packages/_mapscript.so >> #20 0x00000000004c2cc2 in call_ll_exitfuncs () at ../Python/pythonrun.c:1705 >> #21 Py_Finalize () at ../Python/pythonrun.c:534 >> #22 0x00000000004185c2 in Py_Main (argc=<value optimized out>, >> argv=<value optimized out>) at ../Modules/main.c:625 >> #23 0x00007f238c669abd in __libc_start_main (main=<value optimized >> out>, argc=<value optimized out>, ubp_av=<value optimized out>, >> init=<value optimized out>, fini=<value optimized out>, >> rtld_fini=<value optimized out>, stack_end=0x7ffff3914738) at >> libc-start.c:220 >> #24 0x0000000000417ca9 in _start () at ../sysdeps/x86_64/elf/start.S:113 >> >> I have no clue where the problem comes from, however, when I edit the >> installed python2.6/shapely/geos.py module and comment the cleanup >> code, Python does not crash anymore: >> >> def cleanup(): >> if lgeos is not None: >> pass >> #lgeos.finishGEOS() >> >> Any idea? Your help will be much appreciated. > > Hi Jean-Baptiste, > > I suspect at-exit cleanup collision: mapscript's msCleanup is freeing > some memory allocated by libgeos and when Shapely exits, cleanup() > attempts to free that same memory. I've created a ticket in the > tracker: > > http://trac.gispython.org/lab/ticket/217 > > If you've anything to add, please register and do so. In the > meanwhile, do not use Shapely with mapscript. Mapscript provides most > of the functionality if not such a handy API. >
I fixed this problem in a newer version of GEOS (http://trac.osgeo.org/geos/ticket/256) so it will not double free in finishGEOS. Another thing to try.... _______________________________________________ Community mailing list [email protected] http://lists.gispython.org/mailman/listinfo/community
