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 ***
>
>
>
