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Subject: Re: [OMPI users] [openib] segfault when using openib btl
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2010-08-16 12:22:45


Sorry for the delay in replying.

Odd; the values of the callback function pointer should never be 0. This seems to suggest some kind of memory corruption is occurring.

I don't know if it's possible, because the stack trace looks like you're calling through python, but can you run this application through valgrind, or some other memory-checking debugger?

On Aug 10, 2010, at 7:15 AM, Eloi Gaudry wrote:

> Hi,
>
> sorry, i just forgot to add the values of the function parameters:
> (gdb) print reg->cbdata
> $1 = (void *) 0x0
> (gdb) print openib_btl->super
> $2 = {btl_component = 0x2b341edd7380, btl_eager_limit = 12288, btl_rndv_eager_limit = 12288, btl_max_send_size = 65536, btl_rdma_pipeline_send_length = 1048576,
> btl_rdma_pipeline_frag_size = 1048576, btl_min_rdma_pipeline_size = 1060864, btl_exclusivity = 1024, btl_latency = 10, btl_bandwidth = 800, btl_flags = 310,
> btl_add_procs = 0x2b341eb8ee47 <mca_btl_openib_add_procs>, btl_del_procs = 0x2b341eb90156 <mca_btl_openib_del_procs>, btl_register = 0, btl_finalize = 0x2b341eb93186 <mca_btl_openib_finalize>,
> btl_alloc = 0x2b341eb90a3e <mca_btl_openib_alloc>, btl_free = 0x2b341eb91400 <mca_btl_openib_free>, btl_prepare_src = 0x2b341eb91813 <mca_btl_openib_prepare_src>,
> btl_prepare_dst = 0x2b341eb91f2e <mca_btl_openib_prepare_dst>, btl_send = 0x2b341eb94517 <mca_btl_openib_send>, btl_sendi = 0x2b341eb9340d <mca_btl_openib_sendi>,
> btl_put = 0x2b341eb94660 <mca_btl_openib_put>, btl_get = 0x2b341eb94c4e <mca_btl_openib_get>, btl_dump = 0x2b341acd45cb <mca_btl_base_dump>, btl_mpool = 0xf3f4110,
> btl_register_error = 0x2b341eb90565 <mca_btl_openib_register_error_cb>, btl_ft_event = 0x2b341eb952e7 <mca_btl_openib_ft_event>}
> (gdb) print hdr->tag
> $3 = 0 '\0'
> (gdb) print des
> $4 = (mca_btl_base_descriptor_t *) 0xf4a6700
> (gdb) print reg->cbfunc
> $5 = (mca_btl_base_module_recv_cb_fn_t) 0
>
> Eloi
>
> On Tuesday 10 August 2010 16:04:08 Eloi Gaudry wrote:
> > Hi,
> >
> > Here is the output of a core file generated during a segmentation fault
> > observed during a collective call (using openib):
> >
> > #0 0x0000000000000000 in ?? ()
> > (gdb) where
> > #0 0x0000000000000000 in ?? ()
> > #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
> > (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700, byte_len=18) at
> > btl_openib_component.c:2881 #2 0x00002aedbc4e25e2 in handle_wc
> > (device=0x19024ac0, cq=0, wc=0x7ffff279ce90) at
> > btl_openib_component.c:3178 #3 0x00002aedbc4e2e9d in poll_device
> > (device=0x19024ac0, count=2) at btl_openib_component.c:3318 #4
> > 0x00002aedbc4e34b8 in progress_one_device (device=0x19024ac0) at
> > btl_openib_component.c:3426 #5 0x00002aedbc4e3561 in
> > btl_openib_component_progress () at btl_openib_component.c:3451 #6
> > 0x00002aedb8b22ab8 in opal_progress () at runtime/opal_progress.c:207 #7
> > 0x00002aedb859f497 in opal_condition_wait (c=0x2aedb888ccc0,
> > m=0x2aedb888cd20) at ../opal/threads/condition.h:99 #8 0x00002aedb859fa31
> > in ompi_request_default_wait_all (count=2, requests=0x7ffff279d0e0,
> > statuses=0x0) at request/req_wait.c:262 #9 0x00002aedbd7559ad in
> > ompi_coll_tuned_allreduce_intra_recursivedoubling (sbuf=0x7ffff279d444,
> > rbuf=0x7ffff279d440, count=1, dtype=0x6788220, op=0x6787a20,
> > comm=0x19d81ff0, module=0x19d82b20) at coll_tuned_allreduce.c:223
> > #10 0x00002aedbd7514f7 in ompi_coll_tuned_allreduce_intra_dec_fixed
> > (sbuf=0x7ffff279d444, rbuf=0x7ffff279d440, count=1, dtype=0x6788220,
> > op=0x6787a20, comm=0x19d81ff0, module=0x19d82b20) at
> > coll_tuned_decision_fixed.c:63
> > #11 0x00002aedb85c7792 in PMPI_Allreduce (sendbuf=0x7ffff279d444,
> > recvbuf=0x7ffff279d440, count=1, datatype=0x6788220, op=0x6787a20,
> > comm=0x19d81ff0) at pallreduce.c:102 #12 0x0000000004387dbf in
> > FEMTown::MPI::Allreduce (sendbuf=0x7ffff279d444, recvbuf=0x7ffff279d440,
> > count=1, datatype=0x6788220, op=0x6787a20, comm=0x19d81ff0) at
> > stubs.cpp:626 #13 0x0000000004058be8 in FEMTown::Domain::align (itf=
> > {<FEMTown::Boost::shared_base_ptr<FEMTown::Domain::Interface>>
> > = {_vptr.shared_base_ptr = 0x7ffff279d620, ptr_ = {px = 0x199942a4, pn =
> > {pi_ = 0x6}}}, <No data fields>}) at interface.cpp:371
> > #14 0x00000000040cb858 in FEMTown::Field::detail::align_itfs_and_neighbhors
> > (dim=2, set={px = 0x7ffff279d780, pn = {pi_ = 0x2f279d640}},
> > check_info=@0x7ffff279d7f0) at check.cpp:63 #15 0x00000000040cbfa8 in
> > FEMTown::Field::align_elements (set={px = 0x7ffff279d950, pn = {pi_ =
> > 0x66e08d0}}, check_info=@0x7ffff279d7f0) at check.cpp:159 #16
> > 0x00000000039acdd4 in PyField_align_elements (self=0x0,
> > args=0x2aaab0765050, kwds=0x19d2e950) at check.cpp:31 #17
> > 0x0000000001fbf76d in FEMTown::Main::ExErrCatch<_object* (*)(_object*,
> > _object*, _object*)>::exec<_object> (this=0x7ffff279dc20, s=0x0,
> > po1=0x2aaab0765050, po2=0x19d2e950) at
> > /home/qa/svntop/femtown/modules/main/py/exception.hpp:463
> > #18 0x00000000039acc82 in PyField_align_elements_ewrap (self=0x0,
> > args=0x2aaab0765050, kwds=0x19d2e950) at check.cpp:39 #19
> > 0x00000000044093a0 in PyEval_EvalFrameEx (f=0x19b52e90, throwflag=<value
> > optimized out>) at Python/ceval.c:3921 #20 0x000000000440aae9 in
> > PyEval_EvalCodeEx (co=0x2aaab754ad50, globals=<value optimized out>,
> > locals=<value optimized out>, args=0x3, argcount=1, kws=0x19ace4a0,
> > kwcount=2, defs=0x2aaab75e4800, defcount=2, closure=0x0) at
> > Python/ceval.c:2968
> > #21 0x0000000004408f58 in PyEval_EvalFrameEx (f=0x19ace2d0,
> > throwflag=<value optimized out>) at Python/ceval.c:3802 #22
> > 0x000000000440aae9 in PyEval_EvalCodeEx (co=0x2aaab7550120, globals=<value
> > optimized out>, locals=<value optimized out>, args=0x7, argcount=1,
> > kws=0x19acc418, kwcount=3, defs=0x2aaab759e958, defcount=6, closure=0x0)
> > at Python/ceval.c:2968
> > #23 0x0000000004408f58 in PyEval_EvalFrameEx (f=0x19acc1c0,
> > throwflag=<value optimized out>) at Python/ceval.c:3802 #24
> > 0x000000000440aae9 in PyEval_EvalCodeEx (co=0x2aaab8b5e738, globals=<value
> > optimized out>, locals=<value optimized out>, args=0x6, argcount=1,
> > kws=0x19abd328, kwcount=5, defs=0x2aaab891b7e8, defcount=3, closure=0x0)
> > at Python/ceval.c:2968
> > #25 0x0000000004408f58 in PyEval_EvalFrameEx (f=0x19abcea0,
> > throwflag=<value optimized out>) at Python/ceval.c:3802 #26
> > 0x000000000440aae9 in PyEval_EvalCodeEx (co=0x2aaab3eb4198, globals=<value
> > optimized out>, locals=<value optimized out>, args=0xb, argcount=1,
> > kws=0x19a89df0, kwcount=10, defs=0x0, defcount=0, closure=0x0) at
> > Python/ceval.c:2968
> > #27 0x0000000004408f58 in PyEval_EvalFrameEx (f=0x19a89c40,
> > throwflag=<value optimized out>) at Python/ceval.c:3802 #28
> > 0x000000000440aae9 in PyEval_EvalCodeEx (co=0x2aaab3eb4288, globals=<value
> > optimized out>, locals=<value optimized out>, args=0x1, argcount=0,
> > kws=0x19a89330, kwcount=0, defs=0x2aaab8b66668, defcount=1, closure=0x0)
> > at Python/ceval.c:2968
> > #29 0x0000000004408f58 in PyEval_EvalFrameEx (f=0x19a891b0,
> > throwflag=<value optimized out>) at Python/ceval.c:3802 #30
> > 0x000000000440aae9 in PyEval_EvalCodeEx (co=0x2aaab8b6a738, globals=<value
> > optimized out>, locals=<value optimized out>, args=0x0, argcount=0,
> > kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at
> > Python/ceval.c:2968
> > #31 0x000000000440ac02 in PyEval_EvalCode (co=0x1902f9b0, globals=0x0,
> > locals=0x190d9700) at Python/ceval.c:522 #32 0x000000000442853c in
> > PyRun_StringFlags (str=0x192fd3d8 "DIRECT.Actran.main()", start=<value
> > optimized out>, globals=0x192213d0, locals=0x192213d0, flags=0x0) at
> > Python/pythonrun.c:1335 #33 0x0000000004429690 in PyRun_SimpleStringFlags
> > (command=0x192fd3d8 "DIRECT.Actran.main()", flags=0x0) at
> > Python/pythonrun.c:957 #34 0x0000000001fa1cf9 in
> > FEMTown::Python::FEMPy::run_application (this=0x7ffff279f650) at
> > fempy.cpp:873 #35 0x000000000434ce99 in FEMTown::Main::Batch::run
> > (this=0x7ffff279f650) at batch.cpp:374 #36 0x0000000001f9aa25 in main
> > (argc=8, argv=0x7ffff279fa48) at main.cpp:10 (gdb) f 1
> > #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
> > (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700, byte_len=18) at
> > btl_openib_component.c:2881 2881 reg->cbfunc(
> > &openib_btl->super, hdr->tag, des, reg->cbdata ); Current language: auto;
> > currently c
> > (gdb)
> > #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
> > (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700, byte_len=18) at
> > btl_openib_component.c:2881 2881 reg->cbfunc(
> > &openib_btl->super, hdr->tag, des, reg->cbdata ); (gdb) l
> > 2876
> > 2877 if(OPAL_LIKELY(!(is_credit_msg = is_credit_message(frag)))) {
> > 2878 /* call registered callback */
> > 2879 mca_btl_active_message_callback_t* reg;
> > 2880 reg = mca_btl_base_active_message_trigger + hdr->tag;
> > 2881 reg->cbfunc( &openib_btl->super, hdr->tag, des, reg->cbdata
> > ); 2882 if(MCA_BTL_OPENIB_RDMA_FRAG(frag)) {
> > 2883 cqp = (hdr->credits >> 11) & 0x0f;
> > 2884 hdr->credits &= 0x87ff;
> > 2885 } else {
> >
> > Regards,
> > Eloi
> >
> > On Friday 16 July 2010 16:01:02 Eloi Gaudry wrote:
> > > Hi Edgar,
> > >
> > > The only difference I could observed was that the segmentation fault
> > > appeared sometimes later during the parallel computation.
> > >
> > > I'm running out of idea here. I wish I could use the "--mca coll tuned"
> > > with "--mca self,sm,tcp" so that I could check that the issue is not
> > > somehow limited to the tuned collective routines.
> > >
> > > Thanks,
> > > Eloi
> > >
> > > On Thursday 15 July 2010 17:24:24 Edgar Gabriel wrote:
> > > > On 7/15/2010 10:18 AM, Eloi Gaudry wrote:
> > > > > hi edgar,
> > > > >
> > > > > thanks for the tips, I'm gonna try this option as well. the
> > > > > segmentation fault i'm observing always happened during a collective
> > > > > communication indeed... does it basically switch all collective
> > > > > communication to basic mode, right ?
> > > > >
> > > > > sorry for my ignorance, but what's a NCA ?
> > > >
> > > > sorry, I meant to type HCA (InifinBand networking card)
> > > >
> > > > Thanks
> > > > Edgar
> > > >
> > > > > thanks,
> > > > > éloi
> > > > >
> > > > > On Thursday 15 July 2010 16:20:54 Edgar Gabriel wrote:
> > > > >> you could try first to use the algorithms in the basic module, e.g.
> > > > >>
> > > > >> mpirun -np x --mca coll basic ./mytest
> > > > >>
> > > > >> and see whether this makes a difference. I used to observe sometimes
> > > > >> a (similar ?) problem in the openib btl triggered from the tuned
> > > > >> collective component, in cases where the ofed libraries were
> > > > >> installed but no NCA was found on a node. It used to work however
> > > > >> with the basic component.
> > > > >>
> > > > >> Thanks
> > > > >> Edgar
> > > > >>
> > > > >> On 7/15/2010 3:08 AM, Eloi Gaudry wrote:
> > > > >>> hi Rolf,
> > > > >>>
> > > > >>> unfortunately, i couldn't get rid of that annoying segmentation
> > > > >>> fault when selecting another bcast algorithm. i'm now going to
> > > > >>> replace MPI_Bcast with a naive implementation (using MPI_Send and
> > > > >>> MPI_Recv) and see if that helps.
> > > > >>>
> > > > >>> regards,
> > > > >>> éloi
> > > > >>>
> > > > >>> On Wednesday 14 July 2010 10:59:53 Eloi Gaudry wrote:
> > > > >>>> Hi Rolf,
> > > > >>>>
> > > > >>>> thanks for your input. You're right, I miss the
> > > > >>>> coll_tuned_use_dynamic_rules option.
> > > > >>>>
> > > > >>>> I'll check if I the segmentation fault disappears when using the
> > > > >>>> basic bcast linear algorithm using the proper command line you
> > > > >>>> provided.
> > > > >>>>
> > > > >>>> Regards,
> > > > >>>> Eloi
> > > > >>>>
> > > > >>>> On Tuesday 13 July 2010 20:39:59 Rolf vandeVaart wrote:
> > > > >>>>> Hi Eloi:
> > > > >>>>> To select the different bcast algorithms, you need to add an
> > > > >>>>> extra mca parameter that tells the library to use dynamic
> > > > >>>>> selection. --mca coll_tuned_use_dynamic_rules 1
> > > > >>>>>
> > > > >>>>> One way to make sure you are typing this in correctly is to use
> > > > >>>>> it with ompi_info. Do the following:
> > > > >>>>> ompi_info -mca coll_tuned_use_dynamic_rules 1 --param coll
> > > > >>>>>
> > > > >>>>> You should see lots of output with all the different algorithms
> > > > >>>>> that can be selected for the various collectives.
> > > > >>>>> Therefore, you need this:
> > > > >>>>>
> > > > >>>>> --mca coll_tuned_use_dynamic_rules 1 --mca
> > > > >>>>> coll_tuned_bcast_algorithm 1
> > > > >>>>>
> > > > >>>>> Rolf
> > > > >>>>>
> > > > >>>>> On 07/13/10 11:28, Eloi Gaudry wrote:
> > > > >>>>>> Hi,
> > > > >>>>>>
> > > > >>>>>> I've found that "--mca coll_tuned_bcast_algorithm 1" allowed to
> > > > >>>>>> switch to the basic linear algorithm. Anyway whatever the
> > > > >>>>>> algorithm used, the segmentation fault remains.
> > > > >>>>>>
> > > > >>>>>> Does anyone could give some advice on ways to diagnose the issue
> > > > >>>>>> I'm facing ?
> > > > >>>>>>
> > > > >>>>>> Regards,
> > > > >>>>>> Eloi
> > > > >>>>>>
> > > > >>>>>> On Monday 12 July 2010 10:53:58 Eloi Gaudry wrote:
> > > > >>>>>>> Hi,
> > > > >>>>>>>
> > > > >>>>>>> I'm focusing on the MPI_Bcast routine that seems to randomly
> > > > >>>>>>> segfault when using the openib btl. I'd like to know if there
> > > > >>>>>>> is any way to make OpenMPI switch to a different algorithm
> > > > >>>>>>> than the default one being selected for MPI_Bcast.
> > > > >>>>>>>
> > > > >>>>>>> Thanks for your help,
> > > > >>>>>>> Eloi
> > > > >>>>>>>
> > > > >>>>>>> On Friday 02 July 2010 11:06:52 Eloi Gaudry wrote:
> > > > >>>>>>>> Hi,
> > > > >>>>>>>>
> > > > >>>>>>>> I'm observing a random segmentation fault during an internode
> > > > >>>>>>>> parallel computation involving the openib btl and
> > > > >>>>>>>> OpenMPI-1.4.2 (the same issue can be observed with
> > > > >>>>>>>> OpenMPI-1.3.3).
> > > > >>>>>>>>
> > > > >>>>>>>> mpirun (Open MPI) 1.4.2
> > > > >>>>>>>> Report bugs to http://www.open-mpi.org/community/help/
> > > > >>>>>>>> [pbn08:02624] *** Process received signal ***
> > > > >>>>>>>> [pbn08:02624] Signal: Segmentation fault (11)
> > > > >>>>>>>> [pbn08:02624] Signal code: Address not mapped (1)
> > > > >>>>>>>> [pbn08:02624] Failing at address: (nil)
> > > > >>>>>>>> [pbn08:02624] [ 0] /lib64/libpthread.so.0 [0x349540e4c0]
> > > > >>>>>>>> [pbn08:02624] *** End of error message ***
> > > > >>>>>>>> sh: line 1: 2624 Segmentation fault
> > > > >>>>>>>>
> > > > >>>>>>>> \/share\/hpc3\/actran_suite\/Actran_11\.0\.rc2\.41872\/RedHatE
> > > > >>>>>>>> L\ -5 \/ x 86 _6 4\ /bin\/actranpy_mp
> > > > >>>>>>>> '--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/RedHatEL
> > > > >>>>>>>> -5 /x 86 _ 64 /A c tran_11.0.rc2.41872'
> > > > >>>>>>>> '--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3Dreal_m
> > > > >>>>>>>> 4_ n2 .d a t'
> > > > >>>>>>>> '--scratch=/scratch/st25652/LSF_130073_0_47696_0/scratch'
> > > > >>>>>>>> '--mem=3200' '--threads=1' '--errorlevel=FATAL' '--t_max=0.1'
> > > > >>>>>>>> '--parallel=domain'
> > > > >>>>>>>>
> > > > >>>>>>>> If I choose not to use the openib btl (by using --mca btl
> > > > >>>>>>>> self,sm,tcp on the command line, for instance), I don't
> > > > >>>>>>>> encounter any problem and the parallel computation runs
> > > > >>>>>>>> flawlessly.
> > > > >>>>>>>>
> > > > >>>>>>>> I would like to get some help to be able:
> > > > >>>>>>>> - to diagnose the issue I'm facing with the openib btl
> > > > >>>>>>>> - understand why this issue is observed only when using the
> > > > >>>>>>>> openib btl and not when using self,sm,tcp
> > > > >>>>>>>>
> > > > >>>>>>>> Any help would be very much appreciated.
> > > > >>>>>>>>
> > > > >>>>>>>> The outputs of ompi_info and the configure scripts of OpenMPI
> > > > >>>>>>>> are enclosed to this email, and some information on the
> > > > >>>>>>>> infiniband drivers as well.
> > > > >>>>>>>>
> > > > >>>>>>>> Here is the command line used when launching a parallel
> > > > >>>>>>>> computation
> > > > >>>>>>>>
> > > > >>>>>>>> using infiniband:
> > > > >>>>>>>> path_to_openmpi/bin/mpirun -np $NPROCESS --hostfile
> > > > >>>>>>>> host.list --mca
> > > > >>>>>>>>
> > > > >>>>>>>> btl openib,sm,self,tcp --display-map --verbose --version
> > > > >>>>>>>> --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 0
> > > > >>>>>>>> [...]
> > > > >>>>>>>>
> > > > >>>>>>>> and the command line used if not using infiniband:
> > > > >>>>>>>> path_to_openmpi/bin/mpirun -np $NPROCESS --hostfile
> > > > >>>>>>>> host.list --mca
> > > > >>>>>>>>
> > > > >>>>>>>> btl self,sm,tcp --display-map --verbose --version --mca
> > > > >>>>>>>> mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 0 [...]
> > > > >>>>>>>>
> > > > >>>>>>>> Thanks,
> > > > >>>>>>>> Eloi
> > > > >>>>>>
> > > > >>>>>> _______________________________________________
> > > > >>>>>> users mailing list
> > > > >>>>>> users_at_[hidden]
> > > > >>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> --
>
>
> Eloi Gaudry
>
> Free Field Technologies
> Company Website: http://www.fft.be
> Company Phone: +32 10 487 959
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

-- 
Jeff Squyres
jsquyres_at_[hidden]
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