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Subject: Re: [OMPI users] [openib] segfault when using openib btl
From: Eloi Gaudry (eg_at_[hidden])
Date: 2010-09-22 05:23:23


Hi Nysal,

Thanks for your suggestions.

I'm now able to get the checksum computed and redirected to stdout, thanks (I forgot the "-mca pml_base_verbose 5" option, you were right).
I haven't been able to observe the segmentation fault (with hdr->tag=0) so far (when using pml csum) but I 'll let you know when I am.

I've got two others question, which may be related to the error observed:

1/ does the maximum number of MPI_Comm that can be handled by OpenMPI somehow depends on the btl being used (i.e. if I'm using
openib, may I use the same number of MPI_Comm object as with tcp) ? Is there something as MPI_COMM_MAX in OpenMPI ?

2/ the segfaults only appears during a mpi collective call, with very small message (one int is being broadcast, for instance) ; i followed the guidelines given at http://icl.cs.utk.edu/open-
mpi/faq/?category=openfabrics#ib-small-message-rdma but the debug-build of OpenMPI asserts if I use a different min-size that 255. Anyway, if I deactivate eager_rdma, the segfaults remains.
Does the openib btl handle very small message differently (even with eager_rdma deactivated) than tcp ? is there a way to make sure that large messages and small messages are handled the same way ?

Regards,
Eloi

On Friday 17 September 2010 17:57:17 Nysal Jan wrote:
> Hi Eloi,
> Create a debug build of OpenMPI (--enable-debug) and while running with the
> csum PML add "-mca pml_base_verbose 5" to the command line. This will print
> the checksum details for each fragment sent over the wire. I'm guessing it
> didnt catch anything because the BTL failed. The checksum verification is
> done in the PML, which the BTL calls via a callback function. In your case
> the PML callback is never called because the hdr->tag is invalid. So
> enabling checksum tracing also might not be of much use. Is it the first
> Bcast that fails or the nth Bcast and what is the message size? I'm not
> sure what could be the problem at this moment. I'm afraid you will have to
> debug the BTL to find out more.
>
> --Nysal
>
> On Fri, Sep 17, 2010 at 4:39 PM, Eloi Gaudry <eg_at_[hidden]> wrote:
> > Hi Nysal,
> >
> > thanks for your response.
> >
> > I've been unable so far to write a test case that could illustrate the
> > hdr->tag=0 error.
> > Actually, I'm only observing this issue when running an internode
> > computation involving infiniband hardware from Mellanox (MT25418,
> > ConnectX IB DDR, PCIe 2.0
> > 2.5GT/s, rev a0) with our time-domain software.
> >
> > I checked, double-checked, and rechecked again every MPI use performed
> > during a parallel computation and I couldn't find any error so far. The
> > fact that the very
> > same parallel computation run flawlessly when using tcp (and disabling
> > openib support) might seem to indicate that the issue is somewhere
> > located inside the
> > openib btl or at the hardware/driver level.
> >
> > I've just used the "-mca pml csum" option and I haven't seen any related
> > messages (when hdr->tag=0 and the segfaults occurs).
> > Any suggestion ?
> >
> > Regards,
> > Eloi
> >
> > On Friday 17 September 2010 16:03:34 Nysal Jan wrote:
> > > Hi Eloi,
> > > Sorry for the delay in response. I haven't read the entire email
> > > thread, but do you have a test case which can reproduce this error?
> > > Without that it will be difficult to nail down the cause. Just to
> > > clarify, I do not work for an iwarp vendor. I can certainly try to
> > > reproduce it on an IB system. There is also a PML called csum, you can
> > > use it via "-mca pml csum", which will checksum the MPI messages and
> > > verify it at the receiver side for any data corruption. You can try
> > > using it to see if it is able
> >
> > to
> >
> > > catch anything.
> > >
> > > Regards
> > > --Nysal
> > >
> > > On Thu, Sep 16, 2010 at 3:48 PM, Eloi Gaudry <eg_at_[hidden]> wrote:
> > > > Hi Nysal,
> > > >
> > > > I'm sorry to intrrupt, but I was wondering if you had a chance to
> > > > look
> >
> > at
> >
> > > > this error.
> > > >
> > > > Regards,
> > > > Eloi
> > > >
> > > >
> > > >
> > > > --
> > > >
> > > >
> > > > Eloi Gaudry
> > > >
> > > > Free Field Technologies
> > > > Company Website: http://www.fft.be
> > > > Company Phone: +32 10 487 959
> > > >
> > > >
> > > > ---------- Forwarded message ----------
> > > > From: Eloi Gaudry <eg_at_[hidden]>
> > > > To: Open MPI Users <users_at_[hidden]>
> > > > Date: Wed, 15 Sep 2010 16:27:43 +0200
> > > > Subject: Re: [OMPI users] [openib] segfault when using openib btl
> > > > Hi,
> > > >
> > > > I was wondering if anybody got a chance to have a look at this issue.
> > > >
> > > > Regards,
> > > > Eloi
> > > >
> > > > On Wednesday 18 August 2010 09:16:26 Eloi Gaudry wrote:
> > > > > Hi Jeff,
> > > > >
> > > > > Please find enclosed the output (valgrind.out.gz) from
> > > > > /opt/openmpi-debug-1.4.2/bin/orterun -np 2 --host pbn11,pbn10 --mca
> >
> > btl
> >
> > > > > openib,self --display-map --verbose --mca mpi_warn_on_fork 0 --mca
> > > > > btl_openib_want_fork_support 0 -tag-output
> > > > > /opt/valgrind-3.5.0/bin/valgrind --tool=memcheck
> > > > > --suppressions=/opt/openmpi-debug-1.4.2/share/openmpi/openmpi-
> > > > > valgrind.supp --suppressions=./suppressions.python.supp
> > > > > /opt/actran/bin/actranpy_mp ...
> > > > >
> > > > > Thanks,
> > > > > Eloi
> > > > >
> > > > > On Tuesday 17 August 2010 09:32:53 Eloi Gaudry wrote:
> > > > > > On Monday 16 August 2010 19:14:47 Jeff Squyres wrote:
> > > > > > > On Aug 16, 2010, at 10:05 AM, Eloi Gaudry wrote:
> > > > > > > > I did run our application through valgrind but it couldn't
> > > > > > > > find any "Invalid write": there is a bunch of "Invalid read"
> > > > > > > > (I'm using
> > > >
> > > > 1.4.2
> > > >
> > > > > > > > with the suppression file), "Use of uninitialized bytes" and
> > > > > > > > "Conditional jump depending on uninitialized bytes" in
> >
> > different
> >
> > > > ompi
> > > >
> > > > > > > > routines. Some of them are located in btl_openib_component.c.
> > > > > > > > I'll send you an output of valgrind shortly.
> > > > > > >
> > > > > > > A lot of them in btl_openib_* are to be expected -- OpenFabrics
> > > > > > > uses OS-bypass methods for some of its memory, and therefore
> > > > > > > valgrind is unaware of them (and therefore incorrectly marks
> > > > > > > them as
> > > > > > > uninitialized).
> > > > > >
> > > > > > would it help if i use the upcoming 1.5 version of openmpi ? i
> >
> > read
> >
> > > > that
> > > >
> > > > > > a huge effort has been done to clean-up the valgrind output ? but
> > > > > > maybe that this doesn't concern this btl (for the reasons you
> > > > > > mentionned).
> > > > > >
> > > > > > > > Another question, you said that the callback function pointer
> > > >
> > > > should
> > > >
> > > > > > > > never be 0. But can the tag be null (hdr->tag) ?
> > > > > > >
> > > > > > > The tag is not a pointer -- it's just an integer.
> > > > > >
> > > > > > I was worrying that its value could not be null.
> > > > > >
> > > > > > I'll send a valgrind output soon (i need to build libpython
> > > > > > without pymalloc first).
> > > > > >
> > > > > > Thanks,
> > > > > > Eloi
> > > > > >
> > > > > > > > Thanks for your help,
> > > > > > > > Eloi
> > > > > > > >
> > > > > > > > On 16/08/2010 18:22, Jeff Squyres wrote:
> > > > > > > >> 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::Int
> > > >
> > > > > > > >>>> er fa ce>>
> > > > > > > >>>>
> > > > > > > >>>> = {_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\/R
> > > >
> > > > > > > >>>>>>>>>>>>>> ed Ha tE L\ -5 \/ x 86 _6 4\ /bin\/actranpy_mp
> > > >
> > > > '--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/Re
> > > >
> > > > > > > >>>>>>>>>>>>>> dH at EL -5 /x 86 _ 64 /A c tran_11.0.rc2.41872'
> > > >
> > > > '--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3D
> > > >
> > > > > > > >>>>>>>>>>>>>> re al _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
> > > > > > > >>>>>>>>>>>>
> > > > > > > >>>>>>>>>>>> _______________________________________________