Can you pass us the actual mpirun command line being executed? Especially need
to see the argv being passed to your application.
On Sep 27, 2014, at 7:09 PM, Amos Anderson <amos.ander...@protabit.com> wrote:
> FWIW, I've confirmed that the segfault also happens with OpenMPI 1.7.5. Also,
> I have some gdb output (from 1.7.5) for your perusal, including a printout of
> some of the variables' values.
>
>
>
> Starting program: /home/user/myapp/tools/python/bin/python
> test/regression/regression-test.py test/regression/regression-jobs
> [Thread debugging using libthread_db enabled]
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaabc8df1e in opal_argv_join (argv=0xa39398, delimiter=32) at
> argv.c:299
> 299 str_len += strlen(*p) + 1;
> (gdb) where
> #0 0x00002aaaabc8df1e in opal_argv_join (argv=0xa39398, delimiter=32) at
> argv.c:299
> #1 0x00002aaaaab2ce4e in ompi_mpi_init (argc=2, argv=0xa39390, requested=0,
> provided=0x7fffffffba98) at runtime/ompi_mpi_init.c:450
> #2 0x00002aaaaab63e39 in PMPI_Init (argc=0x7fffffffbb8c,
> argv=0x7fffffffbb80) at pinit.c:84
> #3 0x00002aaab7b965d6 in boost::mpi::environment::environment
> (this=0xa3a1d0, argc=@0x7fffffffbb8c, argv=@0x7fffffffbb80,
> abort_on_exception=true)
> at ../tools/boost/libs/mpi/src/environment.cpp:98
> #4 0x00002aaabc7b311d in boost::mpi::python::mpi_init (python_argv=...,
> abort_on_exception=true) at
> ../tools/boost/libs/mpi/src/python/py_environment.cpp:60
> #5 0x00002aaabc7b33fb in boost::mpi::python::export_environment () at
> ../tools/boost/libs/mpi/src/python/py_environment.cpp:94
> #6 0x00002aaabc7d5ab5 in boost::mpi::python::init_module_mpi () at
> ../tools/boost/libs/mpi/src/python/module.cpp:44
> #7 0x00002aaab792a2f2 in
> boost::detail::function::void_function_ref_invoker0<void (*)(), void>::invoke
> (function_obj_ptr=...)
> at ../tools/boost/boost/function/function_template.hpp:188
> #8 0x00002aaab7929e6b in boost::function0<void>::operator()
> (this=0x7fffffffc110) at
> ../tools/boost/boost/function/function_template.hpp:767
> #9 0x00002aaab7928f11 in boost::python::handle_exception_impl (f=...) at
> ../tools/boost/libs/python/src/errors.cpp:25
> #10 0x00002aaab792a54f in boost::python::handle_exception<void (*)()>
> (f=0x2aaabc7d5746 <boost::mpi::python::init_module_mpi()>) at
> ../tools/boost/boost/python/errors.hpp:29
> #11 0x00002aaab792a1d9 in boost::python::detail::(anonymous
> namespace)::init_module_in_scope (m=0x2aaabc617f68,
> init_function=0x2aaabc7d5746 <boost::mpi::python::init_module_mpi()>) at
> ../tools/boost/libs/python/src/module.cpp:24
> #12 0x00002aaab792a26c in boost::python::detail::init_module
> (name=0x2aaabc7f7f4d "mpi", init_function=0x2aaabc7d5746
> <boost::mpi::python::init_module_mpi()>)
> at ../tools/boost/libs/python/src/module.cpp:59
> #13 0x00002aaabc7d5b2b in boost::mpi::python::initmpi () at
> ../tools/boost/libs/mpi/src/python/module.cpp:34
> #14 0x00002aaaab27e095 in _PyImport_LoadDynamicModule (name=0xac9435 "mpi",
> pathname=0xb08c60 "/home/user/myapp/lib/mpi.so", fp=0xaca450) at
> ./Python/importdl.c:53
> #15 0x00002aaaab279fd4 in load_module (name=0xac9435 "mpi", fp=0xaca450,
> pathname=0xb08c60 "/home/user/myapp/lib/mpi.so", type=3, loader=0x0) at
> Python/import.c:1915
> #16 0x00002aaaab27c2e8 in import_submodule (mod=0x2aaaab533a20,
> subname=0xac9435 "mpi", fullname=0xac9435 "mpi") at Python/import.c:2700
> #17 0x00002aaaab27b8fa in load_next (mod=0x2aaab0f075a8,
> altmod=0x2aaaab533a20, p_name=0x7fffffffc3f8, buf=0xac9430 "util.mpi",
> p_buflen=0x7fffffffc408)
> at Python/import.c:2519
> #18 0x00002aaaab27a98d in import_module_level (name=0x0, globals=0xe95a70,
> locals=0xe95a70, fromlist=0x2aaaab533a20, level=-1) at Python/import.c:2224
> #19 0x00002aaaab27aeda in PyImport_ImportModuleLevel (name=0x2aaab0f00964
> "mpi", globals=0xe95a70, locals=0xe95a70, fromlist=0x2aaaab533a20, level=-1)
> at Python/import.c:2288
> #20 0x00002aaaab2419c4 in builtin___import__ (self=0x0, args=0x2aaabc6211f8,
> kwds=0x0) at Python/bltinmodule.c:49
> #21 0x00002aaaab1b19c7 in PyCFunction_Call (func=0x2aaaabf85510,
> arg=0x2aaabc6211f8, kw=0x0) at Objects/methodobject.c:85
> #22 0x00002aaaab14d673 in PyObject_Call (func=0x2aaaabf85510,
> arg=0x2aaabc6211f8, kw=0x0) at Objects/abstract.c:2529
> #23 0x00002aaaab25ad03 in PyEval_CallObjectWithKeywords (func=0x2aaaabf85510,
> arg=0x2aaabc6211f8, kw=0x0) at Python/ceval.c:3890
> #24 0x00002aaaab2543e5 in PyEval_EvalFrameEx (f=0xe8aef0, throwflag=0) at
> Python/ceval.c:2333
> #25 0x00002aaaab258b7e in PyEval_EvalCodeEx (co=0x2aaabc61ce00,
> globals=0xe95a70, locals=0xe95a70, args=0x0, argcount=0, kws=0x0, kwcount=0,
> defs=0x0, defcount=0,
> closure=0x0) at Python/ceval.c:3253
> #26 0x00002aaaab24b5ce in PyEval_EvalCode (co=0x2aaabc61ce00,
> globals=0xe95a70, locals=0xe95a70) at Python/ceval.c:667
> #27 0x00002aaaab2779e2 in PyImport_ExecCodeModuleEx (name=0xaa9080
> "util.myappMPI", co=0x2aaabc61ce00, pathname=0xe7d380
> "/home/user/myapp/src/util/myappMPI.pyc")
> at Python/import.c:709
> #28 0x00002aaaab278629 in load_source_module (name=0xaa9080 "util.myappMPI",
> pathname=0xe7d380 "/home/user/myapp/src/util/myappMPI.pyc", fp=0x76eb00)
> at Python/import.c:1099
> #29 0x00002aaaab279fa0 in load_module (name=0xaa9080 "util.myappMPI",
> fp=0x76eb00, pathname=0x80fe00 "/home/user/myapp/src/util/myappMPI.py",
> type=1, loader=0x0)
> at Python/import.c:1906
> #30 0x00002aaaab27c2e8 in import_submodule (mod=0x2aaab0f075a8,
> subname=0xaa9085 "myappMPI", fullname=0xaa9080 "util.myappMPI") at
> Python/import.c:2700
> #31 0x00002aaaab27b860 in load_next (mod=0x2aaab0f075a8,
> altmod=0x2aaaab533a20, p_name=0x7fffffffcd98, buf=0xaa9080 "util.myappMPI",
> p_buflen=0x7fffffffcda8)
> at Python/import.c:2515
> #32 0x00002aaaab27a98d in import_module_level (name=0x0, globals=0x7a3c70,
> locals=0x7a3c70, fromlist=0x2aaaaf6f53e0, level=-1) at Python/import.c:2224
> #33 0x00002aaaab27aeda in PyImport_ImportModuleLevel (name=0x2aaaaf6e8854
> "myappMPI", globals=0x7a3c70, locals=0x7a3c70, fromlist=0x2aaaaf6f53e0,
> level=-1)
> at Python/import.c:2288
> #34 0x00002aaaab2419c4 in builtin___import__ (self=0x0, args=0x2aaab0a9f7d0,
> kwds=0x0) at Python/bltinmodule.c:49
> #35 0x00002aaaab1b19c7 in PyCFunction_Call (func=0x2aaaabf85510,
> arg=0x2aaab0a9f7d0, kw=0x0) at Objects/methodobject.c:85
> #36 0x00002aaaab14d673 in PyObject_Call (func=0x2aaaabf85510,
> arg=0x2aaab0a9f7d0, kw=0x0) at Objects/abstract.c:2529
> #37 0x00002aaaab25ad03 in PyEval_CallObjectWithKeywords (func=0x2aaaabf85510,
> arg=0x2aaab0a9f7d0, kw=0x0) at Python/ceval.c:3890
> #38 0x00002aaaab2543e5 in PyEval_EvalFrameEx (f=0x79d000, throwflag=0) at
> Python/ceval.c:2333
> #39 0x00002aaaab258b7e in PyEval_EvalCodeEx (co=0x2aaab0253880,
> globals=0x7a3c70, locals=0x7a3c70, args=0x0, argcount=0, kws=0x0, kwcount=0,
> defs=0x0, defcount=0,
> closure=0x0) at Python/ceval.c:3253
> #40 0x00002aaaab24b5ce in PyEval_EvalCode (co=0x2aaab0253880,
> globals=0x7a3c70, locals=0x7a3c70) at Python/ceval.c:667
> #41 0x00002aaaab2779e2 in PyImport_ExecCodeModuleEx (name=0x7153a0 "util",
> co=0x2aaab0253880, pathname=0x7e98a0 "/home/user/myapp/src/util/__init__.pyc")
> at Python/import.c:709
> #42 0x00002aaaab278629 in load_source_module (name=0x7153a0 "util",
> pathname=0x7e98a0 "/home/user/myapp/src/util/__init__.pyc", fp=0x6fe020) at
> Python/import.c:1099
> #43 0x00002aaaab279fa0 in load_module (name=0x7153a0 "util", fp=0x6fe020,
> pathname=0x755e40 "/home/user/myapp/src/util/__init__.py", type=1, loader=0x0)
> at Python/import.c:1906
> ---Type <return> to continue, or q <return> to quit---
> #44 0x00002aaaab2788ef in load_package (name=0x7153a0 "util",
> pathname=0x703390 "/home/user/myapp/src/util") at Python/import.c:1166
> #45 0x00002aaaab279fea in load_module (name=0x7153a0 "util", fp=0x0,
> pathname=0x703390 "/home/user/myapp/src/util", type=5, loader=0x0) at
> Python/import.c:1920
> #46 0x00002aaaab27c2e8 in import_submodule (mod=0x2aaaab533a20,
> subname=0x7153a0 "util", fullname=0x7153a0 "util") at Python/import.c:2700
> #47 0x00002aaaab27b860 in load_next (mod=0x2aaaab533a20,
> altmod=0x2aaaab533a20, p_name=0x7fffffffd818, buf=0x7153a0 "util",
> p_buflen=0x7fffffffd828) at Python/import.c:2515
> #48 0x00002aaaab27a98d in import_module_level (name=0x2aaaac0e0f59
> "myappSubmission", globals=0x6443c0, locals=0x6443c0,
> fromlist=0x2aaaac0f1760, level=-1)
> at Python/import.c:2224
> #49 0x00002aaaab27aeda in PyImport_ImportModuleLevel (name=0x2aaaac0e0f54
> "util.myappSubmission", globals=0x6443c0, locals=0x6443c0,
> fromlist=0x2aaaac0f1760, level=-1)
> at Python/import.c:2288
> #50 0x00002aaaab2419c4 in builtin___import__ (self=0x0, args=0x2aaaac0dbb00,
> kwds=0x0) at Python/bltinmodule.c:49
> #51 0x00002aaaab1b19c7 in PyCFunction_Call (func=0x2aaaabf85510,
> arg=0x2aaaac0dbb00, kw=0x0) at Objects/methodobject.c:85
> #52 0x00002aaaab14d673 in PyObject_Call (func=0x2aaaabf85510,
> arg=0x2aaaac0dbb00, kw=0x0) at Objects/abstract.c:2529
> #53 0x00002aaaab25ad03 in PyEval_CallObjectWithKeywords (func=0x2aaaabf85510,
> arg=0x2aaaac0dbb00, kw=0x0) at Python/ceval.c:3890
> #54 0x00002aaaab2543e5 in PyEval_EvalFrameEx (f=0x71a1a0, throwflag=0) at
> Python/ceval.c:2333
> #55 0x00002aaaab258b7e in PyEval_EvalCodeEx (co=0x2aaaac0dd720,
> globals=0x6443c0, locals=0x6443c0, args=0x0, argcount=0, kws=0x0, kwcount=0,
> defs=0x0, defcount=0,
> closure=0x0) at Python/ceval.c:3253
> #56 0x00002aaaab24b5ce in PyEval_EvalCode (co=0x2aaaac0dd720,
> globals=0x6443c0, locals=0x6443c0) at Python/ceval.c:667
> #57 0x00002aaaab28d492 in run_mod (mod=0x720960, filename=0x7fffffffe6bf
> "test/regression/regression-test.py", globals=0x6443c0, locals=0x6443c0,
> flags=0x7fffffffe220,
> arena=0x6707d0) at Python/pythonrun.c:1370
> #58 0x00002aaaab28d41c in PyRun_FileExFlags (fp=0x6cb7c0,
> filename=0x7fffffffe6bf "test/regression/regression-test.py", start=257,
> globals=0x6443c0, locals=0x6443c0,
> closeit=1, flags=0x7fffffffe220) at Python/pythonrun.c:1356
> #59 0x00002aaaab28bbfe in PyRun_SimpleFileExFlags (fp=0x6cb7c0,
> filename=0x7fffffffe6bf "test/regression/regression-test.py", closeit=1,
> flags=0x7fffffffe220)
> at Python/pythonrun.c:948
> #60 0x00002aaaab28b1be in PyRun_AnyFileExFlags (fp=0x6cb7c0,
> filename=0x7fffffffe6bf "test/regression/regression-test.py", closeit=1,
> flags=0x7fffffffe220)
> at Python/pythonrun.c:752
> #61 0x00002aaaab2a7497 in Py_Main (argc=3, argv=0x7fffffffe3a8) at
> Modules/main.c:640
> #62 0x00000000004006f3 in main (argc=3, argv=0x7fffffffe3a8) at
> ./Modules/python.c:23
> (gdb) p argv
> $1 = (char **) 0xa39398
> (gdb) p *argv
> $2 = 0xa26390 "test/regression/regression-jobs"
> (gdb) p **argv
> $3 = 116 't'
> (gdb) p p
> $4 = (char **) 0xa393a0
> (gdb) p *p
> $5 = 0x20 <Address 0x20 out of bounds>
> (gdb) p str_len
> $6 = 32
>
>
>
>
>
> On Sep 26, 2014, at 5:19 PM, Amos Anderson <amos.ander...@protabit.com> wrote:
>
>> Hello all --
>>
>> I'm trying to get a working configuration for my application and I can get
>> OpenMPI 1.6.5 to work, while OpenMPI 1.8.2 segfaults.
>>
>>
>> Here's how I compile OpenMPI:
>>
>> OPENMPI = openmpi-1.8.2
>> FLAGS = --enable-static
>> cd $(OPENMPI) ; ./configure $(FLAGS) --with-tm=/opt/torque-2.5.9/
>> --prefix=$(CURDIR)
>>
>>
>> I'm able to compile openmpi successfully, and I use a bjam instruction like
>> this to compile my program (which uses boost python boost_1_55_0):
>> using mpi : ../tools/openmpi/bin/mpic++ ;
>>
>> and I run my program in a Torque pbs script like this:
>>
>> /bin/rm -rf jobname.nodes
>> for i in `cat ${PBS_NODEFILE} | sort -u`
>> do
>> echo $i slots \= `grep $i ${PBS_NODEFILE} | wc -l` >> jobname.nodes
>> done
>> /home/user/myapp/tools/openmpi/bin/mpirun -np 2 -hostfile jobname.nodes
>> /home/user/myapp/myapp.exe
>>
>>
>>
>> which also compiles just fine. But when I run my program I get the segfault
>> I printed below. When I switch to:
>> OPENMPI = openmpi-1.6.5
>>
>> then everything works as expected. (As a side question, do I need both
>> -hostfile and --with-tm? I asked this question earlier today on this list).
>> That is, I believe that I'm using the exact same setup in both cases, and
>> 1.6.5 works while 1.8.2 fails. Any suggestions what I might be doing wrong?
>>
>> I suppose if I have a working setup I can give up even if it's with an older
>> version... but this could be evidence of something I'll have to confront
>> eventually.
>>
>> Thanks for any advice!
>> Amos.
>>
>>
>>
>>
>> [local:27921] *** Process received signal ***
>> [local:27921] Signal: Segmentation fault (11)
>> [local:27921] Signal code: Address not mapped (1)
>> [local:27921] Failing at address: 0x40
>> [local:27921] [ 0] /lib64/libpthread.so.0[0x322180e4c0]
>> [local:27921] [ 1] /lib64/libc.so.6(strlen+0x30)[0x3220c78d80]
>> [local:27921] [ 2]
>> /home/user/myapp/tools/openmpi/lib/libopen-pal.so.6(opal_argv_join+0x95)[0x2b87f5c4e175]
>> [local:27921] [ 3]
>> /home/user/myapp/tools/openmpi/lib/libmpi.so.1(ompi_mpi_init+0x82d)[0x2b87f3c9ec0d]
>> [local:27921] [ 4]
>> /home/user/myapp/tools/openmpi/lib/libmpi.so.1(MPI_Init+0xf0)[0x2b87f3cbc310]
>> [local:27921] [ 5]
>> /home/user/myapp/lib/libboost_mpi.so.1.55.0(_ZN5boost3mpi11environmentC1ERiRPPcb+0x36)[0x2b87f3795826]
>> [local:27921] [ 6]
>> /home/user/myapp/lib/mpi.so(_ZN5boost3mpi6python8mpi_initENS_6python4listEb+0x314)[0x2b87f30bc7b4]
>> [local:27921] [ 7]
>> /home/user/myapp/lib/mpi.so(_ZN5boost3mpi6python18export_environmentEv+0xcc6)[0x2b87f30bd5f6]
>> [local:27921] [ 8]
>> /home/user/myapp/lib/mpi.so(_ZN5boost3mpi6python15init_module_mpiEv+0x547)[0x2b87f30d4967]
>> [local:27921] [ 9]
>> /home/user/myapp/lib/libboost_python.so.1.55.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x530)[0x2b87f3558430]
>> [local:27921] [10]
>> /home/user/myapp/lib/libboost_python.so.1.55.0(_ZN5boost6python16handle_exceptionIPFvvEEEbT_+0x38)[0x2b87f3559798]
>> [local:27921] [11]
>> /home/user/myapp/lib/libboost_python.so.1.55.0(_ZN5boost6python6detail11init_moduleEPKcPFvvE+0x63)[0x2b87f3559463]
>> [local:27921] [12]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0xc2)[0x2b87e8c79282]
>> [local:27921] [13]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c771a9]
>> [local:27921] [14]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c776c1]
>> [local:27921] [15]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1b7)[0x2b87e8c77977]
>> [local:27921] [16]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c57bcd]
>> [local:27921] [17]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b87e8bb7ae8]
>> [local:27921] [18]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x2b87e8c58216]
>> [local:27921] [19]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x381c)[0x2b87e8c5c79c]
>> [local:27921] [20]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x8c9)[0x2b87e8c60c89]
>> [local:27921] [21]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b87e8c60d02]
>> [local:27921] [22]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x2b87e8c74432]
>> [local:27921] [23]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c769f0]
>> [local:27921] [24]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c771a9]
>> [local:27921] [25]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c77642]
>> [local:27921] [26]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1b7)[0x2b87e8c77977]
>> [local:27921] [27]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0[0x2b87e8c57bcd]
>> [local:27921] [28]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyObject_Call+0x68)[0x2b87e8bb7ae8]
>> [local:27921] [29]
>> /home/user/myapp/tools/python/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x2b87e8c58216]
>> [local:27921] *** End of error message ***
>>
>>
>>
>
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