[CIG-SHORT] Pylith error
Jiangning Lu
jlu at chandler.mit.edu
Tue Feb 12 16:34:06 PST 2008
Hi Brad,
I believe it's not memory issue. The mesh only has 53026 nodes and
307798 cells.
And my computer has 1 G memory. Besides I have another successful run with the
same size mesh.
I've done as you said. attached are the backtrace.txt and run log(stderr +
stdout)file.
Quoting Brad Aagaard <baagaard at usgs.gov>:
> Jiangning-
>
> Are you sure you are not running out of memory? If you are not running out of
> memory, then rerun with the debugger to get a stacktrace as described below.
>
> In general, if you ever encounter a segmentation fault when running PyLith
> (as you did in this case), you should rerun PyLith and add the command line
> argument --petsc.start_in_debugger. This will open up a debugger window when
> PyLith starts. Enter "c" at the gdb prompt to continue executing PyLith and
> when the error occurs, enter "backtrace" at the gdb prompt to get a
> stacktrace where the segmentation fault occurred. Copy the stacktrace to a
> text file and sent it along with the run log (stderr + stdout).
>
> Brad
>
>
> On Tuesday 12 February 2008, Jiangning Lu wrote:
>> Hi,
>>
>> I run into some new issue here. now the pylith did run further until it
>> got crashed. Anyone has a clue what does the following error mean?
>> Thanks a lot!!
>>
>> Where the error info occurred: (Attached is the detailed run log file).
>> ......
>> -- implicit(info)
>> -- Creating solution field.
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
>> gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on
>> Apple to find memory corruption errors
>> [0]PETSC ERROR: likely location of problem given in stack below
>> [0]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available, [0]PETSC ERROR: INSTEAD the line number of the start of
>> the function [0]PETSC ERROR: is given.
>> [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Development Version 2.3.3, Patch 8, Tue Jan 29
>> 00:02:06 CST 2008 HG revision: 4b0f5f032b0655745a4e6a02aa42852564e2854a
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR:
>> /chandler/home/jlu/scratch1/pylith_workarea/nemesis/trunk/mpinemesis on a
>> linux-gnu named elsasser by jlu Tue Feb 12 11:11:05 2008
>> [0]PETSC ERROR: Libraries linked from
>> /chandler/home/jlu/scratch1/pylith_workarea/petsc-dev/lib
>> [0]PETSC ERROR: Configure run at Tue Jan 29 15:33:02 2008
>> [0]PETSC ERROR: Configure options --with-sieve=1 --with-clanguage=C++
>> --with-shared=1 --download-f-blas-lapack=1 --with-boost=1
>> --download-boost=1 --with-chaco=1 --download-chaco=1 --with-mpi=1
>> --download-mpich=1
>> --with-mpi-shared=1
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> [cli_0]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>
>> Jiangning
>>
>>
>> ---
>> Jiangning Lü
>> 54-521 x3-6389
>> Geophysics
>> EAPS, MIT
>> johnnylu at mit.edu (????
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
---
Jiangning Lü
54-521 x3-6389
Geophysics
EAPS, MIT
johnnylu at mit.edu (????
-------------- next part --------------
(gdb) backtrace
#0 0x00110402 in __kernel_vsyscall ()
#1 0x00548950 in __nanosleep_nocancel () from /lib/libc.so.6
#2 0x0054879f in sleep () from /lib/libc.so.6
#3 0x013a51b3 in PetscSleep (s=10) at psleep.c:40
#4 0x012ecce3 in PetscAttachDebugger () at adebug.c:411
#5 0x0135d8e8 in PetscOptionsCheckInitial_Private () at init.c:377
#6 0x0138a347 in PetscInitialize (argc=0xbf977680, args=0xbf977684, file=0x0,
help=0x0) at pinit.c:561
#7 0x00410724 in Petsc_initialize (argc=0xbf977680, argv=0xbf977684)
at petsc_embed.cpp:13
#8 0x00410231 in __pyx_f_5petsc_petsc_initialize (__pyx_self=0x0,
__pyx_args=0x92ce12c, __pyx_kwds=0x0) at petsc.c:141
#9 0x080c095c in PyEval_EvalFrameEx (f=0x919eb2c, throwflag=0)
at Python/ceval.c:3564
#10 0x080c0d85 in PyEval_EvalFrameEx (f=0x91a768c, throwflag=0)
at Python/ceval.c:3650
#11 0x080c1b95 in PyEval_EvalCodeEx (co=0x8efef50, globals=0x8f4c714,
locals=0x0, args=0x92ca4f8, argcount=1, kws=0x91439a0, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#12 0x0810d036 in function_call (func=0x915e224, arg=0x92ca4ec, kw=0x92cd68c)
at Objects/funcobject.c:517
#13 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x92ca4ec, kw=0x92cd68c)
at Objects/abstract.c:1860
#14 0x080beaf5 in PyEval_EvalFrameEx (f=0x91a2e0c, throwflag=0)
at Python/ceval.c:3844
#15 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7e9e188, globals=0xb7a6b68c,
locals=0x0, args=0x92ca918, argcount=1, kws=0x9248868, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#16 0x0810d036 in function_call (func=0x8ea933c, arg=0x92ca90c, kw=0x92cd8ac)
at Objects/funcobject.c:517
#17 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x92ca90c, kw=0x92cd8ac)
at Objects/abstract.c:1860
#18 0x080beaf5 in PyEval_EvalFrameEx (f=0x91a3264, throwflag=0)
at Python/ceval.c:3844
#19 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7e9e1d0, globals=0xb7a6b68c,
locals=0x0, args=0x92ca878, argcount=1, kws=0x9135568, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#20 0x0810d036 in function_call (func=0x8ea9304, arg=0x92ca86c, kw=0x915fa44)
at Objects/funcobject.c:517
#21 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x92ca86c, kw=0x915fa44)
at Objects/abstract.c:1860
#22 0x080beaf5 in PyEval_EvalFrameEx (f=0x919efc4, throwflag=0)
at Python/ceval.c:3844
#23 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7a897b8, globals=0xb79914f4,
locals=0x0, args=0x8f4ec98, argcount=1, kws=0x9007008, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#24 0x0810d036 in function_call (func=0xb79a6dbc, arg=0x8f4ec8c, kw=0x915f79c)
at Objects/funcobject.c:517
#25 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x8f4ec8c, kw=0x915f79c)
at Objects/abstract.c:1860
#26 0x080beaf5 in PyEval_EvalFrameEx (f=0x9159134, throwflag=0)
at Python/ceval.c:3844
#27 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7ea38d8, globals=0xb7a6b824,
locals=0x0, args=0x8f4ec58, argcount=1, kws=0x9153900, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#28 0x0810d036 in function_call (func=0xb7a861b4, arg=0x8f4ec4c, kw=0x915f714)
at Objects/funcobject.c:517
#29 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x8f4ec4c, kw=0x915f714)
at Objects/abstract.c:1860
#30 0x080beaf5 in PyEval_EvalFrameEx (f=0x91510cc, throwflag=0)
at Python/ceval.c:3844
#31 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7a89410, globals=0xb798d57c,
locals=0x0, args=0x8f4eb78, argcount=1, kws=0x8f96fe0, kwcount=4,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#32 0x0810d036 in function_call (func=0xb798e41c, arg=0x8f4eb6c, kw=0xb799168c)
at Objects/funcobject.c:517
#33 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x8f4eb6c, kw=0xb799168c)
at Objects/abstract.c:1860
#34 0x080beaf5 in PyEval_EvalFrameEx (f=0x8f9675c, throwflag=0)
#35 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7a893c8, globals=0xb798d57c,
locals=0x0, args=0x8f4ea38, argcount=1, kws=0x8f93698, kwcount=3,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#36 0x0810d036 in function_call (func=0xb798e3e4, arg=0x8f4ea2c, kw=0x8f4fbdc)
at Objects/funcobject.c:517
#37 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x8f4ea2c, kw=0x8f4fbdc)
at Objects/abstract.c:1860
#38 0x080beaf5 in PyEval_EvalFrameEx (f=0x8f87a3c, throwflag=0)
at Python/ceval.c:3844
#39 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7a89338, globals=0xb798d57c,
locals=0x0, args=0x8f4e778, argcount=1, kws=0x8d5c2e0, kwcount=3,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#40 0x0810d036 in function_call (func=0xb798e3ac, arg=0x8f4e76c, kw=0x8eabacc)
at Objects/funcobject.c:517
#41 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0x8f4e76c, kw=0x8eabacc)
at Objects/abstract.c:1860
#42 0x080beaf5 in PyEval_EvalFrameEx (f=0x8ed5eb4, throwflag=0)
at Python/ceval.c:3844
#43 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7a897b8, globals=0xb79914f4,
locals=0x0, args=0xb7e8b2b8, argcount=1, kws=0x8ec6518, kwcount=3,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2831
#44 0x0810d036 in function_call (func=0xb79a6dbc, arg=0xb7e8b2ac, kw=0x8eaaacc)
#45 0x0805aa67 in PyObject_Call (func=0xbf9730d4, arg=0xb7e8b2ac, kw=0x8eaaacc)
at Objects/abstract.c:1860
#46 0x080beaf5 in PyEval_EvalFrameEx (f=0x8d46394, throwflag=0)
at Python/ceval.c:3844
#47 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7e9ef08, globals=0xb7a6b79c,
locals=0x0, args=0x8ed3dd4, argcount=1, kws=0x8ed3dd8, kwcount=2,
defs=0xb7990278, defcount=1, closure=0x0) at Python/ceval.c:2831
#48 0x080c0049 in PyEval_EvalFrameEx (f=0x8ed3c74, throwflag=0)
at Python/ceval.c:3660
#49 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7e80530, globals=0xb7a6b46c,
locals=0x0, args=0x8c3f440, argcount=1, kws=0x8c3f444, kwcount=1,
defs=0xb7e90958, defcount=1, closure=0x0) at Python/ceval.c:2831
#50 0x080c0049 in PyEval_EvalFrameEx (f=0x8c3f304, throwflag=0)
at Python/ceval.c:3660
#51 0x080c1b95 in PyEval_EvalCodeEx (co=0xb7e807b8, globals=0xb7eccacc,
locals=0xb7eccacc, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2831
#52 0x080c1c07 in PyEval_EvalCode (co=0xb7e807b8, globals=0xb7eccacc,
locals=0xb7eccacc) at Python/ceval.c:494
#53 0x080e1502 in PyRun_StringFlags (
str=0x8121ef4 "import sys; path = sys.argv[1]; requires = sys.argv[2]; entry = sys.argv[3]; path = path.split(':'); path.extend(sys.path); sys.path = path;
from merlin import loadObject; entry = loadObject(entry); e"..., start=257,
globals=0xb7eccacc, locals=0xb7eccacc, flags=0x0)
at Python/pythonrun.c:1271
#54 0x080e15c5 in PyRun_SimpleStringFlags (
command=0x8121ef4 "import sys; path = sys.argv[1]; requires = sys.argv[2]; entry = sys.argv[3]; path = path.split(':'); path.extend(sys.path); sys.path = path; from merlin import loadObject; entry = loadObject(entry); e"..., flags=0x0)
at Python/pythonrun.c:898
#55 0x08057514 in main (argc=-1080582403, argv=Cannot access memory at address 0xfffffe00
) at nemesis.c:102
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