Regression: Crash when called from Rmpi
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
openmpi (Ubuntu) |
New
|
Undecided
|
Unassigned |
Bug Description
Hi,
we have three machines at different hardy patchlevels,
one with openmpi1-1.2.5-1 (around 2008-03-17)
and two current with 1.2.5-1ubuntu1. All are AMD64 architecture.
When initializing Rmpi I get a
library(Rmpi)
*** caught segfault ***
which actually happens in
Rmpi.c:73 MPI_Init((void *)0,(void *)0);
Program received signal SIGSEGV, Segmentation fault.
0x00007f7e9ffb5b8b in _int_malloc () from /usr/lib/
#0 0x00007f7e9ffb5b8b in _int_malloc () from /usr/lib/
#1 0x00007f7e9ffb6e58 in malloc () from /usr/lib/
#2 0x00007f7e9ff98bfb in opal_class_
#3 0x00007f7e9fface2b in opal_malloc_init () from /usr/lib/
#4 0x00007f7e9ff99d97 in opal_init_util () from /usr/lib/
#5 0x00007f7e9ff99e76 in opal_init () from /usr/lib/
#6 0x00007f7ea0889723 in ompi_mpi_init () from /usr/lib/
#7 0x00007f7ea08ab15f in PMPI_Init () from /usr/lib/
#8 0x00007f7ea0aef866 in mpi_initialize () at Rmpi.c:73
a simple "mpirun -n 4 date" works fine on all machines.
Although all three hachines have completely different libc-versions
(between 2.7-5ubuntu2 and 2.7-9ubuntu2) it is sufficient to copy the
/usr/lib/
to the two other machines. Rebuilding 1.2.5-1ubuntu1 on the
newer machines doesn't help.
Since the only changes in ubuntu-1 are fixed dangling pointers
and a maintainer field, I suspect it has to do with the build process.
Yours,
Steffen
I'm seeing this, too, on released hardy. (1.2.5-1ubuntu1). Here's my stack:
Program received signal SIGSEGV, Segmentation fault. libopen- pal.so. 0 libopen- pal.so. 0 libopen- pal.so. 0 initialize () from /usr/lib/ libopen- pal.so. 0 libopen- pal.so. 0 libopen- pal.so. 0 libopen- pal.so. 0 libmpi. so.0 libmpi. so.0 mpi::environmen t::environment () from /home/andreas/ pool/lib/ libboost_ mpi-gcc42- mt-1_35. so.1.35. 0 mpi::python: :mpi_init () from /home/andreas/ pool/lib/ python2. 5/site- packages/ boost/mpi. so mpi::python: :export_ environment () from /home/andreas/ pool/lib/ python2. 5/site- packages/ boost/mpi. so mpi::python: :init_module_ mpi () from /home/andreas/ pool/lib/ python2. 5/site- packages/ boost/mpi. so function0< void, std::allocator< boost:: function_ base> >::operator() () pool/lib/ libboost_ python- gcc42-mt- 1_35.so. 1.35.0 python: :handle_ exception_ impl () from /home/andreas/ pool/lib/ libboost_ python- gcc42-mt- 1_35.so. 1.35.0 python: :handle_ exception< void (*)()> () from /home/andreas/ pool/lib/ libboost_ python- gcc42-mt- 1_35.so. 1.35.0 python: :detail: :init_module () from /home/andreas/ pool/lib/ libboost_ python- gcc42-mt- 1_35.so. 1.35.0 LoadDynamicModu le () ImportModuleLev el () CallObjectWithK eywords () ExecCodeModuleE x () ImportModuleLev el () CallObjectWithK eywords () veOneFlags () veLoopFlags () Flags ()
[Switching to Thread 0x7f51cbec26e0 (LWP 27918)]
0x00007f51c932fb8b in _int_malloc () from /usr/lib/
(gdb) ]bt
Undefined command: "". Try "help".
(gdb) bt
#0 0x00007f51c932fb8b in _int_malloc () from /usr/lib/
#1 0x00007f51c9330e58 in malloc () from /usr/lib/
#2 0x00007f51c9312bfb in opal_class_
#3 0x00007f51c9326e2b in opal_malloc_init () from /usr/lib/
#4 0x00007f51c9313d97 in opal_init_util () from /usr/lib/
#5 0x00007f51c9313e76 in opal_init () from /usr/lib/
#6 0x00007f51c99d7723 in ompi_mpi_init () from /usr/lib/
#7 0x00007f51c99f90d6 in PMPI_Init () from /usr/lib/
#8 0x00007f51ca11f5cb in boost::
#9 0x00007f51ca5b80a2 in boost::
#10 0x00007f51ca5b8607 in boost::
#11 0x00007f51ca5bdb8c in boost::
#12 0x00007f51c9c6abee in boost::
from /home/andreas/
#13 0x00007f51c9c6a998 in boost::
#14 0x00007f51c9c6b265 in boost::
#15 0x00007f51c9c6af46 in boost::
#16 0x00000000004a39c3 in _PyImport_
#17 0x00000000004a1809 in ?? ()
#18 0x00000000004a1cdb in ?? ()
#19 0x00000000004a1f1a in ?? ()
#20 0x00000000004a23c5 in PyImport_
#21 0x0000000000481a19 in ?? ()
#22 0x0000000000417e73 in PyObject_Call ()
#23 0x0000000000481fc2 in PyEval_
#24 0x0000000000485b61 in PyEval_EvalFrameEx ()
#25 0x000000000048a376 in PyEval_EvalCodeEx ()
#26 0x000000000048a492 in PyEval_EvalCode ()
#27 0x00000000004a0a00 in PyImport_
#28 0x00000000004a1230 in ?? ()
#29 0x00000000004a28c3 in ?? ()
#30 0x00000000004a1809 in ?? ()
#31 0x00000000004a1cdb in ?? ()
#32 0x00000000004a1f1a in ?? ()
#33 0x00000000004a23c5 in PyImport_
#34 0x0000000000481a19 in ?? ()
#35 0x0000000000417e73 in PyObject_Call ()
#36 0x0000000000481fc2 in PyEval_
#37 0x0000000000485b61 in PyEval_EvalFrameEx ()
#38 0x000000000048a376 in PyEval_EvalCodeEx ()
#39 0x000000000048a492 in PyEval_EvalCode ()
#40 0x00000000004ac459 in PyRun_Interacti
#41 0x00000000004ac664 in PyRun_Interacti
#42 0x00000000004ac76a in PyRun_AnyFileEx