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Re: [moose-generic] MOOSE_installation_problem
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From: Vadim A <ast...@nc...> - 2013-03-25 20:42:23
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Hi Subha.
Thanks for your comments. I did try what you've suggested:
1. Modifications was performed in "moosemodule.cpp"
2. I double check that we use g++ :
[astakhov@trestles-login1 moose]$ make BUILD=debug USE_HDF5=0
make[1]: Entering directory `/home/astakhov/moose/moose/moose/basecode'
g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ -I../msg consts.cpp -c
3. And I did "make BUILD=debug"
but we still getting segmentation fault:
>>> import moose
on node 0, numNodes = 1, numCores = 16, numComputeThreads = 1
Segmentation fault (core dumped)
I wonder, is it possible to make a teleconference session where we can call you and share our screen to demonstrate all steps.
May be this way we could find the problem and have MOOSE finally installed for us.
Please let me know how do you feel about that.
Also, I attached trace to the end of this e-mail, may be you can advice us what we are still missing.
#0 0x000000344be7275e in free () from /lib64/libc.so.6
#1 0x00000035f8a9db6a in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string() ()
from /usr/lib64/libstdc++.so.6
#2 0x00002b0af62f6075 in Field<std::vector<Id, std::allocator<Id> > >::get (dest=..., field=...)
at ../basecode/SetGet.h:289
#3 0x00002b0af66e1525 in defineAllClasses (module_dict=0xc826f10) at moosemodule.cpp:4288
#4 0x00002b0af66edd7e in init_moose () at moosemodule.cpp:4953
#5 0x00002b0af07c0705 in _PyImport_LoadDynamicModule (name=0x7fffaa57dda0 "moose._moose",
pathname=0x7fffaa57ccb0 "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value optimized out>)
at ./Python/importdl.c:53
#6 0x00002b0af07be7d8 in import_submodule (mod=0xc54a398, subname=0xc549e34 "_moose",
fullname=0x7fffaa57dda0 "moose._moose") at Python/import.c:2596
#7 0x00002b0af07bed40 in ensure_fromlist (mod=0xc54a398, fromlist=0xc540cd0, buf=0x7fffaa57dda0 "moose._moose",
buflen=5, recursive=0) at Python/import.c:2507
#8 0x00002b0af07bf1b7 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0xc540cd0,
level=1, locals=<value optimized out>) at Python/import.c:2175
#9 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0x2b0af156f644 "", globals=0xc591030,
locals=<value optimized out>, fromlist=0xc540cd0, level=1) at Python/import.c:2189
#10 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#11 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#12 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0xc6153b0,
kw=<value optimized out>) at Python/ceval.c:3881
#13 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#14 0x00002b0af07a6515 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
#15 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
---Type <return> to continue, or q <return> to quit---
locals=<value optimized out>) at Python/ceval.c:666
#16 0x00002b0af07bd342 in PyImport_ExecCodeModuleEx (name=0x7fffaa581390 "moose.moose", co=0xc53f430,
pathname=0x7fffaa5802b0 "/home/astakhov/moose/moose/moose/python/moose/moose.py") at Python/import.c:681
#17 0x00002b0af07bd68e in load_source_module (name=0x7fffaa581390 "moose.moose",
pathname=0x7fffaa5802b0 "/home/astakhov/moose/moose/moose/python/moose/moose.py", fp=<value optimized out>)
at Python/import.c:1021
#18 0x00002b0af07be7d8 in import_submodule (mod=0xc54a398, subname=0x7fffaa581396 "moose",
fullname=0x7fffaa581390 "moose.moose") at Python/import.c:2596
#19 0x00002b0af07bea52 in load_next (mod=0xc54a398, altmod=0xc54a398, p_name=<value optimized out>,
buf=0x7fffaa581390 "moose.moose", p_buflen=0x7fffaa5823a0) at Python/import.c:2416
#20 0x00002b0af07bf062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0xc529290,
level=1, locals=<value optimized out>) at Python/import.c:2137
#21 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0xc549cb4 "moose", globals=0xc57e200,
locals=<value optimized out>, fromlist=0xc529290, level=1) at Python/import.c:2189
#22 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#23 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#24 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0x2b0af162b590,
kw=<value optimized out>) at Python/ceval.c:3881
#25 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#26 0x00002b0af07a6515 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
#27 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#28 0x00002b0af07bd342 in PyImport_ExecCodeModuleEx (name=0x7fffaa5859d0 "moose", co=0x2b0af1653f30,
pathname=0x7fffaa583890 "/home/astakhov/moose/moose/moose/python/moose/__init__.py") at Python/import.c:681
#29 0x00002b0af07bd68e in load_source_module (name=0x7fffaa5859d0 "moose",
---Type <return> to continue, or q <return> to quit---
pathname=0x7fffaa583890 "/home/astakhov/moose/moose/moose/python/moose/__init__.py", fp=<value optimized out>)
at Python/import.c:1021
#30 0x00002b0af07be444 in load_package (name=0x7fffaa5859d0 "moose", pathname=<value optimized out>)
at Python/import.c:1077
#31 0x00002b0af07be7d8 in import_submodule (mod=0x2b0af0a578c0, subname=0x7fffaa5859d0 "moose",
fullname=0x7fffaa5859d0 "moose") at Python/import.c:2596
#32 0x00002b0af07bea52 in load_next (mod=0x2b0af0a578c0, altmod=0x2b0af0a578c0, p_name=<value optimized out>,
buf=0x7fffaa5859d0 "moose", p_buflen=0x7fffaa5869e0) at Python/import.c:2416
#33 0x00002b0af07bf062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x2b0af0a578c0,
level=-1, locals=<value optimized out>) at Python/import.c:2137
#34 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0xc549cb4 "moose", globals=0xc4b8a00,
locals=<value optimized out>, fromlist=0x2b0af0a578c0, level=-1) at Python/import.c:2189
#35 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#36 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#37 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0x2b0af163be68,
kw=<value optimized out>) at Python/ceval.c:3881
#38 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#39 0x00002b0af07a6515 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
#40 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#41 0x00002b0af07c9b02 in run_mod (fp=<value optimized out>, filename=0x2b0af0810fff "<stdin>",
flags=0x7fffaa586f20) at Python/pythonrun.c:1346
#42 PyRun_InteractiveOneFlags (fp=<value optimized out>, filename=0x2b0af0810fff "<stdin>", flags=0x7fffaa586f20)
at Python/pythonrun.c:845
#43 0x00002b0af07c9d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0, filename=0x2b0af0810fff "<stdin>",
---Type <return> to continue, or q <return> to quit---
flags=0x7fffaa586f20) at Python/pythonrun.c:765
#44 0x00002b0af07ca2ec in PyRun_AnyFileExFlags (fp=0x344c1516a0, filename=0x2b0af0810fff "<stdin>", closeit=0,
flags=0x7fffaa586f20) at Python/pythonrun.c:734
#45 0x00002b0af07dc44b in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:599
#46 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6
#47 0x0000000000400619 in _start ()
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 15492]
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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)
On Mar 20, 2013, at 10:18 PM, Subhasis Ray wrote:
> Dear Vadim,
> I could not reproduce this. Are you using g++? In the trace
>
> "Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done."
>
> seems to indicate that you have Intel C++ compiler and related libraries installed (and possibly linked to in moose).
>
> Can you please try out the following in moose/pymoose/moosemodule.cpp: Go to line 4277 and modify:
>
> ------8<------------------------------->8-------
>
> static int defineAllClasses(PyObject * module_dict)
> {
> static vector <Id> classes(Field< vector<Id> >::get(ObjId("/classes"),
> "children"));
>
> ------8<------------------------------->8-------
>
> into ...
>
> ------8<------------------------------->8-------
>
> static int defineAllClasses(PyObject * module_dict)
> {
> static const string children("children");
> static const string path("/classes");
> static vector <Id> classes = Field< vector<Id> >::get(ObjId(path),
> children);
>
> ------8<------------------------------->8-------
> and rebuild.
>
> You can also try reducing the number of threads by setting the NUMPTHREADS environment variable:
>
> export NUMPTHREADS=1
>
> in the shell before starting the Python interpreter. But I doubt if that will help.
>
> Beyond that, you can do a "make clean" and the "make BUILD=debug" to create a debug build, which may avoid some issues caused by compiler optimizations and give more elaborate backtrace.
>
> Best,
> Subha
>
>
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