Menu
▾
▴
Re: [moose-generic] MOOSE_installation_problem
|
From: Vadim A <ast...@nc...> - 2013-03-20 18:34:07
|
Hi Subha, We are trying import MOOSE and having problem. I provide some trace information at the end of this e-mail. And very appreciate any comments. May be we should turn threading off? What would be your suggestions? >>> import moose on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16 Segmentation fault (core dumped) [astakhov@trestles-login1 moose]$ gdb -c core.24245 /home/diag/opt/python2.7/bin/python GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1) Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /home/diag/opt/python2.7/bin/python...done. [New Thread 24275] [New Thread 24274] [New Thread 24273] [New Thread 24272] [New Thread 24271] [New Thread 24270] [New Thread 24269] [New Thread 24268] [New Thread 24267] [New Thread 24266] [New Thread 24265] [New Thread 24264] [New Thread 24263] [New Thread 24262] [New Thread 24261] [New Thread 24260] Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so Reading symbols from /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done. Loaded symbols for /lib64/libpthread.so.0 Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libdl.so.2 Reading symbols from /lib64/libutil.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libutil.so.1 Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libm.so.6 Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libc.so.6 Reading symbols from /usr/lib64/libstdc++.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libstdc++.so.5 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libgcc_s.so.1 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5 Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/ld-linux-x86-64.so.2 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so Reading symbols from /usr/lib64/libreadline.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libreadline.so.5 Reading symbols from /usr/lib64/libncursesw.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libncursesw.so.5 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so Reading symbols from /home/astakhov/moose/moose/moose/python/moose/_moose.so...(no debugging symbols found)...done. Loaded symbols for /home/astakhov/moose/moose/moose/python/moose/_moose.so Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0 Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0 Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libstdc++.so.6 Reading symbols from /opt/pgi/linux86-64/10.5/libso/libpgc.so...(no debugging symbols found)...done. Loaded symbols for /opt/pgi/linux86-64/10.5/libso/libpgc.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so Core was generated by `python'. Program terminated with signal 11, Segmentation fault. #0 0x000000344be7275e in free () from /lib64/libc.so.6 (gdb) where #0 0x000000344be7275e in free () from /lib64/libc.so.6 #1 0x00002b3b34bcc2db in Field<std::vector<Id, std::allocator<Id> > >::get(ObjId const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #2 0x00002b3b34f238e0 in defineAllClasses () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #3 0x00002b3b34f24108 in init_moose () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #4 0x00002b3b2f25d705 in _PyImport_LoadDynamicModule (name=0x7fff9742c950 "moose._moose", pathname=0x7fff9742b860 "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value optimized out>) at ./Python/importdl.c:53 #5 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0, subname=0x189bfd14 "_moose", fullname=0x7fff9742c950 "moose._moose") at Python/import.c:2596 #6 0x00002b3b2f25bd40 in ensure_fromlist (mod=0x189c03d0, fromlist=0x189b6cd0, buf=0x7fff9742c950 "moose._moose", buflen=5, recursive=0) at Python/import.c:2507 #7 0x00002b3b2f25c1b7 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x189b6cd0, level=1, locals=<value optimized out>) at Python/import.c:2175 #8 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x2b3b3000c644 "", globals=0x18a16350, locals=<value optimized out>, fromlist=0x189b6cd0, level=1) at Python/import.c:2189 #9 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #10 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #11 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x18a483b0, kw=<value optimized out>) at Python/ceval.c:3881 #12 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #13 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #14 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 #15 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff9742ff40 "moose.moose", co=0x189b53b0, pathname=0x7fff9742dd50 "/home/astakhov/moose/moose/moose/python/moose/moose.pyc") at Python/import.c:681 #16 0x00002b3b2f25a68e in load_source_module (name=0x7fff9742ff40 "moose.moose", pathname=0x7fff9742dd50 "/home/astakhov/moose/moose/moose/python/moose/moose.pyc", fp=<value optimized out>) at Python/import.c:1021 #17 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0, subname=0x7fff9742ff46 "moose", fullname=0x7fff9742ff40 "moose.moose") at Python/import.c:2596 #18 0x00002b3b2f25ba52 in load_next (mod=0x189c03d0, altmod=0x189c03d0, p_name=<value optimized out>, buf=0x7fff9742ff40 "moose.moose", p_buflen=0x7fff97430f50) at Python/import.c:2416 #19 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x1899f290, level=1, locals=<value optimized out>) at Python/import.c:2137 #20 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54 "moose", globals=0x189f43c0, locals=<value optimized out>, fromlist=0x1899f290, level=1) at Python/import.c:2189 #21 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #22 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #23 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x2b3b300c8590, kw=<value optimized out>) at Python/ceval.c:3881 #24 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #25 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #26 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 ---Type <return> to continue, or q <return> to quit--- #27 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff97434580 "moose", co=0x2b3b300f0eb0, pathname=0x7fff97431340 "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc") at Python/import.c:681 #28 0x00002b3b2f25a68e in load_source_module (name=0x7fff97434580 "moose", pathname=0x7fff97431340 "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc", fp=<value optimized out>) at Python/import.c:1021 #29 0x00002b3b2f25b444 in load_package (name=0x7fff97434580 "moose", pathname=<value optimized out>) at Python/import.c:1077 #30 0x00002b3b2f25b7d8 in import_submodule (mod=0x2b3b2f4f48c0, subname=0x7fff97434580 "moose", fullname=0x7fff97434580 "moose") at Python/import.c:2596 #31 0x00002b3b2f25ba52 in load_next (mod=0x2b3b2f4f48c0, altmod=0x2b3b2f4f48c0, p_name=<value optimized out>, buf=0x7fff97434580 "moose", p_buflen=0x7fff97435590) at Python/import.c:2416 #32 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x2b3b2f4f48c0, level=-1, locals=<value optimized out>) at Python/import.c:2137 #33 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54 "moose", globals=0x1892ea00, locals=<value optimized out>, fromlist=0x2b3b2f4f48c0, level=-1) at Python/import.c:2189 #34 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #35 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #36 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x2b3b300d8e68, kw=<value optimized out>) at Python/ceval.c:3881 #37 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #38 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #39 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 #40 0x00002b3b2f266b02 in run_mod (fp=<value optimized out>, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:1346 #41 PyRun_InteractiveOneFlags (fp=<value optimized out>, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:845 #42 0x00002b3b2f266d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:765 #43 0x00002b3b2f2672ec in PyRun_AnyFileExFlags (fp=0x344c1516a0, filename=0x2b3b2f2adfff "<stdin>", closeit=0, flags=0x7fff97435ad0) at Python/pythonrun.c:734 #44 0x00002b3b2f27944b in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:599 #45 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6 #46 0x0000000000400619 in _start () (gdb) |
