I'm not calling mpirun in this case because this particular calculation doesn't
use more than one processor. What I'm doing on my command line is this:
/home/user/myapp/tools/python/bin/python test/regression/regression-test.py
test/regression/regression-jobs
and internally I check for rank/size. This command is executed in the context
of a souped up LD_LIBRARY_PATH. You can see the variable argv in opal_argv_join
is ending up with the last argument on my command line.
I suppose your question implies that mpirun is mandatory for executing anything
compiled with OpenMPI > 1.6 ?
On Sep 29, 2014, at 10:28 AM, Ralph Castain <r...@open-mpi.org> wrote:
> 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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>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
>> Link to this post:
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>
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